Program and abstracts EMBO Workshop on Microbial Sulfur Metabolism 12–15 April 2015

Program and abstracts EMBO Workshop on Microbial Sulfur Metabolism 12–15 April 2015
EMBO Workshop on
Microbial Sulfur Metabolism
12–15 April 2015
Helsingør, Denmark
Program and abstracts
Thioploca sp., South America
Workshop Organization
Organizers
Kai Finster, Aarhus University, Denmark
Niels-Ulrik Frigaard, University of Copenhagen, Denmark
Scientific Committee
Andy Johnston, University of East Anglia, UK
Mark Dopson, Linnaeus University, Sweden
Judy D. Wall, University of Missouri, US
Ulrike Kappler, University of Queensland, Australia
Casey Hubert, Newcastle University, UK
Heide Schulz-Vogt, Leibniz Institute for Baltic Sea Research, Germany
Alexander Loy, University of Vienna, Austria
Marc Mussmann, Max Planck Institute for Marine Microbiology, Germany
Jan Kuever, Bremen Institute for Materials Testing, Germany
Piet Lens, UNESCO-IHE Institute for Water Education, The Netherlands
Christiane Dahl, University of Bonn, Germany
Erik van Zessen, Paques B.V., The Netherlands
Gerard Muyzer, University of Amsterdam, The Netherlands
Inês A. C. Pereira, New University of Lisbon, Portugal
Venue
Konventum
Gl. Hellebækvej 70
3000 Helsingør
Denmark
http://www.konventum.dk/
2
Sponsors
The following organizations are gratefully acknowledged for their generous support:
European Molecular Biology Organisation (EMBO)
Carlsberg Foundation
Federation of European Microbiological Societies (FEMS)
International Society for Microbial Ecology (ISME)
Cameca GmbH
Unisense A/S
3
Program
Sunday, 12 April 2015
From 14:00
Check-in at conference center
16:00-18:00
Registration
Poster mounting
Coffee in poster area
18:00-19:00
Dinner
19:00-19:55
Welcome and Key Note Lecture
Chairs: Kai Finster and Niels-Ulrik Frigaard
19:00-19:15
Welcome
19:15-19:55
Key note lecture: Lars Peter Nielsen, Denmark (L1)
Electrogenic sulfur oxidation by cable bacteria in sediments and soils
20:00-22:00
Mixer in “Salonerne”
Until 1:00
Bar open
Monday, 13 April 2015
7:00-8:30
Breakfast
8:30-10:00
Session 1: Biogeochemistry (Part 1 of 2)
Chair: Filip Meysman
8:30-9:00
Invited lecture: David Johnston, USA (L2)
The information locked in the oxygen isotope composition of sulfate
9:00-9:20
Boswell Wing, Canada (L3)
Sulfur isotope discrimination during microbial sulfate respiration:
linking biogeochemical signals to biochemical and physiological state
9:20-9:40
Marion Jaussi, Denmark (L4)
Sulfate reduction rates and the size of the sulfate-reducer community
are tightly linked in the subsurface of an arctic fjord (Greenland)
9:40-10:00
Hannah Sophia Weber, Denmark (L5)
Sulfur cycling and isotope fractionation coupled to anaerobic methane
oxidation in a low sulfate environment
10:00-10:30
Coffee break
4
10:30-11:40
Session 1: Biogeochemistry (Part 2 of 2)
Chair: David Johnston
10:30-11:00
Invited lecture: Donald E. Canfield, Denmark (L6)
Interpreting sulfur isotope signatures, progress and problems
11:00-11:20
Filip Meysman, Netherlands (L7)
Electrical currents and cryptic sulphur cycling in coastal sediments
11:20-11:40
Nils Risgaard-Petersen, Denmark (L8)
Cable Bacteria in Freshwater Sediments
12:00-13:00
Lunch
14:00-15:40
Session 2: Ecology and Evolution (Part 1 of 2)
Chair: Casey Hubert
14:00-14:30
Invited lecture: Heide Schulz-Vogt, Germany (L9)
Large sulfur bacteria
14:30-15:00
Invited lecture: Karthik Anantharaman, USA (L10)
Bacterial sulfur oxidation genes in deep-sea viruses
15:00-15:20
Hendrik Schaefer, United Kingdom (L11)
Characterization of uncultured dimethylsulfide degrading
gammaproteobacteria from a coastal saltmarsh using stable isotope
probing and single cell genomics
15:20-15:40
Gerard Muyzer, Netherlands (L12)
Ecogenomics of haloalkaliphilic sulphur bacteria
15:40-16:10
Coffee break
16:10-17:40
Session 2: Ecology and Evolution (Part 2 of 2)
Chair: Heide Schulz-Vogt
16:10-16:40
Invited lecture: Casey Hubert, Canada (L13)
Thermospores of sulfate-reducing bacteria as biogeographic indicators
16:40-17:00
Bela Hausmann, Austria (L14)
The power of the rare: Sulfate reduction in an acidic peatland is driven
by small networks of natively low abundant bacteria
17:00-17:20
Kasper Urup Kjeldsen, Denmark (L15)
Can cable bacteria actually oxidize sulfide? Insights from a genome
17:20-17:40
Vera Thiel, USA (L16)
Metagenomic study reveals first sulfate-reducing member of the
Bacteroidetes-Chlorobi group
18:00-19:00
Dinner
19:00-21:00
Posters and coffee (even numbered posters presented)
Until 1:00
Bar open
5
Tuesday, 14 April 2015
7:00-8:30
Breakfast
8:30-10:00
Session 3: Students’ Contest
Chair: Kai Finster
8:30-8:45
Stefan Dyksma, Germany (L17)
Ubiquitous Gammaproteobacteria dominate dark carbon fixation in
coastal sediments
8:45-9:00
Xiaofen Wu, Sweden (L18)
Metagenomes from the terrestrial deep biosphere reveal sulfur
oxidation and reduction pathways
9:00-9:15
Petra Henke, Germany (L19)
Tight symbiotic interactions in the pelagic sulfur cycle - the case of
phototrophic consortia
9:15-9:30
Jasmine Berg, Germany (L20)
Single-cell investigations into the metabolism of stored sulfur in living
bacteria
9:30-9:45
Diana Vasquez Cardenas, Netherlands (L21)
Microbial carbon metabolism associated with electrogenic sulphur
oxidation in coastal sediments
9:45-10:00
Jon Graf, Germany (L22)
Metagenome and mRNA expression analysis of the bacterial partner of
an AOM-mediating microbial consortium
10:00-10:30
Coffee break
10:30-12:00
Session 4: Physiology and Biochemistry (Part 1 of 2)
Chair: Ulrike Kappler
10:30-11:00
Invited lecture: Inês A. C. Pereira, Portugal (L23)
What is the physiological product of the DsrAB dissimilatory sulfite
reductase?
11:00-11:20
Sofia Venceslau, Portugal (L24)
New insights into the energy metabolism of Desulfovibrio vulgaris: The
role of FlxABCD-HdrABC, a novel NADH dehydrogenaseheterodisulfide reductase
11:20-11:40
André Santos, Portugal (L25)
Crucial role of DsrC in dissimilatory sulfite reduction
11:40-12:00
Rich Boden, United Kingdom (L26)
Chemolithoheterotrophy – new insights into an often forgotten yet
widespread metabolic trait
12:00-13:00
Lunch
6
13:15-14:55
Session 4: Physiology and Biochemistry (Part 2 of 2)
Chair: Inês A. C. Pereira
13:15-13:45
Invited lecture: Christiane Dahl, Germany (L27)
An integrated view on sulfur oxidation in purple sulfur bacteria
13:45-14:15
Invited lecture: Jillian Petersen, Germany (L28)
Sulfur-oxidizing symbionts: novel pathways and novel organisms
14:15-14:35
Marianne Guiral, France (L29)
Oxidation of thiosulfate and sulfite by the hyperthermophilic bacterium
Aquifex aeolicus
14:35-14:55
Ulrike Kappler, Australia (L30)
Organosulfur compound metabolism in the human pathogen
Haemophilus influenzae
15:00-17:00
Posters and coffee (odd numbered posters presented)
17:15-19:00
Excursion to Kronborg Castle
20:00-22:00
Conference Dinner
Until 1:00
Bar open
Wednesday, 15 April 2015
Before 9:00
Check-out of conference center
7:00-8:00
Breakfast
8:00-9:10
Session 5: Sulfur Transformations
Chair: Rich Boden
8:00-8:30
Invited lecture: Silke Leimkühler, Germany (L31)
Biosynthesis of the molybdenum cofactor and its relation to sulfur
metabolism
8:30-8:50
Tom Berben, Netherlands (L32)
Comparative metabolic studies of the halo-alkaliphilic
chemolithoautotrophic sulfur-oxidizing bacterium Thioalkalivibrio
thiocyanoxidans ARh 2
8:50-9:10
Marc Mussmann, Germany (L33)
Ecology and ecogenomics of uncultured sulfate-reducing bacteria
ubiquitous and abundant in marine sediments
9:10-9:40
Coffee break
7
9:40-11:20
Session 6: Biotechnology
Chair: Christiane Dahl
9:40-10:10
Invited lecture: Piet Lens, Netherlands (L34)
Applications of the biological sulfur and selenium cycles in
environmental biotechnology
10:10-10:40
Invited lecture: Ian Head, United Kingdom (L35)
Sulfur-metabolizing microbes in oil degradation and corrosion
10:40-11:00
Barrie Johnson, United Kingdom (L36)
Development and application of acidophilic sulfidogenic bioreactors for
combined pH amelioration, sulfate removal and selective recovery of
metals from acidic waste waters
11:00-11:20
Mark Dopson, Sweden (L37)
Oxidation of inorganic sulfur compounds in metal sulfide processing
wastewaters generates an electrical current in microbial fuel cells
11:20-11:35
Poster and oral presentation awards
Chair: Kai Finster
12:00-13:00
Lunch
13:00-14:20
Session 7: Microbial Interactions and Environmental Impacts
Chair: Marc Mussmann
13:00-13:30
Invited lecture: David Schleheck, Germany (L38)
Sulfoquinovose degradation pathways in bacteria
13:30-14:00
Invited lecture: Jana Milucka, Germany (L39)
The role of sulfur in marine methane oxidation
14:00-14:20
Naoki Kamiya, Japan (L40)
Sulfur disproportionation is achieved by co-metabolism with
photosynthetic sulfide oxidation to sulfur
14:20-15:10
Key Note Lecture and Closing
Chairs: Niels-Ulrik Frigaard and Kai Finster
14:20-15:00
Key note lecture: H. Rex Gaskins, USA (L41)
Microbial sulfur metabolism and colorectal cancer risk
15:00-15:10
Closing
15:30
Departure
8
Abstracts of Lectures
Abstracts are organized according to the sequence of presentation.
9
Key Note Lecture
L1
Electrogenic sulfur oxidation by cable bacteria in sediments
and soils
Lars Peter Nielsen
Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus
University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
Spectacular behavioral, morphological, and physiological traits have evolved among the
prokaryotes competing for the lucrative aerobic oxidation of sulfide in marine
sediments. The most recent and surprising finding is electrical cable bacteria, which use
internal conductors to mediate electron transport over centimeter distances from
sulfide at depth to oxygen at the sediment surface. All sequenced cable bacteria form a
cluster of multicellular filamentous bacteria within the Desulfobulbaceae family and all
show a conspicuous ring of parallel, putative electric wires inside a periplasmic
continuum. The spatial separation of oxidation and reduction processes in distant cells
challenge much conventional thinking in sediment biogeochemistry and microbial
physiology. That cable bacteria have been overlooked until now, despite their
abundance and impact in many environments, further reminds us about all the
unknowns out there. My lecture will summarize present knowledge about biology,
occurrence, importance, electronics and diversity of cable bacteria and then discuss
some of the most exciting open questions. As an example, many single-celled sulfur
oxidizers seem to co-exist with cable bacteria, thus raising the possibility that cable
bacteria themselves are not sulfur bacteria but rather purely electric bacteria needing
the real sulfur bacteria to deliver the electrons from sulfide oxidation.
10
Session: Biogeochemistry
Invited Lecture
L2
The information locked in the oxygen isotope composition of
sulfate
D. Johnston, A. S. Bradley, B. Cowie
Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
Our collective understanding of the modern and geological sulfur cycle benefits from the
fact that microorganisms – the agents of nearly all geochemical S cycling – impart large
isotope effects. Most commonly, sulfur isotopes in sulfate and sulfide (both aqueous and
in mineral form) are employed to track everything from rates of microbial processes (1)
through to the presence/absence of certain metabolic clades in a given environment
(2, 3). In complement to sulfur isotope studies, one under-developed tool to track sulfur
recycling comes from the interrogation of oxygen isotope change in sulfate reservoirs
(marine, pore water, mineralogical) (4, 5). As S-O bonds are broken and formed through
inorganic and biogeochemical activity, the 18O/16O composition of the related sulfate
reservoir evolves. In this work we will document the extraordinary isotopic consistency
across environmental 18O/16O sulfate records and outline a rigorous, mechanismfocused approach to unpacking these records.
A small but rich body of literature sets the stage for our work [see (4)]. Much of the
previous work focus falls on calibrating an inorganic equilibrium between intracellular
water and sulfite (SO32-) – a large isotope effect that significantly influences the O
isotope composition of sulfate (6). Other candidate isotope exchange reactions include
those associated with the generation and destruction of APS, another intracellular
intermediate common in both sulfate reducing bacteria and, at a minimum, sulfur
disproportionating bacteria. In parallel, there is additional and complementary
information gained through the inclusion of 17O measurements (17O/16O). Although in
its infancy, the usage of 17O/16O provides a direct test of hypotheses derived from the
18O/16O studies noted above and provide a unique quantitative glimpse into the direct
linkages between the microorganisms that drive the sulfur cycle and the
contemporaneous atmosphere, all of which is captured in the isotopic composition of
seawater sulfate.
1. W. D. Leavitt, A. S. Bradley, I. Halevy, D. T. Johnston (2013) Influence of sulfate reduction rates on the
Phanerozoic sulfur isotope record. Proc Natl Acad Sci
2. D. E. Canfield, A. Teske (1996) Late Proterozoic rise in atmospheric oxygen concentration inferred from
phylogenetic and sulphur-isotope studies. Nature 382, 127-132
3. D. T. Johnston, B. A. Wing, J. Farquhar, A. J. Kaufman, H. Strauss, T. W. Lyons, L. C. Kah, D. E. Canfield
(2005) Active microbial sulfur disproportionation in the Mesoproterozoic. Science 310, 1477-1479
4. G. Antler, A. V. Turchyn, V. Rennie, B. Herut, O. Sivan (2013) Coupled sulfur and oxygen isotope insight
into bacterial sulfate reduction in the natural environment. Geochim Cosmochim Acta 118, 98-117
5. A. V. Turchyn, D. P. Schrag (2004) Oxygen isotope constraints on the sulfur cycle over the past 10
million years. Science 303, 2004-2007
6. S. D. Wankel, A. S. Bradley, D. L. Eldridge, D. T. Johnston (2014) Determination and application of the
equilibrium oxygen isotope effect between water and sulfite. Geochim Cosmochim Acta 125, 694-711
11
Session: Biogeochemistry
L3
Sulfur isotope discrimination during microbial sulfate
respiration: linking biogeochemical signals to biochemical
and physiological state
Boswell Wing1, Itay Halevy2, André Pellerin1, Jyotsana Singh1
1
2
Department of Earth and Planetary Sciences and GEOTOP, McGill University
Department of Earth and Planetary Sciences, Weizmann Institute of Science
Aqueous sulfate supports widespread anoxic respiratory carbon cycling by microbes.
Aqueous sulfide is produced during this process and, when it escapes re-oxidation, it can
be sequestered in metallic sulfide minerals for geological timescales. The preferential
consumption of 32S-subsituted sulfate during dissimilatory sulfate reduction enables
sulfur isotope measurements to support these inferences. Sulfate in modern
sedimentary porewaters is 34S enriched, while aqueous sulfide is 34S depleted, providing
a rational framework for monitoring the biogeochemistry of microbial sulfur cycling
throughout Earth’s history.
Dissimilatory sulfate reduction was isotopically characterized through culture
experiments more than a half century ago. More recent work has precisely calibrated
how the magnitude of sulfur isotopic discrimination covaries inversely with the average
sulfate reduction rate of a microbial population and directly with sulfate levels in the
local environment. At the low-rate limit, sulfate-reducing microbes preferentially
process 34S-substituted sulfate to a degree that approaches the isotopic partitioning
defined by thermodynamic equilibrium between aqueous sulfate and sulfide. Separation
of 34S from 32S appears to follow a strain-specific trajectory as microbes respire faster
than this limit.
In this presentation, we will discuss how these gross physiological observations provide
a link between isotopic constraints on biogeochemical sulfur cycling and the average
biochemical state of a population of sulfate-reducing microbes. We will focus on
predictions that explicitly link preferential processing of 34S-enriched metabolites to
enzymatic reversibility and intracellular metabolite concentrations. These will focus on,
for example, the in-vivo reversibility of dissimilatory (bi)sulfite reductase, the
covariation of respiratory enzyme production with intracellular sulfate reduction rate,
and the energetic tradeoff between ribosome production and the survival of respiratory
proteins. While the presentation may inspire dissension, we hope it will encourage
discussion that links the isotopic biogeochemistry of microbial sulfur metabolisms to
their biochemical and physiological state.
12
Session: Biogeochemistry
L4
Sulfate reduction rates and the size of the sulfate-reducer
community are tightly linked in the subsurface of an arctic
fjord (Greenland)
Marion Jaussi1, Kasper Urup Kjeldsen1, Marit-Solveig Seidenkrantz2, Bente Aagaard
Lomstein1, 3, Bo Barker Jørgensen1, Hans Røy1
1
Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade
114, Building 1540, DK-8000 Aarhus C, Denmark
2 Centre for Past Climate Studies and Arctic Research Centre, Department of Geoscience,
Aarhus University, Hoegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
3 Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, Building
1540, DK-8000 Aarhus C, Denmark
Sulfate reduction contributes to a major part of the organic matter mineralization in
shelf sediments both in temperate and arctic environments. So far, rates of catabolic
metabolism have rarely been quantified together with community size within the same
sediment samples, although this association is crucial to address the metabolic state of
individual cells. We quantified sulfate reduction rates with radiotracer incubation and
the community size of sulfate reducers together in a highly dynamic fjord system (South
West Greenland). The four sediment cores presented intriguing and diverse depth
patterns of sulfate reduction rates, followed tightly by the abundance of sulfatereducers. The mean cell-specific sulfate reduction rates were constant with depth in
spite of large changes in sulfate reduction rates. Interestingly, the level of the constant
per-cell sulfate reduction rates differed from site to site.
13
Session: Biogeochemistry
L5
Sulfur cycling and isotope fractionation coupled to anaerobic
methane oxidation in a low sulfate environment
Hannah Sophia Weber1, Kirsten Silvia Habicht2, Bo Thamdrup1
1
Nordic Center for Earth Evolution and Department of Biology, University of Southern
Denmark, Campusvej 55, 5230 Odense M, Denmark
2 Unisense A/S, Tueager 1, 8200 Aarhus N, Denmark
Sulfate–dependent anaerobic oxidation of methane (AOM) was described as an efficient
sink of the greenhouse gas methane in various marine habitats. Freshwater sediments
are often low sulfate environments and only since recently, evidence is accumulating for
efficient anaerobic methane consumption under extremely low sulfate conditions.
Taxonomic identities of the AOM–active microorganisms in freshwater sediments and
their metabolic constraints remain unknown. The present study was carried out in
iron–rich Lake Ørn in Denmark, which previously showed AOM activities at sulfate
concentrations as low as 3 µmol L-1 and a the consumption of ~90 % of the produced
methane in a sulfate-methane transition zone well below the oxic realm. The AOM zone
was associated with a large 34S depletion in the reduced sulfur pool and a strong
accumulation of zero–valent sulfur. In slurry incubations, we showed that methane
addition to sediment of the AOM–active zone induced sulfate consumption and
associated isotope fractionation, apparently through a kinetic isotope effect. Our results
strongly suggest that AOM is capable of 34S fractionation at sulfate concentrations
<50 µmol L-1 and that sulfur isotope signatures in low-sulfate environments may be
strongly impacted by AOM. Furthermore, with the aim to identify the AOM–active
microorganisms, we applied RNA–stable isotope probing to AOM–active sediment of
Lake Ørn incubated with 13C–methane or 13C–bicarbonate. 16S rRNA clone library–
derived sequences revealed 13C–incorporation of both substrates mainly into the
environmental clade GoM Arc 1 (Euryarchaeota), whereas anaerobic methane oxidizers
known from marine habitats (AMNE strains) could not be detected. This study suggests
that sulfur cycling in low-sulfate freshwater environments may be impacted by
anaerobic methane oxidizers with taxonomic identities and enzymatic pathways
different from those found in marine habitats.
14
Session: Biogeochemistry
Invited Lecture
L6
Interpreting sulfur isotope signatures, progress and
problems
Donald Canfield
Department of Biology, University of Southern Denmark, Odense, Denmark
The isotopic composition of sulfur species in the environment reflects interplay between
biological processes that impart fractionations and physical/environmental processes
that control the extent to which these fractionations will be expressed. Understanding
the nature of this interplay presents a crucial challenge in interpreting sulfur isotopic
compositions. In my talk I will review recent progress in our understanding of the
capabilities of microbial populations to impart fractionations. Despite this progress, I
will demonstrate, through several examples, many of the challenges that still exist in
interpreting the sulfur isotope record as preserved in modern and ancient sediments.
15
Session: Biogeochemistry
L7
Electrical currents and cryptic sulphur cycling in coastal
sediments
Filip Meysman1, 2, Dorina Seitaj1, Fatimah Sulu-Gambari3, Regina Schauer4, Caroline
Slomp3
1
Department of Ecosystem Studies, Royal Netherlands Institute for Sea Research (NIOZ),
Korringaweg 7, 4401 NT Yerseke, The Netherlands
2 Department of Analytical Environmental and Geo-Chemistry, Vrije Universiteit Brussel
(VUB), Pleinlaan 2, 1050 Brussels, Belgium
3 Department of Earth Sciences (Geochemistry), Faculty of Geosciences, Utrecht University,
Budapestlaan 4, 3584 CD Utrecht, The Netherlands
4 Department of Bioscience, Center of Geomicrobiology, Aarhus University, Ny Munkegade
116, 8000 Aarhus, Denmark
Sulfate reduction is the dominant pathway for organic matter mineralization in coastal
sediments, and hence, vast amounts of free sulphide are produced in the pore water.
Nonetheless, the surface layer of coastal sediments often exhibits a centimeter wide
zone, where neither oxygen nor free sulphide is present, suggesting that intense cryptic
sulphur (S) cycling takes place. We studied the geochemical transformations and
microbial drivers associated with cryptic S cycling in the sediments of a seasonally
hypoxic basin, where recently cable have been found in situ (Marine Lake Grevelingen,
The Netherlands). By combining microbial and geochemical data, distinct geochemical
fingerprints could be linked to specific mechanisms of suboxic zone formation, which
revealed a remarkable temporal succession of different cryptic S cycling pathways.
Electrogenic sulphur oxidation by cable bacteria dominated the sediment geochemistry
in winter and strongly solubilized the Fe-sulphide pool, which led to the formation of a
large pool of Fe-oxides in the surface sediment. In late spring, these Fe-oxides were
reduced to Fe-sulfides thereby acting as a sink for sulfide, whereas after the summer
hypoxic period, Beggiatoa-mats colonized the sediment. Our data show that internal
shifts in microbial communities can induce strong seasonality in sedimentary
biogeochemical cycling, independent of the seasonal variation in bottom water
oxygenation.
16
Session: Biogeochemistry
L8
Cable bacteria in freshwater sediments
Nils Risgaard-Petersen1, Lars Peter Nielsen1, Lars Damgaard2, Jesper Berg2
1
Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus
University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
2 Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade
114, DK-8000 Aarhus C, Denmark
In marine sediments cathodic oxygen reduction at the sediment surface can be coupled
to anodic sulphide oxidation in deeper anoxic layers through electrical currents
mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so
called cable bacteria. In this study we tested if the same occurs in freshwater sediments.
Homogenized sediments collected from the stream Giber Å, Denmark, were incubated in
the laboratory. After two weeks pH signatures and electric fields, signified that anodic
and cathodic reactions had developed. In situ measurements of oxygen, pH and electric
potential distributions in the sediment in waterlogged banks of Giber Å further
confirmed the presence of distant electric redox coupling. Filamentous Desulfobabace,
with microcable morphology were found abundantly in all cases. The results of the
present study indicate that electric currents mediated by cable bacteria could be
important for sulfurcycling in freshwater sediments
17
Session: Ecology and Evolution
Invited Lecture
L9
Large sulfur bacteria
Heide Schulz-Vogt
Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Germany
The family Beggiatoaceae contains several linages of giant bacteria, which have caught
the curiosity of microbiologists since centuries. Locally, they can also be of high
environmental importance, because of the enormous biomasses, that they can build up
in environments with high sulfide fluxes. Even though the genus Beggiatoa was first
described more than 200 years ago, the phylogenetic relationship among members of
this family has only been unveiled recently. Now we have to take into account, that also
in this family, members that appear to be identical, because of a very similar
morphology may not be closely related and possibly very distinct in physiology. Thus,
with the increasing availability of genomic information it becomes more and more
important to distinguish between environmental sequences originating from loosely
related linages, in order to precisely describe the ecological niches of the respective
genera. Lately, we came to learn, that the physiological potential in this family is even
more divers than originally thought, including the use of a mixture of electron donors
and acceptors as well as the use of storage compounds such as PHB or polyphosphate.
Especially the letter can have important consequences for the phosphorus cycling in
marine sediments and represents a poorly investigated link between the sulfur and the
phosphorus cycle.
18
Session: Ecology and Evolution
Invited Lecture
L10
Bacterial sulfur oxidation genes in deep-sea viruses
Karthik Anantharaman
Earth and Planetary Sciences, University of California, Berkeley, California, USA
Microbial chemosynthesis involves the use of reduced chemicals like sulfur to power
carbon fixation and is pervasive throughout the deep sea. Chemosynthetic microbes
drive key biogeochemical cycles that impact all life on earth. Viruses are the most
abundant biological entities in the deep-sea and the primary cause of microbial
mortality. Although viruses infecting phototrophs in the surface oceans are well studied,
little is known about the impacts of viruses that infect lithotrophic primary producers. In
this presentation, we will describe the ecological strategy of viruses that putatively
infect the globally distributed ‘SUP05’ clade of sulfur-oxidizing gammaproteobacteria.
We hypothesize that these viruses have acquired and retained bacterial metabolic genes
to access abundant elemental sulfur in the environment. Metabolic genes in the viruses
supplement sulfur oxidation metabolism in their hosts in order to support viral infection
and replication. Our work implicates viruses as an agent of horizontal gene transfer of
sulfur oxidation genes and an important component of the global biogeochemical cycle
of sulfur.
19
Session: Ecology and Evolution
L11
Characterisation of uncultured dimethylsulfide-degrading
gammaproteobacteria from a coastal saltmarsh using stable
isotope probing and single cell genomics
Hendrik Schäfer1, Jennifer Pratscher2, Hyun Soon Gweon3, Eileen Muhs1, Jonathan D.
Todd4, J. Colin Murrell2, Andrew W. B. Johnston4
1
School of Life Sciences, University of Warwick, Coventry, UK
School of Environmental Sciences, University of East Anglia, Norwich Research Park,
Norwich, UK
3 Centre for Ecology and Hydrology, Wallingford, UK
4 School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich,
UK
2
Coastal saltmarshes are natural hotspots for organic sulfur transformations. Due to their
high productivity and the presence of macroscopic and microscopic algae as well as
macrophytes that have the capacity to produce dimethylsulfoniopropionate (DMSP),
saltmarshes are environments where dimethylsulfide (DMS)-degrading microbial
populations thrive in sediments and in association with plants, but little is known about
the identity of DMS-degrading microorganisms in such environments. In this project we
sought to identify the dominant populations and metabolic pathways in microbial
catabolism of DMS in a saltmarsh at Stiffkey (Norfolk, UK). We combined stable isotope
probing (SIP) with 13C-labelled DMS, together with 454 high-throughput sequencing of
microbial rRNA genes in heavy and light SIP fractions to identify DMS-degrading
microorganisms in sediments and in association with Spartina anglica, a DMSPproducing halophyte. SIP experiments suggested that uncultivated gammaproteobacteria from the Piscirickettsiaceae were actively involved in DMS catabolism.
Metagenomic sequencing of 13C-DNA from SIP-labelled benthic DMS-degrading
populations and comparison to the 12C-community DNA provided insights into
particular functional genes enriched in the metagenome of the DMS-degrading bacteria.
Single-cell genomics allowed us to characterise the phylogeny of these bacteria and
enabled comparison of their genomes to Methylophaga spp., their closest cultivated
DMS-degrading relatives. The analyses provide a first glimpse into the genomes of
gammaproteobacterial DMS degraders which so far have resisted isolation but which
may play key roles in DMS degradation in benthic and pelagic marine habitats.
20
Session: Ecology and Evolution
L12
Ecogenomics of haloalkaliphilic sulphur bacteria
Gerard Muyzer
Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University
of Amsterdam, Amsterdam, The Netherlands
Soda lakes are extreme environments with pH values between 9 and 11, and salinities
up to saturation. However, despite these extreme conditions, soda lakes are highly
productive and harbor diverse microbial communities. The sulfur cycle, driven by
sulfur-oxidizing and sulfidogenic bacteria, is one of the most active element cycles in
these habitats. Members of the genus Thioalkalivibrio have versatile metabolic
capabilities, including sulfide oxidation, denitrification and thiocyanate utilization. We
have isolated more than 70 strains, for which the Joint Genome Institute of the U.S.
Department of Energy has sequenced the genomes. The availability of these sequence
data will allow us to get insight into the diversity of these bacteria, their niche
differentiation, and the molecular mechanisms by which they adapt to the extreme haloalkaline conditions. For this we will use a systems biology approach, combining different
'omics' techniques with physiological experiments under well-defined conditions, and
mathematical modeling. The results of these experiments are of paramount importance,
both for a basic understanding of life under extreme conditions, as well as for the use of
these bacteria in the sustainable removal of noxious sulfur compounds from waste
streams. Here I will discuss the ecogenomics and application of haloalkaliphilic sulfur
bacteria, and present the first results of comparative genomics.
21
Session: Ecology and Evolution
Invited Lecture
L13
Thermospores of sulfate-reducing bacteria as biogeographic
indicators
Casey Hubert
Department of Biological Sciences, University of Calgary, Canada
Sulfate-reducing bacteria (SRB) are well known inhabitants of the deep biosphere, yet
subsurface habitats are leaky due to geological features such as hydrocarbon seeps,
hydrothermal vents, discharging seamounts, and mud volcanoes. Geofluids may
therefore passively transport subsurface dwelling microorganisms through and/or out
of the subsurface. Consistent with this is the discovery of thermophilic SRB present as
dormant endospores in surface marine sediments where in situ conditions are too cold
to support their germination and growth. These “thermospores” are phylogenetically
and physiologically diverse and many are closely related to Clostridia commonly found
in deep anoxic habitats such as petroleum reservoirs or mid ocean ridges. The
distribution of thermospores in marine sediments is spatially variable, both globally and
regionally. In Arctic sediments near Svalbard, certain phylo- and phenotypes of sulfatereducing Desulfotomaculum thermospores appear to be unique to certain fjords, while
others are more widespread. In addition to surviving the cold temperatures in surface
sediments, certain thermospores display remarkable heat resistance and remain viable
after serial autoclaving and/or long-term exposure to temperatures above their growth
limit. Several different thermospore taxa are typically detected in a single surface
sediment location, suggesting multiple sources and dispersal vectors may contribute to
this microbial diversity. Thermospores provide a tractable model for quantitative
studies of microbial dispersal with the potential to highlight previously unconsidered
dispersal mechanisms for marine microorganisms in general.
22
Session: Ecology and Evolution
L14
The power of the rare: Sulfate reduction in an acidic peatland
is driven by small networks of natively low abundant bacteria
Bela Hausmann1, Klaus-Holger Knorr2, Stephanie Malfatti3, Susannah Tringe3, Tijana
Glavina del Rio3, Mads Albertsen4, Per H. Nielsen4, Ulrich Stingl5, Alexander Loy1, Michael
Pester1, 6
1
Division of Microbial Ecology, Department of Microbiology and Ecosystem Science,
Faculty of Life Sciences, University of Vienna, Austria
2 Hydrology Group, Institute of Landscape Ecology, University of Münster, Germany
3 Joint Genome Institute, U.S. Department of Energy, Walnut Creek, California, USA
4 Center for Microbial Communities, Department of Biotechnology, Chemistry and
Environmental Engineering, Aalborg University, Denmark
5 Red Sea Research Center, King Abdullah University of Science and Technology, Saudi
Arabia
6 Chair for Microbial Ecology, Limnology and General Microbiology, Department of Biology,
University of Konstanz, Germany
Peatlands are regarded primarily as methanogenic environments significantly
contributing to global methane emissions. Little attention is given to the fact that
dissimilatory sulfate reduction is maintained by a hidden sulfur cycle in these lowsulfate environments, with sulfate reduction rates being comparable to marine surface
sediments. To deepen our understanding of sulfate reducers in peatlands, anoxic peat
slurries were supplemented with typical degradation intermediates of organic matter at
in situ concentrations and either stimulated with low amounts of externally supplied
sulfate or incubated under endogenous conditions. Changes in the microbial community
were monitored by 16S rRNA gene and cDNA amplicon sequencing and correlated to
sulfate turnover. OTUs most abundant in the native community (Acidobacteria,
Actinobacteria, Alphaproteobacteria, Planctomycetes) showed no significant response to
sulfate stimulation. In contrast, small networks of natively low abundant bacteria
strongly correlated with bulk sulfate turnover under lactate, propionate, and butyrate
amendment. Among the responsive OTUs affiliated to recognized sulfate reducers,
members of the genera Desulfomonile and Desulfovibrio (Deltaproteobacteria)
responded specifically to one of these three substrates, while a Desulfopila OTU
(Deltaproteobacteria) and a Desulfosporosinus OTU (Firmicutes) were always
responsive, exhibiting a generalist lifestyle. Interestingly, the Desulfosporosinus OTU
markedly increased its 16S rRNA and thus ribosome content but stayed at low
abundance throughout the incubation period. This likely mirrors its ecological strategy
in the natural peat soil. Sequencing of a metagenome enriched by DNA-stable isotope
probing allowed almost complete reconstruction of the Desulfosporosinus population
pan-genome and confirmed functional properties of this low abundant peatland sulfate
reducer. The small networks of responsive OTUs always contained at least one member
not affiliated to recognized sulfate reducers (e.g. Alphaproteobacteria) indicating
possible metabolic interaction partners or novel sulfate reducers. In conclusion, our
results show that selected low abundance microorganisms can have a profound effect on
biogeochemical cycling and greenhouse gas production.
23
Session: Ecology and Evolution
L15
Can cable bacteria actually oxidize sulfide? Insights from a
genome
Lars Schreiber1, Kasper Urup Kjeldsen1, Jesper Jensen Bjerg1, Andreas Bøggild2, Jack van
de Vossenberg3, Lars Peter Nielsen1, 2, Andreas Schramm1, 2
1
Department of Bioscience, Center for Geomicrobiology, Aarhus University, Denmark
Department of Bioscience, Section for Microbiology, Aarhus University, Denmark
3 Institute for Water Education, UNESCO-IHE, Delft, The Netherlands
2
Cable bacteria are filamentous members of the family Desulfobulbaceae that can couple
the reduction of oxygen at the surface of aquatic sediments to the oxidation of sulfide in
anoxic layers centimeters below by an unknown electron conducting mechanism. The
goal of the present study was to explore the metabolic and molecular basis for the
unique lifestyle of the so far uncultured cable bacteria using single-filament genomics.
Single cable bacterium filaments were isolated from Aarhus Bay sediment (Denmark) by
micro-manipulation, their genomes amplified and sequenced. By combining the genomic
information of two such filaments, an approx. 90% complete draft genome with a size of
3.7 Mbp was obtained. About 44% of the genome represented novel genes without
homologs in other Desulfobulbaceae. Genes diagnostic for sulfide-oxidizing bacteria, e.g.,
encoding the Sox sulfur oxidation system, sulfide-quinone reductase or reverse-type
dissimilatory sulfite reductase, were not found. Instead, the canonical dissimilatory
sulfate reduction pathway was present, albeit lacking the typical membrane-associated
electron transport proteins (DsrMKJOP), which in sulfate reducers couple the quinone
pool with sulfite reduction. We propose that sulfide oxidation is performed via a
reversal of the sulfate-reduction pathway, in which heterodisulfide reductases transfer
electrons released by sulfide oxidation into the quinone pool. A proton translocating
cytochrome d ubiquinol reductase may then couple the quinone pool to oxygen
reduction. Besides by sulfide oxidation, the quinone pool may also be reduced by NADH
via a proton and a sodium translocating NADH:ubiquinone oxidoreductase conferring
the potential for both lithotrophic and organotrophic growth. Genes coding for the
potentially electron-conducting, string-like structures found in the periplasm of cable
bacteria were not identified. We did, however, identify homologs of multi-heme
cytochromes involved in electron-transport in nanowires. These cytochromes along
with pili could potentially be involved in the electron transport along the cable bacteria.
24
Session: Ecology and Evolution
L16
Metagenomic study reveals first sulfate-reducing member of
the Bacteroidetes-Chlorobi group
Vera Thiel1, Jason Wood2, David Ward2, Donald Bryant1, 3
1
Department of Biochemistry and Molecular Biology, The Pennsylvania State University,
University Park, PA, 16802 USA
2 Department of Land Resources and Environmental Sciences, Montana State University,
Bozeman, MT 59717, USA
3 Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT
59717, USA
Dissimilatory sulfate reduction (DSR) plays major roles in prokaryotic energy
transformation in oxygen-depleted environments as well as in sulfur and carbon cycling.
Horizontal gene transfer is usually invoked to explain the polyphyletic distribution of
DSR in Bacteria and Archaea. We identified a genomic bin defining a novel sulfatereducing bacterium within a metagenome that was derived from the undermat layer of a
phototrophic microbial mat from Mushroom Spring, Yellowstone National Park, WY,
USA. The corresponding uncultured organism is predicted to be a motile, Gram-negative,
anaerobic sulfate-reducing bacterium; it had previously been detected in the microbial
mat by cloning and sequencing studies for dsrAB. Based on phylogenetic marker genes
and BLAST hits, the closest characterized relative is Ignavibacterium album, a
heterotrophic member of the Chlorobi. The metagenomic bin contains all genes
necessary for DSR, and most of these genes are clustered. Phylogenetic analyses of
DsrAB and AprAB, as well as the presence of dsrT and the absence of dsrEFH, support
the assignment of this organism as a sulfate-reducing bacterium. The genes involved in
DSR show significant similarity to sequences associated with uncultured sulfatereducing bacteria in marine sediments. The metagenomic study of this hot spring
microbial mat suggests the presence of the first sulfate-reducing member of the
Bacteroidetes/Chlorobi group, organisms in which only sulfur-oxidizing bacteria were
previously known. Comparative bioinformatics analysis supports the hypothesis that a
genomic island for sulfate respiration may exist, and that horizontal transfer of this
entire gene cluster can sometimes occur. As often observed for photosynthesis gene
clusters, a few required genes were no longer a part of the hypothesized cluster, which
suggests they may have been displaced after acquisition. Analysis of this unconventional
dsrAB-containing member of Bacteroidetes/Chlorobi should provide new insights into
the evolution of DSR and may possibly reveal a missing link between sulfate-reducing
and sulfur-oxidizing prokaryotes.
25
Session: Students’ Contest
L17
Ubiquitous Gammaproteobacteria dominate dark carbon
fixation in coastal sediments
Stefan Dyksma, Bernhard Fuchs, Marc Mußmann
Max Planck Institute for Marine Microbiology, Germany
Nearly half of microbial dark carbon fixation in the oceans occurs in sediments, whereby
oxidation of sulfur is considered the main carbon-fixing process. However, still very little
is known about the identity and physiology of the key CO2-fixing and sulfide-detoxifying
microorganisms in these sediments. We combined isotopic tracer experiments, the 16S
rRNA
approach
and
metatranscriptomics
to
identify
potential
key
chemolithoautotrophic populations in nine coastal surface sediments in Australia and
Europe. Using a novel methodological approach we were able to quantify carbon fixation
by specific populations. Sediment incubations with 14C bicarbonate, subsequent flowsorting of FISH-identified cells and liquid scintillography of the sorted cell fractions
showed that Gammaproteobacteria accounted for 70-86% of carbon fixed by the total
bacterial community. In accordance, 16S rRNA pyrotag sequencing suggested relatives
of gammaproteobacterial, sulfur-oxidizing symbionts and the Acidiferrobacter group as
the main chemolithoautotrophic populations at all sites. Together with the
physiologically yet-unknown JTB255 group these core groups accounted for 36-67% of
gammaproteobacterial sequences and for 62% of gammaproteobacterial carbon
fixation. In support, environmental transcripts of sulfur oxidation and carbon fixation
genes mainly affiliated with those of uncultured sulfur-oxidizing Gammaproteobacteria.
Unexpectedly, gammaproteobacterial genes encoding Ni, Fe uptake hydrogenases
recruited many transcripts. The co-localization and expression of key genes of sulfurand hydrogen oxidation in a metagenomic fragment and in a single cell genome strongly
suggest that sulfur-oxidizing Gammaproteobacteria in coastal sediments can cope with
the fluctuating availability of energy sources. In accordance, sediment incubation
experiments demonstrated a sulfate-independent oxidation of hydrogen. The role of
hydrogen oxidation in dark carbon fixation remains unclear, but this finding provides a
novel perspective on benthic primary production that has been ignored before. Our
study indicates a central function of these ubiquitous, uncultured Gammaproteobacteria
for sulfide detoxification and as a yet-overlooked carbon sink in marine sediments.
26
Session: Students’ Contest
L18
Metagenomes from the terrestrial deep biosphere reveal
sulfur oxidation and reduction pathways
Xiaofen Wu1, Karin Holmfeldt1, Valerie Hubalek3, Mats Åström2, Stefan Bertilsson3, Mark
Dopson1
1
Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus
University, Kalmar, Sweden
2 Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
3 Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala
University, Uppsala, Sweden
Despite scarce carbon and energy sources, microorganisms in the deep terrestrial
subsurface are estimated to constitute approximately 20% of the earth’s biomass.
However, due to the difficulties of accessing samples, details of the diversity and
metabolism of these microorganisms remain largely unexplored. We analyzed the
microbiomes of three dominant deep biosphere water types (“modern marine”, “old
saline”, and an “undefined mix”) at the Äspö Hard Rock Laboratory, Sweden. The
metagenome data has been assigned to twenty-four genome bins constituting near
complete genomes of the dominating microorganisms from the three water types. Most
of the bins were classified as similar to uncultured and uncharacterized bacteria while
four belong to unclassified archaea. Metagenomic bins related to known microbial
species include a Thiobacillus denitrificans-like species identified from the old saline
water that exhibits soxA from the Sox enzyme complex and asrAB coding for subunits of
a reversible anaerobic sulfite reductase. Co-occurrence of these genes may suggest
coupling of inorganic sulfur oxidation to dissimilatory nitrate reduction. In addition, a
Desulfarculus baarsii-like population was found in the old saline water that contains
genes coding for the reductive acetyl coenzyme A pathway that oxidizes carbon sources
such as formate and oxalate potentially coupled to sulfate as the terminal electron
acceptor. These metagenomes will for the first time allow detailed investigation of the
molecular mechanisms underpinning microbial sulfur transformations in the deep
biosphere.
27
Session: Students’ Contest
L19
Tight symbiotic interactions in the pelagic sulfur cycle – the
case of phototrophic consortia
Petra Henke1, Johannes Müller1, Gerhard Wanner2, Shawn McGlynn3, Victoria Orphan3,
Jörg Overmann1
1
Leibniz Institute DSMZ - German Collection of Mikroorganisms and Cell Cultures,
Germany
2 Ludwig Maximilian University of Munich, Germany
3 California Institute of Technology, USA
Green sulfur bacteria are obligate photolithoautotrophs inhabiting a very narrow
ecological niche characterized by the simultaneous presence of light and sulfide. Several
green sulfur bacteria have gained the advantage of mobility by entering into symbiosis
with motile Betaproteobacteria forming multicellular associations termed phototrophic
consortia. In the first cultured model system “Chlorochromatium aggregatum” the
chemoheterotrophic central bacterium is surrounded in a highly ordered fashion by 1220 green sulfur bacteria epibionts. Transcriptomics analyses of intact consortia and pure
epibiont cultures revealed that of 328 differently expressed genes, 25 genes are involved
in amino acid pathways (1). Metabolic coupling appears to involve amino acids and was
studied by tracking the flux of isotopically-labeled CO2 through the two partner
organisms using NanoSIMS analysis and magnetic capture. The epibiont genome also
contains a limited number of unique putative symbiosis genes (1,2). Three of the
putative symbiotic genes (Cag_1919, Cag_0614, Cag_0616) were studied in more detail
and their intracellular localizations determined. All three postulated symbiotic genes are
transported across the cell envelope of the epibiont into the central bacterium.
Cag_1919 contains a RTX domain which is typically found in Gram-negative pathogenic
bacteria. Cag_0614 and Cag_0616 represent the largest open reading frames in the
prokaryotic world known to date. Interestingly, Cag_0616 is predicted to be transcribed
together with a polysulfide reductase and Cag_0614 contains signature sequences for
the α- and β-ATP synthase subunits and might constitute a monitoring system for
motility of the consortium. The results of our physiological, localization and
bioinformatic studies yield novel hypotheses with respect to tight symbiotic interactions
within the pelagic sulfur cycle.
(1) Wenter R et al. (2010) Environ. Microbiol.12:2259-2276.
(2) Vogl K et al. (2008) Environ. Microbiol. 10:2842–2856.
28
Session: Students’ Contest
L20
Single-cell investigations into the metabolism of stored sulfur
in living bacteria
Jasmine Berg, et al.
Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
Zero-valent sulfur is a key intermediate in the microbial oxidation of sulfide to sulfate.
Many sulfide-oxidizing bacteria therefore produce and store large amounts of sulfur
intracellularly. How this stored sulfur is utilized remains a subject of discussion as the
most stable from of S0 under standard biological conditions – orthorhombic α-sulfur – is
most likely not accessible to bacterial enzymes. In this study (Berg et al. 2014), Raman
spectroscopy was employed as an ideal non-destructive technique to investigate
potentially redox- and pH-sensitive sulfur species in single cells of living bacteria. We
compared the chemical nature of sulfur in four different strains of Beggiatoa under
various ecological and physiological conditions. Results showed that in microaerobic
cultures at circumneutral pH, stored intracellular sulfur consisted of S8 rings and
inorganic polysulfides (Sn2-). Linear sulfur chains were detected during both the
oxidation and reduction of stored sulfur suggesting that Sn2- species comprise a pool of
activated sulfur utilized by bacteria. The formation of Sn2- results from the cleavage of
sulfur rings, either biologically by membrane-bound thiol groups and glutathione or
chemically by the strong nucleophile HS-. It is likely that Beggiatoa in the environment
utilize both of these mechanisms to generate Sn2- intermediates as they migrate
vertically between oxic and sulfidic sediment zones. With Raman spectroscopy it was
also possible to further follow the fate of sulfur during its oxidation to sulfate.
Unexpectedly high concentrations (up to ~2 M) of internal sulfate were detected in
Beggiatoa sp. Although the reason for the intracellular accumulation of sulfate remains
unknown we could show for the first time that Beggiatoa contains sulfate in
concentrations 100-1,000-fold higher than in the environment.
29
Session: Students’ Contest
L21
Microbial carbon metabolism associated with electrogenic
sulphur oxidation in coastal sediments
Diana Vasquez Cardenas1, Jack van de Vossenberg1, Lubos Polerecky2, Sairah Malkin3,
Regina Schauer4, Silvia Hidalgo-Martinez1, Veronique Confurius1, Jack Middelburg2, Filip
Meysman1, 3, Henricus Boschker1
1
Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
3 Department of Environmental, Analytical and Geo-chemistry, Vrije Universiteit Brussel,
Brussels, Belgium
4 Department of Bioscience, Aarhus University, Aarhus, Denmark
2
Recently, a novel electrogenic type of sulphur oxidation was documented in marine
sediments, whereby filamentous cable bacteria (Desulfobulbaceae) mediate electron
transport over cm-scale distances. These cable bacteria are capable of developing an
extensive network within days, which implies a highly efficient carbon acquisition
strategy. Presently the carbon metabolism of cable bacteria is unknown, so we adopted a
multi-disciplinary approach to study the carbon substrate utilization of both cable
bacteria and associated microbial community in sediment incubations. Fluorescence in
situ hybridization showed rapid downward growth of cable bacteria, concomitant with
high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling.
We studied heterotrophy and autotrophy by following 13C-propionate and -bicarbonate
incorporation into bacterial fatty acids. This biomarker analysis showed that propionate
uptake was limited to fatty acid signatures typical for the genus Desulfobulbus.
NanoSIMS analysis confirmed heterotrophic rather than autotrophic growth of cable
bacteria. Still high bicarbonate uptake was observed in concert with the development of
cable bacteria. Clone libraries of 16S cDNA showed numerous sequences associated to
chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria while
13C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria
were active far below the oxygen penetration. A targeted manipulation experiment
demonstrated that chemoautotrophic carbon fixation was tightly linked to the
heterotrophic activity of the cable bacteria down to centimetres depth. Overall, results
suggest that electrogenic sulphur oxidation is performed by a microbial consortium,
consisting of chemo-organotrophic cable bacteria and chemo-lithoautotrophic Epsilonand Gammaproteobacteria. The metabolic linkage between these two groups is
presently unknown and needs further study.
30
Session: Students’ Contest
L22
Metagenome and mRNA expression analysis of the bacterial
partner of an AOM-mediating microbial consortium
Jon Graf, Jana Milucka, Timothy Ferdelman, Marcel Kuypers
Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
Sulfate-coupled anaerobic oxidation of methane (AOM) is a major sink of methane in the
ocean and plays an important role in sedimentary biogeochemical cycling of carbon and
sulfur [1]. The Deltaproteobacteria belonging to the Desulfosarcina/Desulfococcus (DSS)
clade associated with the methanotrophic archaea (ANME) are capable of polysulfide
disproportionation and couple the carbon and sulfur cycles during AOM [2]. Biochemical
studies of elemental sulfur and thiosulfate disproportionation in Desulfocapsa
sulfoexigens have shown that enzymes involved in canonical sulfate reduction (sulfate
adenylyl transferase, adenylylsulfate reductase, sulfite reductase) are also mediating
thiosulfate and likely elemental sulfur disproportionation [3]. Using differential
coverage binning we have isolated a draft genome of the AOM bacterial partner from a
metagenome of a highly enriched AOM culture originating from sediments of the
Mediterranean mud volcano Isis. 228 contigs constituted the 3.7 Mb draft genome
containing a full length 16S ribosomal DNA clustering within the SEEP-SRB1 group of
DSS. Metagenome binning validation using essential single copy gene (ESCG) analysis [4]
indicated that the draft genome was almost complete and contamination-free (101 of
104 unique ESCG, 3 duplicates). Within the draft genome we found all key genes for the
canonical sulfate reduction pathway (Sat, AprAB, DsrAB) as well as genes encoding for
putative accessory proteins for sulfate reduction (e.g. DsrC, inorganic pyrophosphatase).
mRNA expression analysis showed that these genes were among the 10 highest
expressed genes and thus are likely involved in sulfur metabolism of DSS. Furthermore
we found in immediate proximity to Sat and Apr genes a well expressed putative operon
comprised of four molybdopterin oxidoreductases, two of which show high similarity to
polysulfide reductase (NrfD-type family).
[1] Reeburgh WS (2007) Chem. Rev. 107(2), 486 – 513.
[2] Milucka J et al. (2012) Nature 491, 541-546.
[3] Frederiksen T and Finster K (2003) Biodegradation 14.3, 189-198.
[4] Albertsen M et al. (2013) Nature biotechnology 31.6, 533-538.
31
Session: Physiology and Biochemistry
Invited Lecture
L23
What is the physiological product of the DsrAB dissimilatory
sulfite reductase?
Inês A. C. Pereira1, André Santos1, Sofia S. Venceslau1, Fabian grein1, William D. Leavit2,
David T. Johnston2, Christiane Dahl3
1
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa,
Oeiras, Portugal
2 Department of Earth & Planetary Science, Harvard University, Cambridge, MA, USA
3 Institut for Microbiology and Biotechnology, University of Bonn, Germany
Many questions remain about how energy is conserved in sulfur-metabolizing
organisms. A key reaction in microbial sulfur metabolism is the reduction of sulfite by
the dissimilatory sulfite reductase, DsrAB. This enzyme is present in sulfate, thiosulfate
and sulfite reducing organisms, and also in sulfur-oxidizers. The mechanism of sulfite
reduction by DsrAB has long been the subject of controversy due to the in vitro
formation of thiosulfate and trithionate, in contrast to the closely-related assimilatory
enzyme that produces only sulfide. Recent studies have identified the small protein DsrC
[1] and the DsrMKJOP membrane complex as physiological partners of DsrAB [2]. In
particular, a crystal structure of DsrAB in complex with DsrC suggested the involvement
of the latter protein in sulfite reduction and led to the proposal of a new mechanism for
this reaction [3]. I will present recent in vivo and in vitro studies that reveal the function
of DsrC in sulfite reduction, identifying the mechanism and physiological product of this
reaction. These results implicate the respiratory membrane complex DsrMKJOP in the
process, providing a direct link to energy conservation.
1. Venceslau SS, Stockdreher Y, Dahl C, Pereira IAC. 2014 Biochim Biophys Acta-Bioenerg 1148
2. Grein F, Ramos AR, Venceslau SS, Pereira IAC. 2013 Biochim Biophys Acta –Bioenerg, 1827, 145
3. Oliveira TF, Vonrheim, Matias PM, Venceslau SS, Pereira IAC, Archer M 2008 J Biol Chem 283, 34141
32
Session: Physiology and Biochemistry
L24
New insights into the energy metabolism of Desulfovibrio
vulgaris: The role of FlxABCD-HdrABC, a novel NADH
dehydrogenase-heterodisulfide reductase
Sofia Venceslau1, Ana Raquel Ramos1, Fabian Grein1, Irene Raccagni1, Gonçalo Oliveira1,
Kimberly Keller2, Judy Wall2, Inês Pereira1
1
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa,
Oeiras, Portugal
2 University of Missouri, Biochemistry Department, Columbia, USA
Flavin-based electron bifurcation (FBEB) has been recently recognized as an important
process for the energy metabolism of anaerobic organisms [1]. Here, we report on a new
family of proteins, the Flavin oxidoreductase (FlxABCD), which is a new NADH
dehydrogenase that, together with a heterodisulfide reductase (HdrABC), seems to be
involved in FBEB [2]. The flxABCD genes are usually found next to hdrABC genes [3], and
this gene cluster is found in a large number of anaerobes, suggesting a general and
important role in their bioenergetics. In the case of the sulfate reducing organism
Desulfovibrio vulgaris Hildenborough the hdr-flx genes are part of the same
transcriptional unit. The levels of transcripts and proteins of the hdr-flx gene cluster
were increased in growth with ethanol/sulfate and to a less extent in pyruvate
fermentation. Two mutant strains were generated, one lacking expression of the hdr-flx
gene cluster and a ΔflxA mutant. Both mutants were impaired in growth with
ethanol/sulfate, whereas growth was restored in a flxA-complemented strain.
Furthermore, the wild-type and complemented strain produce ethanol as a product of
fermentation, which is not observed with both mutants. Our results show that in
D. vulgaris the FlxABCD-HdrABC proteins are essential for NADH oxidation during
growth on ethanol, probably involving a FBEB mechanism that couples reduction of
ferredoxin and DsrC, whereas in fermentation they operate in reverse, reducing NAD+
for ethanol production. This provides the first link between NADH and sulfate (sulfite)
reduction through the DsrC protein [2,4].
[1] Thauer RK, et al. (2008) Nat. Rev. Microbiol. 6, 579-591.
[2] Ramos AR, et al. (2014) Environ. Microbiol. DOI: 10.1111/1462-2920.12689.
[3] Pereira IAC, et al. (2011) Front. Microbiol. 2, 69.
[4] Venceslau SS, et al. (2014) Biochim. Biophys. Acta 1837, 1148-1164
33
Session: Physiology and Biochemistry
L25
Crucial role of DsrC in dissimilatory sulfite reduction
André A. Santos, Sofia S. Venceslau, Fabian Grein, Inês A. C. Pereira
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa,
Oeiras, Portugal
The difference between assimilatory and dissimilatory sulfite reduction is an important
question that remains to be answered. Both assimilatory and dissimilatory sulfite
reductases contain the same unique catalytic site: a siroheme-[4Fe4S] coupled cofactor.
It is also known that the assimilatory sulfite reductase reduces sulfite directly to sulfide.
On the other hand several in vitro studies revealed that the dissimilatory sulfite
reductase (DsrAB) reduces sulfite to a mixture of trithionate, thiosulfate and sulfide. In
2008 Oliveira and coworkers proposed a new mechanism where DsrAB cooperates with
another protein (DsrC) to reduce sulfite to sulfide. The present work reveals the
relationship between DsrAB and DsrC. DsrC increases the activity of DsrAB in sulfite
reduction without formation of sub-products. Our results show that DsrC is directly
involved in dissimilatory sulfite reduction and allow the identification of the mechanism
and physiological product of this essential reaction.
34
Session: Physiology and Biochemistry
L26
Chemolithoheterotrophy – new insights into an often
forgotten yet widespread metabolic trait
Rich Boden, Lee Hutt
University of Plymouth, UK
Oxidation of sulfur anions by heterotrophic Bacteria has been recognised for over 100
years. This can be divided into the so-called 'gratuitous oxidation', occuring with no
apparent increase in yield or benefit to the organism and 'fortuitous oxidation' in which
increases in yield and/or specific growth rate may occur due to additional ATP/[H]
produced in S-oxidation – chemolithoheterotrophy. This is not to be confused with
mixotrophic metabolic modes in which sulfur oxidation supports chemolithoautotrophic
growth occurring simultaneously with heterotrophic growth, as observed in Paracoccus
spp., for example.
We have revisited sulfur oxidation in a number of strains historically dubbed
"Thiobacillus trautweinii" - viz. Pseudomonas sp. T (Trautwein, 1921) and
Achromobacter sp. B (Starkey, 1934). In addition to confirming the nature of the sulfur
oxidation pathways and enzymes involved as well as understanding the bioenergetic
benefits to the organism we have understood the triggers behind fortuitous vs
gratuitous oxidation. We have demonstrated that chemolithoheterotrophy is not
triggered specifically by carbon-limited growth as has previously been proposed as
identical increases in yield can be observed in chemostats limited by carbon, oxygen or
by phosphate when media are supplemented with thiosulfate rather than in growth on
sugars or organic acids alone.
Thiosulfate dehydrogenase (EC. 1.8.2.2) activity was found in all strains examined and
expression was induced by the presence of thiosulfate, however, this alone was not
sufficient to produce an increase in yield. In batch cultures in which cells are not limited
by intracellular ATP levels, no increase in yield occurs but in the chemostat in which
cells are limited by ATP, an intracellular “ATP cap” acts as the trigger – when ATP levels
in the cell fall below this ‘cap’, additional ATP from sulfur oxidation results in a yield
increase, but when ATP in cells is above it, no benefit occurs.
35
Session: Physiology and Biochemistry
Invited Lecture
L27
An integrated view on sulfur oxidation in purple sulfur
bacteria
Christiane Dahl
Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität
Bonn, Bonn, Germany
Among the sulfur-oxidizing anoxygenic phototrophic bacteria, the Gammaproteobacterium Allochromatium vinosum has been developed into a model organism
not only for biochemical and structural analysis of enzymes involved in oxidative sulfur
metabolism but also for a systems biology approach including comparative genome
analysis, genome-wide transcriptional profiling, differential expression proteomics and
metabolomic profiling (1, 2). Thus, a rather comprehensive and coherent picture of
bioenergetic processes and sulfur oxidation via the Dsr (dissimilatory sulfite reductase)
pathway can now be provided. Classical reverse genetics and in vitro analyses of sulfur
transfer reactions via tandem mass spectrometry further aided the detection of new
genes/proteins participating in oxidative sulfur metabolism. The identification of the
cytoplasmically oriented sulfite-oxidizing iron-sulfur molybdoprotein SoeABC as a major
player in the oxidation of sulfite to sulfate and the detection of extensive sulfur
trafficking networks involving rhodanese, TusA, DsrE-like proteins, DsrEFH and DsrC in
the cytoplasm A. vinosum (3) serve as examples. An rhd-tusA-dsrE2 or at least a tusAdsrE2 arrangement also occurs in many photo- and chemotrophic sulfur oxidizers that
do not contain the Dsr pathway. Those sulfur oxidizers include members of the genera
Thiorhodospira, Ectothiorhodospira, Thioalkalivibrio and Acidithiobacillus. Here, the tusAdsrE2 genes are linked with genes encoding a possible heterodisulfide reductase
complex, (a) liponamide-binding protein(s) and proteins involved in biosynthesis of the
latter. These findings again incite discussion about previous suggestions of a new sulfur
oxidation pathway involving an HdrC1B1AHypHdrC2B2 complex (4).
1. Weissgerber, T et al. 2014. Metabolomics 10:1094-1112.
2. Weissgerber, et al. 2014. Appl. Environ. Microbiol. 80:2279-2292.
3. Stockdreher, Y et al. 2014. J. Biol. Chem. 289:12390-12403.
4. Quatrini, R et al. 2009. BMC Genomics 10
36
Session: Physiology and Biochemistry
Invited Lecture
L28
Sulfur and beyond: Energy sources for sulfur-oxidizing
symbionts
Jillian M. Petersen
Symbiosis Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
Chemosynthetic symbioses between sulfur-oxidizing bacteria and marine invertebrates
were first discovered in 1977 at deep-sea hydrothermal vents but are now known to
occur in a wide range of habitats including coral reef sediments, seagrass beds, cold
seeps and sunken whale carcasses. On the host side, these associations have evolved
multiple times in convergent evolution in at least 9 animal groups such as flatworms,
annelids, nematodes, mussels, clams, and snails. Similarly, chemosynthetic symbionts
have evolved – and are continuing to evolve – from numerous bacterial lineages. Many
are so closely related to free-living chemosynthetic bacteria that at the 16S rRNA level,
they can be considered to belong to the same genus or even the same species (Dubilier
et al. 2008).
For the first thirty years after their discovery, sulfur-oxidizing symbionts were assumed
to use reduced sulfur compounds as their sole energy sources. Only a few studies have
examined the genomic potential for other energy sources and even fewer have
investigated which energy sources are used in situ. We recently discovered that
chemosynthetic symbionts use a surprisingly wide range of energy and carbon sources
that includes hydrogen, carbon monoxide, and organic carbon compounds (Petersen et
al., 2011 Nature, Kleiner et al. 2012 PNAS, Unpublished results). In my talk, I will present
an overview of my research in this area and discuss if the metabolic versatility of both
symbiotic and free-living sulfur-oxidizing bacteria may be much greater than previously
recognized. I will also discuss the role of horizontal gene transfer as the mechanism
driving this metabolic versatility.
Dubilier N, Bergin C, Lott C. 2008. Symbiotic diversity in marine animals: the art of harnessing
chemosynthesis. Nature Reviews Microbiology 6: 725-740
Kleiner M, Wentrup C, Lott C, Teeling, H, Wetzel S, Young J, Chang Y-J, Shah M, VerBerkmoes NC, Zarzycki J,
Fuchs G, Markert S, Hempel K, Voigt B, Becher D, Liebeke M, Lalk M, Albrecht D, Hecker M, Schweder T,
Dubilier N. 2012. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal
unusual pathways for carbon and energy use. Proc. Natl. Acad. Sci. USA. 109: E1173-E1182.
Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe
V, Pelletier E, Fink D, Borowski C, Bach W, Dubilier N. 2011. Hydrogen is an energy source for
hydrothermal vent symbioses. Nature 476: 176-180.
37
Session: Physiology and Biochemistry
L29
Oxidation of thiosulfate and sulfite by the hyperthermophilic
bacterium Aquifex aeolicus
Souhéla Boughanemi, David Ranava, Marie-Thérèse Giudici-Orticoni, Marianne Guiral
Bioenergetics and Protein Engineering Laboratory, CNRS-Aix-Marseille University,
Mediterranean Institute of Microbiology, 31 chemin Joseph Aiguier, 13402 Marseille cedex
20, France
Aquifex aeolicus is a hyperthermophilic, chemolithoautotrophic and microaerophilic
bacterium that uses molecular hydrogen or inorganic sulfur compounds as electron
donor to grow. On the basis of genome analysis and biochemical studies, we have
proposed a general model of its sulfur metabolism. A significant effort has been made to
characterize the enzymes of this metabolism, but much remains to be done to better
understand the oxidation of sulfur compounds. We have shown using an Oxygraph that
oxygen is consumed by entire cells or membrane fraction, with thiosulfate or sulfite as
electron donor and developed a protocol to visualize both the thiosulfate- and sulfiteoxidase activity directly in native gel. At least one protein can oxidize these sulfur
compounds in vitro with an artificial electron acceptor. This protocol allowed us to (i)
localize the thiosulfate-oxidase and sulfite-oxidase activity in the membrane fraction,
and (ii) demonstrate that the two activities are localized together in the gel, suggesting
that they arise from the same molecular entity, a complex of about 500 kDa. With the
aim of characterizing this complex, we have started to purify it from the membrane of A.
aeolicus. Mass spectrometry analysis of a partially purified fraction indicated that it
contains a heterodisulfide reductase (HdrABC) and additional proteins encoded by the
hdr operon as well as a molybdenum-dependant three-subunit enzyme annotated as
DMSO reductase. This last, which we had already characterized as a sulfur reductase,
might also catalyze sulfur compounds oxidation and could be, as proposed in the sulfur
bacterium Allochromatium vinosum, a cytoplasmic sulfite-oxidizing complex that was
missing from the sulfur metabolism of A. aeolicus. We are currently purifying this
molybdenum oxidase as well as the Hdr, which seems to be an essential enzyme in
bacterial energy sulfur metabolism, to shed light on their metabolic role.
38
Session: Physiology and Biochemistry
L30
Organosulfur compound metabolism in the human pathogen
Haemophilus influenzae
Dk Seti Maimonah Othman1, Noor Marian Muda1, Rabeb Dhouib1, Horst J Schirra1, 2,
Alastair G McEwan1, Ulrike Kappler1
1
2
School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
Centre for Advanced Imaging, The University of Queensland, Australia
Non-typeable Haemophilus influenzae (NTHi) is a host-adapted pathogen that causes a
variety of acute and chronic infections including otitis media, non-CF bronchiectasis and
chronic obstructive pulmonary disease (COPD). NtHi generates energy via a ‘respiration
assisted fermentation’ that relies on a mixed acid type fermentation linked to a versatile
respiratory chain used for redox balancing. This respiratory chain contains two putative
sulfoxide converting molybdenum enzymes, a DmsA-type dimethylsulfoxide (DMSO)
reductase and a TorZ-like enzyme. Both enzymes were highly expressed under mostly
anaerobic conditions, which is in keeping with established roles and expression patterns
for such enzymes in e.g. E. coli. However, the main substrates for either of these
enzymes, DMSO and trimethylaminoxide (TMAO), are largely absent from the human
body, calling into question the physiological significance of these enzymes is in H.
influenzae.
Our data show that both enzymes are conserved in Pasteurellaceae, and form separate
clades within their respective enzyme families, indicating important roles in pathogen
physiology. In order to elucidate the properties and physiological roles of these
enzymes, we have created and studied dmsA & torZ mutant strains of H. influenzae. The
ΔdmsA strain showed defects in biofilm formation and colonization of epithelial cells,
while the ΔtorZ strain showed minor changes in tissue cell colonization. Our
characterization of the purified TorZ enzyme showed low affinities to DMSO and TMAO,
but high affinity for methionine sulfoxide as a substrate, further corroborating the fact
that this group of enzymes fulfils a novel function in bacterial physiology. Gene
expression patterns varied for the two sulfoxide reductases varied in different strains of
H. influenzae, which may be indicative of niche specific adaptation. Based on our results
we propose that DmsA & TorZ may act on sulfoxides produced from e.g. sulfur
containing amino acids during interaction of NTHi with the immune system.
39
Session: Sulfur Transformations
Invited Lecture
L31
The biosynthesis of the molybdenum cofactor and its relation
to sulfur metabolism
Silke Leimkuehler
University of Potsdam, Germany
Molybdenum is the only second row transition metal essential for biological systems,
which is biologically available as molybdate ion. In eukarya, bacteria and archaea,
molybdenum is bound to a tricyclic pyranopterin, thereby forming the molybdenum
cofactor (Moco). To date more than 50 Moco-containing enzymes have been purified and
biochemically or structurally characterized. The physiological role of molybdenum in
these enzymes is fundamental to organisms, since the reactions include the catalysis of
key steps in carbon, nitrogen and sulfur metabolism. The catalyzed reactions are in most
cases oxo-transfer reactions or the hydroxylation of carbon centers. The biosynthesis of
Moco has been intensively studied, in addition to its insertion into molybdoenzymes. In
particular, a link between the biosynthesis and maturation of molybdoenzymes and the
biosynthesis and distribution of FeS clusters has been identified in the last years. Here,
both pathways are directly linked by the sulfur mobilizing enzyme in the cell: The
sulfurtransferase for the dithiolene group in Moco is common also for the synthesis of
FeS clusters, thiamin and thiolated tRNAs. Here, the main focus is on the biosynthesis of
the molybdenum cofactor in bacteria, its modification and insertion into
molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur
transfer in the cell.
40
Session: Sulfur Transformations
L32
Comparative metabolic studies of the halo-alkaliphilic
chemolithoautotrophic sulfur-oxidizing bacterium
Thioalkalivibrio thiocyanoxidans ARh2
Tom Berben1, Dimitry Sorokin2, 3, Gerard Muyzer1
1
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam,
The Netherlands
2 Winogradsky Institute of Microbiology, RAS, Moscow, Russia
3 Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
Soda lakes are characterized by their extremely high pH and moderate to high salinity.
Carbonate is the dominant anion, leading to a uniquely stable sodium
carbonate/bicarbonate buffer system which has a maximum buffering capacity at pH
9.5-10. Despite these extreme conditions, soda lakes harbor a rich biodiversity that
drives active biogeochemical cycles, of which the sulfur cycle is one of the most active.
One of the dominant genera of sulfur oxidizers is Thioalkalivibrio, a group of high salttolerant, alkaliphilic, chemolithoautotrophic Gammaproteobacteria. They are capable of
oxidizing a variety of inorganic sulfur compounds, such as sulfide, thiosulfate, elemental
sulfur and tetrathionate. Some strains also have the ability to use the C-1 sulfur
compound thiocyanate (NCS-) as electron-donor, sulfur and nitrogen source. We have
performed chemostat cultivations of Thioalkalivibrio thiocyanoxidans ARh2 grown on
either thiosulfate or thiocyanate followed by transcriptomics analysis aiming to uncover
difference in enzymatic profiles expressed with two different substrates. Furthermore,
comparative analysis on a large set of Thioalkalivibrio genomes sequenced at the DOE’s
Joint Genome Institute has raised additional questions regarding the physiology and
biochemistry of sulfur oxidation in this group. In the absence of the sulfane
dehydrogenase SoxCD, the dissimilatory sulfite reductase (DSR) pathway running in the
reverse direction is the only known alternative to oxidize zero-valent sulfur to sulfite,
but comparative genomics has shown that many sequenced genomes of Thioalkalivibrio
lack the DSR cluster as well as SoxCD. A systems biology approach using transcriptomics
was used to investigate the differential expression of genes involved in the sulfur
oxidation in T. thiocyanoxidans ARh2. Closing the gaps in our knowledge of the sulfur
cycle is essential for creating a complete picture of the microbial ecology in soda lakes.
41
Session: Sulfur Transformations
L33
Ecology and ecogenomics of uncultured sulfate-reducing
bacteria ubiquitous and abundant in marine sediments
Marc Mussmann, Stefan Dyksma, David Probandt, David Virant, Kin Ovanesov, Sten
Littmann
Max Planck Institute for Marine Microbiology, Germany
Sulfate reduction is the key electron accepting process that drives anaerobic carbon
mineralization in marine coastal sediments. Despite this, we still know little about the
ecology and ecophysiology of the sulfate-reducing bacteria (SRB) responsible. We used
16S rRNA gene pyrotags and fluorescence in situ hybridization (FISH) to investigate the
identity and abundance of SRB in 9 coastal sediments in Europe and Australia. The
uncultured Sva0081-group, which includes the sulfate-reducing endosymbionts of the
gutless oligochaete Olavius sp., and was first described in clone libraries from Svalbard
sediments, was a ubiquitous and highly abundant member of SRB communities in
diverse habitats from the deep sea to intertidal sediments. Single-cell genomes and
metatranscriptomes revealed that they use diverse energy sources including organic
acids, aromatic compounds and hydrogen. Expression of high-affinity transporters for
carbohydrates, dicarboxylates, polyamines and amino acids/peptides shows that a
diverse range of substrates is used in situ. The broad array of defense mechanisms
against oxidative stress that are encoded in Sva0081-SRB genomes could explain their
remarkable ability to thrive in fluctuating environments such as tidal sediments.
Genome comparisons with other SRB revealed potential physiological properties unique
to Sva0081-SRB compared to other known SRB. For instance, we identified a highly
expressed high-affinity ABC phosphate transporter that had not been previously found
in SRB. Quantification of phosphorus levels in single Sva0081-cells via SEM-EDS
suggested that cells from the uppermost tidal sediment layer (0-2.5 mm) accumulate
significantly more phosphorus/phosphate than cells from deeper layers. The highly
versatile metabolism of the Sva0081-SRB may provide them with a distinct competitive
advantage, and could explain their remarkable success in diverse marine habitats.
42
Session: Biotechnology
Invited Lecture
L34
Applications of the biological sulfur and selenium cycles in
environmental biotechnology
Piet Lens
UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
43
Session: Biotechnology
Invited Lecture
L35
Sulfur-metabolizing microorganisms in oil degradation and
corrosion
Ian Head1, Ana Suarez-Suarez1, Luiza Andrade1, 2, Angela Sherry1, Sven Lahme1, Carolyn
Aitken1, Martin Jones1, Neil Gray1, Casey Hubert1, 3
1
School of Civil Engineering and Geosciences, Newcastle University, UK
Instituto Nacional de Tecnologia –INT, Av. Venezuela, Rio de Janeiro, Brasil
3 Department of Biological Sciences and Energy Bioengineering and Geomicrobiology
Group, University of Calgary, Canada
2
The significance of sulfur-metabolizing microorganism for petroleum and petroleum
systems was first recognized as long ago as the 1920s when Bastin first isolated sulfatereducing bacteria from petroleum reservoirs in Illinois. Since those seminal studies, the
reach of microbial sulfur metabolism in petroleum microbiology has ranged from
fundamental new discoveries in microbial hydrocarbon metabolism to the recognition of
the role of sulfur metabolizing microorganisms in economically significant processes
such as petroleum reservoir souring, corrosion and oil biodegradation. Exploration of
the microbial metabolism of individual hydrocarbon compounds by sulfate-reducing
bacteria has transformed our appreciation of what is biochemically possible in anoxic
systems with the discovery of novel mechanisms for activation of stable hydrocarbons.
However relatively little work has been conducted on the microbial metabolism of crude
oil, one of the most complex natural substances on Earth, containing tens of thousands
of different compounds resolvable with state-of-the-art high resolution massspectrometry techniques. The role of sulfate-reducing microorganisms in
transformations of a range of saturated and aromatic hydrocarbons in crude oil will be
explored both from the view-point of their importance in attenuation of oil pollution in
anoxic sediments but also in relation to their operational significance to the oil industry
and understanding fundamental questions about the deep biosphere. The relationship
between petroleum and sulfur bacteria also encompasses sulfide-oxidizing bacteria
which have been implicated as agents in nitrate-mediated control of reservoir souring.
However these organisms may have a dual personality leading to unintended
consequences in the form of microbial influenced corrosion. The many facets of the
interaction of the sulfur cycle with petroleum systems will be explored in this
presentation.
44
Session: Biotechnology
L36
Development and application of acidophilic sulfidogenic
bioreactors for combined pH amelioration, sulfate removal
and selective recovery of metals from acidic waste waters
Ana Laura Santos1, Roseanne Holanda1, Sabrina Hedrich2, Ivan Ňancucheo3, Carmen
Falagán1, Barry Grail1, Barrie Johnson1
1
College of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655
Hanover, Germany
3 Instituto Tecnológico Vale, Belém, Brazil
2
Acidic, sulfate-enriched waste waters can be generated by different industrial processes.
Mining of metals and coals is notorious in this context, often producing waste streams
that also contain elevated concentrations of various transition metals and aluminium.
Dissimilatory biosulfidogenesis (the production of hydrogen sulfide by microbial
reduction of sulfate and other more oxidized forms of sulfur in anoxic environments)
has great potential for ameliorating such waste waters. Biosulfidogenesis is an acidconsuming process (at pH <7), lowers concentrations of soluble sulfate, and the
hydrogen sulfide generated can react with chalcophilic metals present to produce
insoluble sulfide phases. We have developed continuous flow biofilm sulfidogenic
reactors which, in contrast to similar systems, are populated by consortia of acidophilic
and acid-tolerant sulfate-reducing bacteria, and operate effectively at set pH values
between pH 2.5 and 5. The indigenous communities respond to changes in operating pH
values by, for example, more acidophilic species becoming more dominant at lower pH
values, and vice-versa. We have used the reactors (2 L, working volume) to increase the
pH of acidic, metal-rich waste waters, lower their concentrations of sulfate, and to
remove metals selectively, thereby facilitating their recovery and recycling. The modular
units are highly versatile, operate with minimal control, and can be readily configured to
remediate acidic waters of widely different chemical compositions where the primary
objectives (pH amelioration, sulfate removal or metal recovery) may vary. Examples will
be presented where the acidophilic sulfidogenic bioreactors have been used to remove
sulfate from acidic groundwater (Germany) and mine process water (Chile), and to
selectively recover transition metals (copper, zinc etc.) from metal mine drainage waters
in Sweden, Brazil and Wales.
45
Session: Biotechnology
L37
Oxidation of inorganic sulfur compounds in metal sulfide
processing wastewaters generates an electrical current in
microbial fuel cells
Gaofeng Ni, Mark Dopson
Linnaeus University, Sweden
Acidophilic microorganisms optimally grow at low pH that is often generated by the
oxidation of inorganic sulfur compounds to sulfuric acid. An abundant source of
inorganic sulfur compounds, such as tetrathionate and thiosulfate, is wastewater
generated during sulfide mineral processing. Microbial oxidation of the inorganic sulfur
compounds can be exploited in a microbial fuel cell to generate an electrical current.
Mixed cultures of acidophilic microorganisms from metal sulfide containing
environments including sediment from an acid mine drainage stream and an acid sulfate
soil were tested in a microbial fuel cell. The cultures were investigated for their ability to
donate electrons from anaerobic tetrathionate oxidation to the anode, creating an
electrical current that could be utilized for ferric iron reduction in the cathode. The
oxidation of tetrathionate during current generation was coupled to an increase in
sulfate in solution. An electrical current was also generated from the oxidation of
thiosalts in a sulfide mineral processing wastewater. Microorganisms present in the
mixed cultures were identified by high throughput next generation sequencing of the
16S rRNA gene and included autotrophic inorganic sulfur compound oxidizing
Acidithiobacillus species as well as heterotrophic and ferrous iron oxidizing Ferroplasma
spp. and Sulfobacillus spp. The coupling of inorganic sulfur compound oxidation to
current generation in a microbial fuel cell technology may be suitable for bioremediation
of sulfide mineral processing wastewaters.
46
Session: Microbial Interactions and Environmental Impacts
Invited Lecture
L38
Sulfoquinovose degradation pathways in bacteria
David Schleheck
University of Konstanz, Germany
Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is the polar headgroup of the sulfolipid
(SQDG) in all higher plants, mosses, ferns and algae, and in most photosynthetic
bacteria. SQ represents a significant proportion of the organo-sulfur in nature and, thus,
plays an important role in the biogeochemical sulfur cycle. There is evidence for at least
two SQ-degradative pathways in bacteria, but no enzymic reaction or gene in any
pathway has been defined, though a sulfoglycolytic pathway has been proposed. We
found that Escherichia coli K-12, the most widely-studied prokaryotic model organism, is
able to utilize SQ for growth. SQ is catabolized through “sulfoglycolysis”, involving four
newly discovered reactions that we established using purified, heterologously expressed
enzymes: 6-deoxy-6-sulfoglucose (SQ) isomerase, 6-deoxy-6-sulfofructose (SF) kinase,
6-deoxy-6-sulfofructose-1-phosphate (SFP) aldolase, and 3-sulfolactaldehyde (SLA)
reductase. The pathway yields dihydroxyacetone phosphate (DHAP), which powers
energy conservation and growth of E. coli, and the sulfonate product 2,3dihydroxypropane-1-sulfonate (DHPS), which is excreted. The corresponding SQ-gene
cluster is found in >90% of the known E. coli genomes, and in a wide range of other
Enterobacteriaceae, e.g., Salmonella, Klebsiella and Pantoea species. Hence, we presume
that sulfoglycolysis plays a significant role in bacteria in the alimentary tract of all
herbivores and omnivores, and in human and plant pathogens. We are currently
revealing a second degradative pathway for SQ in a typical soil bacterium, Pseudomonas
putida SQ1. This organism excretes 3-sulfolactate (SL) instead of DHPS during growth
with SQ, and the present enzymic, proteomic and analytical-chemical data indicate that
the pathway proceeds in analogy to the well-known Entner-Doudoroff pathway for
glucose-6-phosphate in Pseudomonas species, through four novel enzymes: NADdependent SQ-dehydrogenase, 6-deoxy-6-sulfogluconolactone (SGL) lactonase, 6-deoxy6-sulfogluconate (SG) dehydratase, 2-keto-3,6-dideoxy-6-sulfogluconate (KDSG)
aldolase, and sulfolactaldehyde (SLA) dehydrogenase. The excreted SL and DHPS can be
mineralized by other environmental bacteria through readily defined degradation
pathways and desulfonative enzymes. Hence, a complete degradation of SQ can be
accomplished by bacterial communities.
47
Session: Microbial Interactions and Environmental Impacts
Invited Lecture
L39
The role of sulfur in marine methane oxidation
Jana Milucka
Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen,
Germany
Methane oxidation coupled to sulfate reduction is a major process responsible for
reducing the emissions of methane, a potent greenhouse gas, from marine sediments.
Sulfate-coupled AOM is believed to be performed by a microbial consortium of
methanotrophic archaea and sulfate-reducing Deltaproteobacteria but the underlying
mechanism remains a geomicrobiological puzzle. We proposed a new model for marine
AOM, in which both methane oxidation and sulfate reduction to zero-valent sulfur is
performed by the methanotrophic archaea. Furthermore, we could show that the
associated Deltaproteobacteria are under AOM conditions capable of disproportionating
the produced sulfur in a form of disulfide to sulfate and sulfide. These new observations
expand the physiological diversity of known microbial sulfur metabolisms. Moreover,
our results suggest that zero-valent sulfur plays a key role in AOM, which has important
implications for biogeochemical carbon and sulfur cycling in marine sediments.
In my talk, I will introduce our ongoing work on sulfur cycling associated with AOM in
marine enrichment cultures, using a combination of molecular, microbiological and
biogeochemical approaches. I will present our preliminary results from metagenomic
and metatranscriptomic analyses of these enrichment cultures which provide first
insights into the enzymatic mechanisms of sulfur-cycling associated with AOM.
48
Session: Microbial Interactions and Environmental Impacts
L40
Sulfur disproportionation is achieved by co-metabolism with
photosynthetic sulfide oxidation to sulfur
Naoki Kamiya, Katsumi Matsuura, Shin Haruta
Department of Biological Sciences, Tokyo Metropolitan University, Japan
We found a novel co-metabolism of sulfur disproportionation and photosynthetic sulfide
oxidation to sulfur resulting in sulfate production from sulfide. Hot spring microbial
mats we analyzed were dominated by green filamentous photosynthetic bacterium,
Chloroflexus aggregans which anaerobically utilized sulfide as an electron donor and
produced sulfur globule. However, the microbial mats anaerobically oxidized sulfide to
sulfate. This study will present sulfur disproportionation in the mats has an important
role of sulfur consumption and sulfide supply for photosynthetic bacteria as a primary
producer. Elemental sulfur disproportionation is an anaerobic metabolism which
utilizes elemental sulfur as both electron donor and acceptor, and produces sulfate and
sulfide. Because produced sulfide decreases the energy efficiency, growth with this
metabolism requires continuous sulfide removal such as abiotic sulfide precipitation
with metal species. We are studying on sulfur metabolism of C. aggregans-dominating
hot spring microbial mats. The mats developed at 65 degree Celsius were anaerobicaly
incubated with sulfide as the sole sulfur and electron source. Sulfide concentration
decreased with increase in sulfate concentration only in the light. This sulfate
production was suppressed by the addition of molybdate, an inhibitor of ATP sulfurylase
indicating sulfur disproportionation involved in sulfate production. We confirmed
isolated C. aggregans did not produced sulfate as a result of sulfide consumption in the
same condition, and previous genome research about C. aggregans indicates this
bacterium oxidizes sulfide to most likely elemental sulfur. In order to confirm the
existence of sulfur disproportionating bacteria, the mats were repeatedly cultivated in
elemental sulfur disproportionating medium containing ferrihydrite as abiotic sulfide
remover. Sulfide production was detected during the cultivation. Our results indicated
C. aggregans acted as biotic sulfide scavenger in the microbial mats to help sulfur
disproportionation. Growth of C. aggregans was also likely promoted through sulfur
consumption and sulfide production by sulfur disproportionating bacteria.
49
Key Note Lecture
L41
Microbial sulfur metabolism and colorectal cancer risk
H. Rex Gaskins
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign,
USA
Despite the centrality of sulfur metabolism to most anaerobic microbial ecosystems,
relatively little is known about the microbial assemblages and ecological constraints that
contribute to microbial sulfur metabolism in the human colon. This gap in knowledge
exists even with compelling evidence that bacterial-derived hydrogen sulfide is linked to
prevalent human colonic disorders, namely inflammatory bowel disease (IBD) and
colorectal cancer. Most of the attention given to the contribution of sulfidogenic
microbes to colonic disorders has focused on sulfate-reducing bacteria (SRB), which are
ubiquitously present in human colonic. Much less is known regarding the abundance of
microbes capable of conserving energy through the utilization of organic sulfur sources
in the human colon.
We are examining the extent to which bacterial-derived hydrogen sulfide may serve as a
proinflammatory and genotoxic insult that modifies colon cancer risk. Data will be
presented which demonstrate that the human colonic mucosa is persistently colonized
by bacteria capable of generating sulfide from both inorganic and organic sulfur sources
along with evidence that sulfide activates molecular pathways that underlie epithelial
inflammation and hyperplasia, a phenotype common to both ulcerative colitis and
colorectal cancer. Published studies will also be summarized, which demonstrate direct
free radical based genotoxicity by exogenous sulfide that is independent of host cell
metabolism. These observations highlight the possible role of bacterial-derived sulfide
as an colonic insult that, given a predisposing genetic background, may lead to genomic
instability or the cumulative mutations characteristic of colorectal cancer.
50
Abstracts of Posters
Abstracts are organized according to the session.
51
Session: Biogeochemistry
P1
Isotopic insights into the metabolism of sulfur
disproportionation
Emma Bertran, David Johnston
Department of Earth and Planetary Sciences, Harvard University, USA
Microbial sulfur disproportionation imparts large, mass-dependent sulfur isotope effects
that are preserved in modern marine and geological materials. For example, this
metabolic pathway has been used to account for the discrepancy between the classic
fractionation limit produced by pure cultures of sulfate reducers and the isotopic
composition of sulfides in modern and paleoenvironments. Despite being attributed this
crucial role, the biochemical underpinning and physiological controls on
disproportionation that allow for such large fractionations are poorly constrained. In
addition, recent work on the capacity of sulfate reduction to produce similarly large
isotope effects has put into question the true role of disproportionation in the sulfur
cycle, accentuating our general lack of understanding of this metabolic pathway. The
very specific environmental niche occupied by disproportionation suggests even further
that identifying a high fidelity isotopic biosignature would be of great utility. Here we
present an early dataset with this longer-term goal. Starting with thiosulfate
disproportionation, the multiple sulfur isotopic composition of substrate thiosulfate, and
products sulfate and sulfide were tracked during the growth of Desulfocapsa sulfexigens
in a series of batch experiments. The time series analysis and inclusion of minor isotopes
allows added information about the isotopic effects associated with each specific step in
the reaction network. These will be used to inform isotope models built to understand
the broad role of disproportionation and oxidative pathways in the sulfur cycle.
52
Session: Biogeochemistry
P2
Motility of electric cable bacteria
Jesper Tataru Bjerg, Lars Riis Damgaard, Simon Agner Holm, Lars Peter Nielsen
Aarhus University, Denmark
Cable bacteria are filamentous sulfide oxidizers which can perform electrogenic sulfide
oxidation using periplasmic structures capable of transmitting electrons over cm
distances. All cable bacteria described so far couple sulfide oxidation with reduction of
oxygen, nitrate, or nitrite and form a monophyletic cluster within Desulfobulbaceae.
Growth studies and geochemical oscillations observed underneath photosynthetic mats
have suggested that cable bacteria are motile and responsive to oxygen and/or sulfide.
The aim of the present study was to characterize cable bacteria motility and to evaluate
its role in establishing and optimize contact with oxic and sulfidic zones. Sediment
enriched with cable bacteria was placed in microscope slide chambers that established a
transparent transition zone from sulfidic sediment to an oxic-anoxic interface. Velocity,
direction, and mode of cable bacterial motility were recorded by time-lapse microscopy.
After analysis, the identity of a subset of cable bacteria was confirmed by fluorescence in
situ hybridization. Cable bacteria exhibited gliding motility over surfaces and in
sediment, with a maximum velocity of 2.2 µm s-1, and a mean of 0.48 µm s-1. Sections of
the cable bacteria frequently formed loops and moved for extended periods with loop
sections first rather than tip first. The filaments apparently rotated around their
longitudinal axis, evidenced by loops tending to twist when parts of a filament were not
attached to a surface. Cable bacteria moved partially into oxic water and curled up near
the oxic-anoxic interface with part of the filament trailing back to the sediment. We
propose that motility serves to position the cables with an optimal balance between
numbers of cells in cathodic and anodic zones and the minimum number of current
bearing cells in between. The mechanism and cell-cell communication underlying the
observed motility are still to be resolved.
53
Session: Biogeochemistry
P3
Cellular and molecular mechanisms underpinning sulfur
isotope fractionation in sulfate reducing bacteria
Alexander Bradley1, William Leavitt1, David Johnston2, et al.
1
2
Washington University in St. Louis, Saint Louis, MO, USA
Harvard University, Cambridge, MA, USA
In this study we focus on the cellular and molecular level mechanisms of isotope
fractionation during dissimilatory sulfate reduction. At the cellular level, we have
examined the concentration dependence of sulfur isotope fractionation in two model
sulfate reducing bacteria: the freshwater strain Desulfovibrio vulgaris str. Hildenborough
and the brine strain Desulfovibrio alaskensis G20. Using continuous culture devices we
have grown each strain under constant growth rates, varying sulfate concentration from
0.1 to 10 mM. Each relationship can be fit with a Monod curve, but the fitted constants
differ markedly between strains. In previous work we held sulfate concentrations
constant and examined the relationship between sulfur isotope fractionation, and sulfate
reduction rates over a wide range of rates – the resulting relationship is a hyperbolic fit
between rate and fractionation.
We have combined these results in a model framework in which we represent the
magnitude of sulfur isotope fractionation as a function incorporating rates of electron
donor supply and sulfate supply to the cellular machinery responsible for
transformation of sulfate to sulfide, and account for strain specific factors, such as
sulfate and electron donor affinity constants.
These results are best understood by casting them into an enzymatic reaction network
in which fluxes and fractionations may be imposed at any given step. In combination
with recent work aimed at uncovering enzyme-specific sulfur isotope fractionations, this
moves us towards an understanding of the biological underpinnings of sulfur isotope
fractionation, and the genetic variations that may impose phenotypic differences
between strains. We consider the effects of selective pressure on the evolution of sulfate
and electron acquisition machinery over the course of evolutionary and Earth history.
These will aid efforts to reconstruct ambient sulfate concentrations from sedimentary
sulfur isotopic compositions.
54
Session: Biogeochemistry
P4
The impact of environmental conditions on sedimentary δ34S
records: rethinking the evolution of the microbial sulfur cycle
David Fike1, Catherine Rose1, 2, Robert Aller3
1
Department of Earth & Planetary Sciences, Washington University, St. Louis, MO 63130,
USA
2 Department of Geology, Trinity College Dublin, Dublin 2, Ireland
3 School of Marine & Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794
USA
Sulfur isotope ratio data (δ34S) have been used to provide significant insights into global
biogeochemical cycling over Earth history, providing a framework for reconstructing
both global redox budgets and microbial metabolic activity. However, as the record of
ancient oceanic conditions becomes better resolved, reports of coeval but divergent
isotopic proxies are becoming increasingly common. These sulfur isotope records are
characterized not just by divergent δ34S values, but also by differences in the spatial
signature and magnitude of isotopic variability. Such discordant data suggest that we do
not fully understand how isotopic signatures are incorporated and eventually preserved
in the rock record. Here we examine the spatial signature and magnitude of isotopic
variability in modern marine systems as a function of depositional environment and
differential microbial metabolic activity. Varying depositional conditions, particularly
sedimentary reworking, are seen to play a major role in generating and modifying the
isotopic signatures of sulfur phases in modern environments. These observations can be
extrapolated to investigate records of sulfur cycling in ancient strata. The results suggest
that many apparent secular δ34S trends may be related to changing depositional
environment rather than changes in the global sulfur cycle – with implications for how
we infer microbial metabolic activity from sulfur isotopic records. Together, these
observations provide new insights that enable us to reflect on and refine our
interpretations of chemostratigraphic δ34S data that have the potential to constrain the
behavior of the microbial sulfur cycle over geological timescales.
55
Session: Biogeochemistry
P5
The kinetics and environmental significance of sulfide
oxidation by a novel green sulfur bacterium isolated from a
stratified estuary
Alyssa J. Findlay, Thomas E. Hanson, George W. Luther III
University of Delaware, College of Earth, Ocean, and Environment, USA
The oxidation of hydrogen sulfide is an important part of the sulfur cycle that is
microbially mediated in many environments. Field studies were conducted during the
summers of 2011- 2014 in the Chesapeake Bay, USA during which the redox chemistry
and microbiology of the stratified water column were characterized. The redox
conditions, bottom water sulfide concentrations, and location of the pycnocline varied
between years. In 2011, 2013, and 2014, phototrophic sulfide oxidizing bacteria (PSOB)
were enriched from waters sampled at and below the oxic/anoxic interface, and in 2012,
2013, and 2014, light dependent sulfide loss was observed in freshly collected anoxic
water column samples. Extremely low levels of light (0.01 – 5 µEi) were found to cause
2-10 fold increases in sulfide loss over that observed in dark incubations. Laboratory
experiments conducted with enrichment cultures of PSOB from the Chesapeake Bay
constrained their sulfide oxidation kinetics under varying light and sulfide conditions.
These experiments indicate a value for Ks of 10 µM and a Vmax of 50 µM/min/mg
protein for the oxidation of sulfide. Phototrophic activity becomes light saturated over 5
µEi, and a significant uptake rate is observed under dark conditions. Oxidation products
include nanoparticulate elemental sulfur and polysulfides. These results are compared
with similar experimental determination of sulfide oxidation kinetics in Chlorobaculum
tepidum and RSC1 (a green sulfur bacterium isolated from a Bahamian sink hole).
Finally, using these results from the field and lab, a productivity model for PSOB in the
Chesapeake Bay was developed, which indicates that PSOB play an important, yet
variable, role in regulating sulfide oxidation at the pycnocline in the Bay.
56
Session: Biogeochemistry
P6
Distribution of electric fields generated by electrogenic
sulfide oxidation in Aarhus Bay sediment
Diego Giao1, 2, Nils Risgaard Petersen1, 2, Lars Peter Nielsen1, 2
1
Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade
114-116, 8000 Aarhus C, Denmark
2 Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade
114-116, 8000 Aarhus C, Denmark
Cable bacteria are long filamentous bacteria of the Desulfobulbaceae family, which are
able to create centimeter-deep suboxic zone in marine sediment by coupling distant H2S
oxidation to O2 reduction (1, 2) The long distance electron transfer between these redox
reactions creates measureable electric fields, which reflect the rates and locations of
cable bacteria activity in the sediment. We aim to describe the in situ centimeter-scale
heterogeneity of the biogenic electric fields in Aarhus Bay, and the correlations with the
distribution of cable bacteria and sulfide sources.
We employed the new electric potential microsensor in box cores of intact sediment to
calculate the current densities associated to the biogenic electric fields and their spatial
distribution. We also measured the depth distribution of cable bacteria and FeS, as they
are potentially the best proxies to understand the in situ distribution of biogenic electric
fields.
The activity and cable bacteria were very heterogeneously distributed with current
densities varying from 6 to 398 mA m-2 among spots only few centimeters apart. These
range of current densities are comparable to the ones we measured in Tokyo Bay
(Japan), and to rates calculated from geochemical data in The Netherlands and the North
Belgium coast (3).
This is the first report of the in situ presence of cable bacteria in Aarhus Bay and their
electric fields associated to electrogenic sulfide oxidation. Our results show a high
spatial heterogeneity that we do not observe in experiments with homogenized
sediment. This suggests that in situ processes like bioturbation, could be key players in
the distribution of electrogenic sulfur oxidation by cable bacteria.
[1] Nielsen, L.P., et al (2010). Nature 463, 1071–1074.
[2] Pfeffer, C., et al (2012). Nature 491, 218–221.
[3] Malkin, S.Y., et al (2014). ISME J 1–12.
57
Session: Biogeochemistry
P7
Geochemical gradients in marine sediment are reflected in
the community composition of sulfate-reducing
microorganisms
Lara M. Jochum1, Lars Schreiber1, Alexander Loy2, 3, Claus Pelikan2, Bo Barker
Jørgensen1, Andreas Schramm1, 4, Kasper U. Kjeldsen1
1
Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus,
Denmark
2 Department of Microbiology and Ecosystem Science, Division of Microbial Ecology,
Faculty of Life Sciences, University of Vienna, Vienna, Austria
3 Austrian Polar Research Institute, Vienna, Austria
4 Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
Sulfate reducing microorganisms (SRM) are key drivers of anaerobic organic matter
mineralization in marine coastal sediments and thereby represent an important link
between the marine sulfur and carbon cycles. Marine sediments are populated by an
uncultured diversity of SRM and the factors controlling their vertical distribution remain
largely unknown. Using qPCR and high throughput sequencing of dsrB, a functional
marker gene for SRM, we aimed to relate SRM community structures to distinct
geochemical zones of coastal sediment.
We analyzed samples from the sediment surface, the underlying sulfate-rich zone, the
Sulfate-Methane-Transition-Zone (SMTZ: the depth at which sulfate becomes depleted
and methanogenesis takes over) and the methanogenesis zone from four stations in
Aarhus Bay at which the SMTZ occurred at different depths.
According to qPCR the relative abundance of SRM compared to the total microbial
population decreased from 5-17% in surface sediments to 1-2% in deep methanogenic
sediments depending on the station. The most striking difference between any two
geochemical zones was a 50% or higher decrease in abundance from surface sediments
to the sulfate-rich zone. Comparative qPCR assays of dsrB and aprA (another functional
marker gene for SRM) showed similar results for surface sediments, while dsrB was
more abundant than aprA in the zones below. This suggests that a proportion of dsrBcarrying microorganisms do not carry aprA genes and thus cannot conserve energy by
sulfate reduction. To describe community structures we analyzed on average 40,000
dsrB reads per sample.
The dsrB diversity dropped with sediment depth. Distinct dsrB-gene variants were
associated with the surface and sulfate-rich sediments, while deeper zones
accommodated more similar communities. However, those were composed of members
that are only distantly related to known SRM. In conclusion, abrupt SRM community
shifts occur at transitions between the sediment surface, the sulfate-rich zone and the
SMTZ where sulfate is depleted.
58
Session: Biogeochemistry
P8
Seasonal variations in concentrations and isotopic
composition of sulfur species in a low-sulfate, warm,
monomictic lake
Alexey Kamyshny1, Nadav Knossow1, Werner Eckert2, Alexandra Turchyn3, Gilad Antler3
1
Ben-Gurion University of the Negev, Beer Sheva, Israel
Israel Oceanographic & Limnological Research Ltd., Migdal, Israel
3 Department of Earth Sciences, University of Cambridge, United Kingdom
2
The main goal of this research was to study the annual variability of the concentrations
and the isotopic composition of main sulfur species and sulfide oxidation intermediates
in the water column of Lake Kinneret, monomictic fresh-water lake, in which sulfate
concentrations are below 1 mM that is similar to concentrations proposed to have
existed in the Paleoproterozoic ocean. At the deepest point of the lake, the sulfate
inventory decreases by more than 20% between March and December due to microbial
sulfate reduction leading to the buildup of hydrogen sulfide. Hydrogen sulfide inventory
in the water column increases from May to December, and sharply decreases during the
lake mixis in January. At the initial stages of stratification, sulfur isotope fractionation
between sulfate and hydrogen sulfide is low (11.6‰) and sulfur oxyanions (e.g.
thiosulfate and sulfite) are the main products of the incomplete oxidation of hydrogen
sulfide. During the stratification and at the beginning of the lake mixing (July –
December), sulfur isotope fractionation increases to 30±4‰ in October. During the
erosion of the chemocline, zero-valent sulfur prevails over sulfur oxyanions. In the
terminal period of the water column mixing (January), the inventory of sulfide oxidation
intermediates increases, and sulfur isotope fractionation decreases to 20±2‰. Sulfur
isotope fractionation between sulfate and hydrogen sulfide as well as concentrations of
sulfide oxidation intermediates can be explained either by microbial sulfate reduction
alone or by microbial sulfate reduction combined with microbial disproportionation of
sulfide oxidation intermediates. No clear positive correlation between concentrations of
sulfide oxidation intermediates in the water column and sulfur isotope fractionation
between sulfate and hydrogen sulfide was observed.
59
Session: Biogeochemistry
P9
Degradation of carbonyl sulfide, an atmospheric sulfur
compound, by Actinobacteria and fungi
Yoko Katayama1, Takahiro Ogawa2, Hiromi Kato3
1
Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Japan
Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Japan
3 Graduate School of Life Science, Tohoku University, Japan
2
Soil environment has been considered as a major sink of carbonyl sulfide (COS). COS is
the most abundant sulfur compound in the troposphere and is an important source of
the stratospheric sulfate aerosol. Therefore, COS influences the Earth’s radiation balance
and ozone chemistry. COS is also a greenhouse gas because of its high global-warming
potential. Soil microorganisms has been considered to play the important roles in the
process of sink of atmospheric COS and the enzymes such as COS hydrolase has been
isolated from chemolithoautotrophic Thiobacillus thioparus. However, distribution of
microorganisms contributing to the degradation of COS is still unknown. In this study,
we report the COS degradation by chemoorganotrophic soil microorganisms such as
Actinobacteria and fungi for better understanding the major soil microorganisms in
degradation of the atmospheric COS.
Total 43 strains of Actinobacteria that is covering 8 major taxonomic groups in this
phylum were obtained from the culture collection or isolated from soil, and the COS
degrading ability were examined. Within these, 36 strains harbored the ability, in which
Dietzia maris showed the highest activity. Fungal strains isolated from the forest soils
were phylogenetically identified based on the gene sequence analysis of the ITS region.
Total 24 fungal strains out of 42 isolates showed degradation of COS, in which 11
isolates can degrade 30 ppmv COS to less than the detection limit within 1.5 h’s
incubation. Trichoderma spp. showed the highest COS degrading activity in the fungal
isolates examined. These results indicate that COS degrading ability can be find out with
high frequencies in Actinobacteria and fungi and these microorganisms share the
important roles in degradation of atmospheric COS in soil environment.
60
Session: Biogeochemistry
P10
The role of electron-bifurcating transhydrogenase in setting
lipid H-isotope ratios in bacterial sulphate reducers
William Leavitt1, Melanie Seuss1, Magdalena Osburn2, Alexander Bradley1
1
Washington University in St. Louis, Department of Earth & Planetary Sciences, St. Louis
MO, USA
2 Northwestern University, Department of Earth & Planetary Sciences, Evanston, IL, USA
Recent studies have shown that lipids of bacterial sulphate reducers (BSRs) are strongly
depleted in deuterium relative to growth water (-250‰) (1). In aerobic
microorganisms, the deuterium to hydrogen (D/H) ratio relative to growth water varies
systematically with central C metabolism (2). However, this pattern does not hold in
sulphate reducers (1). Moreover, we have a poor understanding for the mechanism(s)
by which these isotopic signatures are imparted during lipid biosynthesis. Recent work
in aerobic methylotrophs (3) implicates transhydrogenase activity as a critical control
on lipid D/H. Transhydrogenases are a class of oxidoreductase enzymes that are
responsible for transferring reducing power between intracellular pools of pyrimidine
nucleotides. At least three classes of transhydrogenases have been described: i) proton
translocating transhydrogenase PntAB, which is known to carry an extremely large
hydrogen isotope fractionation (4); ii) soluble energy-independent transhydrogenase
UdhA, present in many proteobacteria; iii) electron-bifurcating transhydrogenase
NfnAB, present in many anaerobic bacteria and archaea. Here we focus on determining
the role of NfnAB-2 in controlling the D/H lipids in Desulfovibrio alaskensis strain G20.
Utilizing mutant strains from a transposon library (5), we have shown NfnAB-2 plays a
large role in inducing fractionation between lipid and water under some growth
conditions. We discuss the implications for understanding H-isotope fractionation
during microbial fatty acid biosynthesis in BSRs, anaerobes in general, and as a
sedimentary microbial metabolic tracer.
1. Osburn (2013) Dissertation (PhD). California Institute of Technology.
2. Zhang et al. (2009) PNAS 106, 12580–12586.3. Bradley et al., unpublished.
4. Jackson et al. FEBS Lett 464, 1–8 (1999).
5. Kuehl et al. (2014). mBio 5.
61
Session: Biogeochemistry
P11
Multiple S isotope biosignatures in Aarhus Bay sediments
Andrew Masterson1, Marc Alperin2, Gail Arnold3, 4, Will Berelson5, David Johnston1
1
Harvard University, USA
Univ. of North Carolina, Chapel Hill, USA
3 Dept. of Geological Sciences, Univ. of Texas, El Paso, USA
4 Center for Geomicrobiology, Aarhus University, DK
5 Dept. of Earth Sciences, Univ. of Southern California, USA
2
The connection between rates of microbial sulfate reduction (MSR) and the magnitude
of an expressed fractionation 34ε = δ34SSO4 - δ34SH2S in continuous cultures of sulfate
reducers has recently been extended to include 33S (Leavitt et al. 2013). The implications
of that finding for S isotope signatures in marine sediments, however, remains to be
explored. Theoretically, dramatic changes in organic matter reactivity towards sulfate
reduction would be reflected in the pore water sulfate isotope profile, caused by changes
in the rates of MSR at the metabolic scale. The purpose of this study is two-fold (1) to
ascertain whether intrinsic changes in cellular-level rates of sulfate reduction are
required to reproduce the minor isotope signatures in pore water sulfate from a shallow
water environment, and (2) to determine how solid phase sulfides reflect the mass
balance of pore water sulfide. We have explored both by carrying out the full S isotope
and geochemical characterization of a gravity core from Aarhus Bay, Denmark.
Aarhus Bay (Site M1) displays an approximately linear sulfate concentration profile, and
there is a consistent ~66‰ offset between coeval pore water SO42- and H2S, and clear
closed system behavior observed in the minor isotope (Δ33S) signatures, however,
sedimentary pyrite (δ34SFeS2, Δ33SFeS2) exhibits little downcore variability. Diagenetic
modeling of the pore water sulfate profile demonstrates that little change in intrinsic
fractionation characteristics of MSR are required to reproduce the profile. Furthermore,
the lack of strong downcore variation in pyrite isotope signatures implies that, while the
pore water sulfur species display strong closed system behavior, solid phase sulfides do
not strongly inherit those characteristics.
Leavitt W. D., Halevy I., Bradley A. S. and Johnston D. T. (2013) Influence of sulfate reduction rates on the
Phanerozoic sulfur isotope record. Proc. Natl. Acad. Sci. U. S. A. 110, 11244–9.
62
Session: Biogeochemistry
P12
The sulphur cycling and sulphide formation in deep
groundwater bedrock
Hanna Miettinen, Minna Vikman, Kaisa Marjamaa, Heikki Salavirta, Merja Itävaara
VTT Technical Research Centre of Finland Ltd, Finland
Sulphur is among the most abundant elements on Earth. It is mainly present as pyrite or
gypsum in rocks and sediments and as sulphate in seawater. In Finland there are areas
where the deep subsurface ground water has a sulphate rich layers originating from the
old Littorina Sea, the predecessor of the Baltic Sea. In some places sulphide formation in
sulphate rich water is underway whereas in other similar circumstances sulphide
formation is not measurable. This study focuses on sampling three different deep
subsurface (100 to 400 m bsl) ground water types situated near each other: Sulphate
and sulphide rich groundwater, sulphate rich groundwater and salty groundwater. The
aim is to sequence the different type of water samples for metapathways related to
sulphur cycle in DNA and mRNA fractions to compare the differences between the
samples and to discover pathways to sulphide formation. Preliminary results show that
the amount of total number of cells in different ground waters vary between 3.5⋅104 to
4.7⋅105 mL-1, the highest cell counts found in the ground water with high sulphide and
sulphate concentration and the lowest count found in the salty groundwater.
63
Session: Biogeochemistry
P13
Sulfate-reducing bacteria in Mediterranean lagoons:
similarities and disparities between the different
biogeographic areas
Christina Pavloudi1, 2, 3, Anastasis Oulas1, Katerina Vasileiadou1, 4, Christos Arvanitidis1
1
Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine
Research, 71500 Heraklion, Crete, Greece
2 Department of Biology, Faculty of Sciences, University of Ghent, 9000 Ghent, Belgium
3 Department of Microbial Ecophysiology, Faculty of Biology, University of Bremen, 28359,
Bremen, Germany
4 Department of Biology, University of Patras, 26504 Rio, Patras, Greece
Lagoons are naturally enriched habitats, with unstable environmental conditions caused
by their confinement from the sea and their shallow depth. Such ecosystems are
characterized by increased hypoxia and high concentrations of hydrogen sulfide. The
aim of the present study was to examine the sulfate reducing bacterial community in the
lagoonal sediments of the Amvrakikos Gulf (Ionian Sea, Western Greece) and to compare
it with the communities reported from other Mediterranean lagoons.
For this purpose, sediment samples were collected from five lagoons, located in
Amvrakikos Gulf (Ionian Sea, Western Greece). In each lagoon, two sampling stations
were chosen, with different connectivity to the sea. DNA was extracted from the
sediment upper layer (0-2cm) and was further processed through next generation
sequencing (454 GS FLX Titanium Series, Roche) of the V5-V6 region of the 16S rRNA
gene and of a region of the dissimilatory sulfite reductase (dsr) gene. Moreover, the dsr
sequences were processed with the SEQenv pipeline and were thus annotated with
environment
descriptive
terms
occurring
in
the
relevant
literature.
Preliminary results indicate that sequencing of the dsr gene, which is found in sulfate
reducing bacteria, provides in depth information regarding this particular phylogenetic
group which is not provided by the commonly used 16S rRNA. Furthermore, our results
indicate that ecosystem function changes in response to the geochemical variables
fluctuation as microbial diversity in the stations closer to the sea varies from the one in
the stations located inside the lagoons. In addition, each lagoonal community is
annotated with different environmental descriptive terms, at least as their abundance is
concerned, which may indicate that the communities have, to some extent, different
sources of origin.
64
Session: Biogeochemistry
P14
Sulfur isotope fractionation during evolution experiments
with sulfate reducing microbes: physiological controls and
genetic associations
Andre Pellerin1, Jyotsana Singh1, Eric Collins2, Luke Anderson-Trocme1, Boswell Wing1
1
2
Dept. of Earth and Planetary Sciences, McGill University, Canada
School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, USA
Sulfur isotope fractionation during dissimilatory sulfate reduction is controlled by the
energy metabolism of sulfate reducing microorganisms. While this metabolism responds
to variability in the local environment, it is ultimately dependent on the underlying
genotype. However, the basic interplay between microbial evolution, which determines
genotype, and S isotope fractionation has not been examined. We investigated the
evolutionary response of S isotope fractionation in Desulfovibrio vulgaris Hildenborough
(DvH) and Desulfomicrobium baculatum (Dbac) through experimental evolution.
Replicate lines of DvH and Dbac were serially transferred in batch cultures for up to
1000 generations. Both the descendant DvH and Dbac strains were more fit than their
ancestors with 20% enhancement in realized growth rates for DvH and 300%
enhancements for DBac. In-situ monitoring of population size showed that these fitness
changes largely reflected improvements in maximum growth rates. Ancestral cultures of
DvH respired more rapidly than ancestral cultures of DBac, and produced sulfide that
was slightly less depleted in 34S/32S relative to sulfate (-7.0±1.3‰ for DvH; -15.4±0.7‰
for Dbac). When the isotope assay was repeated on the evolved lines, Dbac populations
reproducibly showed a lower 34S/32S fractionation than their ancestors (-12.3±0.4‰).
On the other hand, evolved DvH populations displayed very similar fractionations to
their ancestors. As illustrated here changes in S isotope fractionation during
evolutionary adaptation of growth rate mimic, in a broad sense, known physiological
responses of S isotope fractionation to growth within, and between strains of
dissimilatory sulfate reducers. As a result, it may be possible to disentangle metabolic
and environmental effects imprinted by the sulfate reducing metabolism in natural
environments. Community-level metagenome sequencing of Dbac ancestor and evolved
populations is underway to explore the expression changes that are associated with the
evolutionary shifts described here, potentially pointing to a mechanistic bridge between
genotype and phenotype.
65
Session: Biogeochemistry
P15
Benthic sulfur cycling in the oligotrophic and oligohaline
Bothnian Bay
Bo Thamdrup, Marianela Fallas Dotti, Emma Hammarlund, Amelia-Elena Rotaru, Hannah
Sophia Weber
Nordic Centre for Earth Evolution, Department of Biology, University of Southern Denmark
The northernmost basin of the Baltic is characterized by salinities below 5, low
productivity, high riverine inputs of particulate Mn and Fe, and sparse infauna. These
conditions make the sediments relevant for studying microbial sulfur transformations
and their interactions with C, Mn and Fe cycling at low sulfate concentrations. The
biogeochemistry of Bothnian Bay sediments is poorly explored but important for
understanding the basin’s role in the Baltic system, e.g., as a phosphorus sink. At the
same time, its investigation may provide insights to marine biogeochemistry in early,
sulfate-poor oceans.
With this dual aim, we determined the depth distribution of sulfur species, their isotopic
composition, sulfate reduction rates, and pathways of anaerobic carbon oxidation at
several stations in the Bothnian Bay. Sulfate reduction accounted for 35–60 % of carbon
oxidation, being suppressed by Mn and Fe reduction near the surface. Sulfate
penetration varied from 10 to 40 cm between sites, and secondary peaks of sulfate
reduction were located near the depth of depletion, indicating anaerobic methane
oxidation as a major sulfate sink. This link was further supported by the distribution of
methane. The isotopic composition, δ34S, of reduced iron sulfides accumulating in the
sediment was ~60 ‰ lighter than porewater sulfate, indicating a strong fractionation
despite relatively low sulfate concentrations. Such high fractionation may result from
the combined effects of sulfate reduction and sulfur disproportionation in the Mn- and
Fe-rich sediment, in which H2S was generally not detectable. By contrast, fractionation
factors derived from inverse modelling of profiles of concentrations and δ34S of sulfate
indicate fractionation of only ~15‰. Direct determinations of fractionation during
sulfate consumption are underway to resolve the discrepancy between fractionation
factors. Our results demonstrate that the Bothnian Bay provides an excellent setting for
exploring sulfur dynamics and sulfate dependent methane oxidation under low sulfate
conditions.
66
Session: Physiology and Biochemistry
P16
Expression analysis of sulfide oxidizing enzymes and
characterization of flavocytochrome-c sulfide dehydrogenase
in a purple sulfur photosynthetic bacterium
Tímea Balogh1, Ágnes Duzs1, Enikő Kiss1, András Tóth1, 2, Gábor Rákhely1, 2
1
Department of Biotechnology, University of Szeged, Szeged, Hungary
Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences,
Szeged, Hungary
2
Anoxygenic photosynthesis of purple sulfur bacteria requires reduced sulfur compounds
as electron donors. Oxidation of sulfide is mediated by flavocytochrome-c sulfide
dehydrogenase (Fcc) or, just like in colonic mucosa of human gut, by sulfide:quinone
oxidoreductase (Sqr). Resultant electrons are passed into the photosynthetic electron
transport chain at various points. Fcc is a periplasmic enzyme, donates electrons to
small periplasmic c-type cytochromes, while Sqr is membrane associated and transfers
electrons from sulfide oxidation directly to the quinone pool. There are relatively few
experimental data on transcriptional characteristic of enzymes, participating in sulfur
oxidation. Moreover, individual functions of Fcc and Sqr proteins are still to be
understood. Thiocapsa roseopersicina is a phototrophic purple sulfur bacterium. There
are three genes in the genome of T. roseopersicina BBS encoding enzymes potentially
involved in the oxidation of sulfide: a flavocytochrome-c sulfide dehydrogenase (FccAB),
and two different kinds of sulfide:quinone oxidoreductases (SqrD and SqrF). In order to
investigate the function of above mentioned sulfide oxidases, effect of sulfide on the
expression of fcc, sqrD and sqrF genes was characterized in T. roseopersicina BBS.
Furthermore, for biochemical analysis of flavocytochrome-c, affinity tagged recombinant
enzyme was expressed in T. roseopersicina. Subunits of the enzyme were purified by
affinity chromatography and its kinetic features were determined. The observed
transcriptomic responses indicate that Fcc catalyzes sulfide oxidation predominantly in
the presence of low sulfide concentration, while sulfide:quinone oxidoreductases play
role during growth in a media containing sulfide in higher amount. UV-visible
absorption spectroscopy – used for further investigation of Fcc – resulted peaks, that are
characteristic for redox active flavin prosthetic groups and, by measuring in vitro
activity of purified recombinant Fcc, we were proved it catalyzes sulfide dependent
cytochrome c reduction. Biochemical and kinetic properties of the enzyme were
determined and these findings absolutely correlate with experimental data of
transcriptional analysis.
67
Session: Physiology and Biochemistry
P17
Searching for structures supporting electrogenic sulfur
oxidation
Andreas Bøggild1, Poul Nissen1, Lars Peter Nielsen2, Thomas Boesen1
1
2
Department of Molecular Biology and Genetics, Aarhus University, Denmark
Department of Bioscience, Aarhus University, Denmark
Cable bacteria, a filamentous member of the Desulfobulbaceae, were first described in
2012 in marine sediment from Aarhus Bay (Pfeffer et al.), but have since been found at
other sites around the world (Malkin et al.). Their presence in sediments causes a
distinct set of depth profiles for pH, oxygen and hydrogen sulfide, which can be
explained by long distance electron transport along the multicellular filaments, enabling
electrogenic sulfur oxidation in the anoxic environment centimeters below the sediment
surface.
Though the electron transport can easily be observed indirectly in sediment cores, we
still lack an explanation of how they are transported along the bacterial filament.
Electron transport has been observed over micrometer distances in other organisms
utilizing “nanowires”, pili or pili-like appendages over, where electron transport has
been suggested to be facilitated either directly by pilin subunits or by multiheme
cytochromes organized along the nanowire (Gorby et al.). Cable bacteria could utilize
similar structural arrangements or perhaps even a completely novel way of biological
electron transport.
We are working on elucidating the subcellular structures responsible for the electron
transport in the cable bacteria using electron microscopy of the multicellular filaments,
while mass spectrometry, bioinformatics and other molecular biology and biophysical
methods are employed to identify components at the molecular level.
Gorby, Yuri A. et al. “Electrically Conductive Bacterial Nanowires Produced by Shewanella Oneidensis
Strain MR-1 and Other Microorganisms.” Proceedings of the National Academy of Sciences of the United
States of America 103.30 (2006): 11358–63. Web. 22 Aug. 2012.
Malkin, Sairah Y et al. “Natural Occurrence of Microbial Sulphur Oxidation by Long-Range Electron
Transport in the Seafloor.” The ISME journal 8.9 (2014): 1843–54. Web. 4 Aug. 2014.
Pfeffer, Christian et al. “Filamentous Bacteria Transport Electrons over Centimetre Distances.” Nature
491.7423 (2012): 218–221. Web. 2 Nov. 2012.
68
Session: Physiology and Biochemistry
P18
Targeting sulfur assimilation in the development of new
antibiotics: towards the identification and validation of dual
CysK/CysM inhibitors
Barbara Campanini1, Roberto Benoni2, Thelma Pertinhez3, Stefano Bettati2, Marco
Pieroni1, Giannamaria Annunziato1, Claudia Beato1, Gabriele Costantino1, Andrea
Mozzarelli1
1
Dipartimento di Farmacia, Università di Parma, Italy
Dipartimento di Neuroscienze, Università di Parma, Italy
3 Centro Interdipartimentale Misure, Università di Parma, Italy
2
Recent evidence indicates that blocking cysteine biosynthesis represents a valuable
strategy to diminish bacterial resistance to oxidative stress and hence reduce
persistence inside the host and increase antibiotic susceptibility (1-3). O-acetylserine
sulfhydrylase catalyzes the last step of cysteine biosynthesis in bacteria and, being
absent in mammals, represents a potential target for specific inhibitors. However,
pathogens like Salmonella typhimurium possess two isoforms of this enzyme, CysK and
CysM, whose respective roles during infection and persistency are not fully understood.
So far, CysM has been an elusive target for inhibitors development and most of the
molecules shown to be effective on CysK are much less effective on CysM (4,5). Fifteen
cyclopropanecarboxylic acid derivatives were synthesized and tested on CysK and CysM.
The activity of the compounds was measured by a fluorimetric binding assay, to
estimate Kds for the enzyme, and by a 96-well plate activity assay in the presence of Oacetylserine and bisulfide, to calculate IC50s and identify non-competitive inhibitors.
The structural determinants of binding have been evaluated by STD-NMR. With one
exception, all the molecules bind to both CysK and CysM. Differently from previous
observations (5), substituents that increase affinity to CysK also increase affinity to
CysM. The best hit inhibits both isozymes and has a Kd of 60 ± 7 nM for CysK and 1.65 ±
0.06 microM for CysM. The biological activity of the best inhibitor on E. coli grown in
minimal medium is being assessed both in liquid culture and on agar plates.
1. Turnbull, A. L. et al., (2010) Res Microbiol 161, 643.
2. Campanini, B. et al., (2015) Curr Med Chem 22, 187.
3. Amori, L. et al., (2012) MedChemComm 3, 1111.
4. Spyrakis, F. et al., (2013) Biochim Biophys Acta 1834, 169.
5. Spyrakis, F. et al., (2013) PLoS One 8, e77558
69
Session: Physiology and Biochemistry
P19
Metabolic and physiologic investigations of phototrophic
purple sulfur bacteria in vitro and in situ through flow
cytometry
Francesco Danza1, 2, Mauro Tonolla1, 2
1
Microbial Ecology Group, Microbiology Unit, Plant Biology Department, University of
Geneva, CH-1211 Geneva 4, Switzerland
2 Laboratorio Microbiologia Applicata, Dipartimento Ambiente, Costruzione e Design,
Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), 6500 Bellinzona,
Switzerland
Phototrophic purple sulfur bacteria (PSB) are described as anaerobic anoxygenic photoorganisms that utilize reduced sulfur compounds like sulfide (H2S) as electron donor
and light as energy source. In batch cultures the predominant photolithoautotrophic
metabolism is stimulated through light irradiation and H2S supply. However the PSB
natural environment, like the chemocline of Lake Cadagno (Switzerland), is subjected to
continuous fluctuations. Consequently PSB need alternative metabolic strategies. In this
sense, inclusion bodies of elemental sulfur and reduced carbon polymer like
polyhydroxybutyrate (PHB) are essential. Aim of this study is to investigate the dynamic
and ecological significance of inclusion bodies for PSB Thiodictyon syntrophicum Cad16
and Chromatium okenii. The application of flow cytometry (FC) for the characterization
of physiological behavior of natural pigmented cells is a powerful technique allowing a
rapid evaluation of PSB cell activity and dynamic description of intracellular inclusion
bodies formation and depletion. Sideward and forward light scatter (SSC, FSC) values
are linked with sulfide-oxidation and PHB biosynthesis reactions. Intracellular sulfur
globules S0 during light- oxidation of H2S increase the internal cell complexity with a
consequent rise of the SSC value. Decrease of SSC during dark period corresponds to a
reduction of intracellular sulfur inclusions. A similar light/dark dependence is observed
with FC for PHB. These observations suggest the relevance of inclusions for PSB
metabolism during dark period. Moreover a rapid kinetic reactions evaluation is also
possible. Under laboratory conditions C. okenii showed a faster H2S oxidative activity
compared to other tested PSB strains. Similarly C. okenii rapidly reacted to sulfide
addition during in situ experiment. Through FC characterization of PSB culture we have
a tool for rapid description of PSB population activity in situ. The idea is to describe in
situ the fate of a single PSB population over long time, considering the influence of
external biotic and abiotic factors.
70
Session: Physiology and Biochemistry
P20
Catalytic properties of a type VI sulfide quinone
oxidoreductase
Ágnes Duzs1, András Tóth1, 2, Brigitta Németh2, Viven Tejsi2, Tímea Balogh1, Gábor
Rákhely1, 2
1
Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H6726 Szeged, Hungary
2
Despite its toxicity sulfide involves in a variety of important physiological processes for
instance functional in human digestive system, neurotransmitter in mammals or
electron donor for photosynthetic sulfur bacteria. Flavocytochrome c (Fcc) and sulfide
quinone oxidoreductase (Sqr) are ancient flavoproteins, members of the disulfide
oxidoreductase enzyme family, which catalyse the oxidation of sulfide due to regulation
of its concentration or electron release from this reduced sulfur compound. The
photosynthetic purple sulfur bacterium Thiocapsa roseopersicina can utilize various
reduced inorganic sulfur compounds (eg. sulfide) donating electrons for
photolithoautotrophic growth. Three genes encoding sulfide oxidizing disulfide
oxidoreductases were identified in the genome sequence: fcc, sqrD and sqrF. SqrD and
SqrF belong to group IV and VI of the sulfide quinone oxidoreductase type enzymes,
respectively, which proteins have not been characterized in detail yet. For biochemical
analysis the SqrF protein fused to Strep II affinity tag was expressed in T. roseopersicina.
The recombinant membrane-bound SqrF was successfully purified from membrane
fraction to homogeneity by affinity chromatography. UV-vis absorption spectra of
oxidized and reduced forms of purified SqrF protein was recorded. Based on the changes
of characteristic peaks the covalently bound FAD cofactor is redox active in the pure
protein. The recombinant SqrF enzyme catalyzes sulfur-dependent quinone reduction
and prefers ubiquinone-type quinone compounds as electron acceptor. Effect of pH and
temperature on the SqrF activity were examined. Furthermore, kinetic parameters of
the enzyme for sulfide and quinone substrates were determined. The biochemical and
kinetic analysis of the studied type VI sulfide quinone oxidoreductase highlighted that
the affinity of this enzyme for sulfide is low, which propose that SqrF could play role in
the oxidative sulfide metabolism of purple sulfur bacteria at high sulfide concentration
conditions.
71
Session: Physiology and Biochemistry
P21
Genome sequence of an uncultivated population of the purple
sulfur bacterium Chromatium okenii
Niels-Ulrik Frigaard1, Nicole R. Posth2, Raymond P. Cox3
1
Department of Biology, University of Copenhagen, Helsingør, Denmark
Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of
Southern Denmark, Odense, Denmark
3Department of Biochemistry and Molecular Biology and Nordic Center for Earth Evolution
(NordCEE), University of Southern Denmark, Odense, Denmark
2
Chromatium okenii is a large-celled highly-motile purple sulfur bacterium which is
abundant at the top of the anoxic, sulfide-rich portion of the water column in meromictic Lake Cadagno in the Swiss Alps. We have exploited the tendency of this bacterium
to swim to the bottom of containers to physically enrich Chr. okenii from 20 L of water
from the chemocline. The absence of significant amounts of contaminating bacteria was
confirmed by making a clone library using PCR primers for bacterial 16S rRNA. All the
obtained sequences matched that reported for Chr. okenii. Genomic DNA from the
enriched bacteria was sequenced using PacBio RS and assembled into contiguous
sequences. The majority of the expected ribosomal proteins were found, supporting the
idea that most of the complete genome was covered. We will report a comparison of the
genes encoding components of the photosynthetic apparatus with the corresponding
genes from other purple sulfur bacteria.
72
Session: Physiology and Biochemistry
P22
New insights into energy conservation mechanisms in the
sulfate respiring archaeon Archaeoglobus fulgidus VC16
William Hocking, Irene Roalkvam, Runar Stokke, Ida Helene Steen
Center for Geobiology, University of Bergen, Norway
In this study a model of the energy metabolism of the sulfate-reducing archaeon
Archaeoglobus fulgidus is presented. The model is based on comparative transcriptome
profiling of heterotrophic, hydrogenotrophic and carboxidotrophic growth utilizing
either sulfate or thiosulfate as electron acceptors. The model suggests a putative lactate
dehydrogenase complex (LDHs; lldD, dld, lldEFG), also present in sulfate-reducing
bacteria, to specifically link lactate oxidation with APS reduction via the Qmo complex.
Notably these LDHs were also induced during carboxydotrophic growth. High
transcriptional levels of Fqo confirm an important role of F420H2, as well as a
menaquinone-mediated electron transport chain, during heterotrophic and
carboxydotrophic growth when either sulfate or thiosulfate is available. During
hydrogenotrophic growth, energy conservation is probably facilitated via menaquinone
to multiple membrane-bound heterodisulfide reductase (Hdr) complexes and the DsrC
protein—linking periplasmic hydrogenase (Vht) to the cytoplasmic reduction of sulfite.
A cytoplasmic Mvh:Hdl hydrogenase catalyzing putative bifurcation reaction seems
crucial for providing the Fdred needed for CO2-fixation which thus inhibits the utilization
of Fdred for energy conservation. During growth on CO, when sulfate is supplied as
electron acceptor, transcripts of a nitrate reductase-associated respiratory complex was
induced. This complex may play a role in the integration of reduced Fd into the APS
coupled respiratory chain. Genes of a singular bi-functional carbon monoxide
dehydrogenase (cdhAB-2) were continuously highly expressed, indicating a ubiquitous
role in the metabolism of CO. Finally, a putative periplasmic thiosulfate reductase was
identified by specific up-regulation. Altogether, this study has identified new redox
complexes and identified putative electron flow pathways specific for the utilization of
different substrates and terminal electron acceptors in A. fulgidus. Growth on CO seems
an intrinsic capability of A. fulgidus as dissimilatory sulfate and thiosulfate reduction
functions at high partial pressures of CO with little need for induction of novel resistance
mechanisms.
73
Session: Physiology and Biochemistry
P23
Plant sulfate metabolism: how to economise resources under
sulphate stress
Rainer Hoefgen
Max-Planck-Institute of Molecular Plant Physiology, Germany
Plants are dependent on the uptake of sulphur for growth and development. Sulfur
assimilation is a tightly regulated process. Sulphate deplete conditions lead to growth
retardation and yield depressions and specific responses including nutrient depletion
induced senescence. The plant tries though first to mobilize resources by catabolic but
also by regulatory processes which prevent flux to secondary plant metabolites, thus
compromising plant defence, in favour of primary metabolism. We used combined
transcriptomics and metabolomics analyses to identify processes and involved genes.
74
Session: Physiology and Biochemistry
P24
Physiological and biochemical examination of the moderately
thermophilic chemolithoautotroph Thermithiobacillus sp.
ParkerM
Lee Hutt, Rich Boden
University of Plymouth, UK
The genus Thermithiobacillus (Wood & Kelly 2000) comprises one species with a validly
published name, Ttb. tepidarius (DSM 3134T, Wood & Kelly 1985), isolated from the
Roman Baths at Bath (United Kingdom). The genus is one of two genera of the Class
Acidithiobacillia and is poorly understood and seemingly rare – having only two strains
in Culture Collections and no sequence data from molecular ecological studies.
Thermithiobacillus sp. ParkerM (NCIMB 8349) was isolated from the sewers of
Melbourne, Australia (Parker 1947) and originally identified as Thiobacillus thioparus. It
was re-examined recently and found to be a Thermithiobacillus sp. (Boden et al. 2011).
Chemolithoautotrophic growth of this strain was examined and compared with Ttb.
thioparus. In batch culture, thiosulfate was oxidised stoichiometrically to tetrathionate,
via a small intermediary amount of trithionate. The strain was shown to have
significantly larger specific growth rate and yield (0.153 h-1 and 5.4 g dry biomass per
mol thiosulfate) when compared to the type strain (0.047 h-1 and 2.8 g dry biomass per
mol thiosulfate). When grown in a thiosulfate, tetrathionate or trithionate limited
chemostats, it showed very similar maximum specific growth yield (Ymax) and maximum
specific growth rate (μmax) to those of Ttb. tepidarius for all three sulfur oxyanions. The
higher yield and growth rate observed in batch culture could be owing to an increased
acid-tolerance compared to the type species, allowing it to continue growth to a lower
pH. Thiosulfate dehydrogenase (EC 1.8.2.2) activity was detected in cell-free extracts
prepared from cells obtained from thiosulfate, tetrathionate or trithionate-limited
chemostats but was significantly higher in extracts prepared from thiosulfate grown
cells. The enzyme was coupled to cytochrome c552 in both strains of Thermithiobacillus,
in common with other members of the Acidithiobacillia.
75
Session: Physiology and Biochemistry
P25
More than a variation of a there - the structure of the electron
transfer complex between the SorT sulfite dehydrogenase
and its natural electron acceptor
Aaron McGrath1, Megan Maher2, Ulrike Kappler3
1
Structural Biology Program, Centenary Institute, Locked Bag 6, NSW 2042, Australia
School of Molecular Sciences, LaTrobe University, Melbourne, Vic 3086, Australia
3 School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia,
Qld 4072, Australia
2
Enzymatic sulfite oxidation is a key process in detoxification or energy generating
reactions in most living cells, however, the enzymes involved in these processes differ
markedly in their subunit and redox cofactor content. We have solved the structure of
the first heme-free bacterial sulfite oxidizing enzyme (SOE), SorT, from the sulfonatedegrading soil bacterium Sinorhizobium meliloti. The monomers of the homodimeric
SorT enzyme show the typical combination of a Molybdenum cofactor (MoCo) and a
dimerization domain. However, unlike in other SOEs, the ‘dimerization domain’ is not
actually involved in the dimerization of the enzyme, as the monomers are rotated into an
‘upside down’ configuration. This is a completely novel conformation for this type of
enzyme which appears to be the most common type of bacterial SOE and catalytic
implications are at present unclear.
The complex of SorT and its electron acceptor, SorU revealed close contact between the
redox cofactors of the two proteins (Mo-heme 8.2 Å) as well as some distortion of the
SorU protein on binding which may modulate the SorU redox potential and thus have
significance for the reaction mechanism. Compared to the permanent complex between
the SorA and SorB subunits of a previously characterized bacterial SOE the SorT/SorU
complex is less stable as evidenced by a reduced buried surface area, fewer salt bridges
and hydrogen bonds. Despite this, the final position of the heme and Mo redox cofactors
is highly similar to what was seen in the permanent SorAB complex despite a complete
lack of structural similarity between the SorB and SorU proteins. Electron transfer from
SorT to SorU was found to be slower than between SorAB and its external electron
acceptor but was similar to values reported for vertebrate sulfite oxidases which also
require docking of a heme domain near the Mo centre.
76
Session: Physiology and Biochemistry
P26
Bioinformatic analyses indicate a novel multi-enzyme system
for sulfur oxidation in prokaryotes
Tobias Koch, Christiane Dahl
Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität
Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
Broad range database analysis revealed that several chemo- and phototrophic sulfur
oxidizing prokaryotes lacking the Dsr pathway instead contain the gene cluster
hdrC1B1AhyphdrC2B2 encoding a heterodisulfide reductase (Hdr)-like protein complex
[1]. Transcriptomic [2] and proteomic [3] analyses of Acidithiobacillus species support
the notion that this Hdr-like complex is involved in a process functionally replacing the
Dsr system in the generation of sulfite. Here, we established a core set of genes present
in all sulfur oxidizers containing hdr-like genes. Just as the dsr genes, hdr-like genes are
always linked to genes for proteins involved in cytoplasmic sulfur trafficking, i.e. TusA,
DsrE and often also rhodaneses. The DsrE-related proteins fall into distinct groups
depending on their genetic linkage to dsr or hdr genes [4]. Furthermore, genes for
lipoate-binding proteins resembling glycine cleavage system component H and genes for
several enzymes responsible for biosynthesis of liponamide-containing proteins are
always located in direct vicinity of hdr-like genes. Notably, a putative dihydroliponamide
dehydrogenase is encoded immediately adjacent to the hdr-like genes in sulfur oxidizing
archaea like Metallosphaera cuprina [4]. The genomic linkage of genes for proteins
involved in sulfur trafficking, Hdr-like systems, liponamide-binding proteins and in
archaeal sulfur oxidizers also for proteins with the potential for NAD+ reduction in
conjunction with the established potential of HdrA for electron bifurcation [5] guided us
to propose new models for Hdr-linked sulfur oxidation. These include the suggestion
that part of the electrons arising from sulfane sulfur oxidation can be directly
transferred to NAD+, thereby decreasing the need for energy-requiring reverse electron
flow.
1. Venceslau et al. 2014. Biochim Biophys Acta 1837, 1148
2. Quatrini et al. 2009. BMC Genomics 10, 394
3. Mangold et al. 2011. Front Microbiol 2, 17
4. Liu et al. 2014. J Biol Chem 289, 26949
5. Kaster et al. 2011. PNAS 108, 2981
77
Session: Physiology and Biochemistry
P27
Oxidation of molecular hydrogen in the family Beggiatoaceae
Anne-Christin Kreutzmann1, Marc Mußmann1, Heide Schulz-Vogt2
1
2
Max-Planck-Institute for Marine Microbiology, Germany
Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Germany
Large sulfur bacteria of the family Beggiatoaceae are well known for their ability to grow
on reduced sulfur compounds and various organic substrates. Other electron donors
were never reported to support growth and thus are usually not considered to be of
importance for members of this family. Here, we provide evidence that molecular
hydrogen is an electron donor that can contribute significantly to the metabolic
versatility of the Beggiatoaceae. We identified genes putatively encoding [NiFe]hydrogenase catalytic subunits in several distantly related members of the family. These
genes belonged to four phylogenetically distinct groups, which are thought to represent
hydrogenases of different metabolic functions. Most of the screened strains contained
more than one type of [NiFe]-hydrogenase, suggesting that the capacity for hydrogen
oxidation is not only widespread in the family but that hydrogen oxidation may also play
a role under different ecophysiological conditions. In order to assess the importance of
hydrogen in vivo, we studied hydrogen oxidation in the chemolithoautotrophic strain
Beggiatoa sp. 35Flor, which was grown in oxygen-sulfide gradient media with
diffusional hydrogen gradients. Microsensor profiles and rate measurements suggested
that the strain oxidized hydrogen aerobically in the presence of oxygen. Under these
conditions, hydrogen oxidation supplied more than one third of the total electron
demand and hydrogen-supplemented cultures reached significantly higher biomasses.
Beggiatoa sp. 35Flor oxidized hydrogen also under anoxic conditions in cultures with
high sulfide fluxes. Anaerobic hydrogen oxidation was most likely coupled to sulfur
respiration and thus could support the disposal of internally stored sulfur to prevent
physical damage resulting from excessive sulfur accumulation. Overall, molecular
hydrogen could help members of the Beggiatoaceae to adapt more easily to the
fluctuating conditions in microbial mats by supplying energy for maintenance and
assimilatory purposes and by providing additional means to regulate the size of the
internal sulfur store.
78
Session: Physiology and Biochemistry
P28
The bifunctional tetrathionate reductase/thiosulfate
dehydrogenase TsdA: Properties and functions of the
enzymes from Campylobacter jejuni and Allochromatium
vinosum
Julia Kurth1, Kevin Denkmann1, Sam Rowe2, Myles Cheesman2, Julea Butt2, Christiane
Dahl1
1
Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität
Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
2 Centre for Molecular and Structural Biochemistry, School of Chemistry and School of
Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ,
UK
The diheme c type cytochrome TsdA represents a novel class of bifunctional bacterial
tetrathionate reductases/thiosulfate dehydrogenases. In Allochromatium vinosum TsdA
mainly acts as a thiosulfate dehydrogenase [1] whereas the enzyme from Campylobacter
jejuni preferentially catalyses tetrathionate reduction [2]. Both proteins contain an
active site heme with rare axial His/Cys iron coordination (Heme 1). A conserved
methionine is important for binding of the second heme iron (Heme 2). For CjTsdA these
ligands were verified by nIR-MCD. We intend to elucidate the mechanism(s) that govern
the catalytic bias of TsdA. As a first step, we used electrochemical approaches to
determine the standard reduction potential of the tetrathionate/thiosulfate couple as
0.19±0.02 V and to show that CjTsdA hemes 1 and 2 are redox active in the range -450 to
-270 mV and -20 to 190 mV, respectively. Regarding AvTsdA, Heme 2 has a slightly less
positive and Heme 1 a much more positive redox potential than in CjTsdA.
Spectroelectrochemistry revealed a redox-driven change in the axial ligands of at least
Heme 2 for both proteins. Moreover, we performed detailed enzyme kinetic studies and
protein film voltammetry on CjTsdA and derivatives thereof carrying replacements of
the sixth axial ligands of Heme 1 and 2. Wildtype TsdA exhibited much higher substrate
affinity for tetrathionate (19±1.7 µM) than for thiosulfate (440±18 µM). When thiolate
ligation of Heme 1 was removed by Cys138Gly substitution, Vmax decreased dramatically
but substrate affinities remained virtually unchanged. Although the TsdA active site is at
Heme 1, changes in ligation of Heme 2 affected substrate affinity. In summary, these
findings indicate cooperativity between the two hemes and show that Heme 2 plays a
pivotal role in defining the catalytic direction of this enzyme.
[1] Denkmann et al. 2012 Environ Microbiol 14, 2673.
[2] Liu et al. 2013 Mol Microbiol 88, 173
79
Session: Physiology and Biochemistry
P29
The Candidatus “Thiodictyon syntrophicum” strain Cad16T
genome revised
Samuel Luedin1, 2, 3, Francesco Danza1, 2, Pierre Schneeberger3, 4, 5, Matthias Wittwer3,
Mauro Tonolla1, 2
1
University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology
Unit, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
2 Laboratory of applied microbiology (LAM), Department of environment, constructions
and design University of applied sciences of Southern Switzerland – SUPSI, Via Mirasole
22A, CH-6500 Bellinzona, Switzerland
3 Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Austrasse, CH-3700
Spiez, Switzerland
4 Swiss Tropical and Public Health Institute, Department of Epidemiology and Public
Health, CH-4051 Basel, Switzerland
5 Agroscope Changins-Wädenswil ACW, Department of Epidemiology and Molecular
Diagnostics, CH-8820 Wädenswil, Switzerland
The meromictic alpine lake Cadagno (Switzerland) is a model ecosystem for the study of
phototrophic sulfur bacteria (PSB) communities since it provides a stable vertical
physiochemical gradient over time. High concentration of sulfate favors the
development of microbial populations directly involved in the sulfur cycle. Members of
the family Chromatiaceae such as Chromatium okenii, Lamprocystis purpurea and the
genus Thyocystis and Thiodictyon have been extensively studied by 16S rRNA sequence
analysis and have been isolated.
The CO2 fixation capacity of Candidatus “Thiodictyon syntrophicum” has been studied in
vivo and in vitro. Despite “T. syntrophicum” only represents 2% of the total PSB
community, it provides an estimate of 25% of the total primary production in the
chemocline. Further studies on the “T. syntrophicum” sulphur metabolism have led to
the discovery of novel carotene ketolases and the autotrophic dicarboxylate/4hydroxybutyrate cycle, normally found in archaea.
As a basis for further proteogenomic studies of the sulfur metabolism we sequenced the
“T. syntrophicum” 7.3 Mb genome. Here we describe the features of “T. syntrophicum”,
in combination with the draft genome and a preliminary annotation. We thereby
especially focused on the enzymatic pathways involved in sulfur metabolism and
trafficking. For the de novo assembly and finishing of the "T. syntrophicum" genome we
used a hybrid approach combining shorter IonTorrent PGM and MiSeq reads with Single
Molecule, Real-Time (SMRT) PacBio reads. To complete the genome assembly and
scaffolding the MIRA assembler was used together with an in-house developed software
pipeline. We compared this approach with a PacBio-only assembly using HGAP.
80
Session: Physiology and Biochemistry
P31
Nitrate reduction in the sulfate-reducing bacterium
Desulfovibrio desulfuricans 27774
Angeliki Marietou1, 2, Lesley Griffiths1, Jeff Cole1
1
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000
Aarhus C, Denmark
2
Some sulfate reducing bacteria have the ability to use nitrate as alternative terminal
electron acceptor to sulfate. Desulfovibrio desulfuricans strain 27774 genome includes a
six gene operon encoding for components of the periplasmic nitrate reductase system
(nap). A combination of physiological and molecular approaches was used to investigate
the regulation of nitrate reduction in a sulfate reducing bacterium. We report that the
expression of the nap operon is repressed in the absence but induced in the presence of
nitrate, suggesting the existence of a regulatory system in D. desulfuricans. Strain 27774
grew more rapidly and to higher yields of biomass with nitrate than with sulfate or
nitrite as the only electron acceptor. In the presence of both sulfate and nitrate, sulfate
was used preferentially, when cultures were continuously gassed to prevent sulfide
inhibition of nitrate reduction. qPCR experiments confirmed that nap operon expression
is regulated at the level of mRNA transcription by at least two mechanisms: nitrate
induction and sulfate repression.
81
Session: Physiology and Biochemistry
P32
Some studies of the function of the components of thiosulfate
oxidizing multi-enzyme system from the green sulfur
bacterium Chlorobaculum tepidum
Hidehiro Sakurai1, Masaharu Kitashima2, Takaaki Ito2, 3, Kazuhito Inoue1, 2
1
Research Inst. for Photobiological H2 production, Kanagawa University, Japan
Department of Biological Sciences, Faculty of Science, Kanagawa University, Japan
3 Medical Mycology Research Center, Chiba University, Japan (present address)
2
Thiosulfate oxidation is catalyzed by the collaboration of the three proteins (SoxAXK,
SoxB, and SoxYZ: the core TOMES)1,2, and the presence of the fourth component the
flavoprotein SoxF (CT1015) stimulates the reaction in the reconstituted system3) from
the phototrophic green sulfur bacterium Chlorobaculum tepidum. We will discuss some
details of the effects of SoxF on the core TOMES reaction including the inhibition of
sulfite oxidation by SoxF. SoxYZ tends to be inactivated on storage in solution, which is
ascribed in part to the oxidation of the SH group on SoxY essential to the function. The
inactivated SoxY from the heterotrophic bacterium Paracoccus pantotrophus was
reported to be reactivated greatly by incubation with sulfide but only partially with
reductants such as DTT or tris(2-carboxyethyl)phosphine (TCEP) (Quentmeier et al.
2007). The inactivation and the reactivation are explained by the oxidation state of the
SH group on SoxY and also by the conformational change of SoxYZ. We studied the
relationship between the core TOMES activity of various preparations of SoxYZ and the
changes in the molecular mass of SoxY as isolated or after various treatments by MALDITOF mass spectrometry. Our results suggest that in addition to the recovery of the
reduced SH group from the oxidized state, we need additional assumption in order to
explain the stimulating effects of sulfide.
1) Ogawa, T. et al. (2008) J. Bacteriol. 190: 6097-6110 (2008).
2) Sakurai, H. et al. (2010) Photosyn. Res. 104: 163 (2010).
3) Ogawa T. et al. (2010) Biosci. Biotechnol. Biochem. 74: 771 (2010).
82
Session: Physiology and Biochemistry
P33
Study of the respiratory Arx from the purple sulfur bacterium
H. halophila, a versatile enzyme
Barbara SCHOEPP-COTHENET1, Marielle BAUZAN2, Anne-lise DUCLUZEAU3, Florence
CHASPOUL4, Mahmoud HAJJ CHEHADE5, Fabien PIERREL5, Wolfgang NITSCHKE1
1
Bioénergétique et Ingénierie des Protéines (UMR 7281)/CNRS, Aix Marseille University,
IMM FR3479, Marseille, France
2 Institut de Microbiologie de la Méditerranée, FR3479, F-13402 Marseille Cedex 20, France
3 Beadle Center, University of Nebraska-Lincoln, 1901 Vine Street, Lincoln, NE 68588-0660,
USA
4 Unité de Chimie-Physique, Faculté de Pharmacie 13005, Marseille, France
5 Chimie et Biologie des Métaux, (UMR5249), CEA/CNRS/ JFUniversity, Grenoble, France
The three presently known enzymes responsible for arsenic-using bioenergetic
processes are arsenite oxidase (Aio), arsenate reductase (Arr) and alternative arsenite
oxidase (Arx), all of which are molybdoenzymes from the group referred to as the
Mo/W-bisPGD enzyme superfamily. Since arsenite is present in substantial amounts in
hydrothermal environments (frequently considered as vestiges of primordial
biochemistry), arsenite-based bioenergetics has early on been predicted to be ancient.
Conflicting scenarios, however, have been put forward proposing either Arr/Arx or Aio
as operating in the ancestral metabolism. Phylogenetic data argue in favor of Aio
whereas biochemical and physiological data led several authors to propose the Arx/Arr
enzyme as the most ancient anaerobic arsenite oxidising enzyme. Here we combine
phylogenetic approaches with physiological and biochemical experiments, studying the
Arx from the purple sulfur bacterium Halorhodospira halophila. This strain can use
As(III) instead of sulfide as electron donor to sustain photosynthetic growth. We show
that under physiological conditions, Arx reacts with ubiquinone to oxidise arsenite, in
line with thermodynamic considerations. Under non physiological conditions, we can,
however, force Arx to reacts in reverse, with menaquinone to reduce arsenate. The
phylogeny of the quinone biosynthesis pathway, clearly indicates that the ubiquinone
pathway is recent. An updated phylogeny of Arr/Arx furthermore indicates a recent
emergence of this enzyme. We therefore conclude that the As(III) oxidation metabolism
involving Arx is recent and that only the metabolism involving Aio can have performed
anaerobic As(III) oxidation in the Archaean. Phylogeny moreover revealed close
phylogenetic proximity between Arr/Arx and Psr or Ttr, two enzymes involved in the
respiration of sulfur compounds. The evolutionary adaptations linking Arr/Arx and
Ttr/Psr are therefore expected to mainly involve tinkering with substrate affinities in
the catalytic site. With the aim to establish the structural basis of this tinkering, we
initiated the study of Arx reactivity towards sulfur compounds.
83
Session: Physiology and Biochemistry
P34
Exploring the currently unknown pathway of elemental
sulfur disproportionation by comparative transcriptomics
with Desulfurivibrio alkaliphilus
Lars Schreiber1, Casper Thorup2, Kai Finster2
1
2
Department of Bioscience, Center for Geomicrobiology, Aarhus University, Denmark
Department of Bioscience, Section of Microbiology, Aarhus University, Denmark
The microbially mediated disproportionation of elemental sulfur represents the energyyielding transformation of elemental sulfur to sulfate and sulfide. Significant numbers of
bacteria closely related to known disproportionaters are detected in marine
environments, aquifers, and corrosive oil pipeline biofilms which indicates that sulfur
disproportionation may play an important role in many habitats. The exact importance
and ubiquity of sulfur disproportionation, however, is currently difficult to determine as
(1) its end products are quickly removed by sulfide-oxidizing microorganisms or sulfatereducer, and (2) marker genes that could help to determine the presence and activity of
sulfur disproportionators are currently unknown. This study targets the latter problem
and tries to elucidate the genetic basis of the disproportionation pathway by using
transcriptomics. We will present first results of gene expression patterns of
Desulfurivibrio alkaliphilus grown under nitrate-reducing and sulfur disproportionation
conditions.
84
Session: Physiology and Biochemistry
P35
Desulfurivibrio alkaliphilus AHT2 can couple the nitrate
dependent oxidation of sulphide to growth
Casper Thorup1, Lars Schreiber2, Kai Finster1
1
2
Department of Bioscience, Aarhus University, Aarhus, Denmark
Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
Sulphide oxidation has earlier been documented for sulphate reducers in which sulphide
is oxidized to sulphate using nitrate as electron acceptor, but growth could not be
documented. In this study we provide one of the rare examples that shows that a
member of the delta proteobacteria and close relative to Desulfobulbus, namely the
haloakalophilic strain Desulfurivibrio alkaliphilus AHT2, can couple the oxidation of
sulphide and reduction of nitrate to ammonium to growth. Triplicate cultures were
grown in 100 mL screw-capped bottles containing a modified Dethiobacter medium with
the addition of 3 mM nitrate and incubated at 30°C. Samples were taken at eight hour
intervals over two days. Nitrate and sulphate concentrations were determined by ionchromatography and sulphide and ammonium concentrations were determined using
spectrophotometric methods. Cell numbers were obtained by fluorescence microscopy
upon staining with SyBr gold. The consumption of sulphide and nitrate is accompanied
by the concomitant production of ammonium and sulphate. The net change in
concentration of substrates and products can be summarized by the following
stoichiometry: H2S + NO3- + H2O → SO42- + NH4+. This signifies a net flow of eight
electrons from sulfur to the nitrogen. An increase in cell density was observed. The
results clearly demonstrate anaerobic growth in Desulfurivibrio alkaliphilus AHT2 by
sulphide oxidation. The next step is to elucidate the pathway of sulphide oxidation in
strain Desulfurivibrio alkaliphilus AHT2 and to uncover why only few deltaproteobacteria can couple this process to growth.
85
Session: Physiology and Biochemistry
P36
Isolation of novel acidophilic sulfate-reducing bacteria for
bioremediation of acid rock drainage
Irene Sánchez-Andrea1, D. Barrie Johnson2, Alfons J. M. Stams1
1
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB
Wageningen, The Netherlands
2 School of Biological Sciences, University of Wales, Bangor LL57 2UW, UK
Acid rock drainage (ARD) refers to acid and metalliferous waters produced by the
biochemical oxidation of metallic sulfide-ores (e.g. pyrite). It produces long-term
contamination of aquifers, with secondary effects like reduced crop yields, death of fish,
etc. The environmental concern has led to increasing efforts to remediate ARD
environments and biological treatment applying sulfate-reducing bacteria (SRB) has
become a very attractive option. SRB produce alkalinity, neutralizing the AMD; and
sulfide, which reacts with chalcophilic metals in solution and precipitates them as
insoluble metal sulfides. The use of acidophilic SRB may become crucial for the process;
it avoids the need of influent neutralization and it allows a selective metal recovery by
controlling the pH of the bioremediation reactor. While there is widespread evidence of
sulfate reduction in natural and anthropogenic low pH environments, most SRB
obtained from these sites do not grow below pH 5, and there have been relatively few
reports of acidophilic/acid-tolerant isolates. Due to their biotechnological importance,
we have made an exhaustive effort to enrich and isolate novel acidophilic SRB. Two
novel species within the Desulfosporosinus genus have been obtained, one recently
published as D. acididurans. Another strain represents a new genus in the same
Peptococcaceae family, proposed as a Desulfobacillus sp. The strains showed promising
characteristics for their application such as broad range of growth in terms of pH (from
pH 3.8 to pH 7) and temperature (from 15°C to 42°C); high metal tolerance (up to 50
mM ferrous iron and 10 mM aluminium) and broad spectrum of substrate utilization for
sulfate reduction (sugars, alcohols, organic acids and hydrogen). Enrichments and novel
strains have been tested in bioreactors fed with synthetic acid mine drainage waters
containing different mixtures of heavy metals. The experiments showed the ability of the
microorganisms to perform sulfidogenesis on those extreme conditions and their
potential for selective metal recovery.
86
Session: Physiology and Biochemistry
P37
Molecular basis of sulfur metabolism in Rhodococcus sp.
AF21875, a strain that prefers organosulfur compounds over
sulfate
Valeria Tatangelo1, Jonathan Van Hamme2, Eric Bottos2, Giuseppina Bestetti1, Andrea
Franzetti1
1
2
Department of Earth and Environmental Sciences, University of Milano-Bicocca, Italy
Department of Biological Sciences, Thompson Rivers University, Canada
Sulfur is an essential element for bacterial growth and, when bacteria are under sulfatelimiting conditions, they can utilize alternative sulfur sources such as aliphatic
sulfonates. The uptake and utilization of aliphatic sulfonates and taurine are controlled
by the ssu and tau systems, respectively. In both systems an ABC transport system
(ssuABC and tauABC) and an oxygenase system (ssuDE and tauD) are present. Several
mycolata can utilize dibenzothiophene (DBT) and its derivatives as sulfur source using
systems such as the dsz and DOX operons. Rhodococci are well known for their ability to
catabolize organic pollutants and have previously been found to be capable of exploiting
a wide range of organosulfur compounds for sulfur requirements. We have isolated
Rhodococcus species strain AF21875, an organism that uses dibenzothiphene over
sulfate as a preferred sulfur source, and generates 2-hydroxybiphenyl as a byproduct
indicating that it is using the DBT desulfurization pathway encoded by the dsz operon.
Here we present a whole genome shotgun of AF21875 and describe a wide variety of
genes associated with organosulfur transport and assimilation that were identified
during annotation. In the AF21875 genome, both the assimilatory sulfate reduction
pathway and the cysteine biosynthesis pathway have been detected. In addition,
tauABCD and ssuEADCB genes were annotated, along with a putative plasmid harboring
the dszABC genes. Normally sulfate inhibits organosulfur metabolism, so we are
investigating the molecular features in AF21875 resulting in the unique phenotype
observed as there exists significant potential for industrial application.
87
Session: Physiology and Biochemistry
P38
Biochemical and functional analysis of sulfide oxidase
flavoproteins from purple sulfur bacterium, Thiocapsa
roseopersicina
András Tóth1, 2, Ágnes Duzs2, Tímea Balogh2, Brigitta Németh1, Enikő Kiss1, Gábor
Rákhely1, 2
1
Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H6726 Szeged, Hungary
2 Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
Sulfide oxidase flavocytochrome c (Fcc) and sulfide quinone oxidoreductase (Sqr)
enzymes are ancient flavoproteins, widely present in different domains of life. These
enzymes can involve in energy metabolism of microorganisms, regulation of cellular
sulfide concentration in eukaryotic cells or protection against toxic sulfide. The
phototrophic purple sulfur bacterium Thiocapsa roseopersicina has a versatile sulfur
metabolism. Three genes presumably encoding flavocytochrome c (fcc) and two
different sulfide quinone oxidoreductase type enzymes (sqrD, sqrF) were identified in
the genome sequence. Phylogenetic and comparative sequence analysis of these
proteins revealed that SqrD and SqrF belong to partially characterized groups (type IV
and VI) of Sqr enzymes. For identification of function of these proteins ∆fcc and ∆sqrF
T. roseopersicina strains were created and analysed. The Fcc mutant strain completely
lost the periplasmic sulfide oxidase activity. SqrF mutant cells possessed slightly
decreased sulfide consumption rate. The effect of sulfide on the expression of the
identified genes was studied by qRT-PCR. This analysis revealed that expression of the
flavocytochrome c and the sulfide quinone oxidoreductases are activated at different
sulfide concentrations. Fcc and Sqn proteins fused to Strep II tag were expressed in
T. roseopersicina and purified. The reduction and oxidation of the pure recombinant
proteins in the presence of sulfide and appropriate electron acceptor were followed by
UV-Vis spectra. The Fcc and SqrF proteins catalyzed the expected sulfide dependent
cytochrome c or quinone reduction reactions, respectively. Kinetic analysis revealed that
affinity of Fcc and SqrF to sulfide is considerably different which suggests in well
correlation with the expression studies that these enzymes have role in the metabolism
of cells at different sulfide conditions.
88
Session: Physiology and Biochemistry
P39
Comparative proteomics reveals two methanol-degrading
pathways in the sulfate reducing bacterium
Desulfotomaculum kuznetsovii
Michael Visser, et al.
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB
Wageningen, The Netherlands
Several phylogenetic groups of microorganisms are able to grow with methanol as a sole
carbon and energy source. Aerobic and facultative anaerobic methylotrophs generally
oxidize methanol to formaldehyde by using a methanol dehydrogenase, while anaerobic
methylotrophs such as methanogens and acetogens are known to use a methanol
methyltransferase system. However, the methanol metabolism of sulfate-reducing
bacteria has not been extensively studied. Previous work with the sulfate-reducing
bacterium Desulfotomaculum kuznetsovii resulted in a partially purified alcohol
dehydrogenase that showed activity with methanol and ethanol. However, the genome
also indicated the presence of a methanol methyltransferase system. Therefore, the
methanol metabolism in D. kuznetsovii remained unsolved. The methanol
methyltransferase system is vitamin B12 dependent. Therefore, we studied the
methanol metabolism of D. kuznetsovii by growing the cells with methanol and sulfate in
the presence and absence of cobalt and vitamin B12. When cobalt and vitamin B12 were
omitted from the medium D. kuznetsovii showed a decreased rate of methanol
conversion. A subsequent comparative proteomics approach, using nanoLC-MS/MS,
helped to unravel the methanol metabolism of D. kuznetsovii. Cells were grown under
four different conditions: Methanol and sulfate in presence and absence of cobalt and
vitamin B12, lactate and sulfate, and ethanol and sulfate. The lactate growth condition
was used as a reference. Proteomic results indicate the presence of two methanol
degrading pathways in D. kuznetsovii, a cobalt dependent methanol methyltransferase
system and a cobalt independent alcohol dehydrogenase. The alcohol dehydrogenase is
also involved in the ethanol metabolism of D. kuznetsovii. This study is the first evidence
for the occurrence of two methanol degrading systems in a bacterium.
89
Session: Ecology and Evolution
P40
Revealing the genotypic and phylogenetic diversity within the
genus Thioalkalivibrio
Anne-Catherine Ahn1, Lex Overmars1, Michael Richter2, Jan P. Meier-Kolthoff3, Judith
Umbach4, Dimitry Y. Sorokin5, 6, Gerard Muyzer1
1
Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity
and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
2 Ribocon, Bremen, Germany
3 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures,
Braunschweig, Germany
4 Microbial Genomics and Bioinformatics, Max-Planck-Institute for Marine Microbiology,
Bremen, Germany
5 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
6 Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
Members of the genus Thioalkalivibrio are obligate chemolithoautotrophic and
haloalkaliphilic sulfur-oxidizing bacteria. They live in the dual extreme environment of
soda lakes that have a pH ranging from 9.5 to 11 and a salt concentration up to
saturation. A previous study revealed a high genetic diversity through rep-PCR
fingerprint analysis and furthermore suggested an endemic character for members of
this genus. Having now the genome sequences of 77 Thioalkalivibrio strains isolated
from soda lakes from various locations all over the world, different phylogenetic and
genotypic approaches, such as 16S rRNA, supertree analysis of orthologous protein
sequences, ANI (Average Nucleotide Identity) and in silico DDH (DNA-DNA
hybridization) were applied in order to define the diversity within the genus. With these
analyses, the high genetic diversity could be confirmed and the affiliation of the different
strains to the described species could be determined in detail. Based on this approach,
we found 14 new genetic species next to already 10 described species in this genus.
Furthermore, the results show that the monophyletic character of this genus may be
questionable, as strains from other genera were found within the branch of the genus
Thioalkalivibrio in phylogenetic trees. As 3 species were separated from the rest of
Thioalkalivibrio, which are still grouped around their type species Tv. versutus, these
outliers should be redefined within a novel genus.
90
Session: Ecology and Evolution
P41
Genomics and proteomics of Thioploca ingrica, a nitratestoring sulfur oxidizer living in freshwater sediments
Hisaya Kojima, Tomohiro Watanabe, Manabu Fukui
The Institute of Low Temperature Science, Hokkaido University, Japan
Sulfur-oxidizing bacteria which accumulate a high concentration of nitrate are important
constituents of aquatic sediment ecosystems. For these microorganisms, only
fragmented draft genome sequences have been available. In this group, Thioploca ingrica
is the sole species thriving in freshwater environments at present. By performing
metagenomic analysis, the complete genome of Thioploca ingrica was successfully
reconstituted. Sulfur oxidation pathway deduced from the reconstituted genome was
identical to that suggested for the closest relatives of Thioploca. In the genome, a full set
of genes for nitrate reduction to dinitrogen gas was identified. Further, a proteomic
analysis was performed to investigate the physiology of Thioploca in lake sediments. In
the analysis, many proteins involved in sulfur oxidation, nitrate respiration, and
inorganic carbon fixation were detected as major components of the protein extracts.
Kojima,H., Ogura,Y., Yamamoto,N., Togashi,T., Mori,H., Watanabe,T., Nemoto,F., Kurokawa,K., Hayashi,T.,
and Fukui,M. Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence
supplemented with proteomic evidence. The ISME Journal : in press.
91
Session: Ecology and Evolution
P42
Diversity and abundance of sulfate-reducing alkane
degraders in cold marine surficial sediments – microbial
targets in oil and gas exploration
Antje Gittel, Johanna Donhauser, Kasper Kjeldsen, Hans Røy, Bo Barker Jørgensen
Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus,
Denmark
The understanding that hydrocarbons migrate from marine subsurface petroleum
reservoirs to the sediment surface recently led to the usage of gas seep detection as an
oil prospecting tool. Besides remote sensing and analysis of seep gas composition, it has
been hypothesized that the elevated abundance of microbial targets, in particular
sulfate-reducing short-chain alkane (SCA) degraders, might indicate the presence of
seeps and thus petroleum reservoirs. However, the diversity of these microorganisms in
cold marine surficial sediments is largely unexplored and probably underestimated. In
addition, the origin and turnover of short-chain hydrocarbons in these sediments has
not been assessed so far.
A functional gene approach targeting a subunit of the 1-methylalkyl succinate synthase
(masD) gene was combined with single cell genomics and gas analytics to (1) assess the
diversity and abundance of sulfate-reducing SCA degraders in surficial sediments with
and without seepage, (2) unravel novel diversity and (3) determine the potential for
bioprospecting assays using elevated masD gene abundance as a seepage indicator.
Database research and a pilot study on potential oil exploration sites in the North Sea
revealed that existing masD gene primer pairs did not comprehensively target the
known masD gene diversity. We thus developed an improved detection assay and
successfully applied it to sediment samples from seepage and non-seepage sites. masD
genes were found in all these samples, showing that putative SCA degraders were
present both at seepage-impacted sites and reference sites that are currently not
impacted by hydrocarbon seepage. Their ubiquitous presence indicated that, in the
event of seepage, SCA degraders might grow to represent a larger fraction of the
community and will be readily detectable in bioprospecting assays. However, further
data analysis is needed to assess distinct seep-specific diversity and to link increased gas
concentrations to elevated abundances of the respective target genes.
92
Session: Ecology and Evolution
P43
Exploring the pan-genome of the haloalkaliphilic sulfuroxidizing bacteria of the genus Thioalkalivibrio
Lex Overmars1, Dimitry Y. Sorokin2, 3, Gerard Muyzer1
1
Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University
of Amsterdam, Amsterdam, The Netherlands
2 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
3 Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
Thioalkalivibrio is a genus of chemolithoautothrophic sulfur-oxidizing bacteria capable
of growing at pH up to 10.5 and sodium concentrations up to 4.3 M. An insight into their
genomic potential and diversity will help us to better understand their core metabolism
and the molecular mechanisms by which Thioalkalivibrio have adapted to these extreme
conditions.
As part of the community sequence program of the Joint Genome Institute (JGI) the
genomes of 70 Thioalkalivibrio strains were sequenced. These strains were isolated
from soda lakes in Mongolia, Siberia, California, Egypt and Kenya, which vary in salinity
and chemistry. Comparative analysis revealed that the pan-genome consists of more
than 10,000 orthologous groups (OGs), of which ~15% make up the conserved core. The
core genome is mainly composed of housekeeping, (core-) metabolism- and information
storage/processing-related genes, whereas the accessory genome is characterized by an
overabundance of genes involved in signal transduction and cell wall biogenesis. We
have clustered the strains based on presence/absence of OGs and found two major
clusters consisting of isolates from the Asiatic (Siberia and Mongolia) and the African
(Kenya and Egypt) continents, respectively. Interestingly, we observed a relative high
variability in presence of genes involved in the sulfur metabolism among the 70 strains.
We are currently extending our comparative genome analysis with other pathways and
proteins potentially important for the adaptation to their environment to learn more
about how Thioalkalivibrio can flourish at these conditions of high pH and salinity.
93
Session: Ecology and Evolution
P44
Enabling large-scale ecological studies of sulfate/sulfitereducing microorganisms: A new approach for highly parallel
Illumina sequencing of dsrA and dsrB amplicons
Claus Pelikan, Craig Herbold, Alexander Loy
Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty
of Life Sciences, University of Vienna, Vienna, Austria
Microorganisms that anaerobically respire sulfate, sulfite or organosulfonates
contribute significantly to the world's sulfur and carbon cycles. The central step of these
processes is the reduction of sulfite to hydrogen sulfide, which is catalyzed by a
reductive version of the highly conserved enzyme dissimilatory (bi)sulfite reductase
(DsrAB). Several dsrAB-targeted primers are available and commonly applied for
amplicon based community analyses, however next generation sequencing (NGS) library
preparation methods and data analysis tools remain underevaluated for processing of
dsrAB amplicon sequences. Furthermore, most published primers for dsrAB that are
suitable for NGS library preparation have a rather limited coverage. Here, we describe
an Illumina sequence preparation and analysis pipeline for dsrA and dsrB gene
fragments. These were amplified with a new, highly flexible two-step barcoding
procedure, including a first PCR with new highly degenerate dsrA and dsrB primers and
a second PCR with universal barcoding primers. The updated and newly developed dsrA
and dsrB-targted primer sets covered between 97-100% of the known diversity of
bacterial-type, reductive dsrAB and produced NGS-compatible amplicons of about 300
bp and 700 bp in size, respectively. Amplicon preparation, data quality, and analysis
procedures were initially evaluated with two complex mock communities of defined
diversity and subsequently applied to selected environmental samples of unknown
composition. Although single nucleotide primer mismatches and other PCR biases had
notable effects on data structure, most sequences from the mock communities were
retrieved in relative abundances proportional to input relative abundances. The new
primer sets and optimized sequence analysis pipeline now enables large-scale diversity
analyses of bacterial-type, reductive dsrAB-carrying microorganisms in the environment
or under controlled experimental conditions.
94
Session: Ecology and Evolution
P45
Disproportionation of sulfur compounds by thermophilic
microorganisms
Alexander Slobodkin
Winogradsky Institute of Microbiology, Russian Academy of Sciences, Russia
Microorganisms that disproportionate sulfur compounds such as thiosulfate, sulfite or
elemental sulfur are a unique group of sulfur-cycling prokaryotes that play an important
role in modern sedimentary environments and probably have been involved in sulfur
transformations in early archaean ecosystems. Inorganic sulfur compounds
fermentation that supports microbial growth has been reported for 27 species of 14
genera mainly in the Proteobacteria. Most of them are able to dismutate thiosulfate and
sulfite, while the disproportionation of elemental sulfur is more rare physiological
property. Thermodynamic calculations show that S0 disproportionation is more
energetically favorable at elevated temperatures. Elemental sulfur is abundant in
thermal environments, however before our studies, the capacity to grow by
disproportionation of S0 among thermophiles was not known. Recently we have isolated
and characterized two novel thermophilic elemental sulfur-disproportionating bacteria Thermosulfurimonas dismutans and Dissulfuribacter thermophilus from deep-sea
hydrothermal vents (Slobodkin et al., 2012; 2013). Both microorganisms are
chemolithoautotrophs able to gain energy for growth by disproportionation of
elemental sulfur, thiosulfate or sulfite and unable to perform dissimilatory sulfate
reduction. Thermosulfurimonas dismutans represents the new genus of the phylum
Thermodesulfobacteria, while Dissulfuribacter thermophilus forms distinct phylogenetic
branch within Deltaproteobacteria. Further studies on sulfur disproportionation in
continental freshwater hot springs lead us to the isolation of new microorganisms
‘Dissulfurimicrobium hydrothermalis’ that also belong to Deltaproteobacteria.
Investigations of physiological mechanisms of low soluble S0 disproportionation indicate
the involvement of polysulfides in this process. Overall, the data on isolation of
lithoautotrophic
sulfur-disproportionating
microorganisms
from
deep-sea
hydrothermal vents and freshwater hot springs point to important role of this
physiological group in sulfur-rich extreme environments.
1. Slobodkin et al. (2012) Int J Syst Evol Microbiol 62:2565-2571
2. Slobodkin et al. (2013) Int J Syst Evol Microbiol 63: 1967-1971
95
Session: Ecology and Evolution
P46
Novel thermophilic bacteria capable of chemolithotrophic
anaerobic sulfur oxidation
Galina Slobodkina
Winogradsky Institute of Microbiology RAS, Russia
Sulfur-oxidizing microorganisms are phylogenetically diverse and include
photolithotrophic bacteria and chemolithotrophic bacteria and archaea. Thermophilic
sulfur-oxidizing bacteria are known among the phyla Aquificae and Proteobacteria.
Obligately anaerobic species of elemental sulfur oxidizers have not been previously
reported. In present study, we report the isolation of two strains of thermophilic
anaerobic chemolithotrophic bacteria capable of reduced sulfur compounds oxidation.
Strain ST65 was isolated from the deep-sea hydrothermal vent (1910 m deep) on the
Eastern Lau Spreading Center. Cells were straight or slightly curved short rods, 0.5 to 0.6
μm in diameter and 0.8 to 1.5 μm in length. The strain grew at 65oC and pH 6.5-6.8
under anaerobic conditions coupling elemental sulfur oxidation with nitrate reduction.
Nitrate was reduced to ammonia. It was also capable of sulfur disproportionation.
Organic substrates did not stimulate growth. The closest relatives of the isolated
organism were Thermoslfurimonas dismutans and Thermodesulfatator atlanticus (89.8
and 89.5% of 16S rRNA gene similarity respectively). We propose to assign strain ST65
to a new species of a novel genus ‘Thermosulfurisoma ammonica’ in the order
Thermodesulfobacteriales. Strain S2479 was isolated from the marine shallow-water
hydrothermal vent (Kunashir Island, Russia). It had rod-shaped cells that grew
anaerobically at 65°C and pH 6.5-6.8 with elemental sulfur or thiosulfate as electron
donors and nitrate as electron acceptor. 16S rRNA gene sequence analysis revealed that
the strain S2479 belongs to the order Chromatiales being equidistant from the
representatives
of
families
Ectothiorhodospiraceae,
Chromatiaceae
and
Thioalkalispiraceae (91-92%).
96
Session: Ecology and Evolution
P47A
Tracking carbon flow from major classes of biomolecules into
microorganisms under psychrophilic sulfate-reducing
conditions in Arctic marine sediments
Kenneth Wasmund1, Claus Pelikan1, Albert Leopold Müller1, Julia Rosa de Rezende2,
Kasper Urup Kjeldsen2, Bo Barker Jørgensen2, Alexander Loy1
1
2
Division of Microbial Ecology, University of Vienna, Austria
Center for Geomicrobiology, Aarhus University, Denmark
To understand the microbial ecology and biogeochemistry of marine sediments under
permanently cold conditions that prevail at approximately 90% of the seafloor, it is
important to know and understand the organisms involved in the mineralisation of
detrital biomass and major classes of cellular-derived macromolecules. Such
macromolecules comprise most of the bioavailable organic matter and therefore
nutrients and/or energy for microbial communities in marine sediments. This research
therefore investigates microbial communities involved in the degradation of cellular
biomass including selected macromolecules, i.e. proteins, lipids and nucleic acids, in
marine sediments from Arctic sediments under cold (4°C) sulfate-reducing conditions.
To reveal how different sediment microorganisms interact to degrade complex organic
molecules and thus influence the flow of carbon through the anaerobic microbial food
web, we performed microcosm incubations with 13C-labelled cyanobacterial (Spirulina)
biomass and individual 13C-labelled macromolecules (proteins, lipids, nucleic acids) or a
model fermentation product (acetate). We analysed these incubations by amplicon
sequencing of bacterial 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) genes
from different time-points and isopycnic density gradient fractions (i.e. stable isotope
probing). Data currently obtained from 16S rRNA gene sequencing clearly implicates
several taxa as primary degraders of different macromolecule classes. These taxa
exhibited fast responses (i.e. within 2 days) to substrate additions compared to controls,
indicating a primed and active community. Some of these taxa were also observed as
primary-degraders of whole-cell cyanobacterial biomass, and our data thereby provides
insights into the partitioning of carbon derived from this cellular biomass. Sulfatereducing deltaproteobacterial taxa generally displayed a slower response to
macromolecule additions, suggesting they used fermentation products derived from
primary degraders. Incubations with acetate as a model fermentation product also
supported these findings. On-going analyses aim to further elucidate the role of different
sulfate-reducers under the different experimental treatments.
97
Session: Ecology and Evolution
P47B
Changes in Baltic Sea sediment oxygen concentrations
induces changes in facultatively anaerobic sulfide oxidizing
genera Sulfurimonas and Sulfurovum
Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
Linnaeus University, Sweden
Eutrophication of the Baltic Sea increases algal bloom frequency and magnitude.
Eventually these blooms decay and a portion of the biomass reaches the sediment.
Microbial communities degrade this carbon, consuming the available oxygen, which
results in sediments commonly referred to as “dead zones”. This study investigated how
the microbial community structure and metabolic pathways in the surficial sediment
changes as a result of transitions between oxic and anoxic conditions. A transition from
oxic to anoxic conditions resulted in decreased sulfate, nitrite, and nitrate. In contrast,
converting anoxic sediments to oxic conditions caused an increase in sulfate
concentration. Large changes in the microbial community based upon next generation
sequencing of the 16S rRNA gene were primarily related to the relative abundance of the
facultatively anaerobic sulfide oxidizing genera Sulfurimonas and Sulfurovum. These
genera are chemolitoautotrophic bacteria, able to oxidize zero-valence sulfur and
hydrogen sulfide using either oxygen or nitrate as an electron acceptor. This study
allowed identification of the changes in microbial community as a response to oxygen
concentrations that were primarily associated with sulfur redox change.
98
Session: Ecology and Evolution
P47C
Sulfide oxidation by cable bacteria: Getting by with a little
help from their (associated) friends?
Signe Brokjær Nielsen1, Steffen Larsen1,2, Jesper Tataru Bjerg1, Lars Schreiber2, Kasper
U. Kjeldsen2, and Andreas Schramm1,2
1 Section
for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus,
Denmark
2 Center
Cable bacteria are filamentous members of the Desulfobulbaceae that couple oxygen
reduction at the sediment surface with sulfide oxidation in deeper, anoxic sediment
layers by conducting electrons over centimeter distances. No direct proof exists that
cable bacteria themselves oxidize sulfide: they can so far not be grown in pure culture,
and their closest cultured relative is the sulfate reducer Desulfobulbus propionicus. We
have previously found that sulfide-oxidizing bacteria (SOB) co-establish with cable
bacteria in suboxic sediment layers (Schauer et al., 2012), and a recent study
demonstrated that SOB fix CO2 in sediment with intact cable bacteria but not when the
current is interrupted (Vazques et al., 2015).
The aim of the current study was to describe the microbial community associated with
cable bacteria in more detail. We re-investigated data from marine cable enrichments,
analyzed sequences retrieved from single, manually picked and cleaned filaments from
numerous locations, and sequenced autoclaved freshwater sediment inoculated with
cable bacteria. Our combined data show that both marine and freshwater cable bacteria
consistently associate with three main classes of SOB; the exact SOB type may differ
based on the original habitat sampled. Detection of transcripts of key genes for sulfide
oxidation in the suboxic zone furthermore suggests that these SOB are active even
without direct contact to oxygen. We propose that the associated SOB can deliver
electrons from sulfide oxidation to the cable bacteria. The mechanism for such an
interspecies electron transfer, the significance of the associated SOB for electrogenic
sulfide oxidation, and whether cable bacteria at all participate in sulfide oxidation,
remains to be investigated.
1. Schauer R., Risgaard-Petersen N., Kjeldsen U K., Bjerg T J., Jørgensen B B., Schramm A. and Nielsen L.P.
(2014) Succession of cable bacteria and electric currents in marine sediment. ISME J 23, 239.
2. Schauer R., Larsen S., Kjeldsen U K., Bjerg T J., Schreiber L., Risgaard-Petersen N., Nielsen L.P. &
Schramm A. (2012) Development and succession of electrogenic microbial communities in marine
sediment. In: ISME14, Copenhagen, Denmark.
3. Vasquez-Cardenas D., Malkin S.Y., van de Vossenberg J., Polerecky L., Schauer R., Middelburg J.J.,
Meysman F.J.R. & Boschker H.T.S. (2014) Microbial communities and carbon metabolism associated with
electrogenic sulfur oxidation in coastal sediments. In: ISME15, Seoul, South Korea.
99
Session: Sulfur Transformations
P48
A unique isotopic fingerprint during sulfate-driven anaerobic
oxidation of methane
Gilad Antler1, Alexandra V. Turchyn1, Barak Herut2, Orit Sivan3
1
Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
Israel Oceanographic and Limnological Research, National Institute of Oceanography,
Haifa 31080, Israel
3 Department of Geological and Environmental Sciences, Ben Gurion University, Beer Sheva
84105, Israel
2
Bacterial sulfate reduction is responsible for the majority of anaerobic methane
oxidation in modern marine sediments. This sulfate-driven AOM can often metabolize all
the methane produced within marine sediments, preventing any from reaching the
overlying ocean. In certain areas, however, methane concentrations are high enough to
form bubbles, which can reach the seafloor, only partially metabolized through sulfatedriven AOM; these areas where methane bubbles into the ocean are called cold seeps, or
methane seeps. We use the sulfur and oxygen isotopes of sulfate in locations where
sulfate-driven AOM is occurring both in methane seeps as well as lower flux methane
transition zones to show that in methane seeps, the sulfur and the oxygen isotope data
during the coupled sulfate reduction fall into a very narrow range and with a close to
linear relationship (slope 0.37± 0.01—R2= 0.98, n=52, 95% confidence interval). In the
studied environments, considerably different physical properties exist, excluding the
possibility that this linear relationship can be attributed to physical processes such as
diffusion, advection or mixing of two end-members. This unique isotopic signature
emerges during bacterial sulfate reduction by methane in ‘cold’ seeps and differs when
sulfate is reduced by either organic matter oxidation or by a slower, diffusive flux of
methane within marine sediments. We show also that this unique isotope fingerprint is
preserved in the rock record in authigenic build-ups of carbonates and barite associated
with methane seeps, and may serve as a powerful tool for identifying catastrophic
methane release in the geological record.
100
Session: Sulfur Transformations
P49
Thiosulfate dehydrogenase (TsdA) from Allochromatium
vinosum: Structural and functional insights into thiosulfate
oxidation
José A. Brito1, Kevin Denkmann2, Inês A. C. Pereira2, Christiane Dahl2, Margarida Archer1
1
Instituto de Tecnologia Química e Biológica – António Xavier, Universidade Nova de
Lisboa, Oeiras, Portugal
2 Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität
Bonn, Germany
The ability to perform the very simple oxidation of two molecules of thiosulphate to
tetrathionate is widespread among prokaryotes. Despite the pervasive occurrence of
tetrathionate formation, and its well-documented significance within the sulphur cycle,
little is known about the enzymes catalysing the oxidative condensation of two
thiosulphate anions. To fill this gap, the thiosulphate dehydrogenase (TsdA), enzyme
from Allochromatium vinosum, was recombinantly expressed, purified and
characterized. Moreover, we solved the "as isolated" crystal structure of the enzyme and
further obtained X-ray structures of TsdA in several redox states. The protein
crystallized in space group C2 with PEG 3350 as precipitant and one molecule in the
asymmetric unit. TsdA contains two typical class I c-type cytochrome domains with two
hemes axially coordinated by His53/Cys96 and His164/Lys208. The X-ray structure
showed an all-alpha structure with structural similarities to the Rhodovulum
sulfidophilum’s SoxAX (PDB code 2OZ1), and the low-redox-potential cytochrom c6 from
Hizikia fusiformis (PDB code 2ZBO). Interestingly, reduction of the enzyme causes a
Lys208/Met209 ligand switch in heme 2. TsdALys208Asn or Lys208Gly variants exhibit
similar substrate affinities as the wildtype protein but much lower specific activities
pointing at this heme as the electron exit point. Cys96 is essential for catalysis. Overall,
our kinetic, spectroscopic and structural data lead us to propose a mechanism where
two thiosulfate molecules enter the active site, inducing a movement of the Sγ of Cys96
out of the iron coordination sphere; this ligand movement results in an increase of the
redox potential of heme 1, thus allowing the sequential uptake of the two electrons
resulting from the conversion of the two thiosulfates to tetrathionate, leading to the
reduction of both hemes; upon reduction, heme 2 undergoes a ligand switch, which
increases its redox potential and hinders the back reaction.
101
Session: Sulfur Transformations
P50
Comparative analyses of haloalkaliphilic sulfidogens from
soda lakes
Emily Denise Melton1, Kai Finster2, Dimitry Sorokin3, 4, Gerard Muyzer1
1
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam,
the Netherlands
2 Department of Bioscience, Microbiology Section, Aarhus University, Aarhus, Denmark
3 Winogradsy Institute of Microbiology, RAS, Moscow, Russia
4 Department of Biotechnology Delft University of Technology, Delft, the Netherlands
Soda lakes are defined by their high salinity and alkaline pH conditions, designating
them as extreme environments. These lakes support an active microbial sulfur cycle,
enhanced by the chemical stability and low toxicity of sulfide and polysulfides at these
elevated pH conditions. Correspondingly, a wide variety of haloalkaliphilic anaerobes
have been found in these lakes, which can use various sulfur species including elemental
sulfur and thiosulfate for dissimilatory energy conservation. We investigated
sulfidogenic processes of three haloalkaliphilic strains, isolated from soda lakes:
Dethiobacter alkaliphilus, Desulfurivibrio alkaliphilus and Desulfonatronospira
thiodismutans. These strains are able to conserve energy from the metabolism of sulfur
compounds through reduction and disproportionation reactions. They were cultured
anaerobically with different sulfuric electron acceptors and short chain organic electron
donors to investigate their growth dynamics. Their genomes have been sequenced by
the Joint Genome Institute and genes involved in reductive sulfur metabolisms could be
identified using the IMG Data Management & Analysis system by studying the gene
expression levels in the laboratory cultures. By combining physiology experiments with
genomic analyses, we were able to identify metabolic abilities of these microbes and
identify the sulfidogenic pathways. Comparative genomic analyses between these
extremophiles are important as these experiments bring us closer to the identification of
key genes responsible in sulfur transformation with special focus on disproportionation,
a so far poorly understood sulfur-dependent metabolism. It will also contribute to our
understanding of the degree of metabolic flexibility of haloalkaliphiles with respect to
differences between sulfur disproportionation and sulfur reduction reactions. Their
sulfidogenic activity in cultures also holds ecological relevance, as soda lakes contain
many sulfur-oxidizers that depend on the sulfide that is produced by sulfur-reducers.
Therefore, the activity and gene expression of haloalkaliphilic sulfidogens can also
provide an approximation for the activity of the closed sulfur cycle in these extreme
environments.
102
Session: Sulfur Transformations
P51
The hidden sulfur cycle in rice paddy soil: identification of
key sulfate reducing microorganisms by next-generation
amplicon sequencing
Michael Pester1, Jianguo Dan2, 3, Sarah Zecchin4, 5, Alexander Loy4, Ralf Conrad2
1
Department of Biology, University of Konstanz, Germany
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
3 College of Environment and Plant Protection, Hainan University, China
4 Division of Microbial Ecology, University of Vienna, Austria
5 Department of Food, Environmental and Nutritional Sciences, University of Milan, Italy
2
Rice paddy fields are indispensable for human food supply but at the same time are one
of the most important sources of the greenhouse gas methane. A hidden sulfur is
proposed to occur in freshwater wetlands such as rice paddy fields that effectively cycles
the various sulfur species between their oxidized and reduced states and at the same
time counter balances methane production. Dissimilatory sulfate reduction is a major
process within the hidden sulfur cycle in rice paddy soil and operates at rates
comparable to marine surface sediments, despite the significantly lower sulfate
concentrations. As a consequence, sulfate reduction as the thermodynamically favorable
process over fermentations coupled to methanogenesis diverts organic matter
degradation from methane towards more carbon dioxide production. To stimulate and
thus identify the responsible microorganisms, we set up greenhouse experiments where
whole rice plants were grown in soil amended with gypsum (CaSO4) in amounts relevant
for rice agriculture (0.15% w/w). Rice plants grown in soil without gypsum served as
control. Gypsum amendment significantly reduced methane emission from rice plant
mesocosms by up to 98%, showing that sulfate reducers were active and effectively
competed with microorganisms involved in the methanogenic degradation pathways.
16S rRNA gene-targeted high throughput amplicon sequencing revealed a clear effect of
gypsum amendment on the total microbial community in the rhizosphere and bulk soil.
In particular, the abundance of members of the Desulfobulbaceae, Desulfovibrionaceae,
and Synthrophobacteraceae increased under conditions that stimulated sulfate
reduction. In contrast, methanotrophic bacteria belonging to the Methylococcaceae
decreased in abundance, most likely as an effect of less methane supply. Our results
corroborate the importance of the hidden sulfur cycle in controlling production of the
greenhouse gas methane and identified key players involved in sulfate reduction as a
key process in this biogeochemical phenomenon.
103
Session: Sulfur Transformations
P52
“Thiocyanate dehydrogenase” is a novel copper enzyme of the
primary thiocyanate degradation in haloalkaliphilic sulfuroxidizing bacterium Thioalkalivibrio paradoxus ARh1
Stanislav I. Tsallagov1, Tamara V. Tikhonova1, Dimitry Y. Sorokin2, 3, Arnulf Kletzin4,
Vladimir O. Popov1
1
A.N.Bach Institute of Biochemistry Russian Academy of Sciences
Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
3 Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
4 Microbiology - Sulfur Biochemistry and Microbial Bioenergetics, Technische Universität
Darmstadt, Darmstadt, Germany
2
Thiocyanate (NCS-) is a toxic and chemically recalcitrant compound present in natural
and industrial habitats. Few lithotrophic sulfur-oxidizing bacteria are able to utilize
thiocyanate as sole energy and nitrogen source. Primary thiocyanate degradation can
proceed either via carbonyl sulfide (COS) or cyanate (CNO-) as stable intermediates. The
former is performed by a well characterized Co enzyme, thiocyanate hydrolase, while
practically nothing is known about the enzyme(s) of the cyanate pathway of thiocyanate
degradation.
Haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxus degrade
thiocyanate via the cyanate pathway. The responsible enzyme, “thiocyanate
dehydrogenase” (TcDH) is a copper-containing periplasmic oxido-reductase oxidizing
sulfane atom of CNS- to sulfur with formation of CNO- as an intermediate.
Ferricytochrome c can be used as an e-acceptor in vitro. Increasing of copper content in
the growth medium stimulated the rate of thiocyanate utilization and TcDH specific
activity. During purification procedure TcDH loses the copper. The process of copper
dissociation is reversible. X-ray fluorescence analysis and inductively coupled plasma
mass spectrometry have shown that copper content in the enzyme increases from one to
four atoms per protein molecule after Cu2+ reconstitution. Circular dichroism showed
that Cu2+ binding was not accompanied by considerable structural rearrangements. The
process of copper incorporation was rather slow taking 2-3 days of incubation to
achieve maximum enzyme activity. The increase in copper content resulted in a 100-fold
increase in the enzyme activity and 4-fold decrease in the substrate affinity.
Furthermore, the copper-saturated TcDH revealed increased stability during storage.
Copper-complexing compounds with the binding affinity higher than that for
thiocyanate (cyanate and cyanide) inhibited TcDH. Cyanide is a competitive inhibitor.
Redox-inactive metals, such as zinc, inhibited the TcDH activity, probably by replacing
copper ions in the active site. Overall, the data showed a crucial role of copper in
catalytic function of TcDH.
104
Session: Sulfur Transformations
P53
Bacterial genera involved in diverse biological pathways for
inorganic sulfur compounds oxidation in hypersaline soda
lake brines
Charlotte Vavourakis1, Rohit Ghai2, Francisco Rodriguez Valera2, Dimitry Sorokin3, 4,
Gerard Muyzer1
1
Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity
and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
2 Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología,
Universidad Miguel Hernández, San Juan de Alicante, Spain
3 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
4 Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
Hypersaline soda lakes are double-extreme environments with salt concentrations up to
saturation and a pH exceeding 9.5 due to the domination of sodium carbonate salts. Here
we examined snapshots of the microbial community structure of four hypersaline soda
lake brines in the Kulunda Steppe (Altai region, South-Eastern Siberia, Russia) with
salinities varying between 170 and 400 g/L using direct (PCR-independent)
metagenome sequencing. In parallel, we used amplicon sequencing targeting
environmental 16S rRNA gene fragments to obtain a genus-level OTU distribution within
the most abundant bacterial taxa. Analysis of the directly sequenced reads encoding 16S
rRNA gene fragments revealed the dominant abundance of Euryarchaeota in the
hypersaline brines with a minimum salt concentration of 250 g/L. In the brine with
salinity 170 g/L bacterial phyla of Bacteroidetes, Gamma- and Alphaproteobacteria were
dominant. A significant fraction of the bacterial OTUs assigned to the amplicon
sequences belonged to various groups of Alpha- and Gammaproteobacteria known to be
involved in the oxidative part of the microbial sulfur cycle. The most dominant genus in
the brine with the lowest salinity was Thioalkalivibrio, a diverse group of
chemolithoautrophic sulfur oxidizing bacteria (SOB). In the same brine an important
fraction of the alphaproteobacterial amplicon sequences belonged to
Roseinatronobacter, a unique genus of haloalkaliphilic, aerobic bacteriochlorophyll a–
containing (ABC) bacteria capable of lithoheterotrophic growth by oxidation of reduced
sulfur compounds to sulfate. Although Gammaproteobacteria were only low abundant in
the saturated brine (salinity 400 g/L), we still could detect amplicon sequences from
both purple sulfur bacteria from the genus Halorhodospira and SOB from the genus
Thioalkalivibrio. Finally, Halomonas was the most important gammaproteobacterial
genus in this brine, suggesting that there is a potential for bacterial heterotrophic
thiosulfate oxidation to tetrathionate even at saturating salt conditions.
105
Session: Sulfur Transformations
P54
Single cell genomics provides hints into the unexpected roles
of the widely distributed Dehalococcoidia (DEH), phylum
Chloroflexi, in marine subsurface sulfur cycling
Kenneth Wasmund1, 2, Myriel Cooper1, Lars Schreiber3, Karen G. Lloyd3, Dorthe G.
Petersen3, Andreas Schramm3, Ramunas Stepanauskas4, Richard Reinhardt5, Bo Barker
Jørgensen3, Alexander Loy2, Lorenz Adrian1
1
Helmholtz Centre for Environmental Research – UFZ, Germany
Division of Microbial Ecology, University of Vienna, Austria
3 Center for Geomicrobiology, Aarhus University, Denmark
4 Bigelow Laboratory for Ocean Sciences, USA
5 Max Planck Genome Centre Cologne, Germany
2
Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are globally distributed
in shallow and deep marine sediments. Despite the prevalence of DEH in the marine
subsurface, little is known about their metabolic properties or roles in biogeochemical
cycles. In this research, genomic content from 5 single cells of the DEH were obtained
from sediments of Aarhus Bay, Denmark, and analysed in order to predict key metabolic
properties. In one single cell, we identified a gene cluster encoding for dissimilatory
sulfite reductase (Dsr). This suggests some DEH have the capacity to reduce sulfite,
although genes that indicate the source of sulfite, were not recovered in the
corresponding genome. The single cell provides the first report for genes encoding Dsr
in the phylum Chloroflexi and the first phylogenetic identity for a clade of unknown Dsrharbouring organisms known from molecular surveys of dsrAB. We also provided
further genetic evidence for the potential for sulfite reduction by other putative DEH
taxa and at other sites by amplifying genomic fragments containing the dsr gene cluster
directly from sediment-derived DNA. Several genes were also identified in multiple
single cells that encode oxidoreductases of the complex iron-sulfur molybdoenzyme
(CISM) family. These were phylogenetically affiliated with CISM enzymes known to
reduce dimethyl sulfoxide, suggesting various DEH could use these molecules as
electron acceptors. Genes encoding enzymes with organo-sulfur hydrolysis activity also
hinted to the roles of DEH in desulfonating sulfonated organic compounds. Together,
this data provides indications that DEH may play various previously unknown roles in
sulfur cycling within the marine subsurface.
106
Session: Biotechnology
P55
Anaerobic oxidation of methane using different sulphur
compounds as electron acceptors in a bioreactor
Chiara Cassarini1, 2, Eldon R. Rene1, Graciela Gonzalez-Gil1, Piet N. L. Lens1
1
UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig,
Germany
2
Anaerobic oxidation of methane coupled to sulphate reduction (AOM-SR) is a known
natural process occurring in anaerobic environments, but the mechanism has not yet
been fully understood. AOM investigation have another research direction; the
desulphurization of industrial wastewater using methane as the sole electron donor.
However, the slow growing nature of anaerobic methanotrophs (ANME) remains a
major challenge for AOM-SR practical applications. This research focuses on the
development of a bioprocess for AOM using alternative sulphur compounds as electron
acceptors, on the characterization of the biomass, on the identification of the factors
controlling the growth of the microorganisms involved and on the optimization of the
design for biotechnological application.
The slow microorganisms have been enriching in bioreactors with high biomass
retention capability, using marine sediments as inocula to facilitate microbial growth.
Small sized biotrickilng filter (BTF) reactors (0.4 L) were used in order to select the
most suitable sulphur compounds as electron acceptor for methane oxidation. Sulphate,
elemental sulphur and thiosulphate were used as electron acceptors, while methane as
electron donor. In each reactor, sulphide, sulphate, thiosulphate, methane and carbon
dioxide were monitored. The reactor with sulphate showed complete sulphate
consumption and sulphide production along with the enrichment of ANME identified by
FISH (fluorescence in situ hybridization). The reactors with thiosulphate and elemental
sulphur showed disproportionation to sulphide and sulphate. Sulphide production was
less than expected for all the reactors suggesting formation of other sulphur compounds.
Incubations with 13C-labeled methane will be done to determine the AOM rate. The
selected electron acceptor will be tested in the 5 L BTF reactor, by varying different
process parameters. The microorganisms' phylogenetic identity will be correlated to the
metabolic activity by FISH-NanoSIMS. A mathematical model for the BTF, sensitivity
analysis and cost-benefit analysis will be applied to investigate the bioreactors
performance and application.
107
Session: Biotechnology
P56
A sulphur reducer isolated from Tinto River, an acid rock
drainage environment
Anna Patrícya Florentino1, 2, Jan Weijma2, Alfons J. M. Stams1, 3, Irene Sánchez-Andrea1
1
Laboratory of Microbiology, Wageningen University, The Netherlands
Sub-department of Environmental Technology, Wageningen University, The Netherlands
3 CEB-Centre of Biological Engineering, University of Minho, Portugal
2
Sulphidogenesis, especially from sulphate, is widely applied for bioremediation and
metal recovery of acidic streams from mining and metallurgical activities. Application of
elemental sulphur reduction instead of sulphate reduction may also be attractive as 4
times less electron donor is needed to form the same amount of sulphide. We enriched
and isolated microorganisms able to perform sulphur reduction at low pH from
sediments of an extremely acidic environment, Tinto River, Spain. Sediments were
incubated at 30°C and pH 2 to 5 with hydrogen, glycerol, methanol, and acetate as
electron donors. Sulphur-reducing activity was obtained at a minimal pH of 3 with
hydrogen as electron donor and a pH of 4 with acetate. Cloning and sequencing of the
16S rRNA showed for both substrates dominance of the deltaproteobacterial sulphurreducing genus Desulfurella. Similar sequences have been detected in 16S rRNA
pyrosequencing of the sediment used as inoculum and in other studies of acidic
environments. We combined different traditional isolation methods such as serial
dilutions, antibiotic treatment and developed a novel anaerobic agar-medium with
colloidal sulphur. A pure culture of Desulfurella sp. strain TR1 was obtained. A few
features of the isolate link it back to its isolation source especially growth in a pH range
from 3 to 6.5, and its metal tolerance: The sensitivity of Desulfurella sp. strain TR1 to
heavy metals was in the inhibitory order of Pb > Zn > Cu > Ni with Ni inhibiting at 1.7
mM and Pb at 0.04 mM, suggesting the ability of the strain to cope with high metal
concentration and its suitability to recover metals from acidic streams.
108
Session: Biotechnology
P58
Assessing the role of sulfide-oxidizing nitrate-reducing
Epsilonproteobacteria in oil field corrosion
Sven Lahme, et al.
School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne
NE1 7RU, UK
Microbiologically-influenced corrosion (MIC) of metal infrastructure is a multibillion £
problem. In the oil industry MIC is often linked to the production of hydrogen sulfide
(H2S) by sulfate (SO42-)-reducing microorganisms (SRM), e.g. due to injection of sulfaterich seawater into oil reservoirs to maintain in-situ pressure. Nitrate (NO3-) injection, as
a ‘green’ bioengineering strategy, is often used to counteract souring by promoting: i)
organotrophic nitrate-reducing microorganism (oNRM), competing with SRM for oil
organic carbon sources, ii) sulfide-oxidizing NRM (soNRM), consuming the souring agent
H2S and iii) NRM-mediated production of nitrite (NO2-), as a potent SRM inhibitor.
However, soNRM can produce corrosive sulfur intermediates such as elemental sulfur
(S0), thiosulfate (S2O32-) or polysulfides (Sn-S2-). Epsilonproteobacterial soNRM are
frequently detected in oil reservoirs and have been linked to MIC during souring control
by nitrate injection. The oil-field soNRM Sulfurimonas sp. strain CVO initially converts
sulfide to elemental sulfur prior to further oxidation to SO42-. NO3--dosing regimes at
sour oil fields could therefore affect soNRM metabolism and influence corrosion. Strain
CVO was incubated with iron coupons at different initial N/S ratios ranging from 6.0–
0.9. High corrosion rates of 0.23–0.27 mm/y were observed when nitrate was high
relative to sulfide (ratios 6.0–1.5) whereas at a lower relative nitrate dose (ratio 0.9)
corrosion was only 0.14 mm/y. Time-dependent examination of corrosion coupons
revealed initially corrosion at a high rate (0.37-0.48 mm/y), which decreased around
80% after 50 h (0.08-0.09 mm/y). The high initial rate coincided with maximal
abundance of S0 and therefore it may play a key role in the observed high corrosion of
strain CVO. Sulfurimonas spp. contain sox genes for oxidation of reduced sulfur
compound, and their expression may govern the differential accumulation of S
intermediates in response to varying nitrate dose regimes.
109
Session: Biotechnology
P59
Isolation, characterization and genome analysis of a nitrate
reducing Arcobacter sp. isolated from injection water
Irene Roalkvam1, Karine Drønen2, Runar Stokke1, Håkon Dahle1, Ida Helene Steen1
1
2
University of Bergen, Department of Biology, Norway
University of Bergen, UniResearch, Norway
Corrosion of mild steel is a pervasive problem in the oil industry, and the replacement of
pipes and installations is costly. One of the best studied bacterial groups associated with
microbially induced corrosion (MIC) are the sulfate-reducing bacteria (SRB), while less
is known about the other microbial taxa involved in this process. To expand our
knowledge on this, a nitrate reducing Arcobacter strain was isolated from the Oilfield A
in the North Sea, where the saline aquifer water added to the injection water results in a
great corrosion potential. Physiological and metabolic characterization of the Arcobacter
isolate revealed a mesophilic microorganism capable of respiration with nitrate,
elemental sulfur, ferric iron and oxygen (3-10% O2). Organic substrates such as acetate,
lactate, peptone, pyruvate, tryptone, xylan and yeast extract are utilized, as well as H2,
H2S, elemental sulfur and thiosulfate. The genome included genes for flagellar motility,
chemotaxis and biofilm formation, in addition to genes encoding metabolic pathways
corresponding to the substrates mentioned above. A complete sox system and
sulfide:quinone oxidoreductase allowes for oxidation of sulfur species, and presence of
genes for polysulfide reductase and tetrathionate reductase suggests that elemental
sulfur and tetrathionate could be used as terminal electron acceptors. The genome
analyses also revealed an incomplete denitrification pathway (nitrate reduced to
nitrite), a NAD+-reducing hydrogenase (Hox) and an enzyme complex for dissimilatory
iron reduction; thereby expanding our knowledge of the metabolic properties of
Epsilonproteobacteria. Overall, the Arcobacter strain has a great MIC potential as a
result of its capacity for biofilm formation and wide metabolic range. A direct role in MIC
includes production of corrosive agents like nitrite, H2S and sulfuric acids; while an
indirect role includes maintaining favorable growth conditions for SRB by O2 removal,
detoxification of H2S and providing small fatty acids from degradation of complex
organic substrates.
110
Session: Biotechnology
P60
Combined H2S and thiols removal from sour gas streams at
haloalkaline conditions
Pawel Roman1, 2, Martijn Bijmans2, Albert Janssen1, 3
1
Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700
AA Wageningen, The Netherlands
2 Wetsus, Centre of Excellence for Sustainable Water Technology, Oostergoweg 7, 8911 MA
Leeuwarden, The Netherlands
3 Shell Technology Centre Bangalore, RMZ Centennial Campus B, Kundalahalli Main Road,
Bengaluru 560 048, India
Hydrogen sulfide (H2S) is the main sulfur pollutant in fuel gasses. The release of sulfur
compounds to the atmosphere is unwanted because of air pollution and acid deposition.
Besides H2S, volatile organic sulfur compounds (VOSC’s) can be present in sour gasses,
which comprise toxicity, malodorous and negative environmental impact.
Nowadays, removal of H2S and VOSC’s from sour gas streams is of a great urge to reduce
SO2 emission. Treatment of sour gas streams can be achieved by a variety of well-known
physicochemical processes. Main drawbacks of these processes are the high costs for
operation especially for small-size treatment energy use has a large contribution. Next
to the power consumption, relative high costs for chemicals, catalysts and disposal of
physicochemical processes can be overcome by applying biological processes.
A two-step biological treatment process is often used to remove hydrogen sulfide from
sour gas streams. In the first step, H2S is absorbed in a mildly alkaline solution; in the
second step, sulfur-oxidizing bacteria oxidize under oxygen-limiting conditions the
hydrogen sulfide ions (HS-) to elemental sulfur also referred as ‘biosulfur’.
Previous research focused on developing a biological treatment processes for H2S
removal from gaseous and liquid stream. The aim of this project is to develop a process
in which will be possible remove not only H2S but also methanethiol and higher thiols
from gas streams. In addition to that, we will investigate the effect of thiols on sulfur
oxidizing bacteria present in desulfurization systems. Our research demonstrates that it
is possible to remove more than 50 vol.% methanethiol in a system where a scrubber is
integrated with a bioreactor that is operated at haloalkaline conditions whilst at the
same time maintain meeting high selectivity for sulfur production.
111
Session: Biotechnology
P62
Dimethyldisulfide degradation by anaerobic microorganisms
at haloalkaline conditions
João Sousa1, 2, Agnes Jánoska2, Martijn Bijmans2, Alfons Stams1, Caroline Plugge1, 2
1
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB
Wageningen, The Netherlands
2 Wetsus, European centre of excellence for sustainable water technology, Oostergoweg 9,
8911 MA Leeuwarden, The Netherlands
Besides inorganic sulfur compounds, like sulfate and thiosulfate, organic sulfur
compounds, such as dimethylsulfide, dimethyldisulfide and methanethiol, are also
present in nature. These compounds are biologically produced and can be biologically
degraded anaerobically by sulfate reducers or methanogens (Van Leerdam et al 2008).
Degradation of dimethyldisulfide and methanethiol in a biotechnological process at
haloalkaline conditions was previously studied (Van Leerdam et al 2008). In that study,
methanethiol conversion was mainly performed by methanogens, producing sulfide plus
methane. The addition of methanol as extra e-donor resulted in increased degradation of
dimethyldisulfide and methanethiol. However, in some cases H2 might be a preferred edonor since it can be produced on site. As methanethiol degrading methanogens studied
thus far are all methylotrophs that do not use H2/CO2, using H2 as extra e-donor is a
challenge (Jones et al 1998). Thus far, no studies on dimethyldisulfide or methanethiol
degradation were performed by microbial communities enriched in the presence of
hydrogen. In this research two anaerobic fed-batch bioreactors were used to study
dimethyldisulfide conversion with sulfate and with and without H2 as additional
electron donor. The bioreactors were operated at pH 9 and 1.5 M Na+ and the inoculum
was composed of a mixture of sediments originating from soda lakes, salt production
ponds and sludge from sulfide oxidizing reactors operated at microaerophilic
conditions. We showed degradation of dimethyldisulfide, using biomass enriched with
H2. Dimethyldisulfide was converted to methanethiol, which was then degraded by both
methanogens and sulfate-reducing bacteria. The bioreactor fed with H2 as electron
donor was able to resist higher dimethyldisulfide concentrations, 2.5 mM compared to
0.5 mM without H2. Growth was only observed in the bioreactor with H2. This shows that
use of H2 is a good strategy to increase resistance to dimethyldisulfide and methanethiol
and enhance their degradation at haloalkaline conditions.
112
Session: Biotechnology
P63
Ground tire biodesulfurization process: microbial community
characterization and proprieties of compounds containing
bio desulfurized material
Ivan Mangili1, Valeria Tatangelo1, Paola Caracino2, Marina Lasagni1, Giuseppina Bestetti1,
Andrea Franzetti1
1
2
Department of Earth and Environmental Sciences, University of Milano-Bicocca, Italy
Pirelli Labs S.p.A., Italy
The strains Gordonia desulfuricans 213E and Rhodococcus sp. AF21875 are bacteria with
desulfurizing capability; they were tested in a ground tire (GTR) biodesulfurization
process. Two different bioreactors were set up in order to carry out the process in a
controlled environmental system. A community fingerprinting, automated ribosomal
inter-genic spacer analysis (ARISA), was conducted on samples collected after different
times during the experiment to detect the persistence of the inoculated bacteria and to
compare the community of bioreactors. Furthermore, the abundance of total bacteria
(16S rRNA) and biodesulfurization potential (dszA) were estimated through qPCR. The
community fingerprinting analysis showed the persistence of G. desulfuricans 213E, on
the other hand the persistence was not confirmed for Rhodococcus sp. AF21875 due to
the presence of the same ARISA fragments found also in the untreated GTR.
Furthermore, a change in the community was observed in two bioreactors. In particular,
the communities tended to became similar to the untreated GTR community.
Nevertheless, in the bioreactors an increase of dszA was observed. This could be an
indication of bacterial natural selection having this ability to desulfurize GTR. The
desulfurized GTR by each bacterium was blended into fresh natural rubber at a
concentration of 10 part per hundred of rubber (phr) to find out the devulcanized
rubber with the highest compatibility for compounding and revulcanization. The
rheological and mechanical properties of the compounds were investigated and
compared to a compound containing untreated GTR. The results showed that the
biological process led to an increase of the mechanical and rheological properties of
vulcanizates containing biodesulfurized GTRs.
113
Session: Microbial Interactions and Environmental Impacts
P65
The sulfur-iron interplay and its role in the fate of carbon in
salt marsh sediment
Gilad Antler, Jennifer V. Mills, Alexandra V. Turchyn
Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
The carbon budget at Earth’s surface determines Earth’s climate; this is because the
partitioning of carbon among various surface reservoirs determines how much carbon
dioxide is in the atmosphere, where it acts as the dominant greenhouse gas. The fate of
organic carbon in shallow sediments, whether it is buried, oxidized, or made into
methane, is fundamentally tied to other sensitive biogeochemical cycles such as
nitrogen, iron and sulfur, through their redox couplings Salt marshes are highly
productive coastal wetlands that serve a critical role in carbon sequestration and
nutrient trapping. As a marginal environment poised between the terrestrial and marine
realms, salt marshes are extremely vulnerable to changes in environmental conditions
such anthropogenic eutrophication, climate change and sea level rise. The delicate
interplay between the redox cycles of sulfur, carbon and iron, which is critical for the
ultimate fate of organic carbon, can be easily unbalanced through anthropogenic change.
We will present pore fluid geochemical results from sediments from British salt marsh
ponds. Most of the ponds studied have sediments dominated by iron-reduction, while a
few ponds are fully methanic with depleted sulfate reservoirs. We will demonstrate,
using sulfur and oxygen isotopes in dissolved sulfate, how this marginal marine
environment demonstrates a complex interplay between the subsurface iron, sulfur and
carbon cycles. We will discuss how secular variations in space and time can initiate
turnover feedbacks; these feedbacks result in two distinguishable microenvironments
located only few meters apart. Ultimately, we suggest that small changes in the
environmental conditions can switch the ponds from one state to another, and thus that
these salt marshes may become significant sources of methane if the careful balance
among these geochemical species is changed.
114
Session: Microbial Interactions and Environmental Impacts
P66
Investigating sulfur disproportionation and anaerobic
oxidation of methane coupled to iron reduction
Caroline Buckner, Laura Piepgras, Anne Schwedt, Tim Ferdelman, Marcel Kuypers, Jana
Milucka
Max Planck Institute for Marine Microbiology, Germany
It has been proposed that organisms capable of anaerobic oxidation of methane (AOM)
are able to replace sulfate as an electron acceptor with iron and manganese oxides [1].
This metabolism appears problematic, as dissolved sulfate is easily accessible, while iron
and manganese oxides are insoluble and would require some strategy for coping with
these substrates. There has been no molecular evidence to date that suggests that these
organisms have this ability.
However, a recent discovery has shed light on the substrates involved in AOM [2]. The
archaeal partners within the consortium reduce sulfate to zero-valent sulfur, which
reacts with the sulfidic environment to form disulfides that the bacteria can use as
substrates for disproportionation into sulfide and sulfate.
The well-studied abiotic reaction of iron oxides with sulfide produces both elemental
sulfur and disulfides [3]. In the newly discovered mechanism of AOM, the bacteria within
the consortium should be able to disproportionate these substrates, creating sulfide and
sulfate. The sulfate could be used to fuel AOM performed by the archaea and the sulfide
could then create more substrates for the bacteria through its abiotic interaction with
iron. Such a mechanism should be sustainable, a similar experiment with
Sulfurospirillum deleyianum, found that the organism cycled S up to 60 times in
combination with an abiotic reaction with iron oxides [4].
Therefore, the goal of this research is to determine whether the proposed interactions
allow iron-dependent AOM to occur through experiments with enrichment cultures of
the AOM consortia.
[1] Beal et al., 2009. Science 325: 184-187
[2] Milucka et al., 2012. Nature 491: 541-546
[3] Wan et al., 2014. Environmental Science and Technology 48: 5076-5084
[4] Straub and Schink, 2004. Applied and Environmental Microbiology 70: 5744-5749
115
Session: Microbial Interactions and Environmental Impacts
P68
Sulfur metabolism in the human gut microbiota
Yuan Feng1, Irene Sánchez-Andrea1, Alfons J. M. Stams1, 2, Willem M. de Vos1, 3
1
Laboratory of Microbiology, Wageningen University, the Netherlands
IBB – Institute for Biotechnology and Bioengineering, Centre of Biological Engineering,
University of Minho, Portugal
3 Departments of Veterinary Biosciences and Bacteriology and Immunology, University of
Helsinki, Helsinki, Finland
2
Sulfur acquisition is crucial to both humans and their symbiotic gasterointestinal tract
(GI tract) microbiota. The colonic sulfur-containing compounds are either inorganic (e.g.
sulfate, sulfite) or organic (e.g. dietary amino acids, bile and mucins). When it is not
assimilated, the end product of the anaerobic microbial degradation of sulfurcompounds is predominantly hydrogen sulfide (H2S). Gastrointestinal H2S is a
neuromodulator and plays a critical role in controlling physiological responses such as
motility and epithelial cell health. However, it has also been suggested that H2S has a
potential pathogenic role, such as in inflammatory bowel disease, which afflicts 0.1–
0.5% of individuals in western countries. The exact role and fate of sulfide in the human
GI tract is not clear and there are only few sulfidogenic microorganisms described that
use sulfate of sulfite as terminal electron acceptor, such as Desulfovibrio spp. or Bilophila
spp. (via taurine). However, (meta)genomic analysis indicates that there are may more
microbial groups that carry genes involved in H2S production. Hence, the lack of
representative sulfidogenic species limits our understanding of this important
conversion. The aim of the present research is to enrich and isolate sulfidogenic
microorganisms of the anaerobic gut ecosystems, both sulfur-compound respiring and
hydrolyzing ones. Fresh fecal samples were collected from a healthy donor to perform
anaerobic enrichments at 37°C, pH 7.2 with different combinations of relevant electron
donors (e.g. taurine, cysteine) and acceptors (sulfate or sulfite). According to the sulfide
production, we selected 6 enrichment bottles for further processing. The isolation is
being done by a combination of strategies such as tenfold dilution, streaking on agar
plates, antibiotic treatment and pasteurization. Once the isolates are obtained, a
genome-guided characterization and metabolic pathway reconstruction will be
performed to link the isolated microorganisms with their role in the GI tract.
116
Participants
1. Anne-Catherine Ahn
University of Amsterdam, Amsterdam, Netherlands
[email protected]
2. Karthik Anantharaman
UC Berkeley, Berkeley, United States
[email protected]
3. Gilad Antler
University of Cambridge, Cambridge, United Kingdom
[email protected]
4. Cherel Balkema
University of Amsterdam, Amsterdam, Netherlands
[email protected]
5. Tímea Balogh
University of Szeged, Szeged, Hungary
[email protected]
6. Tom Berben
University of Amsterdam, Oegstgeest, Netherlands
[email protected]
7. Jasmine Berg
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
8. Emma Bertran
Harvard University, Cambridge, United States
[email protected]
9. Martijn Bijmans
WETSUS, Leeuwarden, Netherlands
[email protected]
10. Jesper Tataru Bjerg
Aarhus University, Aarhus, Denmark
[email protected]
11. Rich Boden
University of Plymouth, Plymouth, United Kingdom
[email protected]
117
12. Andreas Bøggild
Aarhus University, Aarhus, Denmark
[email protected]
13. Alexander Bradley
Washington University in St. Louis, St. Louis, United States
[email protected]
14. Jose Artur Brito
ITQB-UNL, Oeiras, Portugal
[email protected]
15. Elias Broman
Linnaeus University, Kalmar, Sweden
[email protected]
16. Caroline Buckner
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
17. Julea Butt
University of East Anglia, Norwich, United Kingdom
[email protected]
18. Barbara Campanini
Università di Parma, Parma, Italy
[email protected]
19. Donald Canfield
University of Southern Denmark, Odense, Denmark
[email protected]
20. Diana Vasquez Cardenas
Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, Netherlands
[email protected]
21. Chiara Cassarini
UNESCO-IHE, Delft, Netherlands
[email protected]
22. Christiane Dahl
University of Bonn, Bonn, Germany
[email protected]
23. Lars Damgaard
Aarhus University, Aarhus, Denmark
[email protected]
118
24. Francesco Danza
University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
[email protected]
25. Mark Dopson
Linnaeus University, Kalmar, Sweden
[email protected]
26. Ágnes Duzs
University of Szeged, Szeged, Hungary
[email protected]
27. Stefan Dyksma
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
28. Yuan Feng
Wageningen UR, Wageningen, Netherlands
[email protected]
29. Timothy Ferdelman
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
30. David Fike
Washington University in St. Louis, St. Louis, United States
[email protected]
31. Alyssa Findlay
University of Delaware, Lewes, United States
[email protected]
32. Kai Finster
Aarhus University, Aarhus, Denmark
[email protected]
33. Anna Patrícya Florentino
Wageningen University, Wageningen, Netherlands
[email protected]
34. Niels-Ulrik Frigaard
University of Copenhagen, Helsingør, Denmark
[email protected]
35. Manabu Fukui
Hokkaido University, Sapporo, Japan
[email protected]
119
36. Diego Giao García
Aarhus University, Aarhus, Denmark
[email protected]
37. H. Rex Gaskins
University of Illinois, Urbana, United States
[email protected]
38. Antje Gittel
Aarhus University, Aarhus, Denmark
[email protected]
39. Jon Graf
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
40. Marianne Guiral
CNRS-Aix-Marseille University, Marseille, France
[email protected]
41. Bela Hausmann
University of Vienna, Vienna, Austria
[email protected]
42. Ian Head
Newcastle University, Newcastle upon Tyne, United Kingdom
[email protected]
43. Petra Henke
DSMZ, Braunschweig, Germany
[email protected]
44. William Hocking
University of Bergen, Bergen, Norway
[email protected]
45. Rainer Höfgen
Max Planck Institute of Molecular Plant Physiology, Potsdam (OT) Golm, Germany
[email protected]
46. Roseanne Holanda
Bangor University, Bangor, United Kingdom
[email protected]
47. Casey Hubert
Newcastle University, Newcastle upon Tyne, United Kingdom
[email protected]
120
48. Lee Hutt
University of Plymouth, Saltash, United Kingdom
[email protected]
49. Marion Jaussi
Aarhus University, Aarhus, Denmark
[email protected]
50. Lara M. Jochum
Aarhus University, Aarhus, Denmark
[email protected]
51. Barrie Johnson
Bangor University, Bangor, United Kingdom
[email protected]
52. David Johnston
Harvard University, Cambridge, United States
[email protected]
53. Alexey Kamishny
Ben-Gurion University of the Negev, Beer Sheva, Israel
[email protected]
54. Naoki Kamiya
Tokyo Metropolitan University, Hachioji, Japan
[email protected]
55. Ulrike Kappler
The University of Queensland, St. Lucia, Australia
[email protected]
56. Yoko Katayama
Tokyo University of Agriculture and Technology, Tokyo, Japan
[email protected]
57. Kasper Urup Kjeldsen
Aarhus University, Aarhus, Denmark
[email protected]
58. Tobias Koch
Universität Bonn, Bonn, Germany
[email protected]
59. Anne-Christin Kreutzmann
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
121
60. Jan Kuever
Bremen Institute for Materials Testing, Bremen, Germany
[email protected]
61. Julia Kurth
Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
[email protected]
62. Sven Lahme
Newcastle University, Newcastle upon Tyne, United Kingdom
[email protected]
63. William Leavitt
Washington University in St. Louis, St. Louis, United States
[email protected]
64. Silke Leimkuehler
University of Potsdam, Potsdam, Germany
[email protected]
65. Piet Lens
UNESCO-IHE, Delft, Netherlands
[email protected]
66. Alexander Loy
University of Vienna, Vienna, Austria
[email protected]
67. Samuel Luedin
University of Geneva, Basel, Switzerland
[email protected]
68. Angeliki Marietou
Aarhus University, Aarhus, Denmark
[email protected]
69. Andrew Masterson
Harvard University, Belmont, United States
[email protected]
70. Emily Denise Melton
University of Amsterdam, Amsterdam, Netherlands
[email protected]
71. Filip Meysman
Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, Netherlands
[email protected]
122
72. Snehit Mhatre
Aarhus University, Aarhus, Denmark
[email protected]
73. Hanna Miettinen
VTT Technical Research Centre of Finland Ltd, Espoo, Finland
[email protected]
74. Jana Milucka
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
75. Marc Mussmann
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
76. Gerard Muyzer
University of Amsterdam, Amsterdam, Netherlands
[email protected]
77. Gaofeng Ni
Linnaeus University, Kalmar, Sweden
[email protected]
78. Lars Peter Nielsen
Aarhus University, Aarhus, Denmark
[email protected]
79. Signe B. Nielsen
Aarhus University, Aarhus, Denmark
[email protected]
80. Joerg Overmann
Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH,
Braunschweig, Germany
[email protected]
81. Lex Overmars
University of Amsterdam, Amsterdam, Netherlands
[email protected]
82. Christina Pavloudi
Hellenic Centre for Marine Research, Heraklion, Greece
[email protected]
83. Claus Pelikan
University of Vienna, Vienna, Austria
[email protected]
123
84. Andre Pellerin
McGill University, Montreal, Canada
[email protected]
85. Inês Cardoso Pereira
ITQB/Universidade Nova de Lisboa, Oeiras, Portugal
[email protected]
86. Michael Pester
University of Konstanz, Konstanz, Germany
[email protected]
87. Jillian Petersen
Max Planck Institute for Marine Microbiology, Bremen, Germany
[email protected]
88. Nils Risgaard-Petersen
Aarhus University, Aarhus, Denmark
[email protected]
89. Irene Roalkvam
University of Bergen, Bergen, Norway
[email protected]
90. Pawel Roman
Wageningen University, Leeuwarden, Netherlands
[email protected]
91. Hidehiro Sakurai
Kanagawa University, Hiratsuka, Japan
[email protected]
92. Irene Sánchez-Andrea
Wageningen University, Wageningen, Netherlands
[email protected]
93. Ana Laura Santos
Bangor University, Bangor, United Kingdom
[email protected]
94. André Santos
ITQB-UNL, Oeiras, Portugal
[email protected]
95. Hendrik Schaefer
University of Warwick, Coventry, United Kingdom
[email protected]
124
96. David Schleheck
University of Konstanz, Konstanz, Germany
[email protected]
97. Barbara Schoepp-Cothenet
CNRS, Marseille, France
[email protected]
98. Andreas Schramm
Aarhus University, Aarhus, Denmark
[email protected]
99. Lars Schreiber
Aarhus University, Aarhus, Denmark
[email protected]
100. Heide Schulz-Vogt
Leibniz Institute for Baltic Sea Research Warnemuende (IOW), Rostock, Germany
[email protected]
101. Alexander Slobodkin
Winogradsky Institute of Microbiology RAS, Moscow, Russia
[email protected]
102. Galina Slobodkina
Winogradsky Institute of Microbiology RAS, Moscow, Russia
[email protected]
103. João Sousa
Wageningen University, Leeuwarden, Netherlands
[email protected]
104. Valeria Tatangelo
University of Milano-Bicocca, Milano, Italy
[email protected]
105. Bo Thamdrup
University of Southern Denmark, Odense, Denmark
[email protected]
106. Vera Thiel
The Pennsylvania State University, State College, United States
[email protected]
107. Casper Thorup
Aarhus University, Aarhus, Denmark
[email protected]
125
108. Mauro Tonolla
University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
[email protected]
109. András Tóth
University of Szeged, Szeged, Hungary
[email protected]
110. Stanislav Tsallagov
Bach Institute of Biochemistry RAS, Moscow, Russia
[email protected]
111. Charlotte Vavourakis
University of Amsterdam, Amsterdam, Netherlands
[email protected]
112. Sofia Venceslau
ITQB-UNL, Oeiras, Portugal
[email protected]
113. Michael Visser
Wageningen University, Wageningen, Netherlands
[email protected]
114. Carsten Vogt
Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
[email protected]
115. Kenneth Wasmund
University of Vienna, Vienna, Austria
[email protected]
116. Hannah Sophia Weber
University of Southern Denmark, Odense, Denmark
[email protected]
117. Boswell Wing
McGill University, Montreal, Canada
[email protected]
118. Xiaofen Wu
Linnaeus University, Kalmar, Sweden
[email protected]
126
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