nitrospira spp

nitrospira spp
Techne ® qPCR test
Nitrospira species
Nitrite oxidoreductase beta subunit (nxrB)
150 tests
For general laboratory and research use only
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Introduction to Nitrospira species
Nitrospira is a genus of bacteria in the phylum Nitrospirae.
The first member of this genus was named Nitrospira marina and was isolated from the
Gulf of Maine. The second member of this genus was discovered in 1995 from a corroded
iron pipe in a Moscow heating system. The bacterium was named Nitrospira moscoviensis
and is a gram-negative nitrite-oxidising organism with a helical to vibroid morphology 0.9
-2.2 x 0.2-0.4 uM in size. Nitrospira have doubling time of every 12 - 32 hours.
Nitrospira has a circular chromosome containing approx. 4317kbp which encode for over
4200 genes.
Nitrospira are nitrite-oxidizing bacteria that are important in marine habitats. In aquariums,
for example, if the ammonia/nitrite/nitrate cycle is thrown off, the ecosystems suffers and
fish can get sick or die. Therefore, nitrite-oxidizing bacteria as well as the other bacteria in
this system are important for healthy marine ecosystems. In addition, Nitrospira-like
bacteria are the main nitrite oxidizers in wastewater treatment plants and in laboratory
scale reactors, not Nitrobacter spp., as was previously thought.
Nitrospira is a chemolithoautotrophic nitrite-oxidizing bacterium that is generally found in
freshwater or saltwater. It has been isolated from ocean water, freshwater, aquarium water,
deltaic sediment, deep-sea sediments, soils, and an iron pipe of a heating system.
Nitrospira is part of a nitrification process which is important in the biogeochemical nitrogen
Nitrification is the oxidation of ammonia to nitrite by autotrophic bacteria of the genus
Nitrosomonas and oxidation of the nitrite to nitrate by bacteria in the genus Nitrobacter or
This is important in marine environments because too much ammonia or nitrite can cause
death in fish. However, Nitrospira and similar bacteria are slow-growing organisms, which
means that a newly set-up aquarium without an established population of these bacteria
can accumulate toxic concentrations of ammonia and nitrite.
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
The Techne qPCR Kit for Nitrospira species (Nitrospira_spp) genomes is designed for the
in vitro quantification of Nitrospira_spp genomes. The kit is designed to have the broadest
detection profile possible whilst remaining specific to the Nitrospira_spp genome.
The primers and probe sequences in this kit have 100% homology with a broad range of
Nitrospira_spp sequences based on a comprehensive bioinformatics analysis.
If you require further information, or have a specific question about the detection profile of
this kit then please send an e.mail to [email protected] and our
bioinformatics team will answer your question.
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Kit Contents
• Nitrospira_spp specific primer/probe mix (150 reactions BROWN)
FAM labelled
• Nitrospira_spp positive control template (for Standard curve RED)
• Internal extraction control primer/probe mix (150 reactions BROWN)
VIC labelled as standard
• Internal extraction control DNA (150 reactions BLUE)
• Endogenous control primer/probe mix (150 reactions BROWN)
FAM labelled
• RNAse/DNAse free water (WHITE)
for resuspension of primer/probe mixes and internal extraction control DNA
• Template preparation buffer (YELLOW)
for resuspension of positive control template and standard curve preparation
Reagents and equipment to be supplied by the user
Real-Time PCR Instrument
DNA extraction kit
This kit designed to work well with all processes that yield high quality DNA with minimal
PCR inhibitors.
Lyophilised 2x qPCR Mastermix
This kit is designed to work well with all commercially available Mastermixes.
Pipettors and Tips
Vortex and centrifuge
Thin walled 1.5 ml PCR reaction tubes
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Kit storage and stability
This kit is stable at room temperature but should be stored at -20ºC on arrival. Techne
does not recommend using the kit after the expiry date stated on the pack. Once the
lyophilized components have been re-suspended, unnecessary repeated freeze/thawing
should be avoided. The kit is stable for six months from the date of resuspension under
these circumstances.
If a standard curve dilution series is prepared this can be stored frozen for an extended
period. If you see any degradation in this serial dilution a fresh standard curve can be
prepared from the positive control.
Suitable sample material
All kinds of sample material suited for PCR amplification can be used. Please ensure the
samples are suitable in terms of purity, concentration, and DNA integrity (An internal PCR
control is supplied to test for non specific PCR inhibitors). Always run at least one negative
control with the samples. To prepare a negative-control, replace the template DNA sample
with RNAse/DNAse free water.
Dynamic range of test
Under optimal PCR conditions Techne Nitrospira_spp detection kits have very high priming
efficiencies of >95% and can detect less than 100 copies of target template.
Notices and disclaimers
This product is developed, designed and sold for research purposes only. It is not intended for human diagnostic or drug
purposes or to be administered to humans unless clearly expressed for that purpose by the Food and Drug Administration in the
USA or the appropriate regulatory authorities in the country of use. During the warranty period Techne® detection kits allow
precise and reproducible data recovery combined with excellent sensitivity. For data obtained by violation to the general GLP
guidelines and the manufacturer’s recommendations the right to claim under guarantee is expired. PCR is a proprietary
technology covered by several US and foreign patents. These patents are owned by Roche Molecular Systems Inc. and have
been sub-licensed by PE Corporation in certain fields. Depending on your specific application you may need a license from
Roche or PE to practice PCR. Additional information on purchasing licenses to practice the PCR process may be obtained by
contacting the Director of Licensing at Roche Molecular Systems, 1145 Atlantic Avenue, Alameda, CA 94501 or Applied
Biosystems business group of the Applera Corporation, 850 Lincoln Centre Drive, Foster City, CA 94404. In addition, the 5'
nuclease assay and other homogeneous amplification methods used in connection with the PCR process may be covered by U.
S. Patents 5,210,015 and 5,487,972, owned by Roche Molecular Systems, Inc, and by U.S. Patent 5,538,848, owned by The
Perkin-Elmer Corporation.
Techne™ is a trademark of Bibby Scientific Ltd.
The PCR process is covered by US Patents 4,683,195, and 4,683,202 and foreign equivalents owned by Hoffmann-La Roche
AG. BI, ABI PRISM® GeneAmp® and MicroAmp® are registered trademarks of the Applera Genomics (Applied Biosystems
Corporation). BIOMEK® is a registered trademark of Beckman Instruments, Inc.; iCycler™ is a registered trademark of Bio-Rad
Laboratories, Rotor-Gene is a trademark of Corbett Research. LightCycler™ is a registered trademark of the Idaho Technology
Inc. GeneAmp®, TaqMan® and AmpliTaqGold® are registered trademarks of Roche Molecular Systems, Inc., The purchase of
the Techne® Prime Pro reagents cannot be construed as an authorization or implicit license to practice PCR under any patents
held by Hoffmann-LaRoche Inc.
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Principles of the test
Real-time PCR
A Nitrospira_spp specific primer and probe mix is provided and this can be detected
through the FAM channel.
The primer and probe mix provided exploits the so-called TaqMan® principle. During PCR
amplification, forward and reverse primers hybridize to the Nitrospira_spp DNA. A
fluorogenic probe is included in the same reaction mixture which consists of a DNA probe
labeled with a 5`-dye and a 3`-quencher. During PCR amplification, the probe is cleaved
and the reporter dye and quencher are separated. The resulting increase in fluorescence
can be detected on a range of real-time PCR platforms.
Positive control
For copy number determination and as a positive control for the PCR set up, the kit
contains a positive control template. This can be used to generate a standard curve of
Nitrospira_spp copy number / CT value. Alternatively the positive control can be used at a
single dilution where full quantitative analysis of the samples is not required. Each time the
kit is used, at least one positive control reaction must be included in the run. A positive
result indicates that the primers and probes for detecting the target Nitrospira_spp gene
worked properly in that particular experimental scenario. If a negative result is obtained
the test results are invalid and must be repeated. Care should be taken to ensure that the
positive control does not contaminate any other kit component which would lead to falsepositive results. This can be achieved by handling this component in a Post PCR
environment. Care should also be taken to avoid cross-contamination of other samples
when adding the positive control to the run. This can be avoided by sealing all other
samples and negative controls before pipetting the positive control into the positive control
Negative control
To validate any positive findings a negative control reaction should be included every time
the kit is used. For this reaction the RNAse/DNAse free water should be used instead of
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Internal DNA extraction control
When performing DNA extraction, it is often advantageous to have an exogenous source
of DNA template that is spiked into the lysis buffer. This control DNA is then co-purified
with the sample DNA and can be detected as a positive control for the extraction process.
Successful co-purification and real-time PCR for the control DNA also indicates that PCR
inhibitors are not present at a high concentration.
A separate primer and probe mix are supplied with this kit to detect the exogenous DNA
using real-time PCR. The primers are present at PCR limiting concentrations which allows
multiplexing with the target sequence primers. Amplification of the control DNA does not
interfere with detection of the Nitrospira_spp target DNA even when present at low copy
number. The Internal control is detected through the VIC channel and gives a CT value of
Endogenous control
To confirm extraction of a valid biological template, a primer and probe mix is included to
detect an endogenous gene. Detection of the endogenous control is through the FAM
channel and it is NOT therefore possible to perform a multiplex with the Nitrospira_spp
primers. A poor endogenous control signal may indicate that the sample did not contain
sufficient biological material.
Carry-over prevention using UNG (optional)
Carry over contamination between PCR reactions can be prevented by including uracil-Nglycosylase (UNG) in the reaction mix. Some commercial mastermix preparations contain
UNG or alternatively it can be added as a separate component. UNG can only prevent
carry over from PCR reactions that include deoxyuridine triphosphate (dUTP) in the original
PCR reaction. Techne recommend the application of 0.2U UNG per assay with a 15
minute incubation step at 37°C prior to amplification. The heat-labile UNG is then
inactivated during the Taq polymerase activation step.
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Reconstitution Protocol
To minimize the risk of contamination with foreign DNA, we recommend that all pipetting
be performed in a PCR clean environment. Ideally this would be a designated PCR lab or
PCR cabinet. Filter tips are recommended for all pipetting steps.
Pulse-spin each tube in a centrifuge before opening.
This will ensure lyophilised primer and probe mix is in the base of the tube and is not
spilt upon opening the tube.
Reconstitute the kit components in the RNase/DNase-free water supplied,
according to the table below:
To ensure complete resuspension, vortex each tube thoroughly.
Component - resuspend in water
Pre-PCR pack
Nitrospira_spp primer/probe mix (BROWN)
165 µl
Internal extraction control primer/probe mix (BROWN)
165 µl
165 µl
Endogenous control primer/probe mix (BROWN)
Pre-PCR heat-sealed foil
Internal extraction control DNA (BLUE)
600 µl
Reconstitute the positive control template in the template preparation
buffer supplied, according to the table below:
To ensure complete resuspension, vortex the tube thoroughly.
Component - resuspend in template preparation buffer
Post-PCR heat-sealed foil
Positive Control Template (RED) *
500 µl
* This component contains high copy number template and is a VERY significant
contamination risk. It must be opened and handled in a separate laboratory environment,
away from the other components.
DNA extraction
The internal extraction control DNA can be added either to the DNA lysis/extraction buffer
or to the DNA sample once it has been resuspended in lysis buffer.
DO NOT add the internal extraction control DNA directly to the unprocessed biological
sample as this will lead to degradation and a loss in signal.
Add 4µl of the Internal extraction control DNA (BLUE) to each sample in DNA
lysis/extraction buffer per sample.
Complete DNA extraction according to the manufacturers protocols.
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Real-time PCR detection protocol
For each DNA sample prepare a reaction mix according to the table below:
Include sufficient reactions for positive and negative controls.
2x qPCR MasterMix
Nitrospira_spp primer/probe mix (BROWN)
Internal extraction control primer/probe mix (BROWN)
RNAse/DNAse free water (WHITE)
Final Volume
10 µl
1 µl
1 µl
3 µl
15 µl
For each DNA sample prepare an endogenous control reaction according to the
table below (Optional):
This control reaction will provide crucial information regarding the quality of the
biological sample.
2x qPCR MasterMix
10 µl
Endogenous control primer/probe mix (BROWN)
1 µl
RNAse/DNAse free water (WHITE)
4 µl
15 µl
Final Volume
Pipette 15µl of each mix into individual wells according to your real-time PCR
experimental plate set up.
Prepare sample DNA templates for each of your samples.
Pipette 5µl of DNA template into each well, according to your experimental plate
set up.
For negative control wells use 5µl of RNAse/DNAse free water. The final volume
in each well is 20µl.
If a standard curve is included for quantitative analysis prepare a reaction mix
according to the table below:
2x qPCR MasterMix
10 µl
Nitrospira_spp primer/probe mix (BROWN)
1 µl
RNAse/DNAse free water (WHITE)
4 µl
15 µl
Final Volume
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Preparation of standard curve dilution series.
1) Pipette 90µl of template preparation buffer into 5 tubes and label 2-6
2) Pipette 10µl of Positive Control Template (RED) into tube 2
3) Vortex thoroughly
4) Change pipette tip and pipette 10µl from tube 2 into tube 3
5) Vortex thoroughly
Repeat steps 4 and 5 to complete the dilution series
Standard Curve
Copy Number
Tube 1 Positive control (RED)
Tube 2
2 x 105 per µl
2 x 104 per µl
Tube 3
2 x 103 per µl
Tube 4
2 x 102 per µl
Tube 5
20 per µl
Tube 6
2 per µl
Pipette 5µl of standard template into each well for the standard curve according
to your experimental plate set up.
The final volume in each well is 20µl.
Amplification Protocol
Amplification conditions using Lyophilsed 2x qPCR MasterMix.
50 Cycles
UNG treatment (if required) **
15 mins
37 oC
Enzyme activation
2 mins
95 oC
95 oC
60 oC
* Fluorogenic data for the control DNA should be collected during this step through the FAM and VIC channels
** Required if your Mastermix includes UNG to prevent PCR carryover contamination
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
Interpretation of Results
-ive or +ive
-ive or +ive
Experiment fail
-ive or +ive
Experiment fail
* Where the test sample is positive and the negative control is also positive the
interpretation of the result depends on the relative signal strength of the two results. This
is calculated using the delta CT method by subtracting the target CT value from the
negative control CT value (NC CT value – sample CT value). Where the test sample is
positive and the NC is detected much later (delta CT ≥ 5) then the positive test result is
reliable. Where the NC detection is at a similar level to the test sample (delta CT<5) then
the positive test result is invalidated and a negative call is the correct result.
Internal PCR control
The CT value obtained with the internal control will vary significantly depending on the
extraction efficiency, the quantity of DNA added to the PCR reaction and the individual
machine settings. CT values of 28±3 are within the normal range. When amplifying a
Nitrospira_spp sample with a high genome copy number, the internal extraction control
may not produce an amplification plot. This does not invalidate the test and should be
interpreted as a positive experimental result.
Endogenous control
The signal obtained from the endogenous control primer and probe set will vary according
to the amount of biological material present in a given sample. An early signal indicates
the presence of a good yield of biological material. A late signal suggests that little
biological material is present in the sample.
Quantification of Nitrospira species genomes.
Advanced kit handbook HB10.03.07
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