BON SynthesisReport

BON SynthesisReport

Attaining an Operational Marine Biodiversity

Observation Network (BON) Synthesis Report

Steering Committee:

Linda Amaral-Zettler, J. Emmett Duffy, Daphne Fautin, Gustav Paulay,

Tatiana Rynearson, Heidi Sosik, and John Stachowicz

Attaining an Operational Marine Biodiversity

Observation Network (BON) Synthesis Report

CONTENTS

EXECUTIVE SUMMARY . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

TOWARD AN OPERATIONAL MARINE BIODIVERSITY

OBSERVATION NETWORK . . . . . . . . . . . . . . . . . . . . . . . . 5

CASE STUDIES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

REFERENCES AND WEBSITES CITED . . . . . . . . . . . . . . . . . . . .15

APPENDIX 1. WORKSHOP AGENDA . . . . . . . . . . . . . . . . . . . .16

APPENDIX 2. PARTICIPANT LIST . . . . . . . . . . . . . . . . . . . . . .18

APPENDIX 3. ACRONYMS AND ABBREVIATIONS . . . . . . . . . . . . . . .19

APPENDIX 4. MONITORING APPROACHES AND METHODS . . . . . . . . . .20

APPENDIX 5. MAJOR HABITAT DIVISIONS

AND TAXA TO BE OBSERVED . . . . . . . . . . . . . . . . . . . . . .32

APPENDIX 6. NATIONAL OCEAN POLICY PRIORITY OBJECTIVES . . . . . .33

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EXECUTIVE SUMMARY

Humans depend on the health of the ocean’s ecosystems and associated biogeochemical cycles for food, jobs, and long-term benefits which result in carbon sequestration and oxygen production. Yet many marine habitats are threatened by impacts such as climate change, pollution, overfishing, habitat destruction, and invasive species.

A growing body of research demonstrates that the maintenance of marine biodiversity may be key for sustained ecosystem health and resilience against global change, suggesting that managing for marine biodiversity may help resolve conflicting management objectives, and enhance the nation’s biosecurity. Thus, biodiversity might serve as a master variable in evaluating both the health of marine ecosystems and the success of management efforts. Yet there is no rigorous, standardized, coordinated approach to monitoring biodiversity in a way that produces a coherent picture of status and trends in the 90% of the Earth’s habitable volume that is the ocean.

Developing a marine Biodiversity Observing Network (BON) to understand human impacts on marine systems and predict their consequences should be a national priority. Doing so requires overcoming both the common misperception that the ocean is vast enough to absorb all impacts, and major logistical challenges to access and observe marine biodiversity. Quantifying biodiversity status and trends in a standard, proactive manner will safeguard biodiversity and be less expensive than a reactive response to loss of biodiversity and associated ecosystem resources. With the goal of designing a BON to fill knowledge gaps and provide a sound basis for informing scientific, government, industry, and public decisions, the Interagency Working Group on Ocean Partnerships Ad Hoc Group on

Biodiversity convened a three-day workshop in May 2010 to develop a plan for implementing a sustainable marine

BON. A Steering Committee of nine academic scientists (seven of whom attended) developed the agenda, which included plenary and break-out sessions. Participants included 35 invited scientists spanning a breadth of expertise and 13 representatives of seven federal agency sponsors.

Overarching components of the BON that were discussed involved 1) integrating across levels of biodiversity from intraspecific genetic variation through species to remotely sensed habitat-level diversity -- microsatellites to macrosatellites, 2) linking observations on biodiversity to observations on abiotic environmental variables, 3) siting

BON projects to emphasize environmental forcing factors and biogeography, and 4) incorporating adaptive monitoring to make it possible to address unforeseen questions. Workshop discussions focused on priorities for taxonomic range and resolution, target habitats, and appropriate methodologies. They culminated in recommendations for implementing a marine BON, which would advance most of the National Ocean Policy (NOP) Priority Objectives identified by the Interagency Ocean Policy Task Force (OPTF). The recommendations include activities that are possible with existing technology and infrastructure, as well as those requiring substantial investment and/or more development. In addition to recommendations, case studies illustrating practical pathways of leveraging existing data and infrastructure to realize the recommendations were assembled for deep-sea, continental shelf, coral reef, and Great Lakes ecosystems. For reasons of logistics and maturity of systems and technology on which to build, nearshore and estuarine sites are prime candidates for the first end-to-end integrated marine BON demonstration projects.

Recommendations

1. Coordinate biodiversity sampling across taxa, habitats, hierarchical levels, and methods from microbes to mammals.

2. Maximize compatibility of BON with legacy data.

3. Establish one or more Biodiversity Observation Center(s) to coordinate sample processing, including taxonomic identifications, data management, and training and invest in the computational expertise to handle large datasets in an open access environment.

4. Synthesize and make accessible marine taxonomic resources.

5. Invest in developing new approaches for automated sample processing.

6. Modernize and enhance the nation’s physical infrastructure for marine exploration.

7. Initiate an integrated marine BON demonstration project soon.

INTRODUCTION

Biological diversity, or biodiversity, is defined as the variety of life, encompassing variation at levels of complexity from within species to across ecosystems (Figure 1). Humans depend on biodiversity for food, medicines, recreation, biosecurity, and much more

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. There are also important ethical, cultural and moral justifications for protecting biodiversity.

In recognition of the importance of biodiversity for human well-being, 2010 was proclaimed the International Year of

Biodiversity by the United Nations.

Biodiversity is no less important in the ocean than on land.

Humans depend on the health of the ocean’s ecosystems and associated biogeochemical cycles for food, jobs, and longterm benefits that result in carbon sequestration and oxygen production. In its final recommendations to the President, made on 19 July 2010, the Interagency Ocean Policy Task

Force declared “It is the Policy of the United States to protect, maintain, and restore the health and biological diversity of

3 ocean, coastal, and Great Lakes ecosystems and resources”

. We note that the recommendations emerging from this workshop include specific measures that address several of the Interagency Ocean Policy Task Force’s National Ocean

Policy Priority Objectives (see Appendix 6), as detailed below.

A growing body of experimental research demonstrating that the maintenance of biodiversity – and thus the provision of some of these services -- may be key for sustained ecosystem health and resilience in the face of environmental change

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has led to the suggestion that managing for marine biodiversity may help resolve otherwise conflicting

Figure 1. The lower level includes habitat types within a region; the middle level includes species diversity; and the upper level includes genetic diversity within species (from

Palumbi et al.

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, with permission).

management objectives

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. Thus, biodiversity might be a key master variable useful for determining the health of ecosystems and the success of management efforts.

Surveys and extrapolations based on remotely-sensed habitat loss have produced staggering estimates of the rate of biodiversity loss in many terrestrial habitats

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. By comparison, few data are available to assess how diversity is changing in the 90% of Earth’s habitable volume that is the ocean

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. The paucity of long-term records that hampers our ability to understand exactly how biodiversity in the seas is responding to human activities is largely due to technical challenges, and to a shortage of taxonomic resources. Diversity of some groups has been measured in some places and at some times, but there is no rigorous, standardized, coordinated approach to monitoring marine diversity that could produce a coherent picture of current status and trends. While we can produce convincing data to quantify the increased concentrations of greenhouse gases in our atmosphere over the past 50 years

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, data do not exist to produce graphs tracking marine biodiversity. So, while Earth is undergoing major changes as a result of human activities, we have little sense of the consequences of these changes for the diversity of plant, animal, fungal, and microbial life in the ocean, although well-developed techniques now exist for assessing and quantifying marine diversity at all levels.

Maintaining biodiversity requires knowing its components; to manage for diversity requires understanding its current status and trends over space and time. Knowledge of biodiversity is also essential for monitoring biosecurity

– that is, guarding against threats posed by the introduction of infectious agents, pests, invasive alien species, and the like. A BON can help alert us to the presence of invasive organisms at an early stage, while eradication is still possible. For example, in 2000, divers monitoring the growth of eelgrass in a lagoon near San Diego, California, discovered the highly invasive seaweed Caulerpa taxifolia, a native of tropical seas, which had caused widespread ecological damage in the Mediterranean Sea. In California it was eradicated before it spread because, when detected, the seaweed was restricted to patches within a single cove.

Even well known, large, mobile conspicuous members of the biota such as turtles and mammals must be monitored for effective conservation and management. Recent developments in telemetry and electronic tag technology have greatly enhanced knowledge of their movements and behavior, allowing them to be enlisted in

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4 sampling the environment. Such “animal oceanographers” can be instrumented to identify their critical foraging habitats, migration corridors, and regions of high occupancy, providing critical knowledge about how components of the variable marine habitat influence their distribution, survival, growth, and reproduction.

Oceanographic data provided by these animal-borne sensors could also increase data for understanding other aspects of ecology, including climate change and ocean acidification.

Understanding changes in biodiversity is vital given mounting evidence of the critical role that diversity plays in maintaining marine ecosystem function

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. Several well-documented ecological mechanisms contributing to this effect include: complementarity in the use of resources among species and their responses to environmental variation; positive interactions among species; an increased likelihood of key species being present when species diversity is high; and redundancy, which can provide biological insurance against changes in ecosystem function because species that are similar in many ways may be differentially susceptible to environmental change. It is now clear that in the same way that

Figure 2. Number of observations of biodiversity with depth and distance from shore for pelagic organisms (A = continental shelf, B = continental slope

/ mesopelagic, C = continental slope / bathypelagic , D = abyssal plain , E = hadal zone) (from Webb et al.

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).

long-term financial health is bolstered by a diversified portfolio, ecosystem health and resilience are enhanced by the maintenance of biodiversity

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.

Many marine habitats are under threat from climate change, pollution, overfishing, habitat destruction, and invasive species

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. The resulting changes will undoubtedly have implications for both biodiversity and the services it provides. Thus, developing an observing network for biodiversity to understand the magnitude of these effects and predict their consequences should be a national priority. Some challenges associated with conceptual and practical design of a marine Biodiversity Observing Network (BON) are unique to operating in the ocean. In particular, it is essential to overcome barriers associated with the misperception that the ocean is so vast that it can absorb insults, and, especially for the deep and open ocean areas, the tendency to regard these insults as out of sight, out of mind.

These characteristics also present major logistical challenges for access to and observation of biodiversity. As a consequence, current knowledge about marine biodiversity and ecosystem function declines with distance from land and the ocean surface (Figure 2).

A three-day workshop sponsored by seven federal agencies had the explicit goal of confronting these challenges by providing practical guidance on the way forward to implement a sustainable marine BON (see Appendix 1, the

Workshop agenda). A major outcome was the insight that we are not limited by ideas nor even by technology — expertise and devices exist to monitor marine biodiversity. Significant barriers, however, are lack of coordination and human resources.

TOWARD AN OPERATIONAL MARINE BIODIVERSITY

OBSERVATION NETWORK

The Workshop

The workshop concept arose from discussions among members of the Interagency Working Group on Ocean

Partnerships Ad Hoc Group on Biodiversity, which convened a Steering Committee of nine academic scientists, seven of whom attended the workshop. Workshop participants were invited to span a breadth of expertise in taxonomy, experience in various marine environments, and familiarity with technological solutions. A high acceptance rate to invitations (73%, resulting in 35 attendees: Appendix 2) indicated the interest and importance felt by the scientific community for this endeavor. Representatives of the federal agency sponsors (Appendix 2) NOAA, NASA, MMC,

ONR, NSF, BOEMRE (formerly known as MMS), and the Smithsonian Institution (for abbreviations and acronyms, see

Appendix 3) participated in plenary discussions and attended some break-out sessions as observers.

Workshop discussions focused on priorities for taxonomic range and resolution, target habitats, and appropriate methodologies. The format included presentations of current knowledge by Steering Committee members, small break-out sessions to consider emerging ideas, and plenary discussions to synthesize findings. Themes included how best to produce concrete BON recommendations, questions of scientific and societal concern that should guide BON design and implementation, integration of observations and understanding across spatial and temporal scales, and merging knowledge from various methods. Recommendations were compiled throughout the workshop, which culminated in the development and discussion of preliminary case studies demonstrating application of recommendations to the deep sea, continental shelves (wide and narrow), coral reefs, estuaries, and the Great Lakes.

Structure and major outcomes of break-out groups

Some break-out groups focused on how to determine which habitats and taxa would best characterize the full scope of biodiversity in a marine BON. Habitat types were divided into pelagic and benthic, and the benthic further divided among hard, soft, and biogenic substrata. Taxa were divided mostly by size and whether photosynthetic or habitat-creating.

Break-out discussions set the stage for consideration by the entire group of methods to quantify diversity for each habitat and taxon combination derived from a survey of existing methods provided by workshop participants prior to the meeting (Appendix 4). After voting on methods favored, participants discussed the results of the vote in break-out groups.

Conclusions from these discussions were that many methods are: 1) currently available to capture diversity at multiple levels and across taxa and spatio-temporal scales (Figure 3), although improvements are possible in most, if not all, approaches, and new technologies will certainly be developed; and 2) appropriate for multiple habitat x taxon approaches (Appendix

4). For example, methods used in shallow water can be adapted to deep habitats, and similar

Figure 3. Aquatic biodiversity can be assessed over spatial scales from millimeters to thousands of kilometers using a combination of detection methods

(top panel) and observing infrastructures (bottom panel). Some observing infrastructures can accommodate multiple detection methods, indicated here by different colors: e.g. ships can accommodate all four detection methods whereas satellites use only imaging methods. The relevant spatial scales refer to the range of a single unit and single sortie for each instrument type.

sampling approaches can capture pelagic diversity for a range of microbes, as well as metazoans including zooplankton. A recurring theme was the need to link sampling approaches across scales of space and time. The survey of existing methods suggests that this is possible, but will require significant coordination.

A marine BON will be critically useful for establishing status and trends in marine biodiversity. In addition, such a network will advance both fundamental and applied knowledge for a range of users. Most of the many possibilities for

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6 ancillary benefits raised at a break-out session devoted to the matter fell into the following categories: 1) understanding long-term cyclic changes; 2) providing the baseline for detecting acute human impacts;

3) assessing the effects of multiple stressors on ecosystem health; 4) understanding the causes of diversity differences across water masses (for both species and communities); and 5) defining links between ecosystem services and biodiversity at large scales to complement insights from small-scale studies. These were similar to the results of the breakout session devoted to synthesizing ideas about issues marine BONs should be designed to address (Box 1).

Recommendations

Quantifying biodiversity status and trends in a standardized, proactive manner will foster safeguarding biodiversity, will enhance biosecurity, and will be less expensive than a reactive and curative response to loss of biodiversity and associated ecosystem resources. A central goal of the workshop was to design an operational, marine US BON to fill knowledge gaps and provide a sound basis for informing science, government, industry, and public decisions.

The BON must integrate observations across hierarchical levels of biodiversity from intraspecific genetic variation through species and functional groups to remotely sensed habitat-level diversity.

Biodiversity observations must be systematically linked to and interact with appropriate abiotic environmental variables.

Members of the Steering Committee synthesized these and other themes from the Workshop into specific recommendations for implementing a marine BON. Recommendations include actions that members of the Committee judged could be implemented now or in the near future with existing technology and infrastructure, as well as actions that will require substantial investment and/or development. Besides recommending particular technologies and locations, the committee offered insights for guiding the assembly and implementation of a coherent marine BON that it considered transformative (Box 2).

1. Coordinate biodiversity sampling across taxa, habitats, hierarchical levels, and methods from microbes to mammals. Workshop participants came to some consensus on preferred sampling and observing components of marine biodiversity that should serve as the standard for integrated marine biodiversity observation programs. The many components that can be implemented immediately are listed in Appendix

4. Briefly, they include primarily molecular approaches for sampling microbes; optical

Box 1. Top Issues for a BON (Biodiversity

Observation Network) to Address

(Numbers in parentheses indicate links to National Ocean Policy (NOP) Priority

Objectives of the OPTF)

• How does biodiversity vary among habitats or water masses, and how is biodiversity in habitats or water masses linked? What processes lead to hotspots in biodiversity? Answering these questions requires baseline spatial and taxonomic assessments of

US waters, including mobilizing legacy data. (NOP objectives 3,6,9)

• How do composition and distribution (including geographic and physiologic ranges) of organisms respond to global changes such as warming, altered water carbon chemistry (including acidification), invasive species, deoxygenation, and modified circulation? Do the effects on ecosystem health differ in the face of multiple stressors as compared to a single stressor? (NOP objectives 1,3,5,6,7,9)

• What can we learn about biodiversity and the function of whole systems beyond what we know from studying the parts in isolation? Do diverse and non-diverse systems respond similarly to perturbation, and do they differ in resilience? (NOP objectives 1,5,6)

• What are the consequences of these changes for ecosystem goods and services? What is the relationship between biodiversity and ecosystem health and ecosystem goods and services, especially in sensitive areas and economically important systems

(e.g. how do changes in upwelling affect fisheries)?

Do insights from small-scale studies allow us to understand links between ecosystem services and biodiversity at large scales? (All NOP objectives)

• What drives changes in the state of ecosystems (e.g. alternate states, regime shifts) and what is the relative importance of physical forcing, biotic interactions, and hysteresis? Are there alternate stable states of marine ecosystems? This requires distinguishing long-term cyclic changes from directional signals as a result of global change, as well as characterizing the current disturbance state to detect human impacts (e.g. bottom trawling, oil spills, invasion by alien species, pollution, overfishing). (NOP objectives 1,2,3,5,6,7,8)

• How can areas at risk for loss of biodiversity be detected? How can recovery from loss of biodiversity be detected? How can we understand and reduce the threats to biodiversity? (NOP objectives 2,3,6)

• How do we leverage existing programs and protocols to monitor biodiversity? (NOP objectives 4,9)

• What information is needed to improve ecosystem models that include biodiversity? (NOP objectives

1,2,3,5,6,7,8)

imaging and/or collection of specimens for smaller invertebrates and photosynthetic microbes (i.e. algae, including cyanobacteria and phytoplankton); transect- or quadrat-based sampling for sessile habitat-forming taxa; a range of optical imaging, electronic tagging, and acoustic methods for large, free-ranging animals; and airborne hyperspectral and other remote-sensing methods for assessing biogenic habitat-scale diversity. A common thread is linking molecular to classical specimen-based approaches and images.

A range of pelagic and benthic ecosystems can be sampled with minor variations on this approach. Sharing solutions for, e.g., sampling regimes, and for data handling with NEON

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, which has similar aims in the terrestrial realm of the US, and GEO BON

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, which is a global environmental monitoring network, will help avoid duplication of effort and ensure data are compatible and comparable, while advancing the OPTF National Ocean Policy Priority

Objectives 4 (Coordination and Support) and 9

(Mapping and Infrastructure).

Box 2. Transformative approaches to implementing a marine BON (Biodiversity

Observation Network)

• A coordinated network that integrates existing marine research efforts will greatly improve understanding of the status and trends in biodiversity of US waters at relatively modest cost.

• Biodiversity observation sites should be selected based on oceanographic forcing factors, biogeographic provinces, and water masses to assure insights into global marine biodiversity change and its causes are contextually relevant.

• Elucidating connections among pelagic, benthic, and adjacent terrestrial systems (including human activities) is critical to understanding temporal scales and driving forces of marine biological cycles and ecosystem processes.

2. Maximize compatibility of BON with legacy data. Some central questions motivating establishment of a comprehensive marine

BON involve trends through time, including responses of biodiversity and ecosystems to climate change, fishing pressure, and pollution.

Addressing such questions requires that data from a BON be maximally comparable to historical biodiversity data like those from fisheries surveys and marine bird and mammal surveys, the Continuous Plankton Recorder, and museum collections. Such legacy data are invaluable as indicators of former conditions, but are also highly diverse and idiosyncratic.

Thus, recommendations for a marine BON include designing sampling schemes that,

• Increased use of AUVs, ROVs, drifters, observatory platforms, animal-borne sensors, etc. to complement ship-based activities will enhance flexibility in sampling through time and space; their use will increase the types and quantities of data gathered, and probably will reduce costs.

• Adaptive monitoring, which uses both empirical and model-based data, will allow biodiversity research to evolve, and thus to answer unforeseen questions that cannot be addressed adequately with existing technologies and approaches. Part of deciding which parameters should be monitored should involve determining if proxies can be effective.

• Comprehensive biodiversity inventories should 1) incorporate state-of-the-art assessment techniques from molecular and organismal to community and seascape scales, 2) require depositing voucher specimens (where practical and ethical) in publicly-accessible repositories, and 3) result in products that are widely usable. where possible, produce data that can be meaningfully compared with historical data, and investing in rescuing historical marine biodiversity data (e.g. unpublished environmental impact reports and associated specimen collections) by digitizing and organizing them into user-friendly electronic formats that are made publicly available.

• Capturing and making legacy data readily accessible on line, enhancing tools for automated specimen identification using both morphology and DNA, and developing predictive models based on empirical research all must be integrated for precise, accurate, and useful marine biodiversity observations.

• Developing human resources is as important as technical innovation in creating a successful BON.

Because analysis of environmental change depends on comparisons across time, this recommendation advances OPTF National Ocean Policy Priority Objectives 3 (Inform Decisions), 5 (Climate

Change), and 8 (Changing Arctic).

3. Establish one or more Biodiversity Observation Center(s) to coordinate sample processing, including taxonomic identifications, data management, and training. Workshop participants emphasized that a comprehensive marine BON will not be viable without sustained long-term support for both the personnel to process large volumes of samples and observations (molecular data, physical specimens, images, etc.), and the requisite

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8 information technology infrastructure. Such a facility would ideally combine, in one or more physical centers, a cadre of mission-oriented master taxonomists and parataxonomists who have expertise covering a wide range of marine organisms with IT personnel and infrastructure equipped to handle a huge volume of data, e.g. molecular, image, acoustic, and tagging. The data, managed across scales of time, space, and organism size, would be made available in a timely manner, in user-friendly formats, following community standards

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. A model for part of this goal is the Smithsonian Oceanographic Sorting Center (SOSC, a unit of the US National Museum of Natural History from 1962 until 1992

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), which employed taxonomists to process and sort specimens received from expeditions; the taxonomists identified what they could, and involved other experts for the rest. An important addition to what the SOSC provided would be parataxonomists, trained to make routine identifications, leaving professional taxonomists to assist with difficult identifications, engage collaborating specialists, and develop taxonomic resources for non-specialists, rapidly making taxonomy more accessible and efficient. Workshop participants noted that the US is well behind some other developed nations in having such a marine biodiversity infrastructure (an example is the Aquatic Biodiversity and Biosecurity unit of New

Zealand’s National Institute of Water and Atmospheric Research)

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. This recommendation is key to advancing

OPTF National Ocean Policy Priority Objective 9 (Infrastructure), which underpins most of the other Objectives.

4. Synthesize and make accessible marine taxonomic resources. A major impediment to studying and monitoring biodiversity is that the extensive taxonomic resources that do exist are both scattered and incompletely coordinated. Organizing and synthesizing the taxonomic resources would greatly enhance capacity for a biodiversity inventory, speeding identification of organisms sampled and observed. Among the needs is an accurate and up-to-date checklist of the US marine biota, along with identification tools. The macrobiota is taxonomically relatively well known, so assembly of such a resource would involve mostly coordination and synthesis. A small group of mission-oriented master taxonomists – including those at the Biodiversity

Observation Center(s) -- could produce a checklist and assemble identification tools in about a decade, enhancing them with images and

DNA sequences as they become available. But it is essential to the US to help compile global checklists and identification tools so that invasive organisms can be recognized and identified, a task that should involve all taxonomists of marine organisms in the US.

Linking such resources with initiatives like the Encyclopedia of Life, OBIS, and WoRMS would improve the usefulness of them all. Importantly, collection infrastructure to house and care for the volume of voucher specimens generated by surveys must be enlarged and improved. It is impractical and unwise to have a single central repository for these

Photo by: Mary Lou Frost

specimens; rather, enhancing existing natural history collection facilities in the US that are publicly accessible

(including both personnel and physical facilities) would strengthen another vital component of the biodiversity infrastructure so these facilities could collectively accommodate the many specimens to be archived.

Making biodiversity data accessible and user-friendly is central to advancing all of the OPTF National Ocean

Policy Priority Objectives, but is particularly relevant to Objectives 3 (Improve Understanding), 6 (Ecosystem

Protection), and 9 (Infrastructure).

5. Invest in developing new approaches for automated sample processing. Molecular sequencing and optical and acoustic imaging, as well as traditional specimen-based sampling, result in volumes of data and samples that can rapidly overwhelm the existing capacity of personnel to process and organize. Workshop participants recommended that, in implementing an integrated marine BON, major effort should be devoted to developing systems that can automate processing and organization of biodiversity observations to eliminate this bottleneck. Innovations might include image recognition systems, including automated processing of genetic samples, algorithms for species recognition, and informatics tools to efficiently link molecular data,

morphological data, images, and taxonomic data from new surveys and legacy data. Strategic investments in this area will likely pay for themselves in relatively short order by reducing the labor involved in processing the large streams of data expected from a BON. This recommendation is key to advancing OPTF National Ocean Policy

Priority Objective 9 (Infrastructure), which underpins most of the other

Objectives.

6. Modernize and enhance the nation’s physical infrastructure for marine exploration. The US fleet of marine vehicles capable of working at depths greater than 4500 m was judged inadequate to achieve a basic

Photo by: Paulo Maurin

assessment of deep-sea biodiversity even in US territorial waters. The cost of using most such vehicles for federally funded projects (not including ship costs and mobilization/demobilization) is so high as to make their use prohibitively expensive for most purposes by members of the scientific community. Workshop participants recommended support for an expanded—and affordable—fleet of ROVs and AUVs suited for deep-water deployment, with capacity for event sampling, automated image processing, and other types of modern datagathering currently available; flexibility is essential for accommodating technologies currently in development or to come during the lifetime of the vehicle. This recommendation is key to advancing OPTF National Ocean

Policy Priority Objective 9 (Infrastructure), which underpins most of the other Objectives.

7. Initiate an integrated marine BON demonstration project as soon as possible. The goal is to prove the concept of an end-to-end observation program — from intraspecific genetic variation through species to remotely sensed habitat-level diversity — at one or more sites, preferably by leveraging existing programs and infrastructure that are particularly well developed. This project will serve to field-test and compare several proposed methodological approaches to a BON (Appendix 4) in the same system, and to evaluate the feasibility and cost of integrating across scales and methods in a single system. The latter goal includes 1) linking the catalog of molecular diversity to organism morphologies by means of specimens and images, and linking them, in turn, to valid taxon names; and 2) ground-truthing remotely sensed habitat-level data (which involves collecting both specimens and information on the abiotic environment) to coincide in time and space with satellite observations. This recommendation could be achieved by a targeted call for proposals of projects to be supported by federal agencies with interests in marine biodiversity (through the NOPP process). This recommendation is key to advancing OPTF National Ocean Policy Priority Objective 9 (Infrastructure), which underpins most of the other Objectives.

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CASE STUDIES

Case studies, which were assembled by break-out groups, were meant to outline realistic models of marine BONs by habitat, including specific suggestions for siting and for building on existing facilities and programs. Among the common themes to emerge from these deliberations was the observation that the results of the considerable effort already being expended on monitoring efforts related to marine biodiversity studies and resource management are not integrated. A marine BON must integrate existing programs with new approaches at all levels, explicitly including incentives and resources for coordinating and standardizing. In addition, considerable legacy data exist. Assembling and synthesizing the existing programs and data is necessary to identify trends, as well as gaps in taxonomic, spatial, and temporal coverage. Over all, linking biodiversity surveys that capture data at all scales – from microbes to whales, from instants to centuries, and from bottles that sample water to entire ecosystems – is essential, as is determining the scale for monitoring to address particular questions. Initially, sampling will have to be frequent and intensive; as knowledge of an area grows, it can focus on particular places, taxa, or times of year.

Comprehensive understanding will require use of conventional and new technologies. Extending operational systems is a practical way to capitalize on existing logistics, so planned and recently-launched observing sites and systems should be extended to include additional types of observations and data. Extending these systems will also allow identification of methodologies that can be adapted to study taxa, regions, or processes other than those for which they were designed. In particular, routine automation of some new acoustic and imaging technologies could expand the spatial and temporal ranges and the resolution of the systems.

A notable gap is in understanding the spatial and temporal patterns of diversity not only of small organisms such as archaea, bacteria, protists, and viruses, but also of large, mobile predators like turtles, birds, and marine mammals. The small organisms, which are far less well known taxonomically, are likely to be easiest to sample and to characterize (by molecular methods), and may, coincidentally, be the best indicators of rapid change in habitats and biomes as well. However, although well known taxonomically, the large organisms are more difficult to sample.

Electronic logging tags permit understanding of their spatial and temporal distribution, leading to knowledge of multi-species aggregations or ‘biodiversity hotspots’. For example, areas of high productivity that attract northern elephant seals also are important to a variety of sharks, fishes, turtles, seabirds, and mammals

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. Both unstudied areas and those that have been subject to research should be included in a marine BON, the former in part to assess representativeness of the studied areas, the latter providing an information base. Prime theoretical considerations in selecting sites include richness and representativeness of both taxa and habitats, likelihood of threat by pollution

(including noise), and sensitivity to climate forcing (sites located at the periphery of physico-chemical realms should be targeted). Logistical feasibility is also key to siting decisions.

Understanding biology is strongly contingent on a knowledge base being built, including fostering of taxonomic expertise and resources (guides, museum collections, databases of molecular sequences and geospatial distributions, sampling and data-management protocols, etc.) at appropriate scales of space, time, and taxonomic resolution. To coordinate and help build these, a central facility is needed that would also function as an archival repository for data and for voucher specimens, and where trained professionals routinely identify specimens

(based on molecular sequence analysis or morphology, as appropriate).

Not only would this be efficient, it would help standardize identifications and procedures across studies and habitats.

The Deep Sea

The deep sea is the largest part of the biosphere, consisting of two very different, linked habitats, the pelagic and the benthic realms. For the purposes of a BON, the pelagic realm includes waters from the surface to the bottom that overlie the seabed (the benthic realm) beyond the shelf. A major challenge is determining interactions (including spatial and temporal variability) between sea floor biota and that of the water above it. Because much of the deep sea lies outside national boundaries, international and industry collaborations are essential.

Leveraging existing data sets and observing systems – Because research in the pelagic realm is very sparse except relatively near the surface, little guidance and history are available for it. Repositories of such data as are available (e.g. those assembled by the California Current Ecosystem Long-

Photo by: NOAA

Term Monitoring Project (LTER)) should be mined as part of the planning process. Although the utility of data collected thus far may be limited (e.g. the long-term CalCOFI dataset are restricted to the epipelagic), it may take relatively little effort and expense to increase diversity of biological data collected at long-term stations.

Reliable, long-term research on the biology of the deep benthos extends back only a few decades. Places studied include Site M at 4100 m off southern California, Davidson Seamount, and the Monterey Canyon (deep locations off the east coast, being far off shore, are logistically difficult to study). Systems to which biological sensors may be added include those in place or planned for studying physical phenomena such as earthquakes or volcanoes (e.g.

NeMO). Some examples of technologies being used to study biology in shallower water that could be modified for use in the deep sea are Widder’s “eye in the sea”

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for visualizing bioluminescent organisms and motion-activated imaging at bait stations.

Integration and implementation – To include major water masses, an ideal US system would have sites on the upper and lower Atlantic seaboard of the US, along the coast of the Gulf of Mexico, on the Pacific coast of the continental US, and in the Arctic, the Aleutian Islands, and the tropical Pacific. To promote inter-regional comparisons, sites within regions would include canyons, oxygen-minimum zones, seamounts, and vents and/or seeps.

Practically, to begin to obtain comparative data, priority should be given to one Atlantic and one Pacific system along the US coast, and one in the tropical Pacific. A cabled observing network could be tied to the Discovery

Corridor in the Atlantic that extends from the Fundy Isles region of Canada, and in the Northeast Pacific, a network could be tied to the planned Neptune Observatory (which should extend to the Columbia River to encompass a canyon). The passive and active listening posts recently built along the Pacific coast of North America should be linked to this system; additional ones might be sited at depth, and acoustic sensors might be added to the Argo network. A prime location for a replicate site in the tropics is the Marianas islands, with its history of research on physical and biological aspects of the Mariana Trench and associated environments; logistical support is accessible from extensive facilities in Guam.

Transformative ideas – Two possibilities for continuous sampling are autonomous collectors (such as sediment traps that periodically shift preservative-laden containers) for small organisms and images for larger ones. Both are most practical on the sea floor associated with moorings, where physico-chemical data are being collected, and

AUVs and gliders dock. Samples and images could be retrieved as the vehicles are serviced and data from them are downloaded. In the pelagic realm, drifters and floats might be designed to gather smaller amounts of similar data, but ships will also be needed. As patterns and relationships are uncovered, times and places of sampling can be dictated by proxies such as climatologies. Inferences to be made from legacy data concern trends such as the similarities and differences among Bear Seamount, Davidson Seamount, and seamounts in Hawaii, and changes in the Gulf of Mexico using BOEMRE data collected in connection with mineral exploration.

Continental Shelves

US Northeast Shelf – The US northeast shelf is a highly productive large marine ecosystem influenced by prevailing advection from subpolar regions, dynamic exchanges across coastal and offshore boundaries, and proximity to dense human population centers. Some information about biodiversity status exists but knowledge is uneven and incomplete.

Leveraging existing data sets and observing systems – Long-term monitoring efforts in the region include fisheries stock assessments and protected resource surveys; sampling techniques having included nets, trawls, acoustics, aerial and shipboard observers, and more recent efforts have included acoustics, aerial survey, animal tagging, and some benthic imaging. Process studies such as the GLOBEC Georges Bank program and routine environmental monitoring by national weather buoys are also important assets. Most biological data focus taxonomically on organisms larger than macrozooplankton and spatially on areas shallower than approximately 350m.

Integration and implementation – Extending spatial, temporal, and taxonomic coverage to fill gaps in current observing programs will lead to a comprehensive BON with modest additional ship time. This will, however, require major enhancements in human capital and resources for data analysis and synthesis. Routine survey cruises (for assessment of managed stocks and resources, and environmental monitoring) should be supplemented with automated organism imaging and classification systems for plankton, continuous acoustic measurements for zooplankton and fish, grab sampling for benthic infauna, and enhanced water sampling for microscopic and molecular analyses of microbes. Readily-accessible near-shore sites can contribute to detailed characterization of shelf biodiversity; importantly, they can help ground-truth innovative developments in ship-free offshore sampling, including use of automated underwater vehicles, floats, or moorings for passive acoustic sampling of mammals, and unmanned aerial vehicles for surface surveys of seabirds, mammals, and some turtles.

11

12

Transformative ideas – Focus should be on intense biodiversity monitoring along selected cross-shelf transects

– new Discovery Corridors - in light of historical information that cross-shelf variations in water masses profoundly affect biodiversity. These transects could be done in conjunction with upgraded resources management surveys that span the entire region multiple times per year. The intense surveys would require state-of-art biodiversity assessment techniques ranging from molecular to organism and community scales. Discovery

Corridors could be located to leverage existing near-shore observing systems such as the Martha’s Vineyard Coastal

Observatory and the New Jersey Shelf Observing System, planned shelf break observing infrastructure that is part of

NSF’s Ocean Observatories Initiative, and the slope-to-deep sea time series provided by long term occupation of the Line

W moorings. Combining such sea-based sampling approaches with remote sensing observations would bridge scales of spatial, temporal, and taxonomic variation.

US West Coast Shelf – The narrow continental shelf and slope associated with the California Current large marine ecosystem is highly productive and influenced by a seasonal coastal upwelling that can have large implications for both benthic and pelagic ecosystems and their coupling. The steepness of the slope and its proximity to shore means that

Image by: Monterey Bay National Marine Sanctuary

habitats from intertidal to coastal to open ocean exist within a relatively small area.

Leveraging existing data sets and observing systems – Currently, clusters of activity in ocean monitoring activities are centered in Oregon, Monterey / San Francisco Bays, and Southern California, each spanning a range in latitude, upwelling influence, and degree of human impact / urbanization. For example, the quarterly CalCOFI cruises off southern and central California collect data on phytoplankton biodiversity and zooplankton biomass and biodiversity, as well as a suite of physical parameters. PISCO surveys intertidal and shallow subtidal diversity.

Additional sampling of phytoplankton from piers occurs as part of monitoring for harmful algal blooms. The TOPP program has approximately 2,500 datasets from electronic tags for 23 species of sharks, turtles, seabirds, and marine mammals

22

. Thus, pieces of the infrastructure of a BON are already in place.

Integration and implementation – Among gaps to be filled are those concerning offshore benthic biodiversity.

PacOOS and/or the West Coast Governors’ Agreement on Ocean Health might be used to facilitate integrating projects in Oregon, California, and Washington to produce a coast-wide BON. Integrating pelagic and benthic and nearshore and offshore observations will be key to developing a comprehensive understanding of biodiversity trends.

Transformative ideas – A coordinated network integrating existing efforts with some new ones would permit addressing such fundamental problems as how biodiversity responds to climate fluctuations on scales from interannual to decadal associated with El Niño / La Niña Southern Oscillation (ENSO) and Pacific Decadal Oscillation

(PDO) cycles. A range of locations would allow understanding of how variation in diversity affects resilience of regional assemblages to perturbation. The explicit linking of observing systems across habitat types (benthic-pelagic or nearshore-offshore) would also raise the possibility of assessing whether patterns of mass or energy transfer across ecosystems are paralleled by gradients in diversity.

Nearshore Regions, Estuaries, and Great Lakes

Estuaries, near-shore coastal regions, and the Great Lakes are some of the most productive aquatic habitats in the US, generating a wide array of goods and services. They are also the aquatic regions most impacted by human activities, including being entry points of non-indigenous, invasive organisms.

Leveraging existing data sets and observing systems – A proposed marine BON would make use of the background data available in many near-shore locations and from conservation and monitoring programs such as the

National Estuary Research Reserve System

23

. Among many long-term monitoring programs are two in Narragansett

Bay that have documented decade-scale changes in nutrient cycling, phytoplankton, zooplankton, and fish community dynamics

24

. Chesapeake Bay is the site of several long-term studies on plankton and nutrient dynamics (e.g. LMER/

LTER, ECOHAB, national and state monitoring programs); approximately 50 years of collated biological and physical data are publicly available

25

. Other LTER sites on the east coast with aquatic elements – in Massachusetts, Virginia,

Photo by: Claire Fackler

Georgia, and Florida (see MIRADA-LTERs

26

for some examples) – have biodiversity observations that could become part of integrated long-term studies of ecosystem change, trophic dynamics and biogeochemical processes. In

Lake Michigan, long-term seasonal plankton and benthos monitoring programs are run by the NOAA Great Lakes

Environmental Research Laboratory, the US EPA makes semi-annual observations of the offshore region of the entire lake, and annual lake-wide fisheries surveys are made by the USGS. Several programs aimed at preventing aquatic invasive organisms (Marine Invasions Research Lab, NEMESIS, NBIC, etc.) are located on estuaries and the Great

Lakes. The BON could also leverage the Great Lakes Observing System (GLOS

27

).

Integration and implementation – Marsh/intertidal and shallow vegetated regions can be surveyed for components of plant or habitat biodiversity over relatively large scales using air- or space-borne platforms (e.g. satellite and aircraft imagery, LIDAR). Aerial surveys would be complemented by on-the-ground transects for visual assessment of species composition and collection of specimens for morphological identification and genetic analyses. Deeper waters would be surveyed through a combination of buoy-based instrumentation for semi-continuous sampling (using, e.g., passive imaging, gliders). Data on environmental forcing from such a moored platform would be supplemented by periodic cruises to collect specimens for biotic inventories (bottom grabs for microbes and invertebrates, net tows for bottom and mid-water fishes and zooplankton, and Niskin bottles for microplankton). Cruises should include acoustics for mapping bottom landscapes and habitat diversity, which would be ground-truthed by the collections. The approach described here for estuaries could be adapted to many near-shore marine and freshwater habitats.

Transformative ideas – Near-shore environments provide ideal opportunities for initial tests of several proposed marine BON approaches because of their relative ease of access and long history of exploration, resulting in comparatively well-known taxonomy and ecology, and a good baseline to extend. This aspect also makes them ideal for perceiving aquatic invasive organisms; a thorough and responsive BON could detect new arrivals, supporting attempts to eradicate them before they establish. Many key habitat-formers are emergent plants (for example, marsh grass and mangroves) that are amenable to observation by remote sensing and thus to linking biodiversity observations from regional to micro-scales.

Coral Reefs

Coral reefs are arguably the most diverse and among the most imperiled of marine ecosystems, so a BON focused on reefs is essential as well as challenging. On an areal basis, reefs are minor in the continental US, but vast areas are under US jurisdiction in Micronesia, Samoa, the central Pacific, and the Caribbean, and reefs are important components of one of the largest marine protected areas in the world, the Papah¯anaumoku¯akea Marine National

Monument in the Northwestern Hawaiian Islands. The study and monitoring of reefs, which have a long history, encompass broad spatial, temporal, and taxonomic scales, providing proof of concept for a marine BON extending from intraspecific genetic variation through species to remotely sensed habitat-level diversity.

Leveraging existing data sets and observing systems – Coral reefs are most prevalent in shallow, clear waters, so multi- and hyper-spectral imagery from aircraft and satellites can provide local to global coverage, differentiating habitat and community types, including sea-grass beds, coral rubble, and various types of coral communities. The

Millennium Coral Reef project, a collection currently numbering about 1500 Landsat-acquired multispectral images, provides a baseline for assessing current reef status around the globe. Aircraft-based hyperspectral coverage, with some field spectroradiometric ground-truthing, is also available for large reef tracts including the Florida Keys, Puerto

Rico, and the US Virgin Islands.

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14

Well-established monitoring programs that survey reefs, most with transects and quadrats using observers and video and still imagery, include Australia’s Long Term Monitoring

Project of the Great Barrier Reef and NOAA’s Reef Assessment and Monitoring Program of US Pacific Islands. Because they typically focus on fishes and corals, these surveys miss the bulk of reef diversity, which comprises other invertebrates and microbes. ARMS devices

28

, which sample sessile and sedentary reef organisms by mimicking the structural complexity of hard bottom habitats, were developed to address this taxonomic gap in monitoring. Next-generation sequencing methods that target single gene loci (e.g. 18S,

28S, and 16S mitochondrial ribosomal RNA, COI) are being tested for environmental barcoding to characterize organisms that have colonized ARMS.

Integration and implementation – The components of a marine BON could be readily linked for coral reefs; many are already in place for the French Polynesian island of Moorea.

The Moorea Biocode project intends to document and characterize all species on the island, based on collecting voucher specimens from which images and genetic barcodes have been obtained, and including ARMS, to sample quantitatively the reef cryptobiota for the first time. The

CRIOBE field station has 40 years of reef monitoring data, and the recently-established LTER site (through the University

Photo by: Claire Fackler

of California Gump field station) is collecting geochemical and physical oceanographic measurements, as well as characterizing ecological communities in depth. MIRADA-LTER is also conducting an inventory of microbial diversity in

Moorea’s waters.

Transformative ideas – The broad range of methods available makes coral reefs an excellent proof of concept habitat for a marine BON, allowing capture of data at all scales from microbes to the entire coral reef ecosystem.

Remote sensing could monitor ecosystem response over large spatial scales, with triggers when observations or models predict major stresses having potential for drastic impacts, as is done by the NESDIS Coral Reef Watch

Satellite Monitoring program

29

, which monitors and models ocean temperature data to warn of warming events that could cause coral bleaching. Genetic characterization of some reef biotas would allow applications of environmental

DNA sampling such as sequencing gut contents (for study of food webs) or plankton samples (to understand recruitment dynamics).

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11 Schindler, D. E., R. Hilborn, B. Chasco, C. P.

Boatright, T. P. Quinn, L. A. Rogers, and M. S.

Webster. 2010. Population diversity and the portfolio effect in an exploited species. Nature

465:609-612.

12 Lotze, H. K., H. S. Lenihan, B. J. Bourque, R. H.

Bradbury, R. G. Cooke, M. C. Kay, S. M. Kidwell,

M. X. Kirby, C. H. Peterson, and J. B. C. Jackson.

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312:1806-1809.

13 Halpern, B. S., S. Walbridge, K. A. Selkoe, C. V.

Kappel, F. Micheli, C. D’Agrosa, J. F. Bruno, K. S.

Casey, C. Ebert, H. E. Fox, R. Fujita, D. Heinemann,

H. S. Lenihan, E. M. P. Madin, M. T. Perry, E. R.

Selig, M. Spalding, R. Steneck, and R. Watson.

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17 Yilmaz, P. et al. 2010. The “Minimum Information about a MARKer gene Sequence” (MIMARKS) specification. Nature Preceedings. doi:10.1038/ npre.2010.5252.2

18 http://siarchives.si.edu/findingaids/FARU0610.htm

19 http://www.niwa.co.nz/our-science/aquaticbiodiversity-and-biosecurity

20 http://seamap.env.duke.edu

21 http://www.pbs.org/wnet/nature/episodes/thebeauty-of-ugly/interview-dr-edith-widder/426/

22 http://www. topp.org

23 http://www.nerrs.noaa.gov

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gso.uri.edu/fishtrawl

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aspx?menuitem=14872

26 http://amarallab.mbl.edu

27 http://glos.us

28 http://www.pifsc.noaa.gov/cred/arms.php

29 http://coralreefwatch.noaa.gov/satellite/index.html

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APPENDIX 1. WORKSHOP AGENDA

Attaining Operational Marine Biodiversity Observations: A Workshop to Determine the Status of Current Abilities and Scope Future Solutions

Consortium for Ocean Leadership

1201 New York Avenue NW, Fourth Floor, Washington, DC

May 24–27, 2010

GOAL: Identifying the BEST OPTIONS for IMPLEMENTING a Local, National and Global Biodiversity

Observing Network (BON)

Monday, 24 May

8:30–9:00 Assemble/Breakfast

9:00–9:20 Opening Remarks – Welcome

Ocean Leadership, Federal Sponsors

I. INTRODUCTION

9:20–9:40 Introduction to the Overarching Goal

Regarding Marine Biodiversity Monitoring

– J. Stachowicz

II. HABITATS

9:40–10:10 Overview of Benthic Habitats: Shallow/

Deep

– E. Duffy

10:10–10:30 Q&A

10:30–10:45 Break

10:45–11:15 Overview of Pelagic Habitats: Shallow/

Deep

– T. Rynearson, H. Sosik

11:15–11:45 Q&A

11:45–12:15 Lunch

12:15–1:15 (No. 1) Breakout Groups to Discuss Major

Challenges and Opportunities by Habitat

Facilitated by SC members

1:20–1:50 Breakout Summaries (10 minutes per group)

– SC members

III. TAXONOMY

1:50–2:20 Overview of Taxonomy Issues: Microbes to Metazoa

– G. Paulay, L. Amaral–Zettler

2:20–2:40 Q & A

2:40–2:55 Break

2:55–3:55 (No. 2) Breakout Groups to Discuss Major

Taxonomic Challenges and Opportunities

– Facilitated by SC members

4:00–4:30 Breakout Summaries (10 minutes per group)

– SC members

4:30–5:00 Day 1, Wrap–up Discussion / Review

– SC Chairs

Tuesday, 25 May

8:00–8:30 Breakfast

IV. METHODS

8:30–9:00 Overview of Existing and Anticipated

Biodiversity Observing Methodologies

– T. Rynearson

9:00–9:20 Q&A

9:20–10:20 Breakout Groups to Identify Major

Methodological Challenges and

Opportunities

– Facilitated by SC members

10:20–10:35 Break

10:35–11:20 Breakout Groups continued

– Facilitated by

SC members

11:25–11:55 Breakout Group summaries

– SC members

11:55–12:25 Lunch

12:25–1:25 Small groups to Review Objectives of the BON, formulate 5 most–important questions a BON could address

– Facilitated by SC members

1:30–2:00 Plenary to discuss top 5 questions from each group

2:00–2:15 Break

2:20–4:20 Breakout Groups to Discuss Habitats,

Taxa, Methods that would Best Address

Objectives

– Facilitated by SC members

4:20–5:00 Breakout Summaries (10 minutes per group)

– SC members

5:05–5:30 Wrap–up Discussion / Review

– Steering

Committee Chairs

6:30–9:00 Joint reception with the Revolution of

Science through Scuba Symposium at the

Smithsonian National Museum of Natural

History Ocean Hall.

Wednesday, 26 May

8:30–9:00 Breakfast

VI. Synthesis

9:00–11:00 (No. 5) Breakout Groups Condense and

Prioritize Taxa and Methods, Address

BON Questions – How often to sample as a function of habitat, taxa and methods?

Facilitated by SC members

11:00–11:15 Break

11:15–12:15 Breakout Group Summaries/Plenary

Review of BON Options

– SC members

12:15–12:45 Lunch

12:45–2:30 Breakout Groups Discuss Linking Spatial,

Temporal, and Taxonomic Scales –

What might be transformative? Existing

Programs–What makes them successful?

Legacy data? OOI?

– Facilitated by SC members

2:30–3:00 Break

3:00–4:00 Case Study Examples by Participants

– SC members, Participants

4:00–4:30 Identify Action Items (Online Forum for

Comments) – Participants, Community,

Federal

– SC members, Participants

Thursday, 27 May

Steering Committee Wrap–Up

9:00–2:30 Steering Committee Workshop Synthesis

VII. TIMELINE

June–Dec. Workshop Synthesis Posted to Online

Forum for Public Comments, Moderated by the Steering Committee; Workshop

Results Presented at Major Conferences

Jan. 2011 Workshop Summary, and Online Forum

Comments, Presented to Interagency

Working Group on Ocean Partnerships Ad

Hoc Group on Biodiversity

Feb. 2011 Ad Hoc Group on Biodiversity to Consider

BON Implementation Steps

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APPENDIX 2. PARTICIPANT LIST

Steering Committee

Amaral-Zettler, Linda . Marine Biological Laboratory

Duffy, J. Emmett . . Virginia Institute of Marine

Science

Fautin, Daphne . . . University of Kansas

Paulay, Gustav . . . University of Florida

Rynearson, Tatiana . University of Rhode Island

Sosik, Heidi . . . . Woods Hole Oceanographic

Institution

Stachowicz, John . . University of California-Davis

Workshop Participants

Best, Ben . . . . . Duke University

Bowen, Don . . . . Fisheries and Oceans Canada

Caley, Julian . . . . Australian Institute of Marine

Sciences

Caron, David. . . . University of Southern California

Clark, Chris . . . . Cornell University

Costa, Dan . . . . University of California-Santa

Cruz

Diaz, Bob . . . . . Virginia Institute of Marine

Science

Etter, Ron . . . . . University of Massachusetts-

Boston

Fogarty, Mike . . . National Marine Fisheries Service

Frank, Ken . . . . Dalhousie University

Galagan, James . . Boston University

Geller, Jon . . . . Moss Landing Marine Laboratory

Guild, Liane . . . . National Aeronautics and Space

Administration

Guinotte, John . . . Marine Conservation Biology

Institute

Haddock, Steve. . . Monterey Bay Aquarium

Research Institute

Jaffe, Jules . . . . Scripps Institution of

Oceanography

Lawson, Gareth. . . Woods Hole Oceanographic

Institution

Levin, Lisa . . . . Scripps Institution of

Oceanography

Meyer, Chris . . . . Smithsonian Institution

Ohman, Mark . . . Scripps Institution of

Oceanography

Reid, Philip . . . . University of Plymouth

Scholin, Chris . . . Monterey Bay Aquarium

Research Institute

Short, Fred . . . . University of New Hampshire

Vanderploeg, Hank . Great Lakes Environmental

Research Laboratory

Vecchione, Mike . . National Marine Fisheries Service

Ward, Bess . . . . Princeton University

Watling, Les . . . . University of Hawaii

Westberry, Toby . . Oregon State University

Workshop Sponsors

Beach, Reginald . . National Oceanic and

Atmospheric Administration

/ Office of Oceanic and

Atmospheric Research

Breuer, Eric . . . . National Oceanic and

Atmospheric Administration /

National Marine Fisheries Service

Canonico, Gabrielle . National Oceanic and

Atmospheric Administration /

National Ocean Service

Eckman, Jim . . . . Office of Naval Research

Garrison, Dave . . . National Science Foundation /

Geosciences

Gisiner, Bob . . . . Marine Mammal Commission

Lindstrom, Eric . . . National Aeronautics and Space

Administration / Earth Science

Division

Meyer, Chris . . . . Smithsonian Institution

Snyder, Scott . . . National Science Foundation /

Biological Sciences

Ticco, Paul . . . . National Oceanic and

Atmospheric Administration /

National Ocean Service

Turner, Woody . . . National Aeronautics and Space

Administration / Headquarters

Science Mission Directorate

Valdes, Sally . . . . Bureau of Ocean Energy

Management, Regulation, and

Enforcement

Weise, Michael . . . Office of Naval Research

Additional Attendees

Armaiz-Nolla, Kamil . Consortium for Ocean

Leadership

Bohan, Margot . . . National Oceanic and

Atmospheric Administration

Decker, Cynthia. . . National Oceanic and

Atmospheric Administration

Feldman, Michael . . Consortium for Ocean

Leadership

Ford, Michael . . . National Oceanic and

Atmospheric Administration

Goodwin, Hilary. . . Consortium for Ocean

Leadership

Innes, Mina . . . . Marine Mammal Commission

Moustahfid, Hassan . National Oceanic and

Atmospheric Administration

Simmons, Samantha . Marine Mammal Commission

Wolfe, Bret . . . . US Fish and Wildlife Service

Zimmermann, Leigh . Consortium for Ocean

Leadership

APPENDIX 3. ACRONYMS AND ABBREVIATIONS

ARMS . . . Autonomous Reef Monitoring System

AUV . . . . Autonomous Underwater Vehicle

BOEMRE . . Bureau of Ocean Energy Management,

Regulation and Enforcement

BON . . . . Biodiversity Observing Network

CalCOFI . . California Cooperative Oceanic Fisheries

Investigations

CRIOBE . . Le Centre de Recherches Insulaires et

Observatoire de l’Environnement de

Polynésie Française

DNA . . . . Deoxyribonucleic Acid

ECOHAB . . Ecology and Oceanography of Harmful Algal

Blooms

ENSO . . . El Niño / La Niña Southern Oscillation

EPA . . . . Environmental Protection Agency

GEO BON. . Group on Earth Observations Biodiversity

Observation Network

GLOBEC . . Global Ocean Ecosystem Dynamics

GLOS . . . Great Lakes Observing System

IPCC . . . . Intergovernmental Panel on Climate Change

IT . . . . . Information Technology

IWG . . . . Interagency Working Group

IWG-OP . . . Interagency Working Group on Ocean

Partnerships

JSOST . . . Joint Subcommittee on Ocean Science and

Technology

LIDAR . . . Light Detection And Ranging

LMER . . . Land Margin Ecosystem Research

LTER . . . . Long Term Ecological Research

MEA . . . . Millennium Ecosystem Assessment

MIRADA . . Microbial Inventory Research Across

Diverse Aquatic

MMS . . . Minerals Management Service

NASA . . . National Aeronautics and Space

Administration

NBIC . . . . National Ballast Information Clearinghouse

NEMESIS . . National Exotic Marine and Estuarine

Species Information System

NEON . . . National Ecological Observatory Network

NeMO . . . New Millennium Observatory

NESDIS . . National Environmental Satellite, Data, and

Information Service

NOAA . . . National Oceanic and Atmospheric

Administration

NOP . . . . National Ocean Policy

NOPP . . . National Oceanographic Partnership

Program

NSF . . . . National Science Foundation

OBIS . . . . Ocean Biogeographic Information System

OPTF. . . . Ocean Policy Task Force

ONR . . . . Office of Naval Research

PacOOS . . Pacific Coast Ocean Observing System

PDO . . . . Pacific Decadal Oscillation

PISCO . . . Partnership for Interdisciplinary Studies of

Coastal Oceans

RNA . . . . Ribonucleic Acid

ROV . . . . Remotely Operated Vehicle

R/V . . . . Research Vessel

TOPP. . . . Tagging of Pacific Predators

USGS . . . United States Geological Survey

WoRMS . . World Register of Marine Species

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APPENDIX 4. MONITORING APPROACHES AND METHODS

Preliminary list of approaches and methods considered potentially useful in monitoring marine biodiversity, as well as existing monitoring programs, providing a flavor for the feasability of biodiversity monitoring across a range of spatial and taxonomic scales using currently available technologies. The list was compiled with input from various sources and is not exhaustive. Comments from the community that wil be useful in expanding and filling in the table are welcome.

System/Program Name Taxa Monitored Environment Purpose Analyses Description

1

Colonization-trap methods

1.01

Autonomous Reef Monitoring

System (ARMS)

1.02

Sediment trays

1.03

Granite blocks

1.04

Disc rack - Virtue Project

1.05

Settlement plates

Epifaunal macroinvertebrates: diversity and abundance of colonists

Benthic hard substrata, shallow (Coral Reefs)

Infaunal macroinvertebrates: diversity and abundance of colonists

Benthic soft substrata, deep To quantify recruitment and sea the assembly of of soft-

Invertebrate diversity,

Community structure and sediment communities under different flow regimes temporal dynamics and sediment characteristics. Can be used at various temporal and spatial scales

Trays are used to mimic specific sediment substrates and sample the natural communities.

Epifaunal macroinvertebrates: diversity and abundance of colonists

Benthic hard substrata, shallow

Designed to systematically assess and compare indices of invertebrate biodiversity across gradients of biogeography, environmental conditions, and anthropogenic stress over time.

Morphological taxonomy;

Barcode of Life DNA; Mass parallel sequencing (454) proposed for large-scale efforts.

Long-term devices designed to mimic the structural complexity of benthic habitats for collecting colonizing invertebrates (following Martin et al).

Designed to mimic rock wall Invertebrate diversity, habitats to quantify Community structure and community assembly and to temporal dynamics experimentally manipulate biotic and abiotic forces.

Can be oriented vertically or horizontally

Long-term blocks designed to mimic rock wall habitats (Miller and Etter

2008)

Epifaunal macroinvertebrates: abundance and diversity of colonists

Marine Environment Educational tool, standardized method to look at communities.

Apparently widespread in the EU

Invertebrate diversity,

Community structure and temporal dynamics

A simple rack hung or suspended with CDs separated from one another

(thus providing upper and underside surfaces)

Epifaunal macroinvertebrates: abundance and diversity of colonizing recruits

Benthic substrata, shallow monitor recruitment sessile fauna diversity and ecological interactions

Old-fashioned, "2D ARMS"

2 Field survey methods

2.01

Photoquadrats/rock walls

2.02

2.03

MARINe (Multi-agency Rocky

Intertidal Network: www.marine.gov)

CBS (Coastal Biodiversity

Surveys: http://cbsurveys.ucsc.edu/)

2.04

Long-Term Monitoring Program

2.05

SeagrassNet

Epifaunal macroinvertebrates: abundance and diversity

Benthic hard substrata, shallow

To monitor changes in community dynamics, biodiversity and the impacts of climate change and invasive species. Can be used on larger scales to

Community structure and temporal dynamics explore regional and global biogeographic forces.

Long-term quadrats on existing rock walls that are visited on a regular basis. Diversity and temporal dynamics can be easily quantified from photos.

Designed to assess population and community dynamics as well as size structure over time

Population and community metrics, Size structure analyses (all over time)

Marine Rocky reefs along west coast of NA (since 1992 in many sites)

Epifaunal macroinvertebrates and algae: abundance and diversity

Benthic hard substrata, shallow

Epifaunal macroinvertebrates and algae: abundance and diversity

Benthic hard substrata, shallow fishes and macrobenthic invertebrates: diversity, longcoral reefs term temporal and spatial dynamics

Seagrasses: diversity and abundance. Environmental parameters

Benthic soft substrata, shallow (also some hard, and coral reef)

Designed to provide spatially explicit maps of species distribution at sites across the intertidal gradient long term monitoring of the

GBR

Biogeographic analyses of biodiversity and community composition

Marine Rocky reefs along west coast of NA; Spatially explicit (X,Y,Z) assesment of biodiversity standardized reporting, various scientific papers

Designed to statistically sample seagrass habitats of all species with repeated measures to detect change over time and identify trajectories

Seagrass specied ID, percent cover, biomass, canopy height, density, change in seagrass bed size, plus temperature, light, salinity and sediment

Trained monitoring teams collecting date 4x/yr at fixed transects and reporting to a common database via the internet

Construction Cost Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

POC

~$100 in materials, 3 hours labor.

Diver

$300 but can vary depending on size and style

ROV/Submersible

Diver

ROV/Submersible

Simplicity of design, low cost; Mass parallel sequencing: Quicker (minimal sorting of sample just grind up and sequence), Cost effective for large volume surveys.

Important for quantifying community development in remote settings

Not representative of all species;

Technology not yet optimized for sequencing most invertebrates yet.

Genetic databases often not to species level yet.

Usually isolated from surrounding sediments precluding colonization through sediments.

$100 Diver Diver Good for setting up experimental manipulations (flow, cages, etc) on hard substrates. Can be placed in specific microhabitats and can be monitored photographically.

Can be labor intensive to install and some may be removed by storms.

Probably < $10/rack Diver in shallow water, hang from pier? ROV or sub in deep water

Diver, ROV or SUB

$5 manual manual

Simple, useful educational tool, can engage school children, college students. Can be used globally due to ready materials and low cost

CD surfaces may only attract a subset of the hard substrate fauna.

Isolation from natural simple, very widely used, cheap substrate may create artifacts

ID of recruits challenging morphologically if fauna not well known uncertain. Probably 1-2 years apparently wisespread in

Scandinavia, Europe very widely used, especially in intertidal and harbors

$10 material, 1 hr labor

Diver

Many different pieces of equipment

Field sampling by people

Diver

Field sampling by people

Fast, relatively easy and cheap. Can be easily replicated in space and time.

Some of the community might be obscurred in photos by luxuriant growth

(macroalgae) or overgrowing epifauna

Very detailed and accurate assessments

Cost of personel, need for experts

NA

Many pieces of equipment

Field sampling by people

Field sampling by people

Very detailed and accurate assessments diver

Intertidal or diving n/a long term monitoring

Cost of personel, need for experts much is not ampled n/a

Standardized protocol, works for all species in the world, trains local scientists and managers, comparable date

Start up costs for site location and training required

Along the whole Western coast of US

Along much of Western coast of North America standardized for GBR and other AIMS monitoring

114 sites worldwide

System/Program Name Taxa Monitored Environment Purpose Analyses Description

1

Colonization-trap methods

1.01

Autonomous Reef Monitoring

System (ARMS)

1.02

Sediment trays

1.03

Granite blocks

1.04

Disc rack - Virtue Project

1.05

Settlement plates

Epifaunal macroinvertebrates: diversity and abundance of colonists

Benthic hard substrata, shallow (Coral Reefs)

Infaunal macroinvertebrates: diversity and abundance of colonists

Benthic soft substrata, deep To quantify recruitment and sea the assembly of of soft-

Invertebrate diversity,

Community structure and sediment communities under different flow regimes temporal dynamics and sediment characteristics. Can be used at various temporal and spatial scales

Trays are used to mimic specific sediment substrates and sample the natural communities.

Epifaunal macroinvertebrates: diversity and abundance of colonists

Benthic hard substrata, shallow

Designed to systematically assess and compare indices of invertebrate biodiversity across gradients of biogeography, environmental conditions, and anthropogenic stress over time.

Morphological taxonomy;

Barcode of Life DNA; Mass parallel sequencing (454) proposed for large-scale efforts.

Long-term devices designed to mimic the structural complexity of benthic habitats for collecting colonizing invertebrates (following Martin et al).

Designed to mimic rock wall Invertebrate diversity, habitats to quantify Community structure and community assembly and to temporal dynamics experimentally manipulate biotic and abiotic forces.

Can be oriented vertically or horizontally

Long-term blocks designed to mimic rock wall habitats (Miller and Etter

2008)

Epifaunal macroinvertebrates: abundance and diversity of colonists

Marine Environment Educational tool, standardized method to look at communities.

Apparently widespread in the EU

Invertebrate diversity,

Community structure and temporal dynamics

A simple rack hung or suspended with CDs separated from one another

(thus providing upper and underside surfaces)

Epifaunal macroinvertebrates: abundance and diversity of colonizing recruits

Benthic substrata, shallow monitor recruitment sessile fauna diversity and ecological interactions

Old-fashioned, "2D ARMS"

2 Field survey methods

2.01

Photoquadrats/rock walls

2.02

2.03

MARINe (Multi-agency Rocky

Intertidal Network: www.marine.gov)

CBS (Coastal Biodiversity

Surveys: http://cbsurveys.ucsc.edu/)

2.04

Long-Term Monitoring Program

2.05

SeagrassNet

Epifaunal macroinvertebrates: abundance and diversity

Benthic hard substrata, shallow

To monitor changes in community dynamics, biodiversity and the impacts of climate change and invasive species. Can be used on larger scales to

Community structure and temporal dynamics explore regional and global biogeographic forces.

Long-term quadrats on existing rock walls that are visited on a regular basis. Diversity and temporal dynamics can be easily quantified from photos.

Designed to assess population and community dynamics as well as size structure over time

Population and community metrics, Size structure analyses (all over time)

Marine Rocky reefs along west coast of NA (since 1992 in many sites)

Epifaunal macroinvertebrates and algae: abundance and diversity

Benthic hard substrata, shallow

Epifaunal macroinvertebrates and algae: abundance and diversity

Benthic hard substrata, shallow fishes and macrobenthic invertebrates: diversity, longcoral reefs term temporal and spatial dynamics

Seagrasses: diversity and abundance. Environmental parameters

Benthic soft substrata, shallow (also some hard, and coral reef)

Designed to provide spatially explicit maps of species distribution at sites across the intertidal gradient long term monitoring of the

GBR

Biogeographic analyses of biodiversity and community composition

Marine Rocky reefs along west coast of NA; Spatially explicit (X,Y,Z) assesment of biodiversity standardized reporting, various scientific papers

Designed to statistically sample seagrass habitats of all species with repeated measures to detect change over time and identify trajectories

Seagrass specied ID, percent cover, biomass, canopy height, density, change in seagrass bed size, plus temperature, light, salinity and sediment

Trained monitoring teams collecting date 4x/yr at fixed transects and reporting to a common database via the internet

Construction Cost Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

POC

~$100 in materials, 3 hours labor.

Diver

$300 but can vary depending on size and style

ROV/Submersible

Diver

ROV/Submersible

Simplicity of design, low cost; Mass parallel sequencing: Quicker (minimal sorting of sample just grind up and sequence), Cost effective for large volume surveys.

Important for quantifying community development in remote settings

Not representative of all species;

Technology not yet optimized for sequencing most invertebrates yet.

Genetic databases often not to species level yet.

Usually isolated from surrounding sediments precluding colonization through sediments.

$100 Diver Diver Good for setting up experimental manipulations (flow, cages, etc) on hard substrates. Can be placed in specific microhabitats and can be monitored photographically.

Can be labor intensive to install and some may be removed by storms.

Probably < $10/rack Diver in shallow water, hang from pier? ROV or sub in deep water

Diver, ROV or SUB

$5 manual manual

Simple, useful educational tool, can engage school children, college students. Can be used globally due to ready materials and low cost

CD surfaces may only attract a subset of the hard substrate fauna.

Isolation from natural simple, very widely used, cheap substrate may create artifacts

ID of recruits challenging morphologically if fauna not well known uncertain. Probably 1-2 years apparently wisespread in

Scandinavia, Europe very widely used, especially in intertidal and harbors

$10 material, 1 hr labor

Diver

Many different pieces of equipment

Field sampling by people

Diver

Field sampling by people

Fast, relatively easy and cheap. Can be easily replicated in space and time.

Some of the community might be obscurred in photos by luxuriant growth

(macroalgae) or overgrowing epifauna

Very detailed and accurate assessments

Cost of personel, need for experts

NA

Many pieces of equipment

Field sampling by people

Field sampling by people

Very detailed and accurate assessments diver

Intertidal or diving n/a long term monitoring

Cost of personel, need for experts much is not ampled n/a

Standardized protocol, works for all species in the world, trains local scientists and managers, comparable date

Start up costs for site location and training required

Along the whole Western coast of US

Along much of Western coast of North America standardized for GBR and other AIMS monitoring

114 sites worldwide

21

22

System/Program Name Taxa Monitored Environment Purpose Analyses Description

3 Sample-based methods

3.01

Continuous Plankton Recorder

3.02

Multiple Opening and Closing Net and Environmental Sensing

System (MOCNESS)

Phytoplankton, mesozooplankton, smaller organisms: diversity and abundance. Chlorophyll, physico/chemical parameters

Mesozooplankton,

Micronekton, Nekton: diversity and abundance

Epipelagic

Pelagic (Epi, Meso, Bathy,

Abysso)

Quantitative sampling of mesozooplankton (including DNA anlyses, photography, meroplankton), semibiomass,. Long-term quantitative for

Morphological taxonomy, changes, interocean

The Continuous Plankton Recorder is an approximately 900cm long machine that samples plankton on a moving band of 270um silk at a rate phytoplankton and smaller comparisons, SEM and EM. constituents and fish larvae, Used to measure that is proportional to the speed of the tow ship. A cassette system is presence/absence for coelenterates and some other planktonn on a moving band of silk of biodiversity, non-natives species, biomass, phenology, growing season,

HAB species. Used in used; one cassette equals ~500 nautical miles of tow. The machines are towed by voluntary merchant ships (Ships of Opportunity,

270um mesh. One sample on silk represents 10 nautical miles of tow and 3 m3 filtered water.

Production of a visual acidification, conservation, carrying capacity, trophic mismatch, pelagic benthic estimate of chlorophyll into

4 categories (Phytoplankton coupling.

Colour index). Has been intercalibrted with SeaWifs satellite measurments.

studies of eutrophication, ecosystem stability, ocean

SOOP).Survey started in June 1931, stopped during the Second World

War and has sampled using

Merchant ships on their regular routes each month since January

1946 in the North Sea and North

Atlantic,from 1997 in the North Pacific expanding more recently into other areas of the world. >500 taxa of phytoplankton and zooplankton identified, half to species level; North

Atlantic Ocean and adjacent shelf of

NW Europe and part east coast USA and Canada, North Pacific, Japan to

Canada and Alaskan waters, some sampling in the South Atlantic and sister surveys in the Southern Ocean,

Quantitative sampling of target size class using various sized systems (1/4m, 1-m, 10-m) and nets

(100 um - 2mm)

Morphological taxonomy,

DNA barcoding, live photography, biomass, silhouette photography, 454 pyrosequencing (proposed) environmental data (T/S/D, fluorescence, etc)

3.03

Ship-board DNA sequencing

3.04

3.05

3.06

Classical biological oceanographic sampling

Lake Michigan Pelagic and

Benthic Monitoring Program

Predator diet sampling

All taxa: diversity

Phytoplankton, zooplankton: abundance

(and diversity?).

Chlorophyll, physicochemical parameters

Phytoplankton, zooplankton, benthos, fishes: diversity and abundance. Nutrients, physical parameters

Pelagic (epi)

Pelagic and benthic soft substrata

Fishes and their prey: diversity and abundance

Pelagic

Pelagic, demersal on continental shelf

Accurate DNA-based species identification; species diversity (presence

/ absence)

DNA barcodes from

Identified specimens: PCR and DNA sequencing of target gene region

ABI Automated DNA Sequencer (4capillary GeneScan) time series microscopy for cell counts and spp id tranditional time series program

Designed to describe seasonal dynamics of plankton and benthos in nearshore and offshore waters and to serve as foundation for process studies to understand the causes of changes in the ecology of the lake interannual and seasonal

Morphological taxonomy morphological taxonomy, fatty acid signature analysis

Standard plankton and benthos monitoring using nets and benthic grab samples (ponar) seasonal sampling of predator diets

3.07

Groundfish trawl survey

3.08

Research Vessel (RV) Bottom

Trawl Survey

Fishes: diversity and abundance

Fishes, benthic macroinvertebrates,

(recently added: zooplankton): diversity and abundance. Bottom-water temperature, (recently added: oxygen, chlorophyll)

Demersal on continental shelf

Demersal on continental shelf spatial and temporal indices community analyses stratified random trawl surveys

Designed to provide annual, All species are identified fishery-independent indices and measured (lengths and

For the Scotian Shelf, the RV survey was intiated in 1970 and continued of abundance of commercially exploited species over large spatial weights). For a sub-set of species, aging information is obtained.

un-interrupted to present. Bottom waters of the Northwest Atlantic

Ocean at depths ranging from 50 to

200-300 m scales. All species are assessed, including noncommercial providing useful information on species diversity, dominance and changing compositional patterns over time.

3.09

HPLC pigment analysis

phytoplankton: abundance and higher-taxon diversity

Pelagic (epi) phytoplankton biomass and pigment types decomposition into classspecific pigments through optimization (e.g. Chemtax) discrete water samples, filtered, extracted in organic solvent and analyzed with high pressure liquid chromatography

Construction Cost Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

POC

1CPR + 1Cassette and 1 Ship requiring fitting with a davit.

Cost for 1

CPRs sent to ships in a standard yellow box using a normal carrier.

CPR recovered by the Extensive and well proven ship's crew, If the tow is longer than 500 methodology. Used extensively, more than 200,000 samples processed.

Large standardised computer The machine is unloaded and deployed from the nautical miles the cassette system is changed by them. database of historical data. Large archive of historical samples

CPR/Cassette

$19,000, Davit construct and instal

$11,000 (varies with stern of the vessel by the ship's crew using

When tow completed the CPR is loaded in ship, not needed on

30% of ships) . Cable and block $500

(varies with ship).

Set up costs for new route - assume

500nm tow x 12 tows per annum, the normal winch and equipment on the vessel or when necessary via a small davit or in one case from an articulated arm. A 100m cable is the box and returned to the laboratory for sample analysis and machine servicing.

Relatively inexpensive for detail obtained.

Develops a centre of expertise in plankton taxonomy.

used, marked so 22m is between the surface and the CPR.

preserved in formalin from ~1998 that are available for further analysis. No cost for the ship platform. voluntary help by ship's officers and crew.

Only samples near surface. Shipping routes can change.

Some regions of the

Can be deployed on short coastal to trans-ocean routes.

Operates remotely behind the ship for days. Samples are world rarely traversed by merchant ships.

Some species may be selectively sampled.

Laour intensive use of parataxonmists. Some preserved in excellent condition for many decades.

Now extensively used througout the globe, but still only covering a small area of the global oceans.

organisms not preserved in formalin and disintegrated.

Director

SAHFOS, Prof

Peter Burkill.

Or Philip

(Chris) Reid

$50,000 - $100,000 Coastal to Ocean-

Class Research

Vessel

$75,000 combination of moorings and ships

Coastal to Ocean-

Class Research

Vessel

CTD casts/ship

Coastal to Ocean-

Class Research

Vessel

Coastal to Ocean-

Class Research

Vessel

CTD casts/ships

Quantification and verification of valid sampling, high-volume sampling for rare species, recovery of living specimens

Deployment from research vessels

Rapid at-sea confirmation of species identification

Currently done on individual specimens

(labor-intensive; expensive)

Tow length dependent on depth sampled: 2-3hrs for surface samples; 24+ hrs for deep tows (to 5000m); archived samples preserved in formalin (no end date), alcohol

(2-5 years for DNA), liquid

MOCNESS or similar Erich Horgan instrumented multi-net systems (BESS) or used world-wide Peter Wiebe

(WHOI) nitrogen (no end date)

Appropriate for cruises lasting weeks to months; DNA data permanent record

Not usual yet Ann Bucklin

(UConn) well defined methods, long running sereis limited coverage common Francisco

Chavez

N/A Shipboard Shipboard

$120/sample live-capture

A large, sciencededicated vessel deploying a bottom trawl in pre-detemined geographic areas,

Ship lasting one month each year during July.

The annual cost of the program is $1M CDN.

ship live-capture ship

Ship

The methods are standard and seasonal sampling (if samples are processed immediately) will allow identification of invading species.

Season sampling at inshore and offshore sites is expensive.

Phytoplankton taxonomy is difficult and time consuming.

Zooplankton and benthos samples have indefinite shelf life. Phytoplankton samples last only a year or two unless slides are made.

Standard. Zooplankton and benthos taxonomy is simple.

Phytoplankton and microzooplankton taxonomy is difficult.

relatively inexpensive, consistent temporal sampling, may sample some may not reflect changes in prey field; species better than research trawl surveys subject ot bias by changing foraging distribution of predator

~20 yr large area of consistent temporal and spatial sampling

Data on fish stock status and diversity obtained independently from fishery.

Standardized sampling in existence since 1970 and cover large spatial scales.

low sampling intensity ~40 yr

Some species not adequately sampled.

High cost. broadly continental shelves

Similar surveys of exploited fish species are conducted throughout the United States,

Canada and the European

Seas.

ship, boat, pier, etc.

ship, boat, pier, etc.

Wide taxonomic range, in common use and limited taxonomic expertise required

Subject to uncertainty indefinite storage in liquid due to species-specific nitrogen and physiological variability in pigment ratios; no in situ or automated application to date, requires immediate sample handling in wide use in biological oceanography

System/Program Name Taxa Monitored Environment Purpose Analyses Description

3 Sample-based methods

3.01

Continuous Plankton Recorder

3.02

Multiple Opening and Closing Net and Environmental Sensing

System (MOCNESS)

Phytoplankton, mesozooplankton, smaller organisms: diversity and abundance. Chlorophyll, physico/chemical parameters

Mesozooplankton,

Micronekton, Nekton: diversity and abundance

Epipelagic

Pelagic (Epi, Meso, Bathy,

Abysso)

Quantitative sampling of mesozooplankton (including DNA anlyses, photography, meroplankton), semibiomass,. Long-term quantitative for

Morphological taxonomy, changes, interocean

The Continuous Plankton Recorder is an approximately 900cm long machine that samples plankton on a moving band of 270um silk at a rate phytoplankton and smaller comparisons, SEM and EM. constituents and fish larvae, Used to measure that is proportional to the speed of the tow ship. A cassette system is presence/absence for coelenterates and some other planktonn on a moving band of silk of biodiversity, non-natives species, biomass, phenology, growing season,

HAB species. Used in used; one cassette equals ~500 nautical miles of tow. The machines are towed by voluntary merchant ships (Ships of Opportunity,

270um mesh. One sample on silk represents 10 nautical miles of tow and 3 m3 filtered water.

Production of a visual acidification, conservation, carrying capacity, trophic mismatch, pelagic benthic estimate of chlorophyll into

4 categories (Phytoplankton coupling.

Colour index). Has been intercalibrted with SeaWifs satellite measurments.

studies of eutrophication, ecosystem stability, ocean

SOOP).Survey started in June 1931, stopped during the Second World

War and has sampled using

Merchant ships on their regular routes each month since January

1946 in the North Sea and North

Atlantic,from 1997 in the North Pacific expanding more recently into other areas of the world. >500 taxa of phytoplankton and zooplankton identified, half to species level; North

Atlantic Ocean and adjacent shelf of

NW Europe and part east coast USA and Canada, North Pacific, Japan to

Canada and Alaskan waters, some sampling in the South Atlantic and sister surveys in the Southern Ocean,

Quantitative sampling of target size class using various sized systems (1/4m, 1-m, 10-m) and nets

(100 um - 2mm)

Morphological taxonomy,

DNA barcoding, live photography, biomass, silhouette photography, 454 fluorescence, etc) pyrosequencing (proposed) environmental data (T/S/D,

3.03

Ship-board DNA sequencing

3.04

3.05

3.06

Classical biological oceanographic sampling

Lake Michigan Pelagic and

Benthic Monitoring Program

Predator diet sampling

All taxa: diversity

Phytoplankton, zooplankton: abundance

(and diversity?).

Chlorophyll, physicochemical parameters

Phytoplankton, zooplankton, benthos, fishes: diversity and abundance. Nutrients, physical parameters

Pelagic (epi)

Pelagic and benthic soft substrata

Fishes and their prey: diversity and abundance

Pelagic

Pelagic, demersal on continental shelf

Accurate DNA-based species identification; species diversity (presence

/ absence)

DNA barcodes from

Identified specimens: PCR and DNA sequencing of target gene region

ABI Automated DNA Sequencer (4capillary GeneScan) time series microscopy for cell counts and spp id tranditional time series program

Designed to describe seasonal dynamics of plankton and benthos in nearshore and offshore waters and to serve as foundation for process studies to understand the causes of changes in the ecology of the lake interannual and seasonal

Morphological taxonomy morphological taxonomy, fatty acid signature analysis

Standard plankton and benthos monitoring using nets and benthic grab samples (ponar) seasonal sampling of predator diets

3.07

Groundfish trawl survey

3.08

Research Vessel (RV) Bottom

Trawl Survey

Fishes: diversity and abundance

Fishes, benthic macroinvertebrates,

(recently added: zooplankton): diversity and abundance. Bottom-water temperature, (recently added: oxygen, chlorophyll)

Demersal on continental shelf

Demersal on continental shelf spatial and temporal indices community analyses stratified random trawl surveys

Designed to provide annual, All species are identified fishery-independent indices and measured (lengths and

For the Scotian Shelf, the RV survey was intiated in 1970 and continued of abundance of commercially exploited species over large spatial weights). For a sub-set of species, aging information is obtained.

un-interrupted to present. Bottom waters of the Northwest Atlantic

Ocean at depths ranging from 50 to

200-300 m scales. All species are assessed, including noncommercial providing useful information on species diversity, dominance and changing compositional patterns over time.

3.09

HPLC pigment analysis

phytoplankton: abundance and higher-taxon diversity

Pelagic (epi) phytoplankton biomass and pigment types decomposition into classspecific pigments through optimization (e.g. Chemtax) discrete water samples, filtered, extracted in organic solvent and analyzed with high pressure liquid chromatography

Construction Cost Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

POC

1CPR + 1Cassette and 1 Ship requiring fitting with a davit.

Cost for 1

CPR/Cassette

$19,000, Davit construct and instal

$11,000 (varies with

CPRs sent to ships in a standard yellow box using a normal carrier.

CPR recovered by the Extensive and well proven ship's crew, If the tow is longer than 500 methodology. Used extensively, more than 200,000 samples processed.

The machine is unloaded and deployed from the stern of the vessel by the ship's crew using nautical miles the cassette system is changed by them.

When tow completed the CPR is loaded in

Large standardised computer database of historical data. Large archive of historical samples preserved in formalin from ~1998 that are available for further analysis. No ship, not needed on

30% of ships) . Cable and block $500

(varies with ship).

Set up costs for new route - assume

500nm tow x 12 tows per annum, the normal winch and equipment on the vessel or when necessary via a small davit or in one case from an articulated arm. A 100m cable is the box and returned to the laboratory for sample analysis and machine servicing.

Relatively inexpensive for detail obtained.

cost for the ship platform. voluntary help by ship's officers and crew.

Develops a centre of expertise in plankton taxonomy.

used, marked so 22m is between the surface and the CPR.

Only samples near surface. Shipping routes can change.

Some regions of the world rarely traversed by merchant ships.

Some species may be selectively sampled.

Laour intensive use of parataxonmists. Some organisms not preserved in formalin and disintegrated.

Can be deployed on short coastal to trans-ocean routes.

Operates remotely behind the

Now extensively used througout the globe, but still only covering a small area of the global oceans.

ship for days. Samples are preserved in excellent condition for many decades.

Director

SAHFOS, Prof

Peter Burkill.

Or Philip

(Chris) Reid

$50,000 - $100,000 Coastal to Ocean-

Class Research

Vessel

$75,000 combination of moorings and ships

Coastal to Ocean-

Class Research

Vessel

CTD casts/ship

Coastal to Ocean-

Class Research

Vessel

Coastal to Ocean-

Class Research

Vessel

CTD casts/ships

Quantification and verification of valid sampling, high-volume sampling for rare species, recovery of living specimens

Deployment from research vessels

Rapid at-sea confirmation of species identification

Currently done on individual specimens

(labor-intensive; expensive)

Tow length dependent on depth sampled: 2-3hrs for surface samples; 24+ hrs for deep tows (to 5000m); archived samples preserved in formalin (no end date), alcohol

(2-5 years for DNA), liquid

MOCNESS or similar Erich Horgan instrumented multi-net systems (BESS) or used world-wide Peter Wiebe

(WHOI) nitrogen (no end date)

Appropriate for cruises lasting weeks to months; DNA data permanent record

Not usual yet Ann Bucklin

(UConn) well defined methods, long running sereis limited coverage common Francisco

Chavez

N/A Shipboard Shipboard

$120/sample live-capture

A large, sciencededicated vessel deploying a bottom trawl in pre-detemined geographic areas,

Ship lasting one month each year during July.

The annual cost of the program is $1M CDN.

ship live-capture ship

Ship

The methods are standard and seasonal sampling (if samples are processed immediately) will allow identification of invading species.

Season sampling at inshore and offshore sites is expensive.

Phytoplankton taxonomy is difficult and time consuming.

Zooplankton and benthos samples have indefinite shelf life. Phytoplankton samples last only a year or two unless slides are made.

Standard. Zooplankton and benthos taxonomy is simple.

Phytoplankton and microzooplankton taxonomy is difficult.

relatively inexpensive, consistent temporal sampling, may sample some may not reflect changes in prey field; species better than research trawl surveys subject ot bias by changing foraging distribution of predator

~20 yr large area of consistent temporal and spatial sampling

Data on fish stock status and diversity obtained independently from fishery.

Standardized sampling in existence since 1970 and cover large spatial scales.

low sampling intensity ~40 yr

Some species not adequately sampled.

High cost. broadly continental shelves

Similar surveys of exploited fish species are conducted throughout the United States,

Canada and the European

Seas.

ship, boat, pier, etc.

ship, boat, pier, etc.

Wide taxonomic range, in common use and limited taxonomic expertise required

Subject to uncertainty indefinite storage in liquid due to species-specific nitrogen and physiological variability in pigment ratios; no in situ or automated application to date, requires immediate sample handling in wide use in biological oceanography

23

System/Program Name

3.10

454-Pyrotag sequencing

Taxa Monitored Environment Purpose Analyses Description

Microorganisms, micrometazoans: diversity, some components of abundance

All environments, in principle

Provides both taxonomic and relative abundance data for Bacteria and

Archaea and presence/absence data for

Eukarya rRNA gene hypervariable regions for bacteria, archaea and eukaryotes

Taxonomic resolution to genus or species possible but depends on extent of annotations in database; captures diversity information for both abundant and rare community members; ability to extend this to longer reads and barcoding applications.

24

3.11

PhyloChip: Universal 16S rRNA

Gene Microarray

Microorganisms, micrometazoans: diversity

(and abundance?)

All environments, in principle

3.12

Lab-on-a-chip

3.13

Hand-held Nucleic Acid Sequence

Based Amplification (NASBA) sensor

Microorganisms, micrometazoans: diversity and abundance

Microorganisms, micrometazoans: diversity

(and abundance?)

Pelagic

Pelagic

The Phylochip is a microarray that uses genetic probes on the chip

Microarray uses genetic probes (rRNA gene

The GeneChip Phylochip

Manufactured by Affymetrix fragments) on chip to match Corporation ® can detect up to to match gene sequences in gene sequences in water or a water, air, or soil sample. sediment sample

32,000 unique versions of the bacterieal 16S RNA gene.

Lab-on-a-chip (LOC) probes for any gene fragment on single chip mm to a few cm square. Can be applied to real-time qPCR to detect prototype hand –held reversetranscription Nucleic Acid Sequence

Based Amplification sensor.

3.14

Autonomous Microbial

Genosensor

Microorganisms: diversity

(and abundance?)

Pelagic

3.15

Environmental Sampling Platform Microorganisms, micrometazoans: diversity

(and abundance?). Proteins and biotoxins

Pelagic

3.16

All Taxon Biodiversity Inventories

(ATBI)

All taxa (potentially) All environments

(potentially) in situ sensor for marine microbe detection. Based on NASBA as well.

Can archive and detect in situ, can be coupled with other equipment to obtain environmental data associated with sampling event. Real-time.

Expandable to other techniques.

document "total" biodiversity of area

HABS, and biotoxins DNA and protein array analyses via filtered samples

Taxonomic, genetic Team of taxonomists and collectors document biodiversity by "saturation" sampling

4 Mixed sample/video/acoustic methods

4.01

4.02

ROV transects: mid-water time series

ROV transects: benthic biology

4.03

Bio-Optical Multi-frequency and

Environmental Recorder

(BIOMAPER-II)

Nekton, gelatinous zooplankton: diversity and abundance

Macroinvertebrates and fishes: diversity and abundance

Mesozooplankton: diversity and abundance.

Temperature, salinity, transmittance, fluorescence

Pelagic: mid-water

Benthic soft and hard substrata, deep sea

Pelagic time series/discovery ecology/discovery

Sample zooplankton diversity, abundance, size

Video, various molecular analyses

ROV transcets video/discrete sampling ROV

Multi-sensor system including multifrequency echosounder, VPR, and environmental sensing system

(temperature, salinity, transmittance, fluorescence)

5 Remote sensing (optical / spectral methods)

5.01

Airborne Visible Infrared Imaging

Spectrometer (AVIRIS)

Habitat-forming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Benthic hard and soft substrata, shallow

5.02

Customized Headwall Imaging

Spectrometer

5.03

Spectroradiometer (GER1500,

SpectraVista Corp) and underwater housing

Habitat-forming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Benthic hard and soft substrata, shallow

Designed to support

NASA's research programs with airborne measurements of upwelling spectral radiance in 224 contiguous spectral channels from 400 to 2500 nm.

Spectral analysis of shallow Spectral radiance information for water benthic type and coastal vegetation type terrestrial and shallow water marine ecosystems; Image classification of benthic types, HAB, and coastal terrestrial cover types

Phytoplankton, habitatforming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Pelagic (epi); benthic hard and soft substrata, shallow

Designed to support

NASA's ocean color and marine research airborne missions with measurements of upwelling spectral radiance in 120 contiguous spectral channels from 400 to 1000 nm.

Spectral analysis of shallow Image classification of benthic types, water benthic type and coastal vegetation type

HABs; Spectral radiance information for ocean color and shallow water marine ecosystems

Designed to collect field spectroscopy data of terrestrial and marine ecosystem features

Spectral analysis of shallow Spectral radiance curves (spectral water benthic type and coastal vegetation type library) for terrestrial and shallow water marine ecosystems

Construction Cost Deployment Method Recovery Method

~30K/per run yielding

~ 1 million sequences

Pros Cons

captures diversity information for both abundant and rare community members; ability to extend this to longer reads and barcoding applications.

Currently restricted to labs with available facilities; expensive upfront costs but different platforms promise cost reductions; not available for in situ platforms but resulting data could be adapted for use with in situ instrumentation such as ESP via phylochips, microarrays etc.

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

POC

ICoMM International Census of Linda Amaral-

Marine Microbes project: Zettler

(http://icomm.mbl.edu); data are downloadable at the

VAMPS website

(http://vamps.mbl.edu). Project descriptions, DNA extraction methodology, proposals and associated metadata are found the MICROBIS pages: http://icomm.mbl.edu/microbis/ project_pages/pp_by_name/

The MIRADA-LTERS project will soon have data available for fresh water and marine

LTERS see http://amarallab.mbl.edu/

MIRADA for project details.

<$1000 a chip Taxonomic resolution to genus or species possible. Another advantage is that it can be used with RNA to determine the most metabolically active organisms in a sample.

Targets known diversity and will not capture unknown or novel diversity.

Requires minimal reagents, fast, highthough-put, cost-effective

Still in development, detection issues, etc.

~$190K reasonable efforts start at $100K very expensive

~$1M

Shipboard varied ship

Towed from vessel

Shipboard varied ship

Isothermal amplification does not require thermocycling during the procedure. Has a high sensitivity. Can

No capacity for sample archival.

be used to detect viruses (has been tested with Noroviruses) and other microbes. NASBA assay has also been developed for the detection of rbcL mRNA from the red tide dinoflagellate Karenia brevis by

Marine Microbiology Group USF.

No capacity for sample archival.

real-time monitoring in situ $$$, coastal deployment challenges, as with all in situ instrumentation

– the possibility of vandalism; biofouling most taxonomically thorough; sets background taxonomic knowledge; creates taxonomic tools mostly qualitative; relies on taxonomic experts; utility increased over longterm as samples get further studied robust and long running examples: CReefs, Biocode,

BIOTAS, Bouchet inventories expensive/limited range generally hrs -day/DNA can be archived for extended periods not widely used

Chris Scholin

Bruce

Robison/Steve

Haddock

Jim Barry

Combination of instruments allows cross-comparison, especially the use of video samples to assist in the interpretation of acoustic data

Large (1 tonne), requires a large vessel and handling system

Aircraft Aircraft Cost NASA JPL

Aircraft Aircraft Portable Cost

Diver Diver Portable Time in the field

NASA Ames

Airborne

Sensor Facility

NASA Ames,

Guild, PI

System/Program Name

3.10

454-Pyrotag sequencing

Taxa Monitored Environment Purpose Analyses Description

Microorganisms, micrometazoans: diversity, some components of abundance

All environments, in principle

Provides both taxonomic and relative abundance data for Bacteria and

Archaea and presence/absence data for

Eukarya rRNA gene hypervariable regions for bacteria, archaea and eukaryotes

Taxonomic resolution to genus or species possible but depends on extent of annotations in database; captures diversity information for both abundant and rare community members; ability to extend this to longer reads and barcoding applications.

3.11

PhyloChip: Universal 16S rRNA

Gene Microarray

Microorganisms, micrometazoans: diversity

(and abundance?)

All environments, in principle

3.12

Lab-on-a-chip

3.13

Hand-held Nucleic Acid Sequence

Based Amplification (NASBA) sensor

Microorganisms, micrometazoans: diversity and abundance

Microorganisms, micrometazoans: diversity

(and abundance?)

Pelagic

Pelagic

The Phylochip is a microarray that uses genetic probes on the chip

Microarray uses genetic probes (rRNA gene

The GeneChip Phylochip

Manufactured by Affymetrix fragments) on chip to match Corporation ® can detect up to to match gene sequences in gene sequences in water or a water, air, or soil sample. sediment sample

32,000 unique versions of the bacterieal 16S RNA gene.

Lab-on-a-chip (LOC) probes for any gene fragment on single chip mm to a few cm square. Can be applied to real-time qPCR to detect prototype hand –held reversetranscription Nucleic Acid Sequence

Based Amplification sensor.

3.14

Autonomous Microbial

Genosensor

Microorganisms: diversity

(and abundance?)

Pelagic

3.15

Environmental Sampling Platform Microorganisms, micrometazoans: diversity

(and abundance?). Proteins and biotoxins

Pelagic

3.16

All Taxon Biodiversity Inventories

(ATBI)

All taxa (potentially) All environments

(potentially) in situ sensor for marine microbe detection. Based on NASBA as well.

Can archive and detect in situ, can be coupled with other equipment to obtain environmental data associated with sampling event. Real-time.

Expandable to other techniques.

document "total" biodiversity of area

HABS, and biotoxins DNA and protein array analyses via filtered samples

Taxonomic, genetic Team of taxonomists and collectors document biodiversity by "saturation" sampling

4 Mixed sample/video/acoustic methods

4.01

4.02

ROV transects: mid-water time series

ROV transects: benthic biology

4.03

Bio-Optical Multi-frequency and

Environmental Recorder

(BIOMAPER-II)

Nekton, gelatinous zooplankton: diversity and abundance

Macroinvertebrates and fishes: diversity and abundance

Mesozooplankton: diversity and abundance.

Temperature, salinity, transmittance, fluorescence

Pelagic: mid-water

Benthic soft and hard substrata, deep sea

Pelagic time series/discovery ecology/discovery

Sample zooplankton diversity, abundance, size

Video, various molecular analyses

ROV transcets video/discrete sampling ROV

Multi-sensor system including multifrequency echosounder, VPR, and environmental sensing system

(temperature, salinity, transmittance, fluorescence)

5 Remote sensing (optical / spectral methods)

5.01

Airborne Visible Infrared Imaging

Spectrometer (AVIRIS)

Habitat-forming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Benthic hard and soft substrata, shallow

5.02

Customized Headwall Imaging

Spectrometer

5.03

Spectroradiometer (GER1500,

SpectraVista Corp) and underwater housing

Habitat-forming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Benthic hard and soft substrata, shallow

Designed to support

NASA's research programs with airborne measurements of upwelling spectral radiance in 224 contiguous spectral channels from 400 to 2500 nm.

Spectral analysis of shallow Spectral radiance information for water benthic type and coastal vegetation type terrestrial and shallow water marine ecosystems; Image classification of benthic types, HAB, and coastal terrestrial cover types

Phytoplankton, habitatforming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Pelagic (epi); benthic hard and soft substrata, shallow

Designed to support

NASA's ocean color and marine research airborne missions with measurements of upwelling spectral radiance in 120 contiguous spectral channels from 400 to 1000 nm.

Spectral analysis of shallow Image classification of benthic types, water benthic type and coastal vegetation type

HABs; Spectral radiance information for ocean color and shallow water marine ecosystems

Designed to collect field spectroscopy data of terrestrial and marine ecosystem features

Spectral analysis of shallow Spectral radiance curves (spectral water benthic type and coastal vegetation type library) for terrestrial and shallow water marine ecosystems

Construction Cost Deployment Method Recovery Method

~30K/per run yielding

~ 1 million sequences

Pros Cons

captures diversity information for both abundant and rare community members; ability to extend this to longer reads and barcoding applications.

Currently restricted to labs with available facilities; expensive upfront costs but different platforms promise cost reductions; not available for in situ platforms but resulting data could be adapted for use with in situ instrumentation such as ESP via phylochips, microarrays etc.

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

POC

ICoMM International Census of Linda Amaral-

Marine Microbes project: Zettler

(http://icomm.mbl.edu); data are downloadable at the

VAMPS website

(http://vamps.mbl.edu). Project descriptions, DNA extraction methodology, proposals and associated metadata are found the MICROBIS pages: http://icomm.mbl.edu/microbis/ project_pages/pp_by_name/

The MIRADA-LTERS project will soon have data available for fresh water and marine

LTERS see http://amarallab.mbl.edu/

MIRADA for project details.

<$1000 a chip Taxonomic resolution to genus or species possible. Another advantage is that it can be used with RNA to determine the most metabolically active organisms in a sample.

Targets known diversity and will not capture unknown or novel diversity.

Requires minimal reagents, fast, highthough-put, cost-effective

Still in development, detection issues, etc.

~$190K reasonable efforts start at $100K very expensive

~$1M

Shipboard varied ship

Towed from vessel

Shipboard varied ship

Isothermal amplification does not require thermocycling during the procedure. Has a high sensitivity. Can

No capacity for sample archival.

be used to detect viruses (has been tested with Noroviruses) and other microbes. NASBA assay has also been developed for the detection of rbcL mRNA from the red tide dinoflagellate Karenia brevis by

Marine Microbiology Group USF.

No capacity for sample archival.

real-time monitoring in situ $$$, coastal deployment challenges, as with all in situ instrumentation

– the possibility of vandalism; biofouling most taxonomically thorough; sets background taxonomic knowledge; creates taxonomic tools mostly qualitative; relies on taxonomic experts; utility increased over longterm as samples get further studied robust and long running examples: CReefs, Biocode,

BIOTAS, Bouchet inventories expensive/limited range generally hrs -day/DNA can be archived for extended periods not widely used

Chris Scholin

Bruce

Robison/Steve

Haddock

Jim Barry

Combination of instruments allows cross-comparison, especially the use of video samples to assist in the interpretation of acoustic data

Large (1 tonne), requires a large vessel and handling system

Aircraft Aircraft Cost NASA JPL

25

Aircraft Aircraft Portable Cost

Diver Diver Portable Time in the field

NASA Ames

Airborne

Sensor Facility

NASA Ames,

Guild, PI

26

System/Program Name Taxa Monitored Environment Purpose Analyses Description

5.04

Ocean Color Satellites (SeaWiFS,

MODIS)

Phytoplankton: abundance and higher-taxon diversity

Pelagic (deep, shallow) and Remote assessment of both Hard and Soft Bottom algal pigment stocks; rates environments (shallow) of production; coarse taxonomy

Detect "color" differences in Polar-orbitting satellites designed to surface ocean via maximize global coverage and repeat fluorescence signature of pigment, processesd via biooptical models

6 In situ optical methods

6.01

Video Plankton Recorder (VPR)

Meso- and macrozooplankton: diversity

Pelagic and abundance

Sample zooplankton diversity, abundance, size

Taxonomy Image-forming optical system sampling a field of view of 7x7mm to

42x42mm

6.02

In situ zooplankton imaging systems (VPR, SIPPER, LOPC,

ISIIS, Ocean DIVA, UVP, ZOOVIS, etc; plus some holographic systems: Holocamera, eHolocam,

Digital Holosub, etc.)

Meso- and macrozooplankton: diversity

Pelagic and abundance

Sample zooplankton diversity, abundance, size

Taxonomy video imaging or holographic imaging

6.03

Flow cytometry (many lab systems, plus in situ systems:

Imaging FlowCytobot, FlowCAM,

Cytobuoy/Cytosub)

Phytoplankton, some microzooplankton: diversity and abundance

Pelagic abundance, cell size, and taxonomic groups optical signature analysis, image analysis in appropriate cases scattering/fluorescence and/or video imaging of single cells in flow

6.04

Absorption spectra (ac-9, ac-s,

Optical Plankton Discriminator)

Phytoplankton: abundance

(and higher-taxon diversity?). Other absorbing constituents

Pelagic Assessment of light absorbing constitutents, potential phytoplankton pigment types spectral decomposition, derivative analysis submersible "shiny tube" or liquid waveguide spectrophotometry

6.05

Fluorescence spectra

(FluoroProbe, etc.)

Phytoplankton: abundance and higher-taxon diversity

(pigment types)

Pelagic assess spectral spectral decomposition, fluorescence characteristics derivative analysis indicative of group-specific pigments spectral fluorometer

6.06

Bathysnap camera system

Macroinvertebrates and fishes: diversity and abundance

Benthic hard and soft substrata: deep sea to monitor long term changes in benthic communities

Changes in animals, sediment-water interface

(e.g., color indications of timing and duration of settlement of phytoplankton to bottom)

7 Animal-carried sampling (tags)

7.01

Position-only/ presence-absence

Large vertebrates: position and movements.

All environments

7.02

Environmental sampling

Large vertebrates: position and movements.

Temperature, pressure

(depth), salinity

(conductivity), color

(fluorimetry)

All environments track migrations, habitat use, find ecosystem hotspots

Position, movements of tagged animal: track could be anything from a microchip sized acoustic fish tag to a cigarette migrations, habitat use, find ecosystem hotspots pack sized long term seal or large fish satellite tag (ARGOS) determine physical and biochemical parameters correlated with animal presence, habitat selection use correlative models to determine physical and biochemical parameters correlated with animal presence, habitat selection:

GAM, GLM, EcoSim etc generally about the size of a cigarette pack or small computer speaker.

Potted in material for depth tolerance to 2000+ meters

7.03

Diving and behavior

Large vertebrates: position and movements (depth, 3-D

All environments accelerometry), feeding biology determine how animals sample the water column in

3-D, partitioning of feeding, resting, travelling, energy high resolution 3-D spatial modeling, statistical analyses budgets, more as above

Construction Cost Deployment Method Recovery Method

None several hundred million dollars per satellite

Rocket

Pros

Global coverage; long term deployment

Cons

low spectral resolution; N/A requires groundtruthing

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

Relatively common due to centralized processing and distribution

POC

$75k

$100K

$100K

$20K

$20K

$100K

Profiled or towed from vessel, mounted on

AUVs (eg REMUS), moored ship, AUV, mooring ship, AUV, mooring, etc.

ship, AUV, mooring, etc.

High vertical resolution; processing can be done in real-time taxonomic resolution to genus or species possible; rapid and quantitative abundance estimates; enables unprecedented space / time resolution and range; automated in situ application possible

Small sample volumes; sampling efficiency affected by density of organisms and avoidance behavior

Routine operation with days to months taxonomic resolution requires complex data analysis systems (e.g., supervised machine learning algorithms) and manual development of training sets, cost ship, mooring, large

AUV ship, mooring, large

AUV taxonomic resolution to genus or species possible with imaging

Routine operation with taxonomic resolution months for in situ instruments, sample storage indefinite in systems; rapid and quantitative abundance estimates; enables unprecedented space / time resolution supervised machine and range; automated in situ applications exist requires complex data analysis systems (e.g., liquid nitrogen for lab analysis learning algorithms) and manual development of training sets, cost prototype in situ applications in coastal systems, ship-board analysis common for picoplankton

Wide taxonomic range within phytoplankton, rapid and relatively inexpensive, no reagents, limited taxonomic expertise required; in situ application

Wide taxonomic range, rapid and relatively inexpensive, no reagents, limited taxonomic expertise required; in situ applications exist low taxonomic resolution (maybe class level); subject to uncertainty due to species-specific and physiological variability in spectra; confounding signals from nonweeks to months phytoplankton constituents, biofouling

Subject to uncertainty due to species-specific and physiological weeks to months variability in spectra; confounding signals from nonphytoplankton constituents, biofouling relatively common in marine optics community small user set to date used rarely ship with precise positioning by submersible ship after acoustic release gives very good look at long term variation in bottom community areal coverage quite small months to year

Dan Costa

Dan Costa

$10-800

$1200-4000

$800 - 5000 surface or surgically implanted

FM radio, acoustic, satellite, recapture and download attached to pelage or with suction cops

(short term) or barbed attachments (long term) satellite telemetry, recovery cheap, deployable in large numbers, provides data on migratory routes, habitat usage patterns, ecosystem hotspots doesn't tell you why the animal is there or what the immediate environment is like - coarse movements cheap, deployable in large numbers, only, usually some sensors, like can provide as many CTD casts when conductivity, can be placed on 10 or more animals as could sensitive to animal's be obtained in 100 years of shipelectric field and must based transects. Transport is free.

be carefully calibrated.

Not programmable: animals go where they weeks to years weeks to years want to go.

Fortunately they usually go to interesting parts of the ocean as above as above can provide surprisingly detailed data about energy budgets, foraging success, behavior and habitat use confirmatory sampling of prey fields or other data still requires shipbased sampling. Lab studies often needed to verify caloric costs/benefits weeks to years wide wide wide

Dan Costa

System/Program Name Taxa Monitored Environment Purpose Analyses Description

5.04

Ocean Color Satellites (SeaWiFS,

MODIS)

Phytoplankton: abundance and higher-taxon diversity

Pelagic (deep, shallow) and Remote assessment of both Hard and Soft Bottom algal pigment stocks; rates environments (shallow) of production; coarse taxonomy

Detect "color" differences in Polar-orbitting satellites designed to surface ocean via maximize global coverage and repeat fluorescence signature of pigment, processesd via biooptical models

6 In situ optical methods

6.01

Video Plankton Recorder (VPR)

Meso- and macrozooplankton: diversity

Pelagic and abundance

Sample zooplankton diversity, abundance, size

Taxonomy Image-forming optical system sampling a field of view of 7x7mm to

42x42mm

6.02

In situ zooplankton imaging systems (VPR, SIPPER, LOPC,

ISIIS, Ocean DIVA, UVP, ZOOVIS, etc; plus some holographic systems: Holocamera, eHolocam,

Digital Holosub, etc.)

Meso- and macrozooplankton: diversity

Pelagic and abundance

Sample zooplankton diversity, abundance, size

Taxonomy video imaging or holographic imaging

6.03

Flow cytometry (many lab systems, plus in situ systems:

Imaging FlowCytobot, FlowCAM,

Cytobuoy/Cytosub)

Phytoplankton, some microzooplankton: diversity and abundance

Pelagic abundance, cell size, and taxonomic groups optical signature analysis, image analysis in appropriate cases scattering/fluorescence and/or video imaging of single cells in flow

6.04

Absorption spectra (ac-9, ac-s,

Optical Plankton Discriminator)

Phytoplankton: abundance

(and higher-taxon diversity?). Other absorbing constituents

Pelagic Assessment of light absorbing constitutents, potential phytoplankton pigment types spectral decomposition, derivative analysis submersible "shiny tube" or liquid waveguide spectrophotometry

6.05

Fluorescence spectra

(FluoroProbe, etc.)

Phytoplankton: abundance and higher-taxon diversity

(pigment types)

Pelagic assess spectral spectral decomposition, fluorescence characteristics derivative analysis indicative of group-specific pigments spectral fluorometer

6.06

Bathysnap camera system

Macroinvertebrates and fishes: diversity and abundance

Benthic hard and soft substrata: deep sea to monitor long term changes in benthic communities

Changes in animals, sediment-water interface

(e.g., color indications of timing and duration of settlement of phytoplankton to bottom)

7 Animal-carried sampling (tags)

7.01

Position-only/ presence-absence

Large vertebrates: position and movements.

All environments

7.02

Environmental sampling

Large vertebrates: position and movements.

Temperature, pressure

(depth), salinity

(conductivity), color

(fluorimetry)

All environments track migrations, habitat use, find ecosystem hotspots

Position, movements of tagged animal: track could be anything from a microchip sized acoustic fish tag to a cigarette migrations, habitat use, find pack sized long term seal or large ecosystem hotspots fish satellite tag (ARGOS) determine physical and biochemical parameters correlated with animal presence, habitat selection use correlative models to determine physical and biochemical parameters correlated with animal presence, habitat selection:

GAM, GLM, EcoSim etc generally about the size of a cigarette pack or small computer speaker.

Potted in material for depth tolerance to 2000+ meters

7.03

Diving and behavior

Large vertebrates: position and movements (depth, 3-D

All environments accelerometry), feeding biology determine how animals sample the water column in

3-D, partitioning of feeding, resting, travelling, energy high resolution 3-D spatial modeling, statistical analyses budgets, more as above

Construction Cost Deployment Method Recovery Method

None several hundred million dollars per satellite

Rocket

Pros

Global coverage; long term deployment

Cons

low spectral resolution; N/A requires groundtruthing

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

Relatively common due to centralized processing and distribution

POC

$75k

$100K

$100K

$20K

$20K

$100K

Profiled or towed from vessel, mounted on

AUVs (eg REMUS), moored ship, AUV, mooring ship, AUV, mooring, etc.

ship, AUV, mooring, etc.

High vertical resolution; processing can be done in real-time taxonomic resolution to genus or species possible; rapid and quantitative abundance estimates; enables unprecedented space / time resolution and range; automated in situ application possible

Small sample volumes; sampling efficiency affected by density of organisms and avoidance behavior

Routine operation with days to months taxonomic resolution requires complex data analysis systems (e.g., supervised machine learning algorithms) and manual development of training sets, cost ship, mooring, large

AUV ship, mooring, large

AUV taxonomic resolution to genus or species possible with imaging

Routine operation with taxonomic resolution months for in situ instruments, sample storage indefinite in systems; rapid and quantitative abundance estimates; enables unprecedented space / time resolution supervised machine and range; automated in situ applications exist requires complex data analysis systems (e.g., liquid nitrogen for lab analysis learning algorithms) and manual development of training sets, cost prototype in situ applications in coastal systems, ship-board analysis common for picoplankton

Wide taxonomic range within phytoplankton, rapid and relatively inexpensive, no reagents, limited taxonomic expertise required; in situ application

Wide taxonomic range, rapid and relatively inexpensive, no reagents, limited taxonomic expertise required; in situ applications exist low taxonomic resolution (maybe class level); subject to uncertainty due to species-specific and physiological variability in spectra; confounding signals from nonweeks to months phytoplankton constituents, biofouling

Subject to uncertainty due to species-specific and physiological weeks to months variability in spectra; confounding signals from nonphytoplankton constituents, biofouling relatively common in marine optics community small user set to date used rarely ship with precise positioning by submersible ship after acoustic release gives very good look at long term variation in bottom community areal coverage quite small months to year

Dan Costa

Dan Costa

$10-800

$1200-4000

$800 - 5000 surface or surgically implanted

FM radio, acoustic, satellite, recapture and download attached to pelage or with suction cops

(short term) or barbed attachments (long term) satellite telemetry, recovery cheap, deployable in large numbers, provides data on migratory routes, habitat usage patterns, ecosystem hotspots doesn't tell you why the animal is there or what the immediate environment is like - coarse movements cheap, deployable in large numbers, only, usually some sensors, like can provide as many CTD casts when conductivity, can be placed on 10 or more animals as could sensitive to animal's be obtained in 100 years of shipelectric field and must based transects. Transport is free.

be carefully calibrated.

Not programmable: animals go where they weeks to years weeks to years want to go.

Fortunately they usually go to interesting parts of the ocean as above as above can provide surprisingly detailed data about energy budgets, foraging success, behavior and habitat use confirmatory sampling of prey fields or other data still requires shipbased sampling. Lab studies often needed to verify caloric costs/benefits weeks to years wide wide wide

Dan Costa

27

28

System/Program Name Taxa Monitored Environment

7.04

Multi-sensor tags with acoustics or video

Large vertebrates: position, movements, feeding biology

All environments

Purpose Analyses Description

observe foraging ecology, identify prey species, prey capture behavior. Detect responses to human, conspecifics, predators

Very large data sets (Gb to

Tb). Analytic methods are intensive and time consuming, even with automated processing algorithms devices are generally 1 kg or larger, and therefore usually only attached for hours or a couple days (lg coffee cup to thermos sized)

7.05

Multi-sensor animal tags

Large vertebrates: position, movements, physiology.

All environments

Environmental parameters and acoustics sample throughout ocean position, depth, temperature, oxygen, movement, sound penetration or suction animal tags

8 Acoustic methods

8.01

Autonomous Acoustic Habitat

Monitoring

Sound-producing mammals, fishes, and other

All environments animals: diversity (and abundance)

8.02

Passive Acoustic Recievers

8.03

Mutli-frequency echosounder

Sound-producing mammals, fishes, and other continental shelf animals: diversity (and

Pelagic and benthic: abundance)

Mesozooplankton, micronekton, fishes: abundance (and diversity)

Pelagic

Sample acoustic habitats to quantify spatio-temporal-

Noise statistics; spatiotemporal maps; animations

Acoustic recorders: ambient noise, species-specific acoustic signals spectral variability and detect occurrence and distribution of acoustically active marine animals tuned to species or groups, location, tracking temporal indices community analyses deploymentof fixed station receivers

Sample zooplankton/micronekton/fis h diversity, abundance, size

Acoustic inversions of abundance in size/taxonomic categories

Measures acoustic backscattering

8.04

Passive Acoustic Monitoring - autonomous

Sound-producing mammals, fishes, and other

All environments animals: diversity (and abundance)

8.05

Passive Acoustic Monitoring - towed

8.06

Passive Acoustic Monitoring - cabled

Sound-producing mammals, fishes, and other animals: diversity (and abundance)

All environments

Sound-producing mammals, fishes, and other

All environments animals: diversity (and abundance)

Sample acoustic habitats to Noise statistics; species quantify spatio-temporalspectral variability and detection, spatio-temporal maps; animations tuned to detect occurrence and distribution of acoustically active marine animals species or groups, location, tracking

Autonomous seafloor recorders: ambient noise, species-specific acoustic signals

Detect occurrence and distribution, and estimate relative abundance of acoustically active marine

Beamforming, aurodetection, tracking animals

Sample acoustic habitats to Noise statistics; species quantify spatio-temporalspectral variability and detect occurrence and distribution of acoustically active marine animals detection, spatio-temporal maps; animations tuned to species or groups, location, tracking

Towed hydrophone array

Seafloor, cabled hydrophone arrays

Reduce ship strikes and quantify acoustic impacts

Noise statistics, species detection

Moored with satellite links sample throughout ocean oceanogrphic productivity variables and acoustics passive glider that samples acoustics

8.07

Passive Acoustic Monitoring - moored with surface expression

8.08

Autonomous glider

Sound-producing Pelagic and benthic mammals, fishes, and other animals: diversity (and substrata, coastal abundance)

Sound-producing mammals, fishes, and other animals: diversity (and abundance?)

All environments

9 Potential Future Technologies

9.01

Portable Remote Imaging

Spectrometer

9.02

Next Generation Airborne Visible

Infrared Imaging Spectrometer

(AVIRISng)

Phytoplankton, habitatforming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Habitat-forming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Benthic hard and soft substrata, shallow

Benthic hard and soft substrata, shallow

9.03

Autonomous Acoustic Habitat

Monitoring

Sound-producing mammals, fishes, and other animals: diversity (and abundance)

All environments

Small imaging spectrometer Spectral analysis of shallow intended to fly on a variety water benthic type and of airborne platforms.

Optimized for coastal ocean coastal vegetation type science

Designed to support

NASA's research programs with measurements of

Spectral analysis of shallow water benthic type and coastal vegetation type upwelling spectral radiance in 224 contiguous spectral channels from 400 to 2500 nm.

Sample acoustic habitats to Noise statistics, spatioquantify spatio-temporalspectral variability and temporal maps and

Acoustic recorders w on-board autorecognition, underwater comms to animations tuned to species AUVs and surface buoys or groups detect occurrence and distribution of acoustically active marine animals

9.04

imaging AUVs for water column and benthos

9.05

sample collection AUVs for microbial communities (sample return)

9.06

ecogenomic sensors (real-time analyses + sample return)

Construction Cost

$10k-$30K

$10k

Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

usually harnessed, attached to skin/pelage by adhesive or suction device must usually be recovered due to the volume and bandwidth of data combines environmental and biological sensors with broadband stereo acoustics or hi-res video.

Usually programmable sampling to cup. Can use skinpenetrating tether prevent memory limits to useful lifespan of tag (memory gets better, smaller, cheaper all the time; 100 Gb (barbs) in some cases.

solid state memory on small tags is now in reach) small boats to ships small boats to ships small-scale and large-scale sampling to integrate animal activity with ocean ecology and habitat still too large to put on small animals (<50 kg or so). Great sophistication means more things that can go wrong, greater cost, and greater operator expertise required.

recovery risk usually deployed for days or hours. Data are digital and last relatively few users (tens) indefinitely.

days to many months limited

POC

Dan Costa

Oregon,

UCSC, WHOI, private etc

$8000/ unit Surface vessel or diver; attach to trees, bury in ground

Surface vessel or diver one person can deploy and retreive, lots of data too expensive, deployment too short, data processing intensive duration - 100+ days10+ years all oceans, ca. 120years of data collected per year

C.W. Clark ship ship longer-term continuous monitoring species must vocalize continental shelves, basins

$200k

$1000-8000/ unit

Profiled or towed from vessel, mounted on

AUVs (eg REMUS), moored

Surface vessel or diver; attach to trees, bury in ground

Surface vessel or diver

High temporal sampling frequency, high range resolution to large range

Provides only indirect measurements of zooplankton/fish, discriminating among species/groups present based on acoustic data along is challenging one person can deploy and retreive, lots of data too expensive, deployment too short, data processing intensive, species must produce sound duration - 100+ days10+ years becoming much more common, all oceans, ca.

120years of data collected per year

C.W. Clark

$400/sensor plus ancillaries ship ship C.W. Clark

>$100K ship not augments other survey methods, provides archived record for postprocessing requiresexperienced analyst, back-deck logistics duration of cruise, 10+ yrs usage, long-term archive very limited

Real-time data, beamforming expensive maintenance and repair, fixed location decades very limited C.W. Clark

>$100K

>$25k

Aircraft

Aircraft ship ship

Aircraft

Aircraft ship ship

Near-real-time data for monitoring and expensive mitigation, dual comms for reprogramming maintenance and repair, fixed location

spatial sampling coupled with acoustics

Portable glide, not active propulsion years many months very limited becoming more common

C.W. Clark

WHOI, SIO,

UW, Duke,

Industry, military

NASA Ames

Airborne

Sensor Facility

NASA JPL

$300-400/unit Surface vessel or diver; attach to trees, bury in ground

Surface vessel or diver; detach, unbury

System/Program Name Taxa Monitored Environment

7.04

Multi-sensor tags with acoustics or video

Large vertebrates: position, movements, feeding biology

All environments

Purpose Analyses Description

observe foraging ecology, identify prey species, prey capture behavior. Detect responses to human, conspecifics, predators

Very large data sets (Gb to

Tb). Analytic methods are intensive and time consuming, even with automated processing algorithms devices are generally 1 kg or larger, and therefore usually only attached for hours or a couple days (lg coffee cup to thermos sized)

7.05

Multi-sensor animal tags

Large vertebrates: position, movements, physiology.

All environments

Environmental parameters and acoustics sample throughout ocean position, depth, temperature, oxygen, movement, sound penetration or suction animal tags

8 Acoustic methods

8.01

Autonomous Acoustic Habitat

Monitoring

Sound-producing mammals, fishes, and other

All environments animals: diversity (and abundance)

8.02

Passive Acoustic Recievers

8.03

Mutli-frequency echosounder

Sound-producing mammals, fishes, and other continental shelf animals: diversity (and

Pelagic and benthic: abundance)

Mesozooplankton, micronekton, fishes: abundance (and diversity)

Pelagic

Sample acoustic habitats to quantify spatio-temporal-

Noise statistics; spatiotemporal maps; animations

Acoustic recorders: ambient noise, species-specific acoustic signals spectral variability and detect occurrence and distribution of acoustically active marine animals tuned to species or groups, location, tracking temporal indices community analyses deploymentof fixed station receivers

Sample zooplankton/micronekton/fis h diversity, abundance, size

Acoustic inversions of abundance in size/taxonomic categories

Measures acoustic backscattering

8.04

Passive Acoustic Monitoring - autonomous

Sound-producing mammals, fishes, and other

All environments animals: diversity (and abundance)

8.05

Passive Acoustic Monitoring - towed

8.06

Passive Acoustic Monitoring - cabled

Sound-producing mammals, fishes, and other animals: diversity (and abundance)

All environments

Sound-producing mammals, fishes, and other

All environments animals: diversity (and abundance)

Sample acoustic habitats to Noise statistics; species quantify spatio-temporalspectral variability and detection, spatio-temporal maps; animations tuned to detect occurrence and distribution of acoustically active marine animals species or groups, location, tracking

Autonomous seafloor recorders: ambient noise, species-specific acoustic signals

Detect occurrence and distribution, and estimate relative abundance of acoustically active marine

Beamforming, aurodetection, tracking animals

Sample acoustic habitats to Noise statistics; species quantify spatio-temporalspectral variability and detect occurrence and distribution of acoustically active marine animals detection, spatio-temporal maps; animations tuned to species or groups, location, tracking

Towed hydrophone array

Seafloor, cabled hydrophone arrays

Reduce ship strikes and quantify acoustic impacts

Noise statistics, species detection

Moored with satellite links sample throughout ocean oceanogrphic productivity variables and acoustics passive glider that samples acoustics

8.07

Passive Acoustic Monitoring - moored with surface expression

8.08

Autonomous glider

Sound-producing Pelagic and benthic mammals, fishes, and other animals: diversity (and substrata, coastal abundance)

Sound-producing mammals, fishes, and other animals: diversity (and abundance?)

All environments

9 Potential Future Technologies

9.01

Portable Remote Imaging

Spectrometer

9.02

Next Generation Airborne Visible

Infrared Imaging Spectrometer

(AVIRISng)

Phytoplankton, habitatforming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Habitat-forming plants and macroinvertebrates: areal coverage and higher-taxon diversity

Benthic hard and soft substrata, shallow

Benthic hard and soft substrata, shallow

9.03

Autonomous Acoustic Habitat

Monitoring

Sound-producing mammals, fishes, and other animals: diversity (and abundance)

All environments

Small imaging spectrometer Spectral analysis of shallow intended to fly on a variety water benthic type and of airborne platforms.

Optimized for coastal ocean coastal vegetation type science

Designed to support

NASA's research programs with measurements of

Spectral analysis of shallow water benthic type and coastal vegetation type upwelling spectral radiance in 224 contiguous spectral channels from 400 to 2500 nm.

Sample acoustic habitats to Noise statistics, spatioquantify spatio-temporalspectral variability and temporal maps and

Acoustic recorders w on-board autorecognition, underwater comms to animations tuned to species AUVs and surface buoys or groups detect occurrence and distribution of acoustically active marine animals

9.04

imaging AUVs for water column and benthos

9.05

sample collection AUVs for microbial communities (sample return)

9.06

ecogenomic sensors (real-time analyses + sample return)

Construction Cost

$10k-$30K

$10k

Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

usually harnessed, attached to skin/pelage by adhesive or suction device must usually be recovered due to the volume and bandwidth of data combines environmental and biological sensors with broadband stereo acoustics or hi-res video.

Usually programmable sampling to cup. Can use skinpenetrating tether prevent memory limits to useful lifespan of tag (memory gets better, smaller, cheaper all the time; 100 Gb (barbs) in some cases.

solid state memory on small tags is now in reach) small boats to ships small boats to ships small-scale and large-scale sampling to integrate animal activity with ocean ecology and habitat still too large to put on small animals (<50 kg or so). Great sophistication means more things that can go wrong, greater cost, and greater operator expertise required.

recovery risk usually deployed for days or hours. Data are digital and last relatively few users (tens) indefinitely.

days to many months limited

POC

Dan Costa

Oregon,

UCSC, WHOI, private etc

$8000/ unit Surface vessel or diver; attach to trees, bury in ground

Surface vessel or diver one person can deploy and retreive, lots of data too expensive, deployment too short, data processing intensive duration - 100+ days10+ years all oceans, ca. 120years of data collected per year

C.W. Clark ship ship longer-term continuous monitoring species must vocalize continental shelves, basins

$200k

$1000-8000/ unit

Profiled or towed from vessel, mounted on

AUVs (eg REMUS), moored

Surface vessel or diver; attach to trees, bury in ground

Surface vessel or diver

High temporal sampling frequency, high range resolution to large range

Provides only indirect measurements of zooplankton/fish, discriminating among species/groups present based on acoustic data along is challenging one person can deploy and retreive, lots of data too expensive, deployment too short, data processing intensive, species must produce sound duration - 100+ days10+ years becoming much more common, all oceans, ca.

120years of data collected per year

C.W. Clark

$400/sensor plus ancillaries ship ship C.W. Clark

>$100K ship not augments other survey methods, provides archived record for postprocessing requiresexperienced analyst, back-deck logistics duration of cruise, 10+ yrs usage, long-term archive very limited

Real-time data, beamforming expensive maintenance and repair, fixed location decades very limited C.W. Clark

>$100K

>$25k

Aircraft

Aircraft ship ship

Aircraft

Aircraft ship ship

Near-real-time data for monitoring and expensive mitigation, dual comms for reprogramming maintenance and repair, fixed location

spatial sampling coupled with acoustics

Portable glide, not active propulsion years many months very limited becoming more common

C.W. Clark

WHOI, SIO,

UW, Duke,

Industry, military

NASA Ames

Airborne

Sensor Facility

NASA JPL

29

$300-400/unit Surface vessel or diver; attach to trees, bury in ground

Surface vessel or diver; detach, unbury

30

System/Program Name Taxa Monitored Environment Purpose Analyses Description

9.07

OOI/IOOS sustained observatories

Hydrographic data,

(e.g.,

ENDURANCE,NEPTUNE,MARS,

currents, DO, sound,

Chlorophyll, seismic activity, shelf, slope, vents, seeps

VENUS)

9.08

DNA probes for invasive species

(already used for Asian carp)

nitrate, pH, pCO2

All taxa All environments long term monitoring and research, ecosystem response to climate variability video and still time series, experiments, acoustics all possible

NE Pacific Margin with nodes at 80 m, 150 m, 500 m, 3000 m; Juan de

Fuca Plate

9.09

Autonomous Robot Swarms

Macroinvertebrates and fishes: diversity and abundance. Environmenta parameters

Benthic soft and hard substrata, deep sea

To quantify long (or short)term changes in deep-sea communities, abiotic environment, and ecosystem processes.

Spatial and temporal dynamics

9.10

Broadband acoustic scattering systems (up and coming)

Mesozooplankton, micronekton, fishes: abundance (and diversity?)

Pelagic Sample zooplankton/fish diversity, abundance, size

An autonomous multiple robot system that can recharge while at sea and continue sampling and transmitting data to shore. Will allow us to sample at temporal and spatial scales that would provide novel insights into the functioning of deep-sea ecosystems.

Active acoustic scattering systems capable of greater species discrimination than traditional narrowband multi-frequency systems

9.11

9.14

Stand-off optical systems

(missing?)

9.12

Next Generation Ocean Color satellites (ACE, HySPIRI, HICO,

GEO-CAPE)

9.13

Wormcam

Ship board continuous flow cytometry

Mesozooplankton, micronekton, fishes: abundance (and diversity?)

Phytoplankton: abundance and higher-taxon diversity

Infaunal macroinvertebrates: diversity, abundance, activity

Phytoplankton: highertaxon diversity and abundance

Pelagic

Pelagic (deep, shallow), benthic hard and soft substrata (shallow) benthic soft substrata

(shallow), possibly adaptable to other habitats

Pelagic (epi)

Sample zooplankton/fish diversity, abundance, size

Remote assessment of algal pigment stocks; rates of production; improved taxonomy

Bio-optical models

Designed to assess rates of bioturbation and other

Analysis of collected images.

faunal activity.

Assess abundance and higher-taxon composition analysis of optical data

Image-forming optical system sampling at a distance far enough away from the instrument to minimize avoidance issues associated with current optical systems that sample some small volume near to the instrument

Satellites in appropriate orbit for monitoring coastal ocean or maximizing coverage of global ocean

Ethernet camera in an underwater housing in the shape of a sediment profile prism (Rhoads and Cande

1971) with water quality sensors.

Connected to solar powered surface buoy that telemeters images and data to base station.

Flow cytometer analyses organisms using the flow-through seawater system on-board a ship so spatial data is recovered.

9.15

In-situ microscope

Microorganisms, including phyto- and microzooplankton: diversity and abundance

All environments to determine size spectra of microbes, to assign phytoplankton to taxa standard imaging processing methods

9.16

Underwater bathymetric lidar imaging systems

Habitat-forming plants and macroinvertebrates: areal coverage

Benthic substrata, shallow to obtain high resolution

(~cm) of the sea floor incl topography (~10 cm res) image and signal processing techniques on chip microscopes are just starting to emerge. One for in-situ studies that could be put on a mobile platform that would accomplish in-situ studies w/o requiring specimen retrieval would be a major achievement bathymetric lidars can be used to construct high res optical images of regions that containt both reflectance and depth data

Construction Cost Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

Limited regional access MEGABUCKS…

210M? (approved)

Permanent Nodes, attach instrumentation

ROV, Submersible Infrastruture will be in place, with a host of continuous environmental variables measured. Telemetry to shore in real time.

High cost of placement Unknown and retrieval. Fouling possible

POC

$150k

Any ship transiting an area

Any ship transiting an area

Much less expensive than using existing technology (e.g. mounting repeated expeditions). Can be designed for a variety of different tasks. Can work at sea for extended periods without investigator involvement.

Still under development, actual costs and capabilities unknown.

Towed from vessel, deployed autonomously (AUV, drifters, moorings)

High temporal sampling frequency, high range resolution to large range, improved species classification relative to traditional acoustic systems

Provides only indirect measurements of zooplankton/fish

??

Towed from vessel, deployed autonomously (AUV, drifters, moorings)

Ability to sample larger animals currently not well sampled by most gears, especially micronekton several hundred million dollars per satellite

Rocket

Housing ~$1,000.

Plus off the shelf camera, electronics, buoy ~$7,000.

Electronic tech labor

~$2,000

Surface vessel or diver

None

Surface vessel or diver

Greater spectral and spatial resolution allows for improved species ID and

Timeline uncertain, subject to funding distribution

N/A

Near real-time insitu imaging of faunal responses to day to day variation in

Needs frequent maintenance in high habitat and water quality. Relative low fouling areas/seasons. cost and off the shelf components. Species identification limited to large fauna.

Days to months ship initial: $100k, in large batches, $1-5k any underwater platform ship vehicle recovery

Rela-time in situ analysis of phytoplankton composition

This method can't be used to detect species but can be used to

N/A detect classes of phytoplankton (e.g. dinos vs diatoms) potential high resolution spatial and temporal sampling with multiple systems extensive digital processing

$1M-$2M towed, AUV, ROV either ship based or land based (AUV from great utility for identifying many shore) high resolution optical images have benthic features. The addition of sea floor topography lends a quantitative element to placing organisms into a context that considers sea floor surface area expensive, lots of data

N/A

Emerging techniques developed with NSF funding.

Robert Diaz, go to and click on Wormcam: http://www.vim

s.edu/people/di az_rj/index.php

N/A Ginger

Armbrust

System/Program Name Taxa Monitored Environment Purpose Analyses Description

9.07

OOI/IOOS sustained observatories

Hydrographic data,

(e.g.,

ENDURANCE,NEPTUNE,MARS,

currents, DO, sound,

Chlorophyll, seismic activity, shelf, slope, vents, seeps

VENUS)

9.08

DNA probes for invasive species

(already used for Asian carp)

nitrate, pH, pCO2

All taxa All environments long term monitoring and research, ecosystem response to climate variability video and still time series, experiments, acoustics all possible

NE Pacific Margin with nodes at 80 m, 150 m, 500 m, 3000 m; Juan de

Fuca Plate

9.09

Autonomous Robot Swarms

Macroinvertebrates and fishes: diversity and abundance. Environmenta parameters

Benthic soft and hard substrata, deep sea

To quantify long (or short)term changes in deep-sea communities, abiotic environment, and ecosystem processes.

Spatial and temporal dynamics

9.10

Broadband acoustic scattering systems (up and coming)

Mesozooplankton, micronekton, fishes: abundance (and diversity?)

Pelagic Sample zooplankton/fish diversity, abundance, size

An autonomous multiple robot system that can recharge while at sea and continue sampling and transmitting data to shore. Will allow us to sample at temporal and spatial scales that would provide novel insights into the functioning of deep-sea ecosystems.

Active acoustic scattering systems capable of greater species discrimination than traditional narrowband multi-frequency systems

9.11

9.14

Stand-off optical systems

(missing?)

9.12

Next Generation Ocean Color satellites (ACE, HySPIRI, HICO,

GEO-CAPE)

9.13

Wormcam

Ship board continuous flow cytometry

Mesozooplankton, micronekton, fishes: abundance (and diversity?)

Phytoplankton: abundance and higher-taxon diversity

Infaunal macroinvertebrates: diversity, abundance, activity

Phytoplankton: highertaxon diversity and abundance

Pelagic

Pelagic (deep, shallow), benthic hard and soft substrata (shallow) benthic soft substrata

(shallow), possibly adaptable to other habitats

Pelagic (epi)

Sample zooplankton/fish diversity, abundance, size

Remote assessment of algal pigment stocks; rates of production; improved taxonomy

Bio-optical models

Designed to assess rates of bioturbation and other

Analysis of collected images.

faunal activity.

Assess abundance and higher-taxon composition analysis of optical data

Image-forming optical system sampling at a distance far enough away from the instrument to minimize avoidance issues associated with current optical systems that sample some small volume near to the instrument

Satellites in appropriate orbit for monitoring coastal ocean or maximizing coverage of global ocean

Ethernet camera in an underwater housing in the shape of a sediment profile prism (Rhoads and Cande

1971) with water quality sensors.

Connected to solar powered surface buoy that telemeters images and data to base station.

Flow cytometer analyses organisms using the flow-through seawater system on-board a ship so spatial data is recovered.

9.15

In-situ microscope

Microorganisms, including phyto- and microzooplankton: diversity and abundance

All environments to determine size spectra of microbes, to assign phytoplankton to taxa standard imaging processing methods

9.16

Underwater bathymetric lidar imaging systems

Habitat-forming plants and macroinvertebrates: areal coverage

Benthic substrata, shallow to obtain high resolution

(~cm) of the sea floor incl topography (~10 cm res) image and signal processing techniques on chip microscopes are just starting to emerge. One for in-situ studies that could be put on a mobile platform that would accomplish in-situ studies w/o requiring specimen retrieval would be a major achievement bathymetric lidars can be used to construct high res optical images of regions that containt both reflectance and depth data

Construction Cost Deployment Method Recovery Method Pros Cons

Employment Duration /

Shelf Life of Materials

Collected

Distribution of the

Technique (How Widely

Used?)

Limited regional access MEGABUCKS…

210M? (approved)

Permanent Nodes, attach instrumentation

ROV, Submersible Infrastruture will be in place, with a host of continuous environmental variables measured. Telemetry to shore in real time.

High cost of placement Unknown and retrieval. Fouling possible

POC

$150k

Any ship transiting an area

Any ship transiting an area

Much less expensive than using existing technology (e.g. mounting repeated expeditions). Can be designed for a variety of different tasks. Can work at sea for extended periods without investigator involvement.

Still under development, actual costs and capabilities unknown.

Towed from vessel, deployed autonomously (AUV, drifters, moorings)

High temporal sampling frequency, high range resolution to large range, improved species classification relative to traditional acoustic systems

Provides only indirect measurements of zooplankton/fish

??

Towed from vessel, deployed autonomously (AUV, drifters, moorings)

Ability to sample larger animals currently not well sampled by most gears, especially micronekton several hundred million dollars per satellite

Rocket

Housing ~$1,000.

Plus off the shelf camera, electronics, buoy ~$7,000.

Electronic tech labor

~$2,000

Surface vessel or diver

None

Surface vessel or diver

Greater spectral and spatial resolution allows for improved species ID and

Timeline uncertain, subject to funding distribution

N/A

Near real-time insitu imaging of faunal responses to day to day variation in

Needs frequent maintenance in high habitat and water quality. Relative low fouling areas/seasons. cost and off the shelf components. Species identification limited to large fauna.

Days to months ship initial: $100k, in large batches, $1-5k any underwater platform ship vehicle recovery

Rela-time in situ analysis of phytoplankton composition

This method can't be used to detect species but can be used to

N/A detect classes of phytoplankton (e.g. dinos vs diatoms) potential high resolution spatial and temporal sampling with multiple systems extensive digital processing

$1M-$2M towed, AUV, ROV either ship based or land based (AUV from great utility for identifying many shore) high resolution optical images have benthic features. The addition of sea floor topography lends a quantitative element to placing organisms into a context that considers sea floor surface area expensive, lots of data

N/A

Emerging techniques developed with NSF funding.

Robert Diaz, go to and click on Wormcam: http://www.vim

s.edu/people/di az_rj/index.php

N/A Ginger

Armbrust

31

32

APPENDIX 5. MAJOR HABITAT DIVISIONS

AND TAXA TO BE OBSERVED

Benthic (Biogenic, Hard Bottom and Soft Bottom)

• Sessile Macrobiota

• Demersal Fauna

• Epibiota

• Cryptobiota

• Infauna

• Meiofauna

• Microbes (Bacteria, Archea, Protista and Viruses)

Pelagic

• Microbes (Bacteria, Archea, Protista and Viruses)

• Macrozooplankton

• Mesoplankton

• Gelatinous Zooplankton

• Fish

• Birds

• Mammals

• Turtles

• Squid

APPENDIX 6. NATIONAL OCEAN POLICY PRIORITY

OBJECTIVES

1. Ecosystem-Based Management: Adopt ecosystem-based management as a foundational principle for the comprehensive management of the ocean, our coasts, and the Great Lakes.

2. Coastal and Marine Spatial Planning: Implement comprehensive, integrated, ecosystem based coastal and marine spatial planning and management in the United States.

3. Inform Decisions and Improve Understanding: Increase knowledge to continually inform and improve management and policy decisions and the capacity to respond to change and challenges. Better educate the public through formal and informal programs about the ocean, our coasts, and the Great Lakes.

4. Coordinate and Support: Better coordinate and support Federal, State, tribal, local, and regional management of the ocean, our coasts, and the Great Lakes. Improve coordination and integration across the Federal Government, and as appropriate, engage with the international community.

5. Resiliency and Adaptation to Climate Change and Ocean Acidification: Strengthen resiliency of coastal communities and marine and Great Lakes environments and their abilities to adapt to climate change impacts and ocean acidification.

6. Regional Ecosystem Protection and Restoration: Establish and implement an integrated ecosystem protection and restoration strategy that is science-based and aligns conservation and restoration goals at the Federal, State, tribal, local, and regional levels.

7. Water Quality and Sustainable Practices on Land: Enhance water quality in the ocean, along our coasts, and in the

Great Lakes by promoting and implementing sustainable practices on land.

8. Changing Conditions in the Arctic: Address environmental stewardship needs in the Arctic Ocean and adjacent coastal areas in the face of climate-induced and other environmental changes.

9. Ocean, Coastal, and Great Lakes Observations, Mapping, and Infrastructure: Strengthen and integrate Federal and non-Federal ocean observing systems, sensors, data collection platforms, data management, and mapping capabilities into a national system, and integrate that system into international observation efforts.

33

We would like to thank the sponsors of the “Attaining Operational Marine Biodiversity Observations” workshop (NOAA,

MMC, BOEMRE, NASA, NSF, ONR, and SI), the steering committee, and the participants of the workshop who all contributed to forming these recommendations for a national marine biodiversity observing network.

Design services provided by Jason Mallett, Consortium for Ocean Leadership. Editing provided by Daphne Fautin,

University of Kansas.

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