Karen I. Stocks

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.

Science priorities for seamounts: research links to conservation and management.

Seamounts shape the topography of all ocean basins and can be hotspots of biological activity in the deep sea. The Census of Marine Life on Seamounts (CenSeam) was a field program that examined seamounts as part of the global Census of Marine Life (CoML) initiative from 2005 to 2010. CenSeam progressed seamount science by collating historical data, collecting new data, undertaking regional and global analyses of seamount biodiversity, mapping species and habitat distributions, challenging established paradigms of seamount ecology, developing new hypotheses, and documenting the impacts of human activities on seamounts. However, because of the large number of seamounts globally, much about the structure, function and connectivity of seamount ecosystems remains unexplored and unknown. Continual, and potentially increasing, threats to seamount resources from fishing and seabed mining are creating a pressing demand for research to inform conservation and management strategies. To meet this need, intensive science effort in the following areas will be needed: 1) Improved physical and biological data; of particular importance is information on seamount location, physical characteristics (e.g. habitat heterogeneity and complexity), more complete and intensive biodiversity inventories, and increased understanding of seamount connectivity and faunal dispersal; 2) New human impact data; these shall encompass better studies on the effects of human activities on seamount ecosystems, as well as monitoring long-term changes in seamount assemblages following impacts (e.g. recovery); 3) Global data repositories; there is a pressing need for more comprehensive fisheries catch and effort data, especially on the high seas, and compilation or maintenance of geological and biodiversity databases that underpin regional and global analyses; 4) Application of support tools in a data-poor environment; conservation and management will have to increasingly rely on predictive modelling techniques, critical evaluation of environmental surrogates as faunal “proxies”, and ecological risk assessment.

The role of colonization in establishing patterns of community composition and diversity in shallow-water sedimentary communities

To determine whether pattern and diversity in benthic sedimentary communities are set primarily at colonization or by post-settlement biological interactions, we collected faunal cores and conducted reciprocal sediment transplant experiments at a sandy and a muddy site at 12 m depth, ∼3 km apart off New Jersey. Multivariate analyses of cores collected at these sites in September 1994 indicated differences in the taxa determining local pattern, with the bivalve Spisula solidissima and the polychaete Polygordius sp. being dominant at the sandy site, and oligochaetes, several polychaete species, and the bivalve Nucula annulata dominant at the muddy site. Individual cores from the sandy site were significantly less diverse than those at the muddy site. Short-term experiments (3-5 d) were deployed by divers at three different times (August-September, 1994). Replicate trays (100 cm 2 ) filled with azoic sand or mud were placed flush with the ambient seafloor at both sites. Multivariate comparisons indicated that sediment treatment in trays played a greater role in determining colonization patterns in the first experiment, site played a greater role in the second, and both variables contributed in the third. This pattern suggests that larval settlement and habitat choice played an important role in the first and third experiments, and that local transport of recently settled juveniles from the surrounding sediments was important in the second and third experiments. Sandy-site trays had significantly lower diversity than muddy-site trays, but there was no effect of sediment type in trays on diversity of colonizers. These experiments focused on small spatial scales and three short time periods, but they demonstrate that species patterns in some environments may be set by habitat selection by larvae and by juvenile colonization from the surrounding community. Post-colonization processes such as predation and competition likely play a major role for some species, but patterns of initial colonization corresponded well with those in the local community.

Flume experiments on post-settlement movement in polychaetes

The ability of benthic polychaetes to move as adults and juveniles was examined using flume experiments. The main question asked was whether post-settlement movement is a passive process predictable from the hydrodynamic characteristics of the environment and the individual, or whether active behavior is involved. In one set of experiments, the percent of individuals moving during a six-hour period in low-food conditions was compared among five species of intertidal polychaetes. Flow speed was set at a velocity that did not cause sediment erosion but did cause bedload transport of anesthetized individuals. Species varied significantly in percent of movement, with Laeonereis culveri, Nereis succinea and Lumbrineris tenuis displaying negligible movement, Polydora cornuta having small but consistent movement, and Streblospio benedicti displaying the most movement (27% of individuals leaving original sediments in 6 h). Movement was not related to body size or mode of development, but showed a correlation with depth/feeding preferences: subsurface-feeders moved less than interface-feeders. Experiments with P. cornuta and S. benedicti that were extended to 18 hours indicated that post-settlement movement continued but the rate of movement during hours 6-18 was approximately half that during the first 6 hours. Experiments looking at the effects of experimental conditions on post-settlement movement in S. benedicti found that darkness had no effect, but that adding food, holding adults in still-water culture for 2.5 months, or growing larvae to adults in still-water cultures all significantly decreased movement. Overall, the results indicated an active component to post-settlement movement.

CenSeam, an International Program on Seamounts within the Census of Marine Life: Achievements and Lessons Learned

Seamounts (undersea mountains) continue to be focal areas for marine science, encompassing research that ranges from plate tectonics, oceanic convective heat budgets, the physical structure and dynamics of the oceans water masses, and the composition of the ancient atmosphere [1]–[5]. Research into the ecological function of seamounts is equally varied. Several groups of organisms have demonstrated hotspots of elevated biomass over seamounts, including mobile pelagic fauna [6]–[9] and larger invertebrates on the seafloor [10], [11]. Seamounts can act as refugia: as presumably isolated habitats, they create conditions that favour the existence of ‘living fossils’ and, in a few isolated cases, support archaic assemblages that are more similar to fossil strata than extant communities [12]–[14]. This refugia function of seamounts may gain new importance as future, shallow-water refuge areas for deep-water corals that become displaced from deeper layers by changing ocean chemistry [15], [16] (but see [16]). Conventional wisdom previously held that seamounts mimic islands whose biological communities contain more species of small geographic ranges (i.e. ‘endemics’) than other areas of the oceans, though this notion has been challenged in recent studies, including those employing genetic techniques [12], [17]–[19]. Instead, seamount communities, though they have structural differences, may play a dynamic role in the source-sink dynamics of abutting systems [20]. There is widespread consensus that biological components of seamounts are highly vulnerable and sensitive to human disturbance and exploitation [21], [22]. The best documented, most widespread, and presumably most substantial human impacts on seamounts are caused by fishing. The history of fishing on many seamounts and for many seamount-associated fish stocks shows a classic ‘boom and bust’ pattern, with few seamount fisheries appearing to be sustainable in the longer term [23]. The impacts of fishing extend from detrimental effects on fish stocks to the seafloor: benthic communities are frequently composed of long-lived and fragile invertebrates (e.g. corals) that have very low tolerances to physical encounters with fishing gear [24], [25]. Consequently, impacts from bottom-contact fishing can be massive, and recovery times may be in the range of decades to centuries [26]. Mining for mineral deposits on seamounts presents a new, and potentially large, threat to seamount ecosystems [27], and emphasizes a need for global, scientifically robust conservation and management planning for seamounts [28], [29]. The increasing biological research on seamounts [30], coupled with these growing management concerns, led to the founding of the Global Census of Marine Life on Seamounts (CenSeam) in 2005 as part of the Census of Marine Life program.

Building Environmental Information Systems: Myths and Interdisciplinary Lessons

With databases and information systems playing an increasing role in large scientific research projects, there is a growing stake in understanding how to design a useful information system and in broadening our understanding of what constitutes the scientific work involved in building these systems. Both experience and theory indicate that non-technical considerations, such as management and communication structures, are as important as technical decisions in system development. We examine four case examples of environmental information system development: the Ocean Biogeographic Information System, the Long Term Ecological Research Network, the California Cooperative Oceanic Fisheries Investigation, and SeamountsOnline. We then draw from a wide interdisciplinary literature, including science and technology studies and social informatics, to identify common myths and misconceptions about system development and consider alternatives. Our goal is both to provide a set of concrete models and a theoretical foundation useful to other projects