19:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1a:T489,

Samples were collected at several sites along the East Pacific Rise hydrothermal vent zone. They included ROV/Jason deployments J2-758, J2-759, J2-760, J2-761, J2-762.

About 1 GB of raw sequence data (bacterial ssrRNA) was obtained using the Ion Torrent platform from total RNA extracted from sixteen microbial biofilm samples characterized by different temperature, redox and biological regimes. Samples included background references. Sequence data are currently being analyzed and will be deposited in GenBank prior to publication and will be made available to the scientific community. [2015-02-04]

The use of rRNA transcripts instead of DNA will allow us to identify the fraction of the population actively transcribing in situ. Sixteen microbial biofilm samples characterized by different temperature, redox and biological regimes were used. These samples included biofilm formed on experimental colonizers deployed at selected vents to obtain early stage biofilm. A comparison of early stage and established biofilms will help to understand how the community changes in relation to biofilm age and geochemical regimes.

1b:T50f,The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/1c:T11e7,Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives: 1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities. 2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents. 3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents. 4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms. Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts. Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context. Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), http://www.whoi.edu/GBF-OOI/page.do?pid=41475)6:["$","$L19",null,{"dataset":{"_id":"549138","description":"

This dataset is a sample log of sequenced samples collected by ROV/Jason in the East Pacific Rise, Pacific Ocean. The taxonomic composition of the active microbial community present in biofilm and fluid samples was investigated by sequencing 16S rRNA transcripts.

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We have optimized a RNA extraction protocol from biofilm biomass using the RNeasy kit (Qiagen). Following extraction and DNase treatment, we generated cDNA using random primers (SuperScript III First-Strand kit). cDNA from biolfilm and fluid samples was used to amplify the 16S rRNA gene with tagged primers and subjected to sequencing. Obtained sequences are currently being analyzed using the QIIME pipeline. The reads are being dereplicated, denoised, screened for chimeric sequences and taxonomically classified using the RDP and GreenGenes databases. Multivariate ordination techniques will be used to discriminate among samples with similar community structures.

\n","bcodmoProcessing":"","title":"Samples sequenced from chemosynthetic biofilm communities in deep-sea hydrothermal vents collected on the R/V Atlantis AT26-10 in the East Pacific Rise, Pacific Ocean from 2013 - 2014 (Microbial Communities at Deep-Sea Vents project)","nickname":"Chemosynthetic biofilm diversity","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"2015-02-10","version_date":"2015-02-10T05:00:00.000Z","abstract":"","citation":"Vetriani, C. (2015) Samples sequenced from chemosynthetic biofilm communities in deep-sea hydrothermal vents collected on the R/V Atlantis AT26-10 in the East Pacific Rise, Pacific Ocean from 2013 - 2014 (Microbial Communities at Deep-Sea Vents project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-02-10) Version Date 2015-02-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/549138 [access date]","citationParts":{"identifier":"http://lod.bco-dmo.org/id/dataset/549138","versionDate":"2015-02-10","versionId":"2015-02-10","year":"2015","title":"Samples sequenced from chemosynthetic biofilm communities in deep-sea hydrothermal vents collected on the R/V Atlantis AT26-10 in the East Pacific Rise, Pacific Ocean from 2013 - 2014 (Microbial Communities at Deep-Sea Vents project)","authors":"Vetriani, C.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"","release_date":null,"field_dataset_location":"","temporal_extent":{"start":null,"end":null},"temporal":{"resolution":"","type":"","start":{"value":"","label":""},"end":{"value":"","label":""}},"spatial_extent":{"shape":"polygon","center":{"latitude":9.8423250023218,"longitude":-104.29217502463},"wkt":" POLYGON((-104.29321 9.83798, -104.29114 9.83798, -104.29114 9.84667, -104.29321 9.84667, -104.29321 9.83798))","north":9.84667,"east":-104.29114,"south":9.83798,"west":-104.29321},"dataset_type":["Unknown"],"keywords":["biota","oceans"],"data_files":[{"id":"900446","title":"AT26-10_samples.csv","url":"https://datadocs.bco-dmo.org/dataset/549138/file/N77GrVgUPq3O2q/AT26-10_samples.csv","showTableUrl":"https://www.bco-dmo.org/dataset/549138/data/view/900446","description":"Primary data file for dataset ID 549138","filename":"AT26-10_samples.csv","bytesize":2595,"checksum":{"value":"d459044b425e22288c6c1fa6d0bbba85","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"51298","name":"Costantino Vetriani"},"performedAtOrganization":{"_id":"236","name":"Rutgers University"}},{"role":{"_id":"137","name":"Data Manager"},"performedBy":{"_id":"50396","name":"Nancy Copley"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"50396","name":"Nancy Copley"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"529031","name":"AT26-10","synonyms":[],"dates":{"start":"2013-12-29T00:00:00.000Z","end":"2014-01-27T00:00:00.000Z"},"platform":{"_id":"54003","name":"R/V Atlantis"},"chiefScientists":[{"id":"51416","name":"Stefan M. Sievert","role":"Chief Scientist"}]}],"funding":[{"_id":"54990","name":"OCE-1136451","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1136451"}],"instruments":[{"_id":"549144","name":"Automated Sequencer","description":"Ion Torrent next-generation sequencing platform","type_id":"649","type_name":"Automated DNA Sequencer","type_desc":"A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.","type_acronym":"Automated Sequencer"},{"_id":"550454","name":"McLane Pump","description":"Large Volume Pump (LVP): McLane WTS 6-1-142LV","type_id":"627","type_name":"McLane Pump","type_desc":"McLane pumps sample large volumes of seawater at depth. They are attached to a wire and lowered to different depths in the ocean. As the water is pumped through the filter, particles suspended in the ocean are collected on the filters. The pumps are then retrieved and the contents of the filters are analyzed in a lab.","type_acronym":"McLane Pump"},{"_id":"550449","name":"ROV Jason","description":"","type_id":"638","type_name":"ROV Jason","type_desc":"$1b","type_acronym":"ROV Jason"}],"parameters":[{"_id":"550495","name":"sample_num","format":"","frictionlessType":"","description":"

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