1b: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"] 1c:T434,

In situ carbonate rocks were taken at sites with different seepage activity in 2017 (AT37-13) and 2018 (AT42-03) using HOV Alvin and in 2019 using ROV SuBastian. These were used as control samples for the following experiments: (1) Colonization experiment: Carbonate rocks deployed for 3 months (Oct. 2018- Jan. 2019) and 17 months (Jun. 2017-Oct. 2018) at different seepage activity, (2) Transplant experiment: Carbonate rocks with attached fauna were moved by the HOV to different seepage conditions with exposure for 17 months (Jun. 2017-Oct. 2018).

All substrates were photographed intact upon recovery, and wrapped in aluminum foil to determine the surface area. Photographs were kept for reference. Before preserving, the sample was kept cold and animals were picked to sample tissue for isotope analysis (see related dataset for isotopic data).

The remaining sample was sieved through 0.3 mm mesh, separating the sample in two fractions (a fine fraction with the meiofauna, and a coarser one with the macrofauna), both preserved in 96% Ethanol.

1d:T593,- Downloaded cruise/vehicle metadata from official sources (Marine Geoscience Data System) including dive start dates and cruise IDs and added to files as "ndsf_metadata_AT42-03.csv", "ndsf_metadata_AT37-13.csv", and "event_information_FK190106.csv" - Imported "BCO-DMO_CR Carbonate macrofauna species.xlsx", "ndsf_metadata_AT42-03.csv", "ndsf_metadata_AT37-13.csv", and "event_information_FK190106.csv" into BCO-DMO system -Renamed all parameter names from "BCO-DMO_CR Carbonate macrofauna species" to remove special characters and spaces - Joined "BCO-DMO_CR Carbonate macrofauna species" to "ndsf_metadata_AT42-03.csv", "ndsf_metadata_AT37-13.csv", and "event_information_FK190106.csv" on dive IDs to incorporate dive start dates and cruise IDs for each sample - Replaced species names in parameters with corrected names provided by submitter - Exported file as "960511_v1_carbonate_rock_species.csv" - Checked all scientific names referenced in methods section and the methods section of related dataset using World Register of Marine Species (WoRMS) Taxon Match. All scientific names referenced are valid and accepted names as of 2025-07-03. Included the complete list in Carbonate_rock_species_composition.csv as a supplemental file - Included "ScientificName", "matched_AphiaID", "Match type", "LSID", "AphiaID_accepted", and "ScientificName_accepted" in "Carbonate_rock_species_composition.csv" supplemental file1e:T82e,Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours. Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed. It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability. With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor. It can collect data throughout the water column, produce a variety of maps and perform photographic surveys. Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive. Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor. Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day. Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology. (from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09)1f:T1254,NSF abstract: If life were to disappear from the deep sea, would we notice? We only have a cursory understanding of this vast region and the connectivity among its communities and the rest of the oceans, and yet the ecosystems of the deep sea have been implicated in the larger function of the global marine ecosystems. We now rely on the deep ocean for food, energy, novel drugs and materials, and for its role in the global cycling of carbon, as well as for supporting services such as habitat creation, nutrient replenishment for shallow waters, and the maintenance of biodiversity. Cold seeps, active areas of the seafloor where methane and other chemicals are released, are key features along the continental margins worldwide. To characterize how methane seep communities interact with the surrounding ecosystems and vice versa, we will study methane seeps off the Pacific coast of Costa Rica in 2017 and 2018. It is the sphere of influence around the seep, both along the seafloor and up into the water column, that we seek to better understand. We will map the structure and the chemistry surrounding these habitats using a novel 3-dimensional framework, combining typical transects with vertical characterizations of the water column just above the seafloor. This will include measurements of methane flux into the water column and changes in the overlying carbonate chemistry and oxygen levels that are critical to our understanding of the effect of warming, oxygen loss and ocean acidification in this region. Within this framework, we will collect seep organisms in sediments and on rocks (including all sizes from microbes to large animals), and transplant some of these from within the area of seep influence to the background deep sea, and vice-versa. Together, these studies will help us to measure the size of the seep sphere of influence, and also demonstrate the role of these seeps within the deep sea and the greater, global, marine ecosystem. We will share this information with a group of teachers during a series of workshops in the San Diego area, at an exhibit at the Birch Aquarium, and through the work of an artist who has worked extensively with marine organisms in extreme environments. Chemosynthetic ecosystems are inextricably linked to the broader world-ocean biome and global biogeochemical cycles in ways that we are just beginning to understand. This research will identify the form, extent, and nature of the physical, chemical, and biological linkages between methane seeps and the surrounding deep-sea ecosystem. The proposed research builds critical understanding of the structural and functional processes that underpin the ecosystem services provided by chemosynthetic ecosystems. We target a critical continental margin, Costa Rica, where methane fates and dynamics loom large and play out in an setting that reflects many oceanographic stressors. We will use quantitative sampling and manipulative studies within a 3-dimensional oceanographic framework. We will ask what are the shapes of the diversity and density functions for organisms of different size classes and trophic position over the transition from the seep habitat through the ecotone to the background deep sea? Further, we will ask how do depth, dissolved oxygen concentrations, pH and carbonate ion availability, relative rates of fluid flux, and substrate (biogenic, authigenic carbonate, sediments) alter these linkages and interactions with the surrounding deep sea? Evidence for distinct transitional communities and biotic patterns in density and alpha and beta diversity will be quantified and placed in a global biogeographic context. All of these investigations will occur across biological size spectra: for microorganisms (archaea, bacteria, microeukaryotes), the macrofauna, and the megafauna that form biogenic habitats. Our research results will be interpreted in the context of potential effects of global ocean change in the equatorial Pacific to determine how the linkages with the surrounding deep sea will be altered as anthropogenic impacts proceed in the future. Related publications: Levin, L.A., V.J. Orphan, G.W. Rouse, W. Ussler, A. E. Rathburn, G. S. Cook, S. Goffredi, E. Perez, A. Waren, B. Grupe, G. Chadwick, B. Strickrott. (2012). A hydrothermal seep on the Costa Rica margin: Middle ground in a continuum of reducing ecosystems. Proc. Royal Soc. B. 279: 2580-88 doi: 10.1098/rspb.2012.0205 Sahling, H., Masson, D. G., Ranero, C. R., Hühnerbach, V., Weinrebe, W., Klaucke, I., & Suess, E. (2008). Fluid seepage at the continental margin offshore Costa Rica and southern Nicaragua. Geochemistry, Geophysics, Geosystems 9: doi: 10.1029/2008GC0019786:["$","$L1b",null,{"dataset":{"_id":"960511","description":"","problem":"Quantitative analysis was not performed on all samples, and surface area measurements are not available in some cases. Additionally, certain samples lack collection depth data. For dive 4921, collection latitude and longitude values are missing; however, the dive metadata indicates a start location of 8.85315° N, 84.2155° W.","acquisition":"$1c","processing":"

In the laboratory, the macrofauna samples were washed in distilled water and sorted, and the animals were identified to the lowest level possible, counted and preserved in 96% Ethanol.

\n","bcodmoProcessing":"$1d","title":"Carbonate rock species composition from samples collected by HOV Alvin during R/V Atlantis cruises AT37-13 and AT42-03 and ROV SuBastian during R/V Falkor cruise FK190106 at Pacific margin of Costa Rica from 2017 to 2019","nickname":"Carbonate rock species composition","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2025-07-03T04:00:00.000Z","abstract":"This dataset is a matrix of individuals counts of species by sample of carbonate rocks collected by HOV Alvin during R/V Atlantis cruise AT37-13 (2017) and AT42-03 (2018) and ROV SuBastian during R/V Falkor cruise FK190106 (2019) at the Quepos Landslide, Mound 12, and Jaco Scar methane seeps in the Pacific margin of Costa Rica. It includes cruise, dive, collection, and sample information, as well as the description of seep location and activity level and description of treatment (in situ, colonization, or transplant). ","citation":"Pereira, O. S., Levin, L. A. (2025) Carbonate rock species composition from samples collected by HOV Alvin during R/V Atlantis cruises AT37-13 and AT42-03 and ROV SuBastian during R/V Falkor cruise FK190106 at Pacific margin of Costa Rica from 2017 to 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-07-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.960511.1 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.960511.1","versionDate":"2025-07-03","versionId":"1","year":"2025","title":"Carbonate rock species composition from samples collected by HOV Alvin during R/V Atlantis cruises AT37-13 and AT42-03 and ROV SuBastian during R/V Falkor cruise FK190106 at Pacific margin of Costa Rica from 2017 to 2019","authors":"Pereira, O. S., Levin, L. A.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.960511.1","release_date":null,"field_dataset_location":"Methane seeps on the Costa Rican Pacific margin at depths from ~350-2000 m.","temporal_extent":{"start":"2017-05-20T04:00:00.000Z","end":"2019-01-10T05:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1495252800","label":"2017-05-20"},"end":{"value":"1547096400","label":"2019-01-10"}},"spatial_extent":{"shape":"polygon","center":{"latitude":8.985124999999,"longitude":-84.528091649994},"wkt":"POLYGON ((-84.8422 8.85245, -84.2139833 8.85245, -84.2139833 9.1178, -84.8422 9.1178, -84.8422 8.85245))","north":9.1178,"east":-84.2139833,"south":8.85245,"west":-84.8422},"dataset_type":["Cruise Results"],"keywords":["biota","oceans"],"data_files":[{"id":"966749","title":"960511_v1_carbonate_rock_species.csv","url":"https://datadocs.bco-dmo.org/dataset/960511/file/zqDYpGlfGK6DxA/960511_v1_carbonate_rock_species.csv","showTableUrl":"https://www.bco-dmo.org/dataset/960511/data/view/966749","description":"Primary data file for dataset ID 960511, version 1","filename":"960511_v1_carbonate_rock_species.csv","bytesize":107806,"checksum":{"value":"37dd8fb0c32e14c0f4b822f4c25f3a33","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"bcodmo_dataset_960511_v1","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[{"id":"966750","title":"Carbonate_rock_species_composition.csv","url":"https://datadocs.bco-dmo.org/dataset/960511/file/8XnK25KhO6QYRr/Carbonate_rock_species_composition.csv","showTableUrl":"","description":"Taxon identifiers (AphiaID and LSID) for scientific names listed in this dataset. 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Levin"},"performedAtOrganization":{"_id":"26","name":"University of California-San Diego Scripps"}},{"role":{"_id":"128","name":"Student"},"performedBy":{"_id":"845725","name":"Olívia Soares Pereira"},"performedAtOrganization":{"_id":"26","name":"University of California-San Diego Scripps"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"924467","name":"Audrey Mickle"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"714567","name":"AT37-13","synonyms":[],"dates":{"start":"2017-05-20T00:00:00.000Z","end":"2017-06-11T00:00:00.000Z"},"platform":{"_id":"54003","name":"R/V Atlantis"},"chiefScientists":[{"id":"51539","name":"Erik E. Cordes","role":"Chief Scientist"}]},{"_id":"777903","name":"AT42-03","synonyms":[],"dates":{"start":"2018-10-17T00:00:00.000Z","end":"2018-11-06T00:00:00.000Z"},"platform":{"_id":"54003","name":"R/V Atlantis"},"chiefScientists":[{"id":"51539","name":"Erik E. Cordes","role":"Chief Scientist"}]},{"_id":"806648","name":"FK190106","synonyms":["FK 190106"],"dates":{"start":"2019-01-06T00:00:00.000Z","end":"2019-01-27T00:00:00.000Z"},"platform":{"_id":"54256","name":"R/V Falkor"},"chiefScientists":[{"id":"51539","name":"Erik E. Cordes","role":"Chief Scientist"}]}],"funding":[{"_id":"710021","name":"OCE-1634172","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1634172"}],"instruments":[{"_id":"960532","name":"Camera","description":"All substrates were photographed intact upon recovery, and wrapped in aluminum foil to determine the surface area. ","type_id":"520","type_name":"Camera","type_desc":"All types of photographic equipment including stills, video, film and digital systems.","type_acronym":"camera"},{"_id":"960531","name":"HOV Alvin","description":"In situ carbonate rocks were taken at sites with different seepage activity in 2017 (AT37-13) and 2018 (AT42-03) using HOV Alvin and in 2019 using ROV SuBastian. ","type_id":"880039","type_name":"HOV Alvin","type_desc":"$1e","type_acronym":""},{"_id":"960529","name":"Optical Microscope Wild Heerbrugg Stereomicroscope M5A","description":"In the laboratory, the macrofauna samples were washed in distilled water and sorted, and the animals were identified to the lowest level possible, counted and preserved in 96% Ethanol.","type_id":"708","type_name":"Microscope - Optical","type_desc":"Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".","type_acronym":""},{"_id":"960530","name":"ROV SuBastian","description":"In situ carbonate rocks were taken at sites with different seepage activity in 2017 (AT37-13) and 2018 (AT42-03) using HOV Alvin and in 2019 using ROV SuBastian. ","type_id":"838108","type_name":"ROV SuBastian","type_desc":"ROV SuBastian is operated from the research vessel Falkor and the R/V Falkor(too). The ROV is outfitted with a suite of sensors and scientific equipment to support scientific data and sample collection, as well as interactive research, experimentation, and technology development. More information available at https://schmidtocean.org/technology/robotic-platforms/4500-m-remotely-operated-vehicle-rov/","type_acronym":""}],"parameters":[{"_id":"961231","name":"Cruise_ID","format":"","frictionlessType":"string","description":"

Cruise ID

","units":{"_id":"","name":"unitless"},"type":{"_id":"1102","name":"cruise_id","description":"

cruise designation; name

"}},{"_id":"961232","name":"Cruise_year","format":"","frictionlessType":"integer","description":"

Cruise year (2017, 2018 or 2019)

","units":{"_id":"","name":"unitless"},"type":{"_id":"1062","name":"year","description":"

year, reported as YYYY, e.g. 1995

"}},{"_id":"961233","name":"Vehicle","format":"","frictionlessType":"string","description":"

HOV Alvin or ROV SuBastian vehicle

","units":{"_id":"","name":"unitless"},"type":{"_id":"932","name":"platform","description":"

name of the platform, buoy, tower, fixed site, etc. (see also ship)

"}},{"_id":"961234","name":"Dive_ID","format":"","frictionlessType":"string","description":"

HOV Alvin or ROV SuBastian dive number

","units":{"_id":"","name":"unitless"},"type":{"_id":"1734","name":"dive_id","description":"

Unique dive id or number for ROV, AUV or HOV type system dive or deployment

"}},{"_id":"961235","name":"Dive_Start_Date","format":"%Y-%m-%d","frictionlessType":"date","description":"

Start date of dive where sample was collected

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"961236","name":"Sample_number","format":"","frictionlessType":"string","description":"

Sample number given at collection

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"961237","name":"Sample_ID","format":"","frictionlessType":"string","description":"

Sample number given during laboratory processing

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"961238","name":"Latitude","format":"","frictionlessType":"number","description":"

Latitude of sample location

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"961239","name":"Longitude","format":"","frictionlessType":"number","description":"

Longitude of sample location

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"961240","name":"Depth","format":"","frictionlessType":"number","description":"

Depth of collection

","units":{"_id":"","name":"meters"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"961241","name":"Experiment","format":"","frictionlessType":"string","description":"

Experiment (in situ, colonization or transplant)

","units":{"_id":"","name":"unitless"},"type":{"_id":"1850","name":"exp_type","description":"

Experiment type or description

"}},{"_id":"961242","name":"Seep","format":"","frictionlessType":"string","description":"

Seep site of collection

","units":{"_id":"","name":"unitless"},"type":{"_id":"1740","name":"site_descrip","description":"

Description or characteristics of a sampling site

"}},{"_id":"961243","name":"Seepage_activity","format":"","frictionlessType":"string","description":"

Level of seepage activity at collection

","units":{"_id":"","name":"unitless"},"type":{"_id":"1740","name":"site_descrip","description":"

Description or characteristics of a sampling site

"}},{"_id":"961244","name":"Surface_Area","format":"","frictionlessType":"number","description":"

Measurement of surface area of the rock in cm2

","units":{"_id":"","name":"cm2"},"type":{"_id":"662800","name":"surface_area","description":"

The total area of the surface of a three-dimensional object or organism. For example, a coral colony.

"}},{"_id":"961245","name":"Annelida_unID","format":"","frictionlessType":"integer","description":"

Count: Annelida unID