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:Tee4,

We employed the virus-dilution technique to quantify lytic virus production at nine sampling sites across three distinct habitats (vent, sub-vent, non-vent) along the East Pacific Rise (9°N 50’N and 104°W) in the Tica vent area during expedition FKt230627 aboard R/V Falkor(too). The virus-dilution technique leverages the density-dependent nature of viral infection. In this approach, viruses are largely removed from the sample, and the remaining prokaryotic cells are incubated in virus-free sample water. Due to the extreme dilution of viruses in the sample, new viral infections are prevented during the incubation period. Consequently, any observed increase in viral abundance is attributable to viral infection processes that were already active prior to sample collection (Köstner et al. 2017).

Samples were collected using a suction-sampler operated onboard the remotely-operated vehicle (ROV) SuBastian. Immediately after the ROV was brought on board, a total of 4 L per sample were transferred into two 2L Nalgene flasks subsequently used for setting-up the experimental incubations by sequential filtration. First, the sample was filtered over membrane filters with a pore-size of 3 µm (Isopore, TSTP04700, Millipore) to remove larger particles. Subsequently, prokaryotic cells within the filtrate of this first filtration step were concentrated using a tangential-flow filtration device with a pore-size of 0.22 µm (Vivaflow 200, PES membrane, Sartorius) until the volume of the retentate approached ~200 mL. The retentate from this second filtration step was subjected to another tangential-flow ultrafiltration device with a molecular weight cut-off of 100 kDa (Vivaflow 200, PES membrane, Sartorius) to remove the viruses, yielding a virus-free ultrafiltrate to be used as culture medium in the experimental incubations.

For each sample, duplicate experimental incubations were prepared by mixing 3 mL of prokaryotic concentrate with 47 mL of virus-free water from the same sample, yielding a final volume of 50 mL per incubation. Immediately afterward, 1.5 mL subsamples were taken to enumerate prokaryotes and viruses (see below). Subsequently, for each duplicate incubation, five 2.5 mL glass vials were filled with the prepared dilution of prokaryotic concentrate in virus-free filtrate, tightly sealed, and placed into pressure chambers (Klose et al. 2015, one chamber per duplicate incubation). The experiments were incubated at 250 bar pressure (approximately 2500 m depth), in the dark, and at in situ temperature for 30 hours. Every ~6 hours, the chambers were depressurized to remove one glass vial per duplicate incubation to collect 1.5 mL of water for subsequent enumeration of prokaryotes and viruses (see below). Immediately after subsampling, the chambers containing the remaining glass vials were re-pressurized to 250 bar and incubated in the dark and at in situ temperature until the next subsampling or until the experiments concluded after 30 hours. To assess the impact of pressure on virus production rates, virus-dilution experiments were also conducted at surface pressure conditions at specific sampling sites.

Samples for the enumeration of prokaryotic cells and viruses were immediately fixed with glutaraldehyde at a final concentration of 0.5% at room temperature for 10 minutes, flash-frozen in liquid nitrogen, and stored at -80°C until analysis by flow cytometry (Brussaard et al. 2010). Upon thawing samples were stained with SYBR Green I for 10 minutes at room temperature for prokaryotes or at 80°C for viruses. The samples were then analyzed using a FACSAria III flow cytometer (Becton Dickinson), and prokaryotes and viruses were enumerated on cytograms of side scatter versus green fluorescence (Brussaard et al. 2010).

1b:T42f,BCO-DMO Data Manager Processing Notes: * Data from source file BCODMOData.xls Sheet 1 were imported into the BCO-DMO data system with values "/N" identified as missing data identifiers. This table was attached to this dataset as 936224_v1_virus-production-hydrothermal-vent.csv ** Missing data in the BCO-DMO system displays as a blank (null values) by default and will vary depending upon the file format downloaded (blank in csv files, NaN in .mat matlab files, etc). * Parameters (column names) were renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions * Date format converted to ISO 8601 date format * Time format converted to ISO 8601 time format * timestamp with timezone column added with UTC time (ISO_DateTime_UTC column) from local data and times provided as UTC-6 (local time zone specified by data provider and confirmed to use UTC-6 during entire cruise). * columns "prokaryotes" and "viruses" were rounded to two decimal places to match the displayed format shown in Excel.1c:T48c,We used the virus-dilution technique to quantify lytic virus production at nine sites across vent, sub-vent, and non-vent habitats along the East Pacific Rise during expedition FKt230627 aboard R/V Falkor(too). This technique leverages the density-dependent nature of viral infection, preventing new infections by dilution. Samples were collected via ROV SuBastian, sequentially filtered to remove larger particles, and concentrated using tangential-flow filtration. Duplicate incubations were set up with prokaryotic concentrate and virus-free water, pressurized to 250 bar, and incubated in the dark at in situ temperatures for 30 hours. Subsamples were taken every six hours for enumeration of prokaryotes and viruses via flow cytometry. Parallel experiments were conducted at surface pressure to assess the impact of pressure on virus production rates. The methodology ensures observed increases in viral abundance are due to pre-existing infections. The experiments were conducted aboard R/V Falkor(too) between 5-22 July 2023 by Tinkara Tinta and Nicole Krause. Prokaryotes and viruses were enumerated flow-cytometrically back in the lab by Christian Winter.1d:T5b5,Since the discovery of deep-sea hydrothermal vents in 1977, scientists realize that life exists above and below the seafloor. The extent to which they are interconnected, however, remains poorly understood. We propose to characterize subsurface biosphere diversity, from viruses to animals, at deep-sea hydrothermal vents to elucidate the nature and extent of connectivity between the surficial and subsurface biospheres. We will test the hypotheses that 1) eukaryotic life is also an integral component of the subseafloor biosphere; 2) the subseafloor is inhabited by both cosmopolitan and endemic protists and fungi; and 3) the subseafloor habitats harbor larvae -and perhaps adult life stages- of vent endemic animals. This research will transform our understanding of the ecology/evolution of subseafloor habitats and our thinking about animal recruitment at deep-sea vents. Consistent with SOI's mission, we will expand our knowledge of limits of eukaryotic life. During a three-week cruise with R/V Falkor and ROV SuBastian to "East Pacific Rise" vents at the 9º50'N region, we will use in situ and lab experiments, molecular identification with amplicon sequencing, Illumina NextSeq 500 technology, 2bRAD population genetic analyses, and RT qPCR for functional analyses. Our data management plan includes deposition of metadata/samples to long-term repositories. Outreach includes inquiry-learning telepresence programs for children from USA and Europe.6:["$","$L19",null,{"dataset":{"_id":"936224","description":"","problem":"Occasionally, glass vial seals were not perfect (manufacturing issue).","acquisition":"$1a","processing":"

Submitted data consist of temporal developments of prokaryotic and viral abundances (both in Nx10⁴ mL^-1) within the experimental incubations.

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Description from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm","type_acronym":"Flow Cytometer"},{"_id":"936236","name":"","description":"customized pressure vessel: Pressure vessels are custom items (see Klose et al. 2015; www.pnas.org/cgi/doi/10.1073/pnas.1501160112).","type_id":"923517","type_name":"Pressure Vessel","type_desc":"A pressure vessel is a container designed to hold gases or liquids at a pressure substantially different from the ambient pressure. Construction methods and materials may be chosen to suit the pressure application, and will depend on the size of the vessel, the contents, working pressure, mass constraints, and the number of items required. Examples include glassware, autoclaves, compressed gas cylinders, compressors (including refrigeration), vacuum chambers and custom designed laboratory vessels. ","type_acronym":"pressurized container"},{"_id":"936237","name":"Waters 515 HPLC Pump","description":"Waters 515 HPLC Pump: Glass vials were placed into pressure vessels and pressurized using a Waters 515 HPLC Pump up to 250 bar.","type_id":"726","type_name":"Pump","type_desc":"A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps","type_acronym":""},{"_id":"936235","name":"","description":"ROV SuBastian and its Multi-Chamber Suction Sampler: Water samples were collected with ROV SuBastian suction sampler at the vent sites.","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":""},{"_id":"936241","name":"Vivaflow 200 tangential-flow filtration device","description":"Vivaflow 200 tangential-flow filtration device: self-contained tangential-flow filter (0.22 µm poresize and 100 kDa molecular weight cut-off) used to obtain prokaryotic concentrates and virus-free ultrafiltrate","type_id":"936239","type_name":"water filtration device","type_desc":"A manufactured device which is used to remove contaminants from water impeding the flow of particles or solutes. ","type_acronym":""}],"parameters":[{"_id":"936244","name":"dive","format":"","frictionlessType":"string","description":"

Dive number of ROV

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

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

"}},{"_id":"936245","name":"sample_id","format":"","frictionlessType":"string","description":"

Identification code of sample as collected by the ROV.

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

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

"}},{"_id":"936246","name":"subsample_id","format":"","frictionlessType":"string","description":"

ID of the sample (subsample of ROV sample_id)

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

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

"}},{"_id":"936247","name":"habitat","format":"","frictionlessType":"string","description":"

Habitat. vent=vent fluid; sub ven=sampled from within the vent using a hose; non vent=deep sea not within direct influence of vents

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

Description or characteristics of a sampling site

"}},{"_id":"936248","name":"latitude","format":"","frictionlessType":"number","description":"

latitude

","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":"936249","name":"longitude","format":"","frictionlessType":"number","description":"

longitude

","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":"936250","name":"depth","format":"","frictionlessType":"number","description":"

meters below surface

","units":{"_id":"","name":"meters (m)"},"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":"936251","name":"temperature","format":"","frictionlessType":"number","description":"

in situ water temperature

","units":{"_id":"","name":"degrees Celsius (degC)"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"936252","name":"incubated_at_250bar","format":"","frictionlessType":"string","description":"

Whether incubated at 250 bar pressure (yes/no)

","units":{"_id":"","name":"unitless"},"type":{"_id":"489066","name":"treatment","description":"

Experimental conditions applied to experimental units. In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.

"}},{"_id":"936253","name":"date_local","format":"%Y-%m-%d","frictionlessType":"date","description":"

date (local) of day aboard ship (UTC-6). Date when subsamples from the experiments were taken to enumerate prokaryotic and viral abundances.

","units":{"_id":"","name":"unitless"},"type":{"_id":"799","name":"date_local","description":"

local month, day and year, usually as a text string, e.g. feb10_1995. It is better to use one of the other forms of presenting date and time data so that the data can be used in computations and for comparisons. Note, if the string begins with numbers but also includes letters, there may be problems using the field name for retrieval.

"}},{"_id":"936254","name":"time_local","format":"%H:%M","frictionlessType":"time","description":"

time (local) of day aboard ship (UTC-6). Time when subsamples from the experiments were taken to enumerate prokaryotic and viral abundances.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1007","name":"time_local","description":"

time of day, local time, using 2400 clock format

"}},{"_id":"936255","name":"ISO_DateTime_UTC","format":"%Y-%m-%dT%H:%MZ","frictionlessType":"datetime","description":"

timestamp with timezone in ISO 8601 format (UTC). Datetime when subsamples from the experiments were taken to enumerate prokaryotic and viral abundances.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1908","name":"ISO_DateTime_UTC","description":"

Date/Time (UTC) ISO formatted
\nThis standard is based on ISO 8601:2004(E) and takes on any of the following forms:
\n2009-08-30T09:05:00[.xx] (local time)
\n2009-08-30T14:05:00[.xx]Z (UTC time)
\n2009-08-30T14:05:00[.xx]-05:00
\nThe dashes and the colons can be dropped.
\nThe T can also be dropped \"by mutual agreement\", but one needs the trailing Z if the time is UTC.

Sample ISO_datetime_utc:
\n2009-08-30T14:05:00[.xx]Z (UTC time)

Format: YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC time)

"}},{"_id":"936256","name":"prokaryotes","format":"","frictionlessType":"number","description":"

prokaryotic abundance

","units":{"_id":"","name":"Nx10^4 mL^-1"},"type":{"_id":"735","name":"abundance","description":"

Amount (number, mass, diversity/species variation) of the specific taxa/group counted per unit area or volume

"}},{"_id":"936257","name":"viruses","format":"","frictionlessType":"number","description":"

viral abundance

","units":{"_id":"","name":"Nx10^4 mL^-1"},"type":{"_id":"735","name":"abundance","description":"

Amount (number, mass, diversity/species variation) of the specific taxa/group counted per unit area or volume

"}}],"related_publications":[{"id":"936242","citation":"Brussaard, C. P. D., Payet, J. P., Winter, C., & Weinbauer, M. G. (2010). Quantification of aquatic viruses by flow cytometry. Manual of Aquatic Viral Ecology, 102–109. https://doi.org/10.4319/mave.2010.978-0-9845591-0-7.102\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"923673","citation":"Klose, J., Polz, M. F., Wagner, M., Schimak, M. P., Gollner, S., & Bright, M. (2015). Endosymbionts escape dead hydrothermal vent tubeworms to enrich the free-living population. Proceedings of the National Academy of Sciences, 112(36), 11300–11305. https://doi.org/10.1073/pnas.1501160112\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"936243","citation":"Köstner, N., Scharnreitner, L., Jürgens, K., Labrenz, M., Herndl, G. J., & Winter, C. (2017). High viral abundance as a consequence of low viral decay in the Baltic Sea redoxcline. PLOS ONE, 12(6), e0178467. https://doi.org/10.1371/journal.pone.0178467\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/936224/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"ERDDAP","items":[{"name":"SUBSET DATA","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.html","contentType":"text/html","actionType":"tool"},{"name":"VIEW TABLE","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.htmlTable","contentType":"text/html","actionType":"view"},{"name":"CSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.csv","contentType":"text/csv","actionType":"download"},{"name":"TSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.tsv","contentType":"text/tsv","actionType":"download"},{"name":"GeoJSON","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.geoJson","contentType":"application/geo+json","actionType":"download"},{"name":"MATLAB","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.mat","contentType":"text/x-matlab","actionType":"download"},{"name":"netCDF","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.nc","contentType":"application/x-netcdf","actionType":"download"},{"name":"ODV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936224_v1.odvTxt","contentType":"text/plain","actionType":"download"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/936224/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/936224/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/936224/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"920699","name":"The Underworld of Hydrothermal Vents","acronym":"Vent Underworld","description":"$1d"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.936224.1","url":"https://doi.org/10.26008/1912/bco-dmo.936224.1","date_assigned":"2025-02-05","version_date":"2024-08-23","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":143},"downloads":{"count":225}}}}]