http://lod.bco-dmo.org/id/dataset/936224 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2024-08-23 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Virus and prokaryote abundances from experiments conducted with samples collected at a hydrothermal vent site by ROV SuBastian during R/V Falkor (too) expedition FKt230627 along the East Pacific Rise in July of 2023 2024-08-23 publication 2024-08-23 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-02-05 publication https://doi.org/10.26008/1912/bco-dmo.936224.1 Christian Winter University of Vienna principalInvestigator Monika Bright University of Vienna principalInvestigator Tinkara Tinta National Institute of Biology, Slovenia principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Tinta, T., Krause, N., Bright, M., Winter, C. (2025) Virus and prokaryote abundances from experiments conducted with samples collected at a hydrothermal vent site by ROV SuBastian during R/V Falkor (too) expedition FKt230627 along the East Pacific Rise in July of 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.936224.1 [access date] Methods and Sampling: &lt;p&gt;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).&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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).&lt;/p&gt; Funding provided by Schmidt Ocean Institute (SOI) Award Number: FKt230627 completed Christian Winter University of Vienna Althanstr. 14 Vienna Austria christian.winter@univie.ac.at pointOfContact Monika Bright University of Vienna +43 1 4277 76430 Department of Functional and Evolutionary Ecology Djerassiplatz 1 Vienna Austria monika.bright@univie.ac.at pointOfContact Tinkara Tinta National Institute of Biology, Slovenia tinkara.tinta@nib.si pointOfContact asNeeded Dataset Version: 1 Unknown dive sample_id subsample_id habitat latitude longitude depth temperature incubated_at_250bar date_local time_local ISO_DateTime_UTC prokaryotes viruses FACS Aria III flow cytometer Waters 515 HPLC Pump Vivaflow 200 tangential-flow filtration device theme None, User defined dive_id sample identification site description latitude longitude depth water temperature at measurement depth treatment date_local time_local ISO_DateTime_UTC abundance featureType BCO-DMO Standard Parameters Flow Cytometer Pressure Vessel Pump ROV SuBastian water filtration device instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. The Underworld of Hydrothermal Vents https://schmidtocean.org/cruise/underworld-of-hydrothermal-vents/ The Underworld of Hydrothermal Vents <p>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.</p> Vent Underworld largerWorkCitation project eng; USA oceans -104.291922 -104.291555 9.839953 9.840335 2023-07-06 2023-07-23 East Pacific Rise 0 BCO-DMO catalogue of parameters from Virus and prokaryote abundances from experiments conducted with samples collected at a hydrothermal vent site by ROV SuBastian during R/V Falkor (too) expedition FKt230627 along the East Pacific Rise in July of 2023 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/936244.rdf Name: dive Units: unitlesss Description: <p>Dive number of ROV</p> http://lod.bco-dmo.org/id/dataset-parameter/936245.rdf Name: sample_id Units: unitlesss Description: <p>Identification code of sample as collected by the ROV.</p> http://lod.bco-dmo.org/id/dataset-parameter/936246.rdf Name: subsample_id Units: unitlesss Description: <p>ID of the sample (subsample of ROV sample_id)</p> http://lod.bco-dmo.org/id/dataset-parameter/936247.rdf Name: habitat Units: unitlesss Description: <p>Habitat.  vent=vent fluid; sub ven=sampled from within the vent using a hose; non vent=deep sea not within direct influence of vents</p> http://lod.bco-dmo.org/id/dataset-parameter/936248.rdf Name: latitude Units: decimal degrees Description: <p>latitude</p> http://lod.bco-dmo.org/id/dataset-parameter/936249.rdf Name: longitude Units: decimal degrees Description: <p>longitude</p> http://lod.bco-dmo.org/id/dataset-parameter/936250.rdf Name: depth Units: meters (m) Description: <p>meters below surface</p> http://lod.bco-dmo.org/id/dataset-parameter/936251.rdf Name: temperature Units: degrees Celsius (degC) Description: <p>in situ water temperature</p> http://lod.bco-dmo.org/id/dataset-parameter/936252.rdf Name: incubated_at_250bar Units: unitless Description: <p>Whether incubated at 250 bar pressure (yes/no)</p> http://lod.bco-dmo.org/id/dataset-parameter/936253.rdf Name: date_local Units: unitless Description: <p>date (local) of day aboard ship (UTC-6). Date when subsamples from the experiments were taken to enumerate prokaryotic and viral abundances.</p> http://lod.bco-dmo.org/id/dataset-parameter/936254.rdf Name: time_local Units: unitless Description: <p>time (local) of day aboard ship (UTC-6). Time when subsamples from the experiments were taken to enumerate prokaryotic and viral abundances.</p> http://lod.bco-dmo.org/id/dataset-parameter/936255.rdf Name: ISO_DateTime_UTC Units: unitless Description: <p>timestamp with timezone in ISO 8601 format (UTC). Datetime when subsamples from the experiments were taken to enumerate prokaryotic and viral abundances.</p> http://lod.bco-dmo.org/id/dataset-parameter/936256.rdf Name: prokaryotes Units: Nx10^4 mL^-1 Description: <p>prokaryotic abundance</p> http://lod.bco-dmo.org/id/dataset-parameter/936257.rdf Name: viruses Units: Nx10^4 mL^-1 Description: <p>viral abundance</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 17432 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/2dc884af-e603-430d-b950-38831fdf8c49/content download https://doi.org/10.26008/1912/bco-dmo.936224.1 download onLine dataset &lt;p&gt;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).&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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).&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Submitted data consist of temporal developments of prokaryotic and viral abundances (both in Nx10&lt;sup&gt;4&lt;/sup&gt; mL&lt;sup&gt;-1&lt;/sup&gt;) within the experimental incubations.&lt;/p&gt; Specified by the Principal Investigator(s) BCO-DMO Data Manager Processing Notes: * Data from source file BCODMOData.xls Sheet 1 were imported into the BCO-DMO data system with values &quot;/N&quot; 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 &quot;prokaryotes&quot; and &quot;viruses&quot; were rounded to two decimal places to match the displayed format shown in Excel. Specified by BCO-DMO Data Managers asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact FACS Aria III flow cytometer FACS Aria III flow cytometer PI Supplied Instrument Name: FACS Aria III flow cytometer PI Supplied Instrument Description:FACS Aria III flow cytometer: The instrument was used to enumerate prokarytes and viruses after staining with the dsDNA-specific stain SYBR Green I. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/ PI Supplied Instrument Name: PI Supplied Instrument Description:customized pressure vessel: Pressure vessels are custom items (see Klose et al. 2015; www.pnas.org/cgi/doi/10.1073/pnas.1501160112). Instrument Name: Pressure Vessel Instrument Short Name:pressurized container Instrument Description: 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.   Waters 515 HPLC Pump Waters 515 HPLC Pump PI Supplied Instrument Name: Waters 515 HPLC Pump PI Supplied Instrument Description:Waters 515 HPLC Pump: Glass vials were placed into pressure vessels and pressurized using a Waters 515 HPLC Pump up to 250 bar. Instrument Name: Pump Instrument Short Name: Instrument Description: 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 PI Supplied Instrument Name: PI Supplied Instrument Description:ROV SuBastian and its Multi-Chamber Suction Sampler: Water samples were collected with ROV SuBastian suction sampler at the vent sites. Instrument Name: ROV SuBastian Instrument Short Name: Instrument Description: 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/ Vivaflow 200 tangential-flow filtration device Vivaflow 200 tangential-flow filtration device PI Supplied Instrument Name: Vivaflow 200 tangential-flow filtration device PI Supplied Instrument 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 Instrument Name: water filtration device Instrument Short Name: Instrument Description: A manufactured device which is used to remove contaminants from water impeding the flow of particles or solutes.