http://lod.bco-dmo.org/id/dataset/949101 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 2025-01-22 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014 2025-01-22 publication 2025-01-22 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-02-14 publication https://doi.org/10.26008/1912/bco-dmo.949101.1 Kyle F. Edwards University of Hawaiʻi at Mānoa principalInvestigator Grieg Steward University of Hawaiʻi at Mānoa principalInvestigator Christopher Schvarcz University of Hawaiʻi at Mānoa principalInvestigator Julie Thomy University of Hawaiʻi at Mānoa 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: Thomy, J., Schvarcz, C., McBeain, K., Edwards, K. F., Steward, G. (2025) NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-01-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.949101.1 [access date] Eukaryotic viruses encode the ribosomal protein eL40 Dataset Description: Methods and Sampling: &lt;p&gt;&lt;em&gt;Note:&lt;/em&gt; The detailed protocols are described in Thomy et al., 2024&lt;/p&gt; &lt;p&gt;For eukaryote isolation, seawater sampling was carried out on March 02, 2011 from the oligotrophic open-ocean site at Station ALOHA, in the North Pacific Subtropical Gyre at a depth of 45 meters. Seawater samples were enriched with Keller (K) medium and unialgal cultures were then isolated by serial dilution to extinction. &lt;em&gt;Florenciella&lt;/em&gt; sp. strain UHM3020 was further identified by small subunit ribosomal RNA gene (18S rRNA gene) sequencing. DNA was extracted from the pellets using the MasterPure Complete DNA and RNA Purification Kit (Epicentre). &lt;em&gt;Florenciella&lt;/em&gt; 18S rRNA was amplified by PCR then cloned and extracted using the Zyppy Plasmid Miniprep Kit (Zymo Research). Near-full-length 18S rRNA gene for &lt;em&gt;Florenciella&lt;/em&gt; was sequenced using Sanger method.&lt;/p&gt; &lt;p&gt;For virus isolation, seawater sampling was carried out on&amp;nbsp;September 15, 2014 from the same site as described previously for the host isolation at a depth of 25 meters. Forty liters of seawater was filtered through 0.8 μm pore size filters to remove larger cells while minimizing losses of large viruses. Viral particles in the filtrate were concentrated by tangential flow filtration (TFF; 30 kDA molecular weight cut-off). The concentrate was amended with nutrients to match K medium and then used to challenge a culture of a healthy &lt;em&gt;Florenciella&lt;/em&gt; culture isolated previously from the same water.&amp;nbsp;Viruses in the filtrate were concentrated by TFF (30 kDa) to 300 mL volume, further concentrated to 0.5 mL by centrifugal ultrafiltration (30 kDa)&amp;nbsp;and then purified in a CsCl buoyant density gradient. DNA was extracted from the virus peak in the gradient using Masterpure Complete DNA and RNA Purification Kit (LGC Biosearch Technologies). DNA was sequenced using Illumina (NextSeq System) and PacBio methods.&lt;/p&gt; &lt;p&gt;The FloV-SA2 complete genome sequence was deposited in GenBank with accession number PP542043 (see related datasets) as well as the ubiquitin-60S ribosomal protein eL40 gene sequence encoded in the &lt;em&gt;Florenciella&lt;/em&gt; sp. host genome PP665604 (see related datasets). The gene annotations were published as Supplementary Table 1 in Thomy et al., 2024.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2129697 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2129697 Funding provided by Simons Foundation (Simons) Award Number: 566853 Award URL: https://www.simonsfoundation.org/grant/simons-early-career-investigator-in-aquatic-microbial-ecology-and-evolution-awards/?tab=awardees Funding provided by NSF Office of Integrative Activities (NSF OIA) Award Number: OIA-1736030 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736030 completed Kyle F. Edwards University of Hawaiʻi at Mānoa 808-956-6198 Department of Oceanography 1000 Pope Road Honolulu HI 96822 kfe@hawaii.edu pointOfContact Grieg Steward University of Hawaiʻi at Mānoa 808-956-6775 Department of Oceanography, CMORE Hale 1950 East-West Rd. Honolulu HI 96822 USA grieg@hawaii.edu pointOfContact Christopher Schvarcz University of Hawaiʻi at Mānoa (808) 956-0577 University of Hawaiʻi at Mānoa, CMORE Hale 1950 East-West Road Honolulu, HI 96822 United States schvarcz@gmail.com pointOfContact Julie Thomy University of Hawaiʻi at Mānoa thomy@hawaii.edu pointOfContact asNeeded Dataset Version: 1 Unknown Taxa_name Source_of_sample Genbank_accession Bioproject_number Latitude Longitude Date_Isolated Illumina (NextSeq System) PacBio P6 C4 centrifugal ultrafiltration PCR theme None, User defined taxon sample type accession number NCBI BioProject accession latitude longitude date featureType BCO-DMO Standard Parameters Automated DNA Sequencer Automated DNA Sequencer Centrifuge Thermal Cycler instrument BCO-DMO Standard Instruments KM1419 KM1108 service Deployment Activity Hawaiian Islands, HOT Site place Locations 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. Giant viruses in the open ocean: Is large size adaptive where cells are scarce? https://osprey.bco-dmo.org/project/889946 Giant viruses in the open ocean: Is large size adaptive where cells are scarce? <p><strong>NSF Award Abstract:</strong><br /> Viruses can infect all forms of life. Viruses are highly diverse, and one aspect of diversity is size: genomes of viruses vary more than a thousandfold in length, and the size of viral particles varies nearly a millionfold. The discovery of “giant” viruses was astounding because they can be physically larger and code for more genes than many free-living microorganisms. There is growing evidence that giant viruses are widespread and diverse in the ocean, but much about their ecology remains unknown. What critical ecological tradeoffs vary with virus size, allowing small and large viruses to coexist? Do these tradeoffs cause the distribution of virus sizes to vary across habitats? This project aims to answer these questions for viruses that infect phytoplankton, the microscopic plants that are the foundation of ocean productivity. This research can also influence a diverse array of scientific fields because virus size varies greatly in other ecosystems and host-associated microbiomes. The fundamental constraints on size may be broadly similar across systems, but the processes driving virus size have not been thoroughly investigated in any of them. This project supports the training of a postdoctoral researcher, two graduate students, and undergraduate students in integrative science that includes field, laboratory, and modeling components. National Science Foundation-supported Research Experience for Undergraduates and Tribal Colleges and Universities programs at UH Manoa that serve Pacific Islanders and other underrepresented groups are used for recruiting students. In addition, science outreach at public events in Hawai’i includes an interactive game to communicate ideas about giant viruses and their role in the ocean.</p> <p>Large viruses may have four advantages over smaller viruses: i) ability to infect a greater diversity of host genotypes, ii) better control of host metabolism, iii) large enough size to enter host cells by ingestion, and iv) greater persistence in the extracellular environment. These advantages may compensate for the advantages held by smaller viruses: higher contact rates with their hosts and greater offspring number per infection. The advantages of large size may be more consequential in oligotrophic habitats, where the microbial eukaryote community is primarily small phagotrophic flagellates (mixotrophs and heterotrophs), at low population densities, with resource-limited growth. The project goals are: (1) To test whether giant viruses indeed dominate in the oligotrophic ocean compared to a productive coastal location, as suggested by initial observations of this research team; (2) To test the above four hypotheses about the advantages of large size by conducting laboratory experiments with diverse viral isolates, and (3) To use an eco-evolutionary model of eukaryotic microbes and their viruses to explain observed size patterns.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> GVs NPSG largerWorkCitation project eng; USA biota oceans Hawaiian Islands, HOT Site -159.107376 -157.886274 21.246098 22.90065 2011-03-27 2014-09-15 North Pacific 0 BCO-DMO catalogue of parameters from NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014 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/949154.rdf Name: Taxa_name Units: unitless Description: <p>Taxa name of genome of FloV-SA2 (phylum Nucleocytoviricota) and Florenciella sp.strain UHM3020</p> http://lod.bco-dmo.org/id/dataset-parameter/949155.rdf Name: Source_of_sample Units: unitless Description: <p>Source of sample used for derived genome</p> http://lod.bco-dmo.org/id/dataset-parameter/949156.rdf Name: Genbank_accession Units: unitless Description: <p>Genbank assession number associated with FloV-SA2 and Florenciella sp.strain UHM3020</p> http://lod.bco-dmo.org/id/dataset-parameter/949157.rdf Name: Bioproject_number Units: unitless Description: <p>Bioproject number associated with FloV-SA2 and Florenciella sp.strain UHM3020</p> http://lod.bco-dmo.org/id/dataset-parameter/949158.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude for sample collection in decimal degrees, postive values are North</p> http://lod.bco-dmo.org/id/dataset-parameter/949159.rdf Name: Longitude Units: decimal degrees Description: <p>Coordinates for sample collection in decimal degrees, postive values are East</p> http://lod.bco-dmo.org/id/dataset-parameter/949160.rdf Name: Date_Isolated Units: unitless Description: <p>Date genome was isolated from Pacific ocean at Station Aloha in Marine Viral Ecology Laboratories</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 297 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8f110989-a802-456e-9e92-96688c32e58b/content download https://doi.org/10.26008/1912/bco-dmo.949101.1 download onLine dataset &lt;p&gt;&lt;em&gt;Note:&lt;/em&gt; The detailed protocols are described in Thomy et al., 2024&lt;/p&gt; &lt;p&gt;For eukaryote isolation, seawater sampling was carried out on March 02, 2011 from the oligotrophic open-ocean site at Station ALOHA, in the North Pacific Subtropical Gyre at a depth of 45 meters. Seawater samples were enriched with Keller (K) medium and unialgal cultures were then isolated by serial dilution to extinction. &lt;em&gt;Florenciella&lt;/em&gt; sp. strain UHM3020 was further identified by small subunit ribosomal RNA gene (18S rRNA gene) sequencing. DNA was extracted from the pellets using the MasterPure Complete DNA and RNA Purification Kit (Epicentre). &lt;em&gt;Florenciella&lt;/em&gt; 18S rRNA was amplified by PCR then cloned and extracted using the Zyppy Plasmid Miniprep Kit (Zymo Research). Near-full-length 18S rRNA gene for &lt;em&gt;Florenciella&lt;/em&gt; was sequenced using Sanger method.&lt;/p&gt; &lt;p&gt;For virus isolation, seawater sampling was carried out on&amp;nbsp;September 15, 2014 from the same site as described previously for the host isolation at a depth of 25 meters. Forty liters of seawater was filtered through 0.8 μm pore size filters to remove larger cells while minimizing losses of large viruses. Viral particles in the filtrate were concentrated by tangential flow filtration (TFF; 30 kDA molecular weight cut-off). The concentrate was amended with nutrients to match K medium and then used to challenge a culture of a healthy &lt;em&gt;Florenciella&lt;/em&gt; culture isolated previously from the same water.&amp;nbsp;Viruses in the filtrate were concentrated by TFF (30 kDa) to 300 mL volume, further concentrated to 0.5 mL by centrifugal ultrafiltration (30 kDa)&amp;nbsp;and then purified in a CsCl buoyant density gradient. DNA was extracted from the virus peak in the gradient using Masterpure Complete DNA and RNA Purification Kit (LGC Biosearch Technologies). DNA was sequenced using Illumina (NextSeq System) and PacBio methods.&lt;/p&gt; &lt;p&gt;The FloV-SA2 complete genome sequence was deposited in GenBank with accession number PP542043 (see related datasets) as well as the ubiquitin-60S ribosomal protein eL40 gene sequence encoded in the &lt;em&gt;Florenciella&lt;/em&gt; sp. host genome PP665604 (see related datasets). The gene annotations were published as Supplementary Table 1 in Thomy et al., 2024.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;The FloV-SA2 genome was assembled from PacBio sequencing reads using Canu v1.0 and polished using a combination of pbalign v0.2.0.141024 and Quiver v2.0.0.&amp;nbsp;&amp;nbsp;&lt;/p&gt; &lt;p&gt;Initial gene prediction was conducted with Prokka v1.14.5. Functional annotations&amp;nbsp; were performed using a BLASTp search using Diamond (v2.1.4) against:&amp;nbsp;&lt;/p&gt; &lt;p&gt;*NCBI Refseq databases (O’Leary et al., 2015)&lt;/p&gt; &lt;p&gt;*InterProScan (Jones et al., 2014)&lt;/p&gt; Specified by the Principal Investigator(s) -imported &quot;Data-samples-info-V2-2024-10-15.xlsx&quot; into the BCO-DMO data system -split column containing lat and lon -converted lon to negative to represent decimal degrees -converted date to YYYY-mm-dd -renamed fields to conform with BCO-DMO naming conventions -exported file as &quot;949101_v1_eukaryotic_viruses_flov-sa2.csv&quot; 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 Illumina (NextSeq System) Illumina (NextSeq System) PI Supplied Instrument Name: Illumina (NextSeq System) PI Supplied Instrument Description:DNA was sequenced using Illumina (NextSeq System) and PacBio methods. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. PacBio P6 C4 PacBio P6 C4 PI Supplied Instrument Name: PacBio P6 C4 PI Supplied Instrument Description:DNA was sequenced using Illumina (NextSeq System) and PacBio methods. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. centrifugal ultrafiltration centrifugal ultrafiltration PI Supplied Instrument Name: centrifugal ultrafiltration PI Supplied Instrument Description:Viruses in the filtrate were concentrated by TFF (30 kDa) to 300 mL volume, further concentrated to 0.5 mL by centrifugal ultrafiltration (30 kDa) and then purified in a CsCl buoyant density gradient.  Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids. PCR PCR PI Supplied Instrument Name: PCR PI Supplied Instrument Description:Florenciella 18S rRNA was amplified by PCR then cloned and extracted using the Zyppy Plasmid Miniprep Kit (Zymo Research). Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html) Cruise: KM1419 KM1419 R/V Kilo Moana Community Standard Description International Council for the Exploration of the Sea R/V Kilo Moana vessel KM1419 Fernando Santiago-Mandujano University of Hawai'i Cruise: KM1108 KM1108 R/V Kilo Moana Community Standard Description International Council for the Exploration of the Sea R/V Kilo Moana vessel KM1108 Susan E. Curless University of Hawai'i R/V Kilo Moana Community Standard Description International Council for the Exploration of the Sea R/V Kilo Moana vessel