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:T665,

Detailed protocols, including suggestions from the scientific community, are published on the lab website at https://u.osu.edu/viruslab/protocols/ and maintained on protocols.io at https://www.protocols.io/workspaces/sullivan-lab.

Samples were collected from the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) during the OMZ Microbial Biogeochemistry Expedition cruise (R/V NewHorizon,13-28 June 2013). Seawater was collected from 16 depths spanning the mixed layer, oxycline, OMZ core, and below the OMZ. Collections were made using Niskin bottles on a rosette. Samples were preserved with EM-grade glutaraldehyde (2% final concentration), flash-frozen in liquid nitrogen and stored between -72 °C and -80 °C until analysis.

Viruses were deposited onto TEM grids with an air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA) and positively stained by immersion in 2% uranyl acetate (Ted Pella, Redding, CA, USA). Prepared grids were examined using a transmission electron microscope (Phillips CM12, FEI, Hilsboro, OR, USA) with 100 kV accelerating voltage. Micrographs of 100 viruses per sample were collected using a Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA). Viruses were classified as myoviruses, podoviruses, siphoviruses or non-tailed viruses based on their morphology. Viral capsid diameters and tail lengths were measured using ImageJ software (US National Institutes of Health, Bethesda, MD, USA).

1d:Ta9a,NSF Award Abstract: Marine oxygen minimum zones (OMZs) are regions of the world's oceans that have low or no oxygen. Often referred to as "dead zones" because of their lack of larger organisms, OMZs actually support specific microbial communities adapted to survive in these low-oxygen regions. These microbes perform metabolic processes that produce greenhouse gases such as methane, and significantly alter global nitrogen budgets. In turn, viruses can alter every aspect of microbial communities by causing mortality and altering microbial functions; yet we know little regarding how viruses affect OMZ ecosystems, which is limiting our ability to predict future changes to the Earth system as these OMZs expand over time. This proposed research seeks to fill this knowledge gap by examining the types of viruses that are present in OMZs, as well as how they alter microbial communities and their impact on global processes. In the broader perspective, this proposed work will provide extensive datasets for 7 marine OMZ regions that can be interrogated through publically-available analysis tools, thus enabling environmental science for both research and educational purposes including real-world research experience in undergraduate classes to strengthen scientific education. One postdoc, two graduate students, and undergraduate students will be trained and mentored during this project. Furthermore, the work will facilitate international collaboration with leading microbial oceanographers from across the world. This project will use recent advances in quantitative environmental viral analysis to rapidly enhance our knowledge of OMZ viral communities through examination of 100s of samples from 7 globally-distributed marine OMZ regions with varying levels of oxygen depletion. The specific aims of the project are to (i) gain a basic understanding of viral abundances, viral-induced microbial mortality, and viral community structure, as well as the environmental conditions that drive differences in these parameters, and (ii) assess the effects of viruses on nutrient and gas cycling in OMZs. These aims will be accomplished through analyzing viral metagenomes to assess how viral communities differ among the 7 diverse OMZ regions, and how they diverge from communities in oxygenated waters. Further, the viral metagenomes will be coupled with microbial metagenomes to assess virus-host dynamics and the effects of viral-induced mortality on microorganisms performing key metabolic functions. Finally, the abundance and expression of viral-encoded metabolic genes will be used to perform gene-based biogeochemical modeling to determine the extent of viral influences in OMZ biogeochemical cycling.6:["$","$L1b",null,{"dataset":{"_id":"823131","description":"

Morphotypes, capsid widths, and tail lengths of viruses in samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013. Viruses were deposited onto TEM grids, positively stained, and examined using a transmission electron microscope. Micrographs were collected and characterized by morphotype, as well as measured using ImageJ software.

\n","problem":"","acquisition":"$1c","processing":"

Virus capsid diameters and tail lengths were measured using ImageJ software (US National Institutes of Health, Bethesda, MD, USA).

BCO-DMO Processing:
\n- added station latitude and longitude;
\n- added date (from related dataset https://www.bco-dmo.org/dataset/629125).

\n","bcodmoProcessing":"","title":"Morphotypes, capsid widths, and tail lengths of viruses from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013","nickname":"ETNP Viral Morphology","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2020-09-02T04:00:00.000Z","abstract":"Morphotypes, capsid widths, and tail lengths of viruses in samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013. Viruses were deposited onto TEM grids, positively stained, and examined using a transmission electron microscope. Micrographs were collected and characterized by morphotype, as well as measured using ImageJ software.","citation":"Brum, J. (2020) Morphotypes, capsid widths, and tail lengths of viruses from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.823131.1 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.823131.1","versionDate":"2020-09-02","versionId":"1","year":"2020","title":"Morphotypes, capsid widths, and tail lengths of viruses from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013","authors":"Brum, J.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.823131.1","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2013-06-19T04:00:00.000Z","end":"2013-06-22T04:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1371614400","label":"2013-06-19"},"end":{"value":"1371873600","label":"2013-06-22"}},"spatial_extent":{"shape":"point","center":{"latitude":18.92,"longitude":-108.799},"wkt":" POINT (-108.799 18.92)","north":0,"east":0,"south":0,"west":0},"dataset_type":["Cruise Results"],"keywords":["oceans"],"data_files":[{"id":"903075","title":"viral_morphology.csv","url":"https://datadocs.bco-dmo.org/dataset/823131/file/A88rzApHVOLgEw/viral_morphology.csv","showTableUrl":"https://www.bco-dmo.org/dataset/823131/data/view/903075","description":"Primary data file for dataset ID 823131","filename":"viral_morphology.csv","bytesize":76513,"checksum":{"value":"349405c2ccdb1a2e0069edffb1a84966","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":"739617","name":"Jennifer R. Brum"},"performedAtOrganization":{"_id":"528919","name":"University of Arizona"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"51498","name":"Shannon Rauch"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"628427","name":"NH1315","synonyms":["OMZoMBiE"],"dates":{"start":"2013-06-13T00:00:00.000Z","end":"2013-06-28T00:00:00.000Z"},"platform":{"_id":"54011","name":"R/V New Horizon"},"chiefScientists":[{"id":"536436","name":"Frank James Stewart","role":"Chief Scientist"}]}],"funding":[{"_id":"739614","name":"OCE-1658040","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658040"}],"instruments":[{"_id":"823143","name":"Macrofire Monochrome CCD camera","description":"Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA)","type_id":"520","type_name":"Camera","type_desc":"All types of photographic equipment including stills, video, film and digital systems.","type_acronym":"camera"},{"_id":"823142","name":"Air-driven ultracentrifuge (Beckman)","description":"Air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA)","type_id":"629890","type_name":"Centrifuge","type_desc":"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.","type_acronym":""},{"_id":"823138","name":"Phillips CM12 transmission electron microscope","description":"Epifluorescence microscope (Axio Imager. D2, Zeiss, Jena, Germany)","type_id":"709","type_name":"Electron Microscope","type_desc":"Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.","type_acronym":""},{"_id":"823137","name":"Niskin bottles","description":"","type_id":"413","type_name":"Niskin bottle","type_desc":"A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.","type_acronym":"Niskin bottle"}],"parameters":[{"_id":"823283","name":"Station","format":"","frictionlessType":"","description":"

Station where sample was collected

","units":{"_id":"","name":"unitless"},"type":{"_id":"987","name":"station","description":"

Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.

"}},{"_id":"823284","name":"Depth","format":"","frictionlessType":"","description":"

Depth of sample

","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":"823285","name":"Capsid_width","format":"","frictionlessType":"","description":"

Capsid width

","units":{"_id":"","name":"nanometers (nm)"},"type":{"_id":"511577","name":"width","description":"

Width is a one-dimenstional extent equal to the distance from one side of an object to another side that is opposite. See dataset for units.

"}},{"_id":"823286","name":"Tail_length","format":"","frictionlessType":"","description":"

Tail length (where applicable)

","units":{"_id":"","name":"nanometers (nm)"},"type":{"_id":"1097","name":"length","description":"

Length is a one-dimensional extent equal to the distance between two points.

"}},{"_id":"823287","name":"Morphotype","format":"","frictionlessType":"","description":"

Morphotype (siphovirus, myovirus, podovirus, non-tailed)

","units":{"_id":"","name":"unitless"},"type":{"_id":"1741","name":"sample_descrip","description":"

text description or other traits of the sample collected

"}},{"_id":"823288","name":"Latitude","format":"","frictionlessType":"","description":"

Station latitude

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

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

"}},{"_id":"823289","name":"Longitude","format":"","frictionlessType":"","description":"

Station longitude

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

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

"}},{"_id":"823290","name":"Date","format":"","frictionlessType":"","description":"

Date; format: YYYY-MM-DD

","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)

"}}],"related_publications":[{"id":"824699","citation":"Brum, J. (2015). Adsorbing Viruses on TEM Grids v1. Protocols.io. doi:10.17504/protocols.io.dar2d5\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"824705","citation":"Brum, J. (2015). Analysis of Viral Morphological Characteristics v1. Protocols.io. doi:10.17504/protocols.io.dde23d\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"824698","citation":"Brum, J. (2015). Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device v1. Protocols.io. doi:10.17504/protocols.io.c54y8v\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"824697","citation":"Brum, J. (2015). Positive and Negative Staining of Viruses on TEM Grids v1. Protocols.io. doi:10.17504/protocols.io.day2fv\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"824706","citation":"Brum, J. (2015). Using ImageJ to Measure Viral Dimensions in Micrographs v1. Protocols.io. doi:10.17504/protocols.io.ddf23m\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/823131/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/823131/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/823131/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/823131/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"739615","name":"Ecology and biogeochemical impacts of viruses in marine oxygen minimum zones","acronym":"OMZ Viruses","description":"$1d"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.823131.1","url":"https://doi.org/10.26008/1912/bco-dmo.823131.1","date_assigned":"2020-09-16","version_date":"2020-09-02","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":87},"downloads":{"count":295}}},"fileId":"903075"}]