Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014 (NCEI Accession 0277280)
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title: Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014 (NCEI Accession 0277280)
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abstract: This dataset contains biological and survey - biological data collected on R/V Melville during cruise MV1405 in the North Pacific Ocean from 2014-07-04 to 2014-07-24. These data include abundance and depth. The instruments used to collect these data include Flow Cytometer. These data were collected by Dr Kimberlee Thamatrakoln of Rutgers University and Mark Brzezinski of University of California-Santa Barbara as part of the "Linking physiological and molecular aspects of diatom silicification in field populations (Diatom Silicification)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2023-01-23. The following is the text of the dataset description provided by BCO-DMO: Bacteria and virus abundance data from the MV1405 cruise. Dataset Description: Bacteria and virus abundance data from the MV1405 cruise. Samples were collected by CTD.
purpose: This dataset is available to the public for a wide variety of uses including scientific research and analysis.
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title: Thamatrakoln, K., Brzezinski, M. (2016) Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Dataset version 2016-07-21. https://doi.org/10.1575/1912/bco-dmo.652259.1
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date: 2016-07-21
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code: https://doi.org/10.1575/1912/bco-dmo.652259.1
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Anchor: http://lod.bco-dmo.org/id/person/558200 Kimberlee Thamatrakoln
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Anchor: https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/225 Rutgers, The State University of New Jersey
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Anchor: http://lod.bco-dmo.org/id/person/50663 Mark A. Brzezinski
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Anchor: https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1444 University of California - Santa Barbara (UCSB)
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Anchor: http://lod.bco-dmo.org/id/person/558200 Thamatrakoln, Kimberlee
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Anchor: http://lod.bco-dmo.org/id/person/50663 Brzezinski, Mark A.
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LanguageCode: eng; USA
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topicCategory: (MD_TopicCategoryCode) environment
topicCategory: (MD_TopicCategoryCode) oceans
topicCategory: (MD_TopicCategoryCode) biota
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westBoundLongitude: -126.616
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southBoundLatitude: 34.231
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beginPosition: 2014-07-04
endPosition: 2014-07-24
supplementalInformation: Acquisition Description: Environmental Sample Collection Transfer 1 ml of whole seawater to a 2 ml cryovial. Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%. Incubate at 4 degrees celsius for 30 min. Flash freeze in liquid N 2 and store at -80 degrees celsius. Fluorescent DNA staining (for bacterial and viral abundances) Thaw samples. To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below) Heat to 80 degrees celsius for 10 min in the dark Cool at RT for 5 min Analyze via flow cytometry Analysis (for bacterial and viral abundances) Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Software (BD Biosciences). An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using Molecular Probes Flow Cytometry Sub-micron particles size reference kit (Cat#F13839) consisting of 0.02, 0.1, 0.5, 1.0 and 2.0 um fluorescent beads. A gating hierarchy is established using both beads and previously determined virus and bacteria populations as reference (Sybr Gold Fluorescence versus SSC cytogram). Samples are analyzed using a 488 nm laser for excitation and a minimum trigger threshold is established using 542/15 nm (SYBR Gold) emission. TE buffer with SYBR Gold recipe 1X TE (for 100 mls) 1 ml of 1M Tris, pH 8.0 1 ml of 0.5 mM EDTA 98 mls MQ water Store 4 degrees celsius 1X TE + SYBR Gold (for 10 mls) Filter 10 mls 1 TE buffer, 0.22 um filter 1:20,0000 dilution of SYBR Gold stock (Molecular Probes) (0.5 ul stock to 10 mls TE buffer)
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Anchor: https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1730 NOAA National Centers for Environmental Information
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fees: In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
orderingInstructions: Contact NCEI for other distribution options and instructions.
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linkage: ftp://ftp-oceans.ncei.noaa.gov/nodc/archive/arc0211/0277280/
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description: NCEI Accession 0277280 v1.1 was published.
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DateTime: 2023-03-30T20:25:28Z
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acquisitionInformation: (MI_AcquisitionInformation)
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code: Flow Cytometer
type: Flow Cytometer
description: A method to enumerate bacterial and phytoplankton cells in seawater and estimate their spherical diameter Flow cytometers are laboratory based instruments used to measure cells and particles from aqueous samples. The instrument was initially developed for analysis of Human blood cells for medical purposes, but this technology was adopted by the ocean science community by several investigators, principally Penny Chischolm out of the Massachusetts Institute of Technology, in late 20th century. Since then, the technique has been broadly applied, and it is a unique measurement of microbial populations in the ocean because it provides one at a time measures of cells, to extrapolate features such as fluorescence and cell size. Flow cytometers have been adapted for a number of oceanographic applications such as ship board measurement, and more precise measurement of planktonic fractions. Additionally, the flow cytometer has been adapted for in-situ deployment (see the corresponding nodc instrument code).
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code: R/V Melville
description: Hull Classification: AGOR-14. It is a research vessel operated by Scripps Institution of Oceanography. Commissioned on 10 July 1968 and the current status is active. https://scripps.ucsd.edu/ships/melville
instrument: (missing)
