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Title Sum-
Institution Dataset ID
   set  data   graph     files  public Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California
coastline during 2014
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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt
attribute NC_GLOBAL acquisition_description String Environmental Sample Collection

1. Transfer 1 ml of whole seawater to a 2 ml cryovial.

2. Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%.

3. Incubate at 4 degrees celsius for 30 min.

4. Flash freeze in liquid N2\u00a0and store at -80 degrees celsius.

Fluorescent DNA staining (for bacterial and viral abundances)

1. Thaw samples.

2. To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below)\u00a0

3. Heat to 80 degrees celsius for 10 min in the dark

4. Cool at RT for 5 min

5. 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).

1. 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.

2. A gating hierarchy is established using both beads and previously determined virus and bacteria populations as\u00a0reference\u00a0(Sybr Gold Fluorescence versus SSC cytogram).

3. 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\u00a0mls)
1 ml of 1M Tris, pH 8.0
1 ml of 0.5 mM EDTA
98\u00a0mls\u00a0MQ water
Store 4 degrees celsius

1X TE + SYBR Gold (for 10\u00a0mls)

1. Filter 10\u00a0mls\u00a01 TE buffer, 0.22 um filter

2. 1:20,0000 dilution of SYBR Gold stock (Molecular Probes) (0.5 ul stock to 10\u00a0mls\u00a0TE buffer)\u00a0
attribute NC_GLOBAL awards_0_award_nid String 558197
attribute NC_GLOBAL awards_0_award_number String OCE-1333929
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1333929 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL awards_1_award_nid String 558203
attribute NC_GLOBAL awards_1_award_number String OCE-1334387
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1334387 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String David L. Garrison
attribute NC_GLOBAL awards_1_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Bacteria and Virus Abundance
K. Thamatrakoln and M. Brzezinski, PIs
Version 20 July 2016
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2016-07-20T20:46:58Z
attribute NC_GLOBAL date_modified String 2019-06-06T15:37:18Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.652259.1
attribute NC_GLOBAL Easternmost_Easting double -120.02587
attribute NC_GLOBAL geospatial_lat_max double 42.6495
attribute NC_GLOBAL geospatial_lat_min double 34.23125
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -120.02587
attribute NC_GLOBAL geospatial_lon_min double -126.6157
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 60.0
attribute NC_GLOBAL geospatial_vertical_min double 2.0
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/652259 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Samples analyzed on flow cytometer using BD Software (BD Biosciences).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 652268
attribute NC_GLOBAL instruments_0_description String 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)
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_0_instrument_nid String 660
attribute NC_GLOBAL instruments_0_supplied_name String Influx Model 209S Mariner Flow Cytometer
attribute NC_GLOBAL keywords String bacteria, bco, bco-dmo, biological, chemical, conductivity, cruise, cruise_id, ctd, data, dataset, date, date_GMT, depth, dmo, erddap, iso, latitude, longitude, management, oceanography, office, preliminary, sonde, station, temperature, time, time_GMT, virus, yearday, yearday_GMT
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/652259/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/652259 (external link)
attribute NC_GLOBAL Northernmost_Northing double 42.6495
attribute NC_GLOBAL param_mapping String {'652259': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'flag - time'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/652259/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Rutgers University
attribute NC_GLOBAL people_0_affiliation_acronym String Rutgers IMCS
attribute NC_GLOBAL people_0_person_name String Kimberlee Thamatrakoln
attribute NC_GLOBAL people_0_person_nid String 558200
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String University of California-Santa Barbara
attribute NC_GLOBAL people_1_affiliation_acronym String UCSB-LifeSci
attribute NC_GLOBAL people_1_person_name String Mark A. Brzezinski
attribute NC_GLOBAL people_1_person_nid String 50663
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Rutgers University
attribute NC_GLOBAL people_2_affiliation_acronym String Rutgers IMCS
attribute NC_GLOBAL people_2_person_name String Kimberlee Thamatrakoln
attribute NC_GLOBAL people_2_person_nid String 558200
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Hannah Ake
attribute NC_GLOBAL people_3_person_nid String 650173
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Diatom Silicification
attribute NC_GLOBAL projects_0_acronym String Diatom Silicification
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:
Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression.
It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.
attribute NC_GLOBAL projects_0_end_date String 2016-08
attribute NC_GLOBAL projects_0_geolocation String Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
attribute NC_GLOBAL projects_0_name String Linking physiological and molecular aspects of diatom silicification in field populations
attribute NC_GLOBAL projects_0_project_nid String 558198
attribute NC_GLOBAL projects_0_start_date String 2013-09
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 34.23125
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String cruise_id
attribute NC_GLOBAL summary String Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014
attribute NC_GLOBAL time_coverage_end String 2014-07-24T19:20:00Z
attribute NC_GLOBAL time_coverage_start String 2014-07-04T16:20:00Z
attribute NC_GLOBAL title String Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -126.6157
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable cruise_id   String  
attribute cruise_id bcodmo_name String cruise_id
attribute cruise_id description String cruise where samples were collected
attribute cruise_id long_name String Cruise Id
attribute cruise_id units String unitless
variable CTD   byte  
attribute CTD _FillValue byte 127
attribute CTD actual_range byte 1, 29
attribute CTD bcodmo_name String cast
attribute CTD description String CTD cast
attribute CTD long_name String CTD
attribute CTD units String unitless
variable station   byte  
attribute station _FillValue byte 127
attribute station actual_range byte 1, 29
attribute station bcodmo_name String station
attribute station description String station where samples were collected
attribute station long_name String Station
attribute station units String unitless
variable date_GMT   String  
attribute date_GMT bcodmo_name String date_gmt
attribute date_GMT description String GMT date of cast; mm/dd/yy
attribute date_GMT long_name String Date GMT
attribute date_GMT units String unitless
variable time_GMT   String  
attribute time_GMT bcodmo_name String time_gmt
attribute time_GMT description String GMT time of cast; HH:MM
attribute time_GMT long_name String Time GMT
attribute time_GMT units String unitless
variable yearday_GMT   short  
attribute yearday_GMT _FillValue short 32767
attribute yearday_GMT actual_range short 185, 205
attribute yearday_GMT bcodmo_name String yrday
attribute yearday_GMT description String GMT day of year.
attribute yearday_GMT long_name String Yearday GMT
attribute yearday_GMT units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 34.23125, 42.6495
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String latitude
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -126.6157, -120.02587
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String longitude
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 2.0, 60.0
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String depth of sample collection
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable bacteria   float  
attribute bacteria _FillValue float NaN
attribute bacteria actual_range float 1680000.0, 4260000.0
attribute bacteria bcodmo_name String abundance
attribute bacteria description String bacteria-like particle abundance
attribute bacteria long_name String Bacteria
attribute bacteria nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute bacteria units String bacteria per milliliter
variable virus   float  
attribute virus _FillValue float NaN
attribute virus actual_range float 6880000.0, 2.8E7
attribute virus bcodmo_name String abundance
attribute virus description String virus-like particle abundance (VLP)
attribute virus long_name String Virus
attribute virus nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute virus units String VLP per milliliter
variable time   double  
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.4044908E9, 1.4062296E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_UTC
attribute time description String DateTime (UTC) ISO formatted
attribute time ioos_category String Time
attribute time long_name String ISO Date Time UTC
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/ (external link)
attribute time source_name String ISO_DateTime_UTC
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01T00:00:00Z
attribute time units String seconds since 1970-01-01T00:00:00Z

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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