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Title Sum-
Institution Dataset ID
     data   graph     files  public Virioplankton abundance from multiple cruises at the Bermuda AtlanticTime Series
Station (BATS), Western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory project)
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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
attribute NC_GLOBAL acquisition_description String Methodology:\u00a0from\u00a0Parsons et al (2011):

Study site and sample collection:
Samples were collected aboard the\u00a0RV Weatherbird II\u00a0or the\u00a0RV
Atlantic Explorer\u00a0at the BATS site (31\u00b0 40\u2032 N, 64\u00b010\u2032
W). All cruises were conducted as part of the larger BATS program and sampled
at least monthly with biweekly sampling between February and April. This
sampling strategy has been successful in revealing the major temporal
microbial and biogeochemical patterns at this site (Carlson and Ducklow,
1996;\u00a0Steinberg et al., 2001;\u00a0Morris et al., 2005;\u00a0Carlson et
al., 2009;\u00a0Treusch et al., 2009;\u00a0Lomas et al., 2010). A broader
assessment of the BATS biogeochemical data is presented in\u00a0Deep Sea
Research II\u00a0in 1996 (volume 43, issues 2\u20133) and 2001 (volume 48,
issues 8\u20139).

Samples for virioplankton (0, 20, 40, 60, 80, 100, 140, 160, 200, 250 and
300\u2009m) and bacterioplankton (0, 10, 20, 40, 60, 80, 100, 120, 140, 160,
200, 250 and 300\u2009m) were collected at the BATS site from January 2000 to
December 2009 via conductivity, temperature, depth profiling rosette equipped
with 12\u2009l Niskin bottles. The 120\u2009m virioplankton sample was added
after October 2007. Throughout the entire time-series, all virioplankton
samples were fixed with 0.02\u2009um filtered formalin (1% final
concentration), placed in 5\u2009ml cryovials and flash frozen in liquid
nitrogen (Wen et al., 2004) until processing (within 12 weeks of collection).
Samples for bacterioplankton abundance were fixed with 0.2\u2009um filtered
gluteraldehyde (1% final concentration) and stored at either 4\u2009\u00b0C
for 72\u2009h or flash frozen and subsequently stored at \u221280\u2009\u00b0C
for up to 6 months until processing as described in\u00a0Steinberg et al
(2001). Storage tests demonstrated no appreciable loss of virioplankton or
bacterioplankton abundance when stored in liquid nitrogen for periods up to 6
months (unpublished data). Picophytoplankton samples were collected at the
same depths through 250\u2009m from October 2001 to December 2009 (Casey et
al., 2007). Samples for fluorescence\u00a0in situ\u00a0hybridization (FISH) of
specific heterotrophic bacterioplankton lineages were collected from the upper
300\u2009m from January 2003 to December 2005 (Carlson et al., 2009).

Biogeochemical and physical data collected at the BATS site are available
at\u00a0[http://bats.bios.edu](\\"http://bats.bios.edu\\"). The MLD was
determined as the depth where potential density (sigma-t) of the water was
equal to sea surface sigma-t\u00a0plus the equivalent in sigma-t\u00a0to a
0.2\u2009\u00b0C decrease in temperature (Sprintall and Tomczak, 1992).
Contour plots were created in Ocean Data View (R
Schlitzer,\u00a0[http://odv.awi.de/](\\"http://odv.awi.de/\\")) with VG
Gridding and linear mapping adjusted to the median of each data set.
Statistics (Pearson's correlation and two-tailed Student's\u00a0t-test for
unequal variances), ratios and percent contributions were determined using
Microsoft Excel.

Virioplankton abundance:
Virioplankton abundance was enumerated according to the methods
of\u00a0Noble and Fuhrman (1998). Briefly, water samples were filtered on to
0.02\u2009um Anodisc aluminum oxide filters (Whatman, Kent, UK), stained with
SYBR Green I (Molecular Probes Inc., Eugene, OR, USA), and enumerated via
epifluorescence microscopy using an Olympus AX70 microscope (Olympus, Tokyo,
Japan) equipped with a Toshiba CCD video camera (Irvine, CA, USA) and Pro-
series Capture Kit version 4.5 (I-CUBE, Crofton, MD, USA). Ten images from
each sample were processed with scripts written in Image Pro Plus (Media
Cybernetics, Bethesda, MD, USA) for particles sized 0.01\u20130.27\u2009um2,
using the clean borders function (cells touching the edge of the image or grid
were omitted). We consider these estimates of viral abundance conservative
because it is possible that some viral particles less than one pixel were
omitted from the final count. We performed pairwise comparisons of automated
versus manual enumeration of virioplankton abundance to determine any
discrepancies between the two approaches. Samples collected along a gradient
from offshore (BATS;\u00a0n=92) to onshore waters of Bermuda (n=32) were
highly correlated with automated counts being slightly greater than manual
counts (slope=1.07,\u00a0r=0.99,\u00a0n=134). The lower estimates of viral
abundance from manual counts may have resulted from image fading during
enumeration and/or operator fatigue. We argue that for this study, the
automated image analysis was the most reliable approach for viral particle
enumeration. The coefficient of variation for the automated counts averaged
11% (n=1517).
attribute NC_GLOBAL awards_0_award_nid String 514363
attribute NC_GLOBAL awards_0_award_number String OCE-0802004
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=0802004 (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 cdm_data_type String Other
attribute NC_GLOBAL comment String Virioplankton abundance at BATS site, 2000-2011
C. Carlson (UC-SB)
version: 2020-05-04
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 dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2014-12-23T18:13:37Z
attribute NC_GLOBAL date_modified String 2020-05-11T19:09:23Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.543808.1
attribute NC_GLOBAL Easternmost_Easting double -63.988
attribute NC_GLOBAL geospatial_lat_max double 31.81
attribute NC_GLOBAL geospatial_lat_min double 31.352
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -63.988
attribute NC_GLOBAL geospatial_lon_min double -64.312
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 502.375
attribute NC_GLOBAL geospatial_vertical_min double 0.9
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/543808 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Niskin bottle
attribute NC_GLOBAL instruments_0_dataset_instrument_description String 12 liter Niskin bottles
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 543815
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Niskin bottle
attribute NC_GLOBAL instruments_0_instrument_nid String 413
attribute NC_GLOBAL instruments_0_supplied_name String Niskin bottle
attribute NC_GLOBAL instruments_1_acronym String CTD
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 543816
attribute NC_GLOBAL instruments_1_description String The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/130/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String CTD profiler
attribute NC_GLOBAL instruments_1_instrument_nid String 417
attribute NC_GLOBAL instruments_1_supplied_name String CTD
attribute NC_GLOBAL instruments_2_acronym String Fluorescence Microscope
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Olympus AX70 microscope (Olympus, Tokyo, Japan) equipped with a Toshiba CCD video camera (Irvine, CA, USA)
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 543818
attribute NC_GLOBAL instruments_2_description String A Fluorescence (or Epifluorescence) Microscope Image Analysis System uses semi-automated color image analysis to determine cell abundance, dimensions and biovolumes from an Epifluorescence Microscope. An Epifluorescence Microscope (conventional and inverted) includes a camera system that generates enlarged images of prepared samples. The microscope uses excitation ultraviolet light and the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light.
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB06/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Fluorescence Microscope Image Analysis System
attribute NC_GLOBAL instruments_2_instrument_nid String 508
attribute NC_GLOBAL instruments_2_supplied_name String Epifluorescence Microscope
attribute NC_GLOBAL instruments_3_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_3_dataset_instrument_description String Becton Dickenson (Franklin Lakes, NJ, USA; formerly Cytopeia) high speed jet-in-air InFlux flow cytometer, using a 488 nm blue excitation laser, appropriate Chl-a (692±20 nm) and phycoerythrin (580±15 nm) bandpass filters.
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 543819
attribute NC_GLOBAL instruments_3_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_3_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_3_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_3_instrument_nid String 660
attribute NC_GLOBAL instruments_3_supplied_name String Flow Cytometer
attribute NC_GLOBAL keywords String abund, abund_vir, abund_vir_sd, bco, bco-dmo, biological, chemical, cruise, cruise_ID, data, dataset, date, date_in, decyear, depth, depth_mixed, depth_nom, dmo, erddap, latitude, longitude, management, oceanography, office, preliminary, station, vir
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/543808/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/543808 (external link)
attribute NC_GLOBAL Northernmost_Northing double 31.81
attribute NC_GLOBAL param_mapping String {'543808': {'lat_in': 'master - latitude', 'depth': 'master - depth', 'lon_in': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/543808/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of California-Santa Barbara
attribute NC_GLOBAL people_0_affiliation_acronym String UCSB
attribute NC_GLOBAL people_0_person_name String Craig Carlson
attribute NC_GLOBAL people_0_person_nid String 50575
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 Oregon State University
attribute NC_GLOBAL people_1_affiliation_acronym String OSU
attribute NC_GLOBAL people_1_person_name String Dr Stephen Giovannoni
attribute NC_GLOBAL people_1_person_nid String 514364
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 Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Nancy Copley
attribute NC_GLOBAL people_2_person_nid String 50396
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Ocean Microbial Observatory
attribute NC_GLOBAL projects_0_acronym String Ocean Microbial Observatory
attribute NC_GLOBAL projects_0_description String (Adapted from the NSF award abstract)
The premise of this project is that stratified bacterioplankton clades engage in specialized biogeochemical activities that can be identified by integrated oceanographic and microbiological approaches. Specifically, the objective of this project is to assess if the mesopelagic microbial community rely on diagenetically altered organic matter and subcellular fragments that are produced by microbial processes in the euphotic zone and delivered into the upper mesopelagic by sinking or mixing. In past efforts this microbial observatory had greater success cultivating members of the euphotic zone microbial community, and revealed an unanticipated growth requirement for reduced sulfur compounds in alphaproteobacteria of the SAR11 clade. Genomic information showed that intense competition for substrates imposes trade-offs on bacterioplankton - there are regions of N dimensional nutrient space where specialists win. We postulate that specific growth requirements may explain some the regular spatial and temporal patterns that have been observed in upper mesopelagic bacterioplankton communities, and the difficulties of culturing some of these organisms.
The specific objectives of this project are: 1) to produce 13C and 15N labeled subcellular (e.g., soluble, cell wall, and membrane) and DOM fractions from photosynthetic plankton cultures and use stable isotope probing to identify specific clades in the surface and upper mesopelagic microbial community that assimilate fractions of varying composition and lability. 2) to use fluorescence in situ hybridization approaches to monitor temporal and spatial variability of specific microbial populations identified from the SIP and HTC experiments. To increase resolution we will use CARD-FISH protocols. 3) to measure the proteomes of bacterioplankton communities to identify highly translated genes in the surface layer and upper mesopelagic, and community responses to seasonal nutrient limitation. 4) and, to cultivate these organisms via high throughput culturing (HTC) by pursuing the hypothesis that they require specific nutrient factors and/or diagenetically altered organic substrates. Complete genome sequences from key organisms will be sought and used as queries to study patterns of natural variation in genes and populations that have been associated with biogeochemically important functions.
attribute NC_GLOBAL projects_0_end_date String 2014-07
attribute NC_GLOBAL projects_0_geolocation String Bermuda Atlantic Time-Series study site
attribute NC_GLOBAL projects_0_name String Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory
attribute NC_GLOBAL projects_0_project_nid String 514365
attribute NC_GLOBAL projects_0_project_website String http://www.bios.edu/research/projects/oceanic-microbial-observatory/ (external link)
attribute NC_GLOBAL projects_0_start_date String 2008-08
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 31.352
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Virioplankton abundances were measured from samples collected from January 2000 to December 2011 at the Bermuda Atlantic Time Series Station (BATS), Western Sargasso Sea, as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/).
attribute NC_GLOBAL title String Virioplankton abundance from multiple cruises at the Bermuda AtlanticTime Series Station (BATS), Western Sargasso Sea from 2000-2011 (Ocean Microbial Observatory project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -64.312
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable station   String  
attribute station bcodmo_name String station
attribute station description String BATS cruise number during which sample was collected
attribute station long_name String Station
attribute station units String unitless
variable cruise_ID   int  
attribute cruise_ID _FillValue int 2147483647
attribute cruise_ID actual_range int 101360101, 2026700416
attribute cruise_ID bcodmo_name String cruise_id
attribute cruise_ID description String BATS cruise ID for the sample that matches the BATS sample collected from the same niskin
attribute cruise_ID long_name String Cruise ID
attribute cruise_ID units String unitless
variable date_in   String  
attribute date_in bcodmo_name String date
attribute date_in description String date of collection at the time of CTD entry year month day
attribute date_in long_name String Date In
attribute date_in nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date_in units String unitless
variable decyear   double  
attribute decyear _FillValue double NaN
attribute decyear actual_range double 2000.0761, 2011.93973
attribute decyear bcodmo_name String year_decimal
attribute decyear description String decimal year
attribute decyear long_name String Decyear
attribute decyear units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 31.352, 31.81
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 at the time of CTD entry in degrees N
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 source_name String lat_in
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 -64.312, -63.988
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 at the time of CTD entry in degrees W
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 source_name String lon_in
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 0.9, 502.375
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 the actual depth in meters
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 depth_nom   short  
attribute depth_nom _FillValue short 32767
attribute depth_nom actual_range short 1, 400
attribute depth_nom bcodmo_name String depth_n
attribute depth_nom colorBarMaximum double 8000.0
attribute depth_nom colorBarMinimum double -8000.0
attribute depth_nom colorBarPalette String TopographyDepth
attribute depth_nom description String bottle target depths in meters
attribute depth_nom long_name String Depth
attribute depth_nom standard_name String depth
attribute depth_nom units String meters
variable depth_mixed   short  
attribute depth_mixed _FillValue short 32767
attribute depth_mixed actual_range short 8, 248
attribute depth_mixed bcodmo_name String depth_mixed_layer
attribute depth_mixed colorBarMaximum double 8000.0
attribute depth_mixed colorBarMinimum double -8000.0
attribute depth_mixed colorBarPalette String TopographyDepth
attribute depth_mixed description String mixed layer depth in meters; MLD was determined as the depth where potential density (sigma-t) of the water was equal to sea surface sigma-t plus the equivalent in sigma-t to a 0.2 1C decrease in temperature (Sprintall and Tomczak 1992).
attribute depth_mixed long_name String Depth
attribute depth_mixed standard_name String depth
attribute depth_mixed units String meters
variable abund_vir   float  
attribute abund_vir _FillValue float NaN
attribute abund_vir actual_range float 0.14, 11.703
attribute abund_vir bcodmo_name String cell_concentration
attribute abund_vir description String Virioplankton abundance 10^9 cells per liter
attribute abund_vir long_name String Abund Vir
attribute abund_vir units String 10^9 cells per liter
variable abund_vir_sd   float  
attribute abund_vir_sd _FillValue float NaN
attribute abund_vir_sd actual_range float 0.014, 5.308
attribute abund_vir_sd bcodmo_name String cell_concentration
attribute abund_vir_sd colorBarMaximum double 50.0
attribute abund_vir_sd colorBarMinimum double 0.0
attribute abund_vir_sd description String standard deviation for Virioplankton Abundance in 10^9 cells per liter
attribute abund_vir_sd long_name String Abund Vir Sd
attribute abund_vir_sd units String 10^9 cells per liter

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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