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Title Sum-
Institution Dataset ID
   set  data   graph     files  public Experimental results and survey of biogeochemical and microbial data collected on the R/V
Atlantic Explorer (AE1516) at the Bermuda Atlantic Time-series study site during
2015 (Bacterial DOC cycling 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
attribute NC_GLOBAL acquisition_description String Methodology References:

Tangential flow filtration methods are described in Giovannoni, et al (1990).
Methods for DOM oxidation measurements are described in Sun, et al (2011).
Methods for rRNA gene diversity analysis are described in Vergin, et al
Methods for DOM analysis are described in Carini, et al (2014).
attribute NC_GLOBAL awards_0_award_nid String 615542
attribute NC_GLOBAL awards_0_award_number String OCE-1436865
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1436865 (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 DOM sample log
S. Giovannoni (OSU)
version: 2015-10-23
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 2015-10-22T13:02:07Z
attribute NC_GLOBAL date_modified String 2019-09-30T19:51:20Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.616269.1
attribute NC_GLOBAL geospatial_vertical_max double 300.0
attribute NC_GLOBAL geospatial_vertical_min double 0.0
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/616269 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, cruise, cruise_id, data, dataset, date, depth, descrip, dmo, erddap, filter, filter_size, filtrand, filtrand_id, incubation, management, oceanography, office, person, preliminary, preservation, sample, sample_descrip, sample_id, sample_volume, size, stored, temp_stored, temperature, time, time2, toc, TOC_id, volume
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/616269/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/616269 (external link)
attribute NC_GLOBAL param_mapping String {'616269': {'depth': 'master - depth'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/616269/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Oregon State University
attribute NC_GLOBAL people_0_affiliation_acronym String OSU
attribute NC_GLOBAL people_0_person_name String Dr Stephen Giovannoni
attribute NC_GLOBAL people_0_person_nid String 514364
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 Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Bacterial DOC cycling
attribute NC_GLOBAL projects_0_acronym String Bacterial DOC cycling
attribute NC_GLOBAL projects_0_description String SAR11 (Pelagibacterales) are the most abundant group of bacterioplankton in the oceans. Globally, they are estimated to oxidize to carbon dioxide (CO2) between 5 and 22% of all the organic carbon produced by photosynthesis each day. The activities of bacterioplankton such as SAR11 determine the residence times of different forms of organic carbon, and ultimately shape the composition of dissolved organic pools in the oceans, which rival atmospheric CO2 in mass. Accurate and detailed information about the oceanic carbon cycle is used in models that are valued for their potential to predict and understand future changes in ocean ecosystems. This grant supports analyses of genomic data that predict the carbon oxidation functions of SAR11 cells, and supports experiments with cells in culture, where high-resolution mass spectrometry technology is applied to discover new organic carbon oxidation biochemistry. To assess the importance of SAR11 carbon oxidation functions in ocean ecosystems, this project includes four short oceanographic cruises to the Bermuda Atlantic Time-series Study (BATS) site, in the western Sargasso Sea. On these cruises the concentrations and oxidation rates of organic compounds will be measured, and linked to variation in planktonic SAR11 populations. 

It is a paradox that SAR11 cells are the most abundant in the oceans, but also have among the smallest genomes known. The central goal of this proposal is to understand what types of dissolved organic matter (DOM) are oxidized to CO2 by SAR11. Implicit to this approach is the perspective that some abundant chemoheterotrophic bacterioplankton taxa, particularly those with small genomes, have evolved specialist strategies for oxidizing organic matter. Understanding these strategies can lead to a more detailed and accurate understanding of the biological processes that recycle biological production to CO2. Major project aims are: 1) investigate SAR11 genomes and assay cells in culture with high-resolution mass spectrometry approaches and isotopic labeling to identify the range of compounds these cells can oxidize to CO2; 2) at BATS, measure biological oxidation rates of DOM compounds used by SAR11; 3) link spatiotemporal SAR11 genome variation to patterns of DOM oxidation in the ocean surface layer (0-300 m). This projects includes four short cruises to BATS that target the four microbial plankton community types at this site: upper euphotic zone, deep chlorophyll maximum, spring bloom and upper mesopelagic. Products of this activity will include new information about variation in labile DOM oxidation across the surface layer, and specific links to genome features that will improve the accuracy of interpretation of global ocean metagenomic data.
attribute NC_GLOBAL projects_0_end_date String 2017-09
attribute NC_GLOBAL projects_0_geolocation String Western Sargasso Sea, Bermuda Atlantic Time Series Site: Hydrostation S
attribute NC_GLOBAL projects_0_name String Dissolved Organic Carbon Cycling by SAR11 Marine Bacteria
attribute NC_GLOBAL projects_0_project_nid String 615543
attribute NC_GLOBAL projects_0_start_date String 2014-10
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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String cruise_id
attribute NC_GLOBAL summary String This dataset is a log of samples collected on AE1516 at the Bermuda Atlantic Time-series study site (BAT) Hydrostation S. The samples were analyzed for microbial diversity, dissolved organic carbon (DOC), total DOC, single celled genomics, and an osmolyte inculation experiment.
attribute NC_GLOBAL title String Experimental results and survey of biogeochemical and microbial data collected on the R/V Atlantic Explorer (AE1516) at the Bermuda Atlantic Time-series study site during 2015 (Bacterial DOC cycling project)
attribute NC_GLOBAL version String 1
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 identification
attribute cruise_id long_name String Cruise Id
attribute cruise_id units String unitless
variable sample_descrip   String  
attribute sample_descrip bcodmo_name String sample_descrip
attribute sample_descrip description String samples taken for this purpose
attribute sample_descrip long_name String Sample Descrip
attribute sample_descrip units String unitless
variable person   String  
attribute person bcodmo_name String person
attribute person description String person who handles the sample
attribute person long_name String Person
attribute person units String unitless
variable date   String  
attribute date bcodmo_name String date
attribute date description String date in yyyy-mm-dd format.
attribute date long_name String Date
attribute date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date units String unitless
variable time2   String  
attribute time2 bcodmo_name String time
attribute time2 description String time; UTC or local?
attribute time2 long_name String Time
attribute time2 nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/ (external link)
attribute time2 units String hh:mm
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 0.0, 300.0
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 sample collection depth
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 sample_id   String  
attribute sample_id bcodmo_name String sample
attribute sample_id description String sample identification (date and depth); taken with PPL cartridge
attribute sample_id long_name String Sample Id
attribute sample_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_id units String unitless
variable filtrand_id   String  
attribute filtrand_id bcodmo_name String sample
attribute filtrand_id description String filtrand identification (date and depth); from Sterivex filter
attribute filtrand_id long_name String Filtrand Id
attribute filtrand_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute filtrand_id units String unitless
variable TOC_id   String  
attribute TOC_id bcodmo_name String sample
attribute TOC_id description String total organic carbon sample id (date_time_depth); given to Craig Carlson for analysis
attribute TOC_id long_name String TOC Id
attribute TOC_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute TOC_id units String unitless
variable sample_volume   short  
attribute sample_volume _FillValue short 32767
attribute sample_volume actual_range short 1, 4000
attribute sample_volume bcodmo_name String sample_volume
attribute sample_volume description String sample volume filtered
attribute sample_volume long_name String Sample Volume
attribute sample_volume units String milliliters
variable filter_size   String  
attribute filter_size bcodmo_name String filter_size
attribute filter_size description String filter pore size and membrane type
attribute filter_size long_name String Filter Size
attribute filter_size units String unitless
variable preservation   String  
attribute preservation bcodmo_name String unknown
attribute preservation description String preservative/buffer used
attribute preservation long_name String Preservation
attribute preservation units String unitless
variable incubation   byte  
attribute incubation _FillValue byte 127
attribute incubation actual_range byte 24, 48
attribute incubation bcodmo_name String incubation time
attribute incubation description String incubation period
attribute incubation long_name String Incubation
attribute incubation nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AZDRZZ01/ (external link)
attribute incubation units String hours
variable temp_stored   byte  
attribute temp_stored _FillValue byte 127
attribute temp_stored actual_range byte -80, -80
attribute temp_stored bcodmo_name String temperature
attribute temp_stored description String temperature at which samples were stored
attribute temp_stored long_name String Temp Stored
attribute temp_stored nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp_stored units String degrees Celsius

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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