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   set  data   graph     files  public Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the
subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in
zooplankton 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,.odvTxt
attribute NC_GLOBAL acquisition_description String Samples were collected from Niskin bottles, filtered, and processed for DNA
analyses. For detailed methods see Benavides et al. 2016.
attribute NC_GLOBAL awards_0_award_nid String 542156
attribute NC_GLOBAL awards_0_award_number String OCE-1130495
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1130495 (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 qPCR Data
Moisander and Benavidas, PIs
Version 2 February 2017
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 2017-02-02T20:50:59Z
attribute NC_GLOBAL date_modified String 2019-04-04T18:19:43Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.680935.1
attribute NC_GLOBAL Easternmost_Easting double -13.3
attribute NC_GLOBAL geospatial_lat_max double 27.8
attribute NC_GLOBAL geospatial_lat_min double 24.5
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -13.3
attribute NC_GLOBAL geospatial_lon_min double -76.2
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/680935 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to process PCR samples
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 680992
attribute NC_GLOBAL instruments_0_description String General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute NC_GLOBAL instruments_0_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_0_instrument_nid String 471582
attribute NC_GLOBAL instruments_0_supplied_name String PCR
attribute NC_GLOBAL keywords String a11, bco, bco-dmo, biological, chemical, data, dataset, date, dmo, erddap, fraction, gamma, Gamma_24774A11, group, group_B, het1, iso, latitude, longitude, management, number, oceanography, office, preliminary, project, size, size_fraction, station, time, time2, tricho, ucyn, UCYN_A
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/680935/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/680935 (external link)
attribute NC_GLOBAL Northernmost_Northing double 27.8
attribute NC_GLOBAL param_mapping String {'680935': {'lat': 'master - latitude', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'master - time'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/680935/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Massachusetts Dartmouth
attribute NC_GLOBAL people_0_affiliation_acronym String UMASSD-SMAST
attribute NC_GLOBAL people_0_person_name String Dr Pia Moisander
attribute NC_GLOBAL people_0_person_nid String 564454
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 Université de Toulon
attribute NC_GLOBAL people_1_person_name String Mar Benavides
attribute NC_GLOBAL people_1_person_nid String 680979
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 Hannah Ake
attribute NC_GLOBAL people_2_person_nid String 650173
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 Microbial associations in zooplankton
attribute NC_GLOBAL projects_0_acronym String Microbial associations in zooplankton
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:
Nitrogen (N2) fixation is a key biogeochemical process providing new N for the marine ecosystem. Current estimates of the global rates suggest that the inputs and outputs of N are not in balance, leaving an apparent deficiency in N2 fixation in the oceanic N budget. Based on recovery of N2 fixation gene fragments, however, numerous potential N2-fixing microbes are present in the euphotic layer and below, yet evidence for their contribution to N2-fixation is lacking. The goal of this study is to identify and determine the importance of potentially diazotrophic, heterotrophic prokaryotes occupying a previously unstudied niche in the upper ocean.
This project PIs hypothesize that N2 fixation in zooplankton-associated microbial communities is an important source of new N in the open ocean contributing to the oceanic N budget. In oligotrophic, N-limited open ocean waters, zooplankton are faced with the same low N availability in their diets that limits growth of primary producers and heterotrophic microbes in the open ocean. Zooplankton guts would be a particularly suitable environment for heterotrophic N2-fixers as the nitrogenase enzyme is inhibited by oxygen. In many terrestrial insects, N2 fixation by gut microbes serves as a source of N. The aim of this study is to investigate whether similar associations occur in marine zooplankton that live on N-limited phytoplankton. The PIs will investigate specific associations between copepods from N-limited and non-N limited oceanic waters with microorganisms that are potentially or actively fixing N. They will also investigate the fate of this N to study whether the new N is incorporated into the zooplankton host. The main research objectives are to determine whether:
1. diazotrophic microflora exist in copepods and what is their seasonal and spatial variability,
2. microbial communities associated with copepods are actively fixing N2,
3. diazotroph communities contribute to the N nutrition of their zooplankton hosts.
Monthly samples will be collected in the oligotrophic Sargasso Sea, in association with BATS sampling cruises. In addition, experiments and field studies will be conducted in Bermuda during the summer. For comparison to a site that is not severely N limited, and for methods development, additional studies will be carried out in coastal Gulf of Maine waters. Selected copepod species and their fecal pellets will be analyzed for the presence of nifH genes and their expression using cloning and sequencing and Reverse Transcriptase-PCR. Quantitative PCR will be employed to investigate the seasonal distributions of dominant phylotypes. Anaerobic cultivation will be used for the enrichment of the gut microflora. Zooplankton will be incubated with 15N2 to quantify microbial N2 fixation activity and its fate of N through zooplankton overall 15N content and nanoSIMS determination of 15N localization. Products of this study will include novel microbial isolates or consortia, evidence regarding taxa-specific expression of N2 fixation in these microhabitats, and a first estimate for the importance of this process for the oceanic N budget.
This project addresses fundamental issues regarding the sources of oceanic nitrogen and will test hypotheses regarding previously overlooked diazotrophic niches. As open ocean productivity is frequently N limited, characterization of new sources of N will have global impacts.
attribute NC_GLOBAL projects_0_end_date String 2016-08
attribute NC_GLOBAL projects_0_geolocation String Sargasso Sea, Eastern and Western North Atlantic.
attribute NC_GLOBAL projects_0_name String Microbial associations in zooplankton: significance for the marine nitrogen cycle
attribute NC_GLOBAL projects_0_project_nid String 564455
attribute NC_GLOBAL projects_0_start_date String 2011-09
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 24.5
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String project
attribute NC_GLOBAL summary String Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in zooplankton project)
attribute NC_GLOBAL time_coverage_end String 2011-03-09T15:10:00Z
attribute NC_GLOBAL time_coverage_start String 2011-01-28T08:25:00Z
attribute NC_GLOBAL title String Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in zooplankton project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -76.2
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable project   String  
attribute project bcodmo_name String project
attribute project description String PI issued project name
attribute project long_name String Project
attribute project units String unitless
variable date   String  
attribute date bcodmo_name String date
attribute date description String Date of sampling; YYYY/mm/dd
attribute date long_name String Date
attribute date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date time_precision String 1970-01-01
attribute date units String unitless
variable time2   String  
attribute time2 bcodmo_name String time
attribute time2 description String Time of sampling; HH:MM
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 unitless
variable station   short  
attribute station _FillValue short 32767
attribute station actual_range short 1, 139
attribute station bcodmo_name String station
attribute station description String Station where sampling occurred
attribute station long_name String Station
attribute station units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 24.5, 27.8
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; N is positive
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 -76.2, -13.3
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; E is positive
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 number   short  
attribute number _FillValue short 32767
attribute number actual_range short 5691, 5735
attribute number bcodmo_name String sample
attribute number colorBarMaximum double 100.0
attribute number colorBarMinimum double 0.0
attribute number description String Sample ID number
attribute number long_name String Number
attribute number nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute number units String unitless
variable size_fraction   float  
attribute size_fraction _FillValue float NaN
attribute size_fraction actual_range float 0.2, 10.0
attribute size_fraction bcodmo_name String filter_size
attribute size_fraction colorBarMaximum double 1.0
attribute size_fraction colorBarMinimum double 0.0
attribute size_fraction description String Filter size
attribute size_fraction long_name String Size Fraction
attribute size_fraction units String microns
variable UCYN_A   float  
attribute UCYN_A _FillValue float NaN
attribute UCYN_A actual_range float 0.0, 198531.3
attribute UCYN_A bcodmo_name String genetic_conc
attribute UCYN_A description String UCYN-A gene copy concentration
attribute UCYN_A long_name String UCYN A
attribute UCYN_A units String genes per liter
variable Gamma_24774A11   float  
attribute Gamma_24774A11 _FillValue float NaN
attribute Gamma_24774A11 actual_range float 0.0, 3320.6
attribute Gamma_24774A11 bcodmo_name String genetic_conc
attribute Gamma_24774A11 description String Gamma 24774A11 gene copy concentration
attribute Gamma_24774A11 long_name String Gamma 24774 A11
attribute Gamma_24774A11 units String genes per liter
variable group_B   float  
attribute group_B _FillValue float NaN
attribute group_B actual_range float 0.0, 1934.5
attribute group_B bcodmo_name String genetic_conc
attribute group_B description String Group B gene copy concentration
attribute group_B long_name String Group B
attribute group_B units String genes per liter
variable Tricho   float  
attribute Tricho _FillValue float NaN
attribute Tricho actual_range float 0.0, 875890.7
attribute Tricho bcodmo_name String genetic_conc
attribute Tricho description String Tricho gene copy concentration
attribute Tricho long_name String Tricho
attribute Tricho units String genes per liter
variable Het1   float  
attribute Het1 _FillValue float NaN
attribute Het1 actual_range float 0.0, 342.5
attribute Het1 bcodmo_name String genetic_conc
attribute Het1 description String Het1 gene copy concentration
attribute Het1 long_name String Het1
attribute Het1 units String genes per liter
variable time   double  
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.2962031E9, 1.2996834E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_UTC
attribute time description String Date/Time (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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