http://lod.bco-dmo.org/id/dataset/982905
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-08-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Non-cyanobacterial diazotroph nifH-qPCR-based abundances collected from various cruises in the global ocean between 2000-2019
2025-08-21
publication
2025-08-21
revision
BCO-DMO Linked Data URI
2025-08-21
creation
http://lod.bco-dmo.org/id/dataset/982905
Kendra Turk-Kubo
University of California-Santa Cruz
principalInvestigator
Matthew M. Mills
Stanford University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Turk-Kubo, K., Mills, M. M. (2025) Non-cyanobacterial diazotroph nifH-qPCR-based abundances collected from various cruises in the global ocean between 2000-2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-08-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/982905 [access date]
Methods and Sampling: <p>This is a formal meta analysis of all available NDC qPCR datasets published between 2000 and 2019. Seawater DNA and RNA samples were collected using two main field approaches, via Niskin bottles attached to rosettes with CTDs, are using the ship's underway seawater systems). Samples were collected by numerous different research groups. DNA and RNA samples were generally filtered through 0.2 µm filers, using a variety of materials, and in some cases, size fractionated samples were collected (e.g. 3 µm and 0.2 µm filters in series). DNA and RNA samples were typically extracted using on column purification-based kits, and in the case where nifH transcription was quantified cDNA (derived from RNA) was typically generated using Superscript reverse transcriptase kits. &nbsp;Purified DNA/RNA/cDNA were typically stored at -80oC prior to analysis. Quantitative PCR assays (55 total), were developed by multiple different groups, and his database only includes data generated using qPCR using Taqman(R) chemistry.<br />
<br />
This dataset was compiled/formatted for CMAP by Mary R Gradoville and Kendra Turk-Kubo from the Zehr Research Group at the University of California Santa Cruz.&nbsp;</p>
<p><strong>Data sources:&nbsp;</strong> Individual dataset sources are listed in the "source_data" column for each observation (from 59 published studies).&nbsp; Column "source_doi" is the DOI&nbsp;for the reference provided in "source_data."&nbsp; Additional details about the specific data used are provided in the "source_location_of_data" column (e.g., specific tables, figures, whether data provided by the authors,&nbsp;or databases).&nbsp; &nbsp;<br />
<br />
<strong>Cruise description: </strong>This dataset is a compilation of multiple cruises, collectively carried out by numerous research groups, not all funded by NSF. The original citations are provided in the metadata for the dataset.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023498 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023498
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023278 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023278
onGoing
Kendra Turk-Kubo
University of California-Santa Cruz
831.421.9293
Ocean Sciences Department UCSC Marine Microbiology Laboratory/Zehr Lab 1156 High Street
Santa Cruz
CA
95064
USA
kturk@ucsc.edu
pointOfContact
Matthew M. Mills
Stanford University
605-736-0688
Geophysics, Mitchell Bldg 397 Panama Mall, Room 324
Stanford
CA
94305-2215
USA
mmmills@stanford.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
time
lat
lon
depth
source_data
source_data_doi
source_location_of_data
notes
NCD_a24809A06_nifH_gene
NCD_aETSP1_nifH_gene
NCD_Alpha_MH144511_nifH_gene
NCD_BAL398_nifH_gene
NCD_BT5667A01_nifH_gene
NCD_CB914H4_nifH_gene
NCD_CE1_45m_12_a_nifH_gene
NCD_OTU0014_Brady_nifH_gene
NCD_alpha1_nifH_gene
NCD_alpha2_nifH_gene
NCD_EVHVF_nifH_gene
NCD_M6411A02_nifH_gene
NCD_PlanctH08_nifH_gene
NCD_PlanctH09_nifH_gene
NCD_Cluster_III_nifH_gene
NCD_Cluster_III_C_nifH_gene
NCD_Cluster_III_L_nifH_gene
NCD_CB907H22_nifH_gene
NCD_cIII_ETSP_nifH_gene
NCD_Cluster_3_nifH_gene
NCD_M6413A02_nifH_gene
NCD_P4_nifH_gene
NCD_D0CY3_nifH_gene
NCD_ECI27_nifH_gene
NCD_AT2LU_nifH_gene
NCD_Arc_nifH_gene
NCD_P6_nifH_gene
NCD_g24774A11_nifH_gene
NCD_gammaA_nifH_gene
NCD_AO15_nifH_gene
NCD_BAL354_nifH_gene
NCD_Azo_nifH_gene
NCD_BAL281_nifH_gene
NCD_BT19215A01_nifH_gene
NCD_CE2_5m_1_g_nifH_gene
NCD_EP19212A1_nifH_gene
NCD_ETSP1_nifH_gene
NCD_ETSP2_nifH_gene
NCD_ETSP3_nifH_gene
NCD_Gamma_1_nifH_gene
NCD_Gamma_2_nifH_gene
NCD_Gamma_3_nifH_gene
NCD_Gamma_4_nifH_gene
NCD_Gamma_P_nifH_gene
NCD_M6433A04_nifH_gene
NCD_EQF91_nifH_gene
NCD_ALHOU_nifH_gene
NCD_Vib_nifH_gene
NCD_OcSpi_nifH_gene
NCD_P8_nifH_gene
NCD_OTU0001_Pseudo_nifH_gene
NCD_OTU0009_Kleb_nifH_gene
NCD_P3_nifH_gene
NCD_P7_nifH_gene
NCD_P1_nifH_gene
NCD_P2_nifH_gene
NCD_Alpha_MH144511_nifH_transcript
NCD_BT5667A01_nifH_transcript
NCD_OTU0014_Brady_nifH_transcript
NCD_EVHVF_nifH_transcript
NCD_Cluster_III_nifH_transcript
NCD_Cluster_III_L_nifH_transcript
NCD_D0CY3_nifH_transcript
NCD_ECI27_nifH_transcript
NCD_AT2LU_nifH_transcript
NCD_Arc_nifH_transcript
NCD_g24774A11_nifH_transcript
NCD_gammaA_nifH_transcript
NCD_AO15_nifH_transcript
NCD_Azo_nifH_transcript
NCD_ETSP2_nifH_transcript
NCD_Gamma_1_nifH_transcript
NCD_Gamma_2_nifH_transcript
NCD_Gamma_3_nifH_transcript
NCD_Gamma_4_nifH_transcript
NCD_EQF91_nifH_transcript
NCD_ALHOU_nifH_transcript
NCD_Vib_nifH_transcript
NCD_OTU0001_Pseudo_nifH_transcript
NCD_OTU0009_Kleb_nifH_transcript
sst
sss
chl
PAR
POC
wind_speed
wind_stress
wind_stress_curl
sla
AOD
NO3
PO4
Fe
O2
Si
PP
PHYC
DIN
FeT
SiO2
sea_water_temp_WOA_clim
density_WOA_clim
salinity_WOA_clim
nitrate_WOA_clim
phosphate_WOA_clim
silicate_WOA_clim
oxygen_WOA_clim
AOU_WOA_clim
o2sat_WOA_clim
conductivity_WOA_clim
theme
None, User defined
Date and time
latitude
longitude
depth
reference_paper
DOI
sample description
comments
genetic material concentration
sea surface temperature
sea surface salinity
chlorophyll a
PAR
particulate organic Carbon (POC)
wind_speed
No BCO-DMO term
Nitrate
reactive phosphorus (PO4)
Iron
dissolved Oxygen
silicate, silicon dioxide SiO2
primary production
count
Dissolved Inorganic Nitrogen
density
Dissolved oxygen (percent)
conductivity
featureType
BCO-DMO Standard Parameters
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Quantifying N2 fixation rates of noncyanobacterial diazotrophs and environmental controls on their activity
https://osprey.bco-dmo.org/project/815423
Collaborative Research: Quantifying N2 fixation rates of noncyanobacterial diazotrophs and environmental controls on their activity
<p><em>NSF Award Abstract:</em><br />
Nitrogen (N) is an important element in the ocean that limits the growth of the microscopic marine plants, phytoplankton. Estimates suggest N inputs and losses may not be balanced in the modern ocean, and thus an underestimation of N inputs may explain this imbalance. The conversion of gaseous N2 to biologically available N (N2 fixation) is the largest source of new N to the ocean. It is possible that the "missing" N can be explained by identifying new sources of N2 fixation. N2 fixation relies on a group of microorganisms, termed "diazotrophs", that utilize N2 for growth, unlike other marine microorganisms. Diazotrophs fall into two groups, cyanobacterial diazotrophs, which are able to derive energy through photosynthesis, and non-cyanobacterial diazotrophs (NCDs), which require a non-light-based energy source. Next to nothing is known about the ecology and biology of NCDs, except that they are ubiquitous in the ocean and contain the nitrogen fixing gene, but no direct measurements of their N2 fixation activity exist. Recent molecular advances for studying organisms at the single cell level now makes the measurement of N2 fixation by NCDs possible. This study is focused on determining whether marine NCDs are actually fixing N2 in the environment and understanding how their N2 fixation is modulated. Determining if NCD activity is an important missing N source in the global oceans has the potential to fill a critical gap in our understanding of the marine N cycle. This project supports early career STEM researchers including a graduate student and a postdoctoral scientist, as well as undergraduate students through several programs including UCSC's California Alliance for Minority Participation (CAMP).</p>
<p>Nitrogen fixation, the microbial process of converting N2 into biologically available ammonia, is an important source of N in the oceans. Historically, research has focused on the most conspicuous diazotrophs, such as Trichodesmium, but the discovery of unicellular cyanobacterial and non-cyanobacterial diazotrophs (NCDs) in the open ocean revealed a broader diversity than previously thought. Much of what is known about NCDs is restricted to presence, abundance estimates and transcriptional activity from gene surveys. NCDs are globally distributed throughout coastal and oligotrophic environments, however, it is not known whether NCDs supply N to support primary productivity. Measurements of marine NCDs are needed to determine if NCDs are actively fixing N2. This study is focused on measuring single cell NCD N2 fixation rates from a variety of taxa living in well-lit, oxygen-rich coastal and oligotrophic surface waters in the North Pacific and Arctic Oceans. The investigators are using a cultivation-independent technique called geneFISH to microscopically visualize and localize NCDs and measuring the incorporation of 15N2 into single cells using nanoscale secondary ion mass spectrometry. Beyond measuring in situ NCD N2 fixation rates, experiments are being conducted to determine environmental controls on single cell NCD N2 fixation (light, temperature, dissolved organic matter, dissolved inorganic N, and iron). Obtaining single cell NCD N2 fixation rates from a range of taxa, under different experimental conditions and in coastal and oligotrophic environments will provide information to link their presence to N2 fixation activity, determine the quantitative significance of NCDs in the marine environment, and set the stage for their inclusion in biogeochemical models.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
NCDN2FIX
largerWorkCitation
project
eng; USA
oceans
-180
180
-90
90
2000-12-01
2019-11-24
Scripps Institution of Oceanography, Tropical and Subtropical Pacific, Chukchi and Beaufort Sea
0
BCO-DMO catalogue of parameters from Non-cyanobacterial diazotroph nifH-qPCR-based abundances collected from various cruises in the global ocean between 2000-2019
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/983034.rdf
Name: time
Units: unitless
Description: <p>date, time (local). Local time zone varies by source location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983035.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/983036.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/983037.rdf
Name: depth
Units: meters (m)
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/983038.rdf
Name: source_data
Units: unitless
Description: <p>The reference for the source data publication</p>
http://lod.bco-dmo.org/id/dataset-parameter/983039.rdf
Name: source_data_doi
Units: unitless
Description: <p>Digital object identifier (DOI) for the source_data (reference)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983040.rdf
Name: source_location_of_data
Units: unitless
Description: <p>Additional information about the source data from original publication</p>
http://lod.bco-dmo.org/id/dataset-parameter/983041.rdf
Name: notes
Units: unitless
Description: <p>comments on the source data from original publication</p>
http://lod.bco-dmo.org/id/dataset-parameter/983042.rdf
Name: NCD_a24809A06_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'a24809A06', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983043.rdf
Name: NCD_aETSP1_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'aETSP1', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983044.rdf
Name: NCD_Alpha_MH144511_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Alpha_MH144511', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983045.rdf
Name: NCD_BAL398_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'BAL398', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983046.rdf
Name: NCD_BT5667A01_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'BT5667A01', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983047.rdf
Name: NCD_CB914H4_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'CB914H4', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983048.rdf
Name: NCD_CE1_45m_12_a_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'CE1_45m_12_a', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983049.rdf
Name: NCD_OTU0014_Brady_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OTU0014_Brady', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983050.rdf
Name: NCD_alpha1_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'alpha1', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983051.rdf
Name: NCD_alpha2_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'alpha2', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983052.rdf
Name: NCD_EVHVF_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'EVHVF', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983053.rdf
Name: NCD_M6411A02_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'M6411A02', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983054.rdf
Name: NCD_PlanctH08_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'PlanctH08', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983055.rdf
Name: NCD_PlanctH09_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'PlanctH09', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983056.rdf
Name: NCD_Cluster_III_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Cluster_III', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983057.rdf
Name: NCD_Cluster_III_C_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Cluster_III_C', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983058.rdf
Name: NCD_Cluster_III_L_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Cluster_III_L', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983059.rdf
Name: NCD_CB907H22_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'CB907H22', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983060.rdf
Name: NCD_cIII_ETSP_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'cIII_ETSP', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983061.rdf
Name: NCD_Cluster_3_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Cluster_3', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983062.rdf
Name: NCD_M6413A02_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'M6413A02', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983063.rdf
Name: NCD_P4_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P4', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983064.rdf
Name: NCD_D0CY3_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'D0CY3', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983065.rdf
Name: NCD_ECI27_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ECI27', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983066.rdf
Name: NCD_AT2LU_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'AT2LU', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983067.rdf
Name: NCD_Arc_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Arc', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983068.rdf
Name: NCD_P6_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P6', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983069.rdf
Name: NCD_g24774A11_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'g24774A11', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983070.rdf
Name: NCD_gammaA_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'gamma A', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983071.rdf
Name: NCD_AO15_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'AO15', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983072.rdf
Name: NCD_BAL354_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'BAL354', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983073.rdf
Name: NCD_Azo_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Azo', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983074.rdf
Name: NCD_BAL281_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'BAL281', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983075.rdf
Name: NCD_BT19215A01_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'BT19215A01', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983076.rdf
Name: NCD_CE2_5m_1_g_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'CE2_5m_1_g', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983077.rdf
Name: NCD_EP19212A1_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'EP19212A1', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983078.rdf
Name: NCD_ETSP1_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ETSP1', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983079.rdf
Name: NCD_ETSP2_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ETSP2', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983080.rdf
Name: NCD_ETSP3_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ETSP3', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983081.rdf
Name: NCD_Gamma_1_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_1', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983082.rdf
Name: NCD_Gamma_2_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_2', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983083.rdf
Name: NCD_Gamma_3_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_3', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983084.rdf
Name: NCD_Gamma_4_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_4', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983085.rdf
Name: NCD_Gamma_P_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_P', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983086.rdf
Name: NCD_M6433A04_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'M6433A04', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983087.rdf
Name: NCD_EQF91_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'EQF91', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983088.rdf
Name: NCD_ALHOU_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ALHOU', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983089.rdf
Name: NCD_Vib_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Vib', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983090.rdf
Name: NCD_OcSpi_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OcSpi', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983091.rdf
Name: NCD_P8_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P8', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983092.rdf
Name: NCD_OTU0001_Pseudo_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OTU0001_Pseudo', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983093.rdf
Name: NCD_OTU0009_Kleb_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OTU0009_Kleb', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983094.rdf
Name: NCD_P3_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P3', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983095.rdf
Name: NCD_P7_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P7', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983096.rdf
Name: NCD_P1_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P1', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983097.rdf
Name: NCD_P2_nifH_gene
Units: gene copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'P2', nifH gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/983098.rdf
Name: NCD_Alpha_MH144511_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Alpha_MH144511', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983099.rdf
Name: NCD_BT5667A01_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'BT5667A01', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983100.rdf
Name: NCD_OTU0014_Brady_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OTU0014_Brady', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983101.rdf
Name: NCD_EVHVF_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'EVHVF', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983102.rdf
Name: NCD_Cluster_III_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Cluster_III', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983103.rdf
Name: NCD_Cluster_III_L_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Cluster_III_L', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983104.rdf
Name: NCD_D0CY3_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'D0CY3', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983105.rdf
Name: NCD_ECI27_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ECI27', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983106.rdf
Name: NCD_AT2LU_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'AT2LU', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983107.rdf
Name: NCD_Arc_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Arc', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983108.rdf
Name: NCD_g24774A11_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'g24774A11', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983109.rdf
Name: NCD_gammaA_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'gamma A', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983110.rdf
Name: NCD_AO15_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'AO15', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983111.rdf
Name: NCD_Azo_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Azo', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983112.rdf
Name: NCD_ETSP2_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ETSP2', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983113.rdf
Name: NCD_Gamma_1_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_1', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983114.rdf
Name: NCD_Gamma_2_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_2', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983115.rdf
Name: NCD_Gamma_3_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_3', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983116.rdf
Name: NCD_Gamma_4_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Gamma_4', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983117.rdf
Name: NCD_EQF91_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'EQF91', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983118.rdf
Name: NCD_ALHOU_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'ALHOU', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983119.rdf
Name: NCD_Vib_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'Vib', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983120.rdf
Name: NCD_OTU0001_Pseudo_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OTU0001_Pseudo', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983121.rdf
Name: NCD_OTU0009_Kleb_nifH_transcript
Units: transcript copies per liter (L-1)
Description: <p>Non-cyanobacterial diazotroph type 'OTU0009_Kleb', nifH transcript</p>
http://lod.bco-dmo.org/id/dataset-parameter/983122.rdf
Name: sst
Units: degrees Celsius (degC)
Description: <p>sea surface temperature; CMAP table: tblSST_AVHRR_OI_NRT. Metadata colocated using CMAP</p>
http://lod.bco-dmo.org/id/dataset-parameter/983123.rdf
Name: sss
Units: Practical Salinity Units (PSU)
Description: <p>sea surface salinity; CMAP table: tblSSS_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983124.rdf
Name: chl
Units: milligrams per cubic meter (mg/m^3)
Description: <p>chlorophyl a; CMAP table: tblCHL_REP</p>
http://lod.bco-dmo.org/id/dataset-parameter/983125.rdf
Name: PAR
Units: Einstein per meter squared per day (E m-2 day-1)
Description: <p>photosynthetically active radiation; CMAP table: tblModis_PAR</p>
http://lod.bco-dmo.org/id/dataset-parameter/983126.rdf
Name: POC
Units: milligrams per cubic meter (mg/m^3)
Description: <p>particulate organic carbon; CMAP table: tblModis_POC</p>
http://lod.bco-dmo.org/id/dataset-parameter/983127.rdf
Name: wind_speed
Units: meters per second (m/s)
Description: <p>wind speed; CMAP table: tblWind_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983128.rdf
Name: wind_stress
Units: pascals (Pa)
Description: <p>wind stress; CMAP table: tblWind_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983129.rdf
Name: wind_stress_curl
Units: pascals (Pa)
Description: <p>wind stress curl; CMAP table: tblWind_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983130.rdf
Name: sla
Units: meters (m)
Description: <p>sea level anomaly; CMAP table: tblAltimetry_REP</p>
http://lod.bco-dmo.org/id/dataset-parameter/983131.rdf
Name: AOD
Units: unitless
Description: <p>Aerosol Optical Depth; CMAP table: tblModis_AOD_REP</p>
http://lod.bco-dmo.org/id/dataset-parameter/983132.rdf
Name: NO3
Units: millimoles per cubic meter (mmol/m^3)
Description: <p>nitrate; CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983133.rdf
Name: PO4
Units: millimoles per cubic meter (mmol/m^3)
Description: <p>phosphate; CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983134.rdf
Name: Fe
Units: millimoles per cubic meter (mmol/m^3)
Description: <p>iron; CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983135.rdf
Name: O2
Units: millimoles per cubic meter (mmol/m^3)
Description: <p>oxygen; CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983136.rdf
Name: Si
Units: micromoles per liter (umol/L)
Description: <p>silicate (SiO2); CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983137.rdf
Name: PP
Units: grams per cubic meter per day (g/m^3/day)
Description: <p>primary productivity; CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983138.rdf
Name: PHYC
Units: millimoles per cubic meter (mmol/m^3)
Description: <p>phytoplankton concentration; CMAP table: tblPisces_NRT</p>
http://lod.bco-dmo.org/id/dataset-parameter/983139.rdf
Name: DIN
Units: millimoles (mmol DIN)
Description: <p>dissolved inorganic nitrogen (DIN); CMAP table: tblDarwin_Nutrient</p>
http://lod.bco-dmo.org/id/dataset-parameter/983140.rdf
Name: FeT
Units: millimoles (mmol Fe)
Description: <p>total iron (Fe); CMAP table: tblDarwin_Nutrient</p>
http://lod.bco-dmo.org/id/dataset-parameter/983141.rdf
Name: SiO2
Units: millimoles (mmol Si)
Description: <p>silicate (SiO2); CMAP table: tblDarwin_Nutrient</p>
http://lod.bco-dmo.org/id/dataset-parameter/983142.rdf
Name: sea_water_temp_WOA_clim
Units: degrees Celsius (degC)
Description: <p>sea surface temperature; CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983143.rdf
Name: density_WOA_clim
Units: kilograms per cubic meter (kg/m^3)
Description: <p>sea surface density; CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983144.rdf
Name: salinity_WOA_clim
Units: Practical Salinity Units (PSU)
Description: <p>sea surface salinity; CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983145.rdf
Name: nitrate_WOA_clim
Units: micromoles per liter (mcmol/L)
Description: <p>nitrate (NO3); CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983146.rdf
Name: phosphate_WOA_clim
Units: micromoles per liter (mcmol/L)
Description: <p>phosphate (PO4); CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983147.rdf
Name: silicate_WOA_clim
Units: micromoles per liter (mcmol/L)
Description: <p>silicate (SiO2); CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983148.rdf
Name: oxygen_WOA_clim
Units: milliliters per liter (mL/L)
Description: <p>oxygen; CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983149.rdf
Name: AOU_WOA_clim
Units: milliliters per liter (mL/L)
Description: <p>apparent oxygen utilization; CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983150.rdf
Name: o2sat_WOA_clim
Units: percent (%)
Description: <p>oxygen saturation; CMAP table: tblWOA_Climatology</p>
http://lod.bco-dmo.org/id/dataset-parameter/983151.rdf
Name: conductivity_WOA_clim
Units: Siemens per meter (S m-1)
Description: <p>conductivity; CMAP table: tblWOA_Climatology</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/982905/data/download
download
onLine
dataset
<p>This is a formal meta analysis of all available NDC qPCR datasets published between 2000 and 2019. Seawater DNA and RNA samples were collected using two main field approaches, via Niskin bottles attached to rosettes with CTDs, are using the ship's underway seawater systems). Samples were collected by numerous different research groups. DNA and RNA samples were generally filtered through 0.2 µm filers, using a variety of materials, and in some cases, size fractionated samples were collected (e.g. 3 µm and 0.2 µm filters in series). DNA and RNA samples were typically extracted using on column purification-based kits, and in the case where nifH transcription was quantified cDNA (derived from RNA) was typically generated using Superscript reverse transcriptase kits. &nbsp;Purified DNA/RNA/cDNA were typically stored at -80oC prior to analysis. Quantitative PCR assays (55 total), were developed by multiple different groups, and his database only includes data generated using qPCR using Taqman(R) chemistry.<br />
<br />
This dataset was compiled/formatted for CMAP by Mary R Gradoville and Kendra Turk-Kubo from the Zehr Research Group at the University of California Santa Cruz.&nbsp;</p>
<p><strong>Data sources:&nbsp;</strong> Individual dataset sources are listed in the "source_data" column for each observation (from 59 published studies).&nbsp; Column "source_doi" is the DOI&nbsp;for the reference provided in "source_data."&nbsp; Additional details about the specific data used are provided in the "source_location_of_data" column (e.g., specific tables, figures, whether data provided by the authors,&nbsp;or databases).&nbsp; &nbsp;<br />
<br />
<strong>Cruise description: </strong>This dataset is a compilation of multiple cruises, collectively carried out by numerous research groups, not all funded by NSF. The original citations are provided in the metadata for the dataset.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>All data would be retrieved off the qPCR instrument as a simple matrix of sample number and relative fluorescence units, including standards (with known quantities of the target gene). Additional software products are not needed.&nbsp;</p>
<p>For this dataset, data was extrapolated, when possible, using Web Plot digitizer (https://automeris.io/WebPlotDigitizer/).&nbsp;</p>
Specified by the Principal Investigator(s)
* Sheet "data" of submitted file "NCDReview_qPCR_database_06092025.xlsx" was exported from excel to capture the formatted values as displayed in excel. The exported csv file was imported into the BCO-DMO data system for this dataset. Table will appear as Data File: 982905_v1_ncd-qpcr-database.csv (along with other download format options).
Additional metadata included in excel sheet "variable metadata" was attached to this dataset as supplemental file 982905_v1_additional_variable_metadata.csv
Additional metadata include in excel sheet "dataset metadata" were added to fields on this BCO-DMO dataset page.
Added DOIs for each source_data reference publication.
* A unique list of each unique reference included in the column "source_data" was made and each provided reference text was matched to a DOI using Crossref's SimpleQuery Tool. And additional column was added to the dataset table "source_doi." The reference text was cleaned for any special characters that didn't display properly in UTF-8 (e.g. "Bostr√ɬ∂m et al. (2007)" -> "Boström et al. (2007)")
The following character replacements were made:
√¢¬Ä¬ê → -
√¢¬Ä¬ì → –
√Ǭ† → make a space (instead of deleting this char)
√ɬ° → á
√ɬ± → ñ
√ɬ© → é
√ɬ≠ → í
√ɬ∂ → ö
√ɬº → ü
√ɬ≥ → ñ
√ɬü → ß
Additional databases included in "source_location_of_data" doi:10.1594/PANGAEA.818214,doi:10.1594/PANGAEA.833791 were added to the section "Related Datasets" on this page.
Missing Data Identifiers:
* In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact