Dataset Overview | National Centers for Environmental Information (NCEI)

Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 (NCEI Accession 0278402)

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This dataset contains biological and survey - biological data collected on R/V Atlantis and R/V Melville during cruises AT15-61 and MV1104 in the South Pacific Ocean from 2010-02-02 to 2011-04-20. These data include abundance and depth. The instruments used to collect these data include CTD Sea-Bird 9, Niskin bottle, and qPCR Thermal Cycler. These data were collected by Karen L. Casciotti of Stanford University as part of the "Expression of Microbial Nitrification in the Stable Isotopic Systematics of Oceanic Nitrite and Nitrate (Microbial Nitrification)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2021-05-07.

The following is the text of the dataset description provided by BCO-DMO:

Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific

Dataset Description:
These data appear in the following:

Figure S7 of Santoro, et al. (2020) Table S5 of Santoro, et al. (2020) Figure S6 in pre-print on ESSOAr ( doi.org/10.1002/essoar.10503499.1 )

Dataset Citation

Cite as: Casciotti, Karen L. (2023). Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 (NCEI Accession 0278402). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0278402. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0278402

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Download Data	HTTPS (download) Navigate directly to the URL for data access and direct download. FTP (download) These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
Distribution Formats	TSV
Ordering Instructions	Contact NCEI for other distribution options and instructions.
Distributor	NOAA National Centers for Environmental Information +1-301-713-3277 NCEI.Info@noaa.gov
Dataset Point of Contact	NOAA National Centers for Environmental Information ncei.info@noaa.gov

Time Period	2010-02-02 to 2011-04-20
Spatial Bounding Box Coordinates	West: -100 East: -80 South: -20.01 North: -9.943
Spatial Coverage Map

General Documentation

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Descriptive Information
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Associated Resources

Biological, chemical, physical, biogeochemical, ecological, environmental and other data collected from around the world during historical and contemporary periods of biological and chemical oceanographic exploration and research managed and submitted by the Biological and Chemical Oceanography Data Management Office (BCO-DMO)
- NCEI Collection
  Navigate directly to the URL for data access and direct download.
Casciotti, K. L., Santoro, A. E. (2020) Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-10-14. https://doi.org/10.26008/1912/bco-dmo.826781.1
- https://doi.org/10.26008/1912/bco-dmo.826781.1 (download)
  originator dataset

gov.noaa.nodc:BCO-DMO

Publication Dates	publication: 2023-05-18
Data Presentation Form	Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status	Complete - production of the data has been completed Historical archive - data has been stored in an offline storage facility
Data Update Frequency	As needed
Supplemental Information	Acquisition Description: Seawater samples were obtained during the R/V Atlantis (AT15-61) and R/V Melville (MV1104) cruises in Jan-Feb 2010 and Mar-Apr 2011. Water samples were collected at discrete depths using a standard 24-bottle Niskin rosette sampler equipped with an SBE9plus conductivity-temperature-depth (CTD) sensor package (SeaBird Electronics, Bellevue, WA). Samples for nucleic acid extraction and qPCR were collected from the rosette in 2-4 L polycarbonate bottles. Cells were harvested by pressure filtration onto 25 mm diameter, 0.2 µm pore-size polyethersulfone membrane filters (Supor-200, Pall Corporation, Port Washington, NY) housed in polypropylene filter holders (Whatman SwinLok, GE Healthcare, Pittsburgh, PA) using a peristaltic pump and silicone tubing. DNA was extracted according to Santoro,et al. (2010). For DNA extraction and analysis methods followed Santoro, et al. (2010). Sample volumes of 1-4 liters were filtered depending on the biomass present at each station and depth, and the filters were flash frozen in liquid nitrogen in 2 mL gasketed bead beating tubes (Fisher Scientific).
Purpose	This dataset is available to the public for a wide variety of uses including scientific research and analysis.
Use Limitations	accessLevel: Public Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.

Dataset Citation	Cite as: Casciotti, Karen L. (2023). Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 (NCEI Accession 0278402). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0278402. Accessed [date].
Cited Authors	Casciotti, Karen L. Stanford University
Principal Investigators	Karen L. Casciotti Stanford University
Contributors	Stanford University
Resource Providers	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Points of Contact	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0961098 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0961098

Theme keywords	NODC DATA TYPES THESAURUS DEPTH - OBSERVATION species abundance NODC OBSERVATION TYPES THESAURUS biological survey - biological WMO_CategoryCode oceanography BCO-DMO Standard Parameters abundance cast date_local day_local depth latitude longitude month_local standard deviation station volume of water filtered year Originator Parameter Names AOA_amoA AOA_amoA_SD AOB_amoA AOB_amoA_SD Cast Day Depth ISO_Date_Local Latitude Longitude Month NIT_16S NIT_16S_SD Station Vol_filtered WCA_amoA WCA_amoA_SD WCB_amoA WCB_amoA_SD Year
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS Stanford University NODC SUBMITTING INSTITUTION NAMES THESAURUS Biological and Chemical Oceanography Data Management Office Global Change Master Directory (GCMD) Data Center Keywords BCO-DMO > Biological and Chemical Oceanography Data Management Office
Platform keywords	NODC PLATFORM NAMES THESAURUS R/V Atlantis R/V Melville BCO-DMO Platform Names R/V Atlantis R/V Melville Global Change Master Directory (GCMD) Platform Keywords Ships ICES/SeaDataNet Ship Codes ATLANTIS (call sign: KAQP, ICES code: 33AT, 1997) MELVILLE (call sign: WECB, ICES code: 318M, 1969)
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS CTD Niskin bottle PCR machine BCO-DMO Standard Instruments CTD Sea-Bird 9 Niskin bottle qPCR Thermal Cycler Global Change Master Directory (GCMD) Instrument Keywords CTD > Conductivity, Temperature, Depth NISKIN BOTTLES Originator Instrument Names 24-bottle Niskin rosette sampler BioRad CFX96 quantitative PCR machine CTD Sea-Bird 9 plus
Place keywords	NODC SEA AREA NAMES THESAURUS South Pacific Ocean Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > SOUTH PACIFIC OCEAN Provider Place Names Eastern Tropical South Pacific
Project keywords	BCO-DMO Standard Projects Expression of Microbial Nitrification in the Stable Isotopic Systematics of Oceanic Nitrite and Nitrate (Microbial Nitrification) Provider Cruise IDs AT15-61 MV1104 Provider Funding Award Information Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0961098
Keywords	NCEI ACCESSION NUMBER 0278402

Use Constraints	Cite as: Casciotti, Karen L. (2023). Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 (NCEI Accession 0278402). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0278402. Accessed [date].
Data License	This dataset is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License. SPDX License: Creative Commons Attribution 4.0 International (CC-BY-4.0)
Access Constraints	Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
Fees	In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.

Lineage information for: dataset
Processing Steps	2023-05-18T05:28:32Z - NCEI Accession 0278402 v1.1 was published.
Output Datasets	NCEI Accession 0278402 v1.1 NCEI Accession 0278402 v1.1 (download) published 2023-05-18T05:28:32Z

Acquisition Information (collection)
Instrument	CTD Niskin bottle PCR machine
Platform	R/V Atlantis R/V Melville

Last Modified: 2024-05-31T15:15:28Z
For questions about the information on this page, please email: ncei.info@noaa.gov

Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 (NCEI Accession 0278402)

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