http://lod.bco-dmo.org/id/dataset/647792
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
2016-05-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Rates of water column nitrification determined from bottle incubations with 15N tracers (15NH4Cl); samples collected on METZYME cruise.
2016-05-27
publication
2016-05-27
revision
BCO-DMO Linked Data URI
2016-05-27
creation
http://lod.bco-dmo.org/id/dataset/647792
Alyson E. Santoro
University of California-Santa Barbara
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: Santoro, A. E. (2016) Rates of water column nitrification determined from bottle incubations with 15N tracers (15NH4Cl); samples collected on METZYME cruise. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 27 May 2016) Version Date 2016-05-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/647792 [access date]
Rates of water column nitrification determined from bottle incubations with 15N tracers (15NH4Cl). Dataset Description: <p>Rates of water column nitrification determined from bottle incubations with 15N tracers (15NH4Cl); sample collected on METZYME cruise (KM1128).</p>
<p><strong>Related references:</strong><br />
Santoro, A.E., Casciotti, K.L., and C.A. Francis. 2010. Activity, abundance,and diversity of nitrifying archaea and bacteria in the central California Current.&nbsp;Environmental Microbiology 12: 1989-2006. doi:<a href="http://dx.doi.org/10.1111/j.1462-2920.2010.02205.x" target="_blank">10.1111/j.1462-2920.2010.02205.x</a></p>
<p>Santoro, A.E., Saito, M.A., Goepfert, T.J., Lamborg, C.H., Dupont, C.L., G.R. DiTullio. Thaumarchaeal ecotype distributions across the equatorial Pacific and their potential roles in nitrification and sinking flux attenuation. Submitted to <em>Limnology &amp; Oceanography, April 2016</em>.</p> Methods and Sampling: <p>Nitrification rate incubations were conducted at Stations 1, 3, and 5 at four depths and followed procedures described in Santoro et al. 2010, Environ. Micro. Timecourse samples of d15NNOx were analyzed by isotope ratio mass spectrometer using the ‘denitrifier method.’&nbsp; Complete methods specific to the MetZyme cruise dataset deposited here are described in Santoro et al., submitted to L&amp;O.</p>
<p>Rates for Station 1 were initiated from the ship’s rosette; Stations 3 and 5 used a trace metal clean rosette.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1031271 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1031271
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260006 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260006
completed
Alyson E. Santoro
University of California-Santa Barbara
805-893-5318
2155 Marine Biotech Lab
Santa Barbara
CA
93106
USA
asantoro@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 27 May 2016
Unknown
cruise
cast
station
lon
lat
depth
bottle
nitr_rate
nitr_rate_SE
theme
None, User defined
Cruise identfier
cast
station
longitude
latitude
depth
bottle
No BCO-DMO term
standard error
featureType
BCO-DMO Standard Parameters
KM1128
service
Deployment Activity
tropical North Pacific along 150 degrees West from 18 degrees North to the equator
place
Locations
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.
U.S. GEOTRACES
http://www.geotraces.org/
U.S. GEOTRACES
GEOTRACES is a SCOR sponsored program; and funding for program infrastructure development is provided by the U.S. National Science Foundation.
GEOTRACES gained momentum following a special symposium, S02: Biogeochemical cycling of trace elements and isotopes in the ocean and applications to constrain contemporary marine processes (GEOSECS II), at a 2003 Goldschmidt meeting convened in Japan. The GEOSECS II acronym referred to the Geochemical Ocean Section Studies To determine full water column distributions of selected trace elements and isotopes, including their concentration, chemical speciation, and physical form, along a sufficient number of sections in each ocean basin to establish the principal relationships between these distributions and with more traditional hydrographic parameters;
* To evaluate the sources, sinks, and internal cycling of these species and thereby characterize more completely the physical, chemical and biological processes regulating their distributions, and the sensitivity of these processes to global change; and
* To understand the processes that control the concentrations of geochemical species used for proxies of the past environment, both in the water column and in the substrates that reflect the water column.
GEOTRACES will be global in scope, consisting of ocean sections complemented by regional process studies. Sections and process studies will combine fieldwork, laboratory experiments and modelling. Beyond realizing the scientific objectives identified above, a natural outcome of this work will be to build a community of marine scientists who understand the processes regulating trace element cycles sufficiently well to exploit this knowledge reliably in future interdisciplinary studies.
Expand "Projects" below for information about and data resulting from individual US GEOTRACES research projects.
U.S. GEOTRACES
largerWorkCitation
program
Connecting Trace Elements and Metalloenzymes Across Marine Biogeochemical Gradients (GPc03)
https://osprey.bco-dmo.org/project/2236
Connecting Trace Elements and Metalloenzymes Across Marine Biogeochemical Gradients (GPc03)
<p>MetZyme project researchers will determine the role of enzymatic activity in the cycling of trace metals. Specifically the research will address the following questions: (1) degradation of sinking particulate organic material in the Tropical North Pacific can be influenced by the ability of microbes to synthesize zinc proteases, which in turn is controlled by the abundance or availability of zinc, and (2) methylation of mercury is controlled, in part, by the activity of cobalt-containing enzymes, and therefore the supply of labile cobalt to the corrinoid-containing enzymes or co-factors responsible for methylation. To attain their goal, they will collect dissolved and particulate samples for trace metals and metalloenzymes from three stations along a biogeochemical gradient in the Tropical North Pacific (along 150 degrees West from 18 degrees North to the equator). Sinking particles from metal clean sediment traps will also be obtained. The samples will also be used to carry out shipboard incubation experiments using amendments of metals, metal-chelators, B12, and proteases to examine the sensitivity and metal limitation of heterotrophic, enzymatic degradation of organic matter within the oceanic "Twilight Zone" (100-500 m). This study will result in a novel metaproteomic/metalloenzyme datasets that should provide insights into the biogeochemical cycling of metals, as well as co-limitation of primary productivity and controls on the export of carbon from the photic zone. In addition to the final data being contributed to BCO-DMO, an online metaproteomic data server will be created so the community has access to the raw data files generated by this research.</p>
MetZyme
largerWorkCitation
project
Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea
https://osprey.bco-dmo.org/project/555307
Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea
<p><em>NSF award abstract:</em></p>
<p>Intellectual Merit. How organisms respond to their physical and chemical and environment is a central question in marine ecology. For microbes living in the mesopelagic - the ocean's "twilight zone" - an efficient response is particularly important to capitalize on the intermittent delivery of organic and inorganic compounds sinking from the surface ocean. These organisms must have a suite of metabolic and regulatory strategies used to cope with environmental variability, but these strategies are largely unknown. Understanding when and why metabolic genes are expressed is critical to our understanding of nutrient remineralization in the ocean. Marine group 1 (MG1) archaea are ubiquitous, abundant microbes in the meso- and bathypelagic and promising model organisms for investigating these questions. MG1 archaea are chemolithoautotrophs that oxidize ammonia for energy and fix carbon for biomass, and as such, play a central role in the ocean's coupled carbon and nitrogen cycles. Though MG1 have historically eluded cultivation, recent efforts have been successful at bringing representative MG1 archaea from the open ocean into culture and demonstrating their importance in the production of the greenhouse gas nitrous oxide. This project takes advantage of unique MG1 cultures and the recently sequenced draft genome of one of the organisms - strain CN25 - to investigate the physiological and transcriptional responses of MG1 archaea to variations in their chemical environment, specifically:</p>
<p>1. Comparative transcriptomics of CN25 cells grown under a range of energy availability and nitrosative stress will identify select genes that can be used to diagnose the physiological state of natural populations</p>
<p>2. Improvements in the genomic and transcriptomic knowledge of MG1 archaea will facilitate a thorough reinterpretation of existing metagenomic and metatranscriptomic datasets, as well as provide a better contextual understanding in future studies</p>
<p>The investigators will conduct comparative transcriptomics of CN25 cells harvested in mid-exponential growth and stationary phase versus starved cells. Transcriptomes of cells grown at high nitrate concentrations and low pO2 with those grown in standard conditions will be characterized. A strand-specific, high-density RNAseq approach will be used to examine the expression of putative ORFs, polycistronic operons, and small RNAs, which, in addition to gene expression profiling, has the ancillary benefit of improving genome annotation. Finally, the investigators will sequence the genomes of two additional MG1 strains isolated from the open ocean, as well as single cells from environmental surveys, and leverage the combination with the CN25 genome to reanalyze available metagenomic and metatranscriptomic datasets. The results will define the transcriptional response of a model mesopelagic microbe to a range of chemical environments, and show how the physicochemical environment induces changes in gene expression and gene content that result in greenhouse gas production. This work will rapidly generate new knowledge of how some of the most ubiquitous, yet heretofore elusive, microorganisms respond to geochemical variability and shape our evolving understanding of the marine nitrogen cycle.</p>
<p>Broader Impacts. The scientific and societal impact of the project will be to elucidate the mechanisms of greenhouse gas production in a model marine organism that is of broad interest to biological and chemical oceanographers. Transcriptome sequencing will improve the assembly of the CN25 genome, the first genome of an MG1 archaeon from the open ocean. Both the genome and transcriptomes will be important references for researchers using metagenomics, metatranscriptomics, and metaproteomics in the ocean, as these techniques are reliant on a knowledgebase composed of both DNA sequence and physiology. Thus, the results add value to both existing and future studies. The proposed research will advance education, teaching, and training for the next generation of marine scientists by providing support for two early-career investigators, one postdoctoral researcher, and a secondary school teacher.</p>
AmoA Archaea
largerWorkCitation
project
eng; USA
oceans
tropical North Pacific along 150 degrees West from 18 degrees North to the equator
2016-05-27
From projects that focused on the following 2 locations: 1. Tropical North Pacific along 150 degrees West from 18 degrees North to the equator 2. Epipelagic and mesopelagic, Equatorial Pacific
0
BCO-DMO catalogue of parameters from Rates of water column nitrification determined from bottle incubations with 15N tracers (15NH4Cl); samples collected on METZYME cruise.
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/647798.rdf
Name: cruise
Units: unitless
Description: <p>Cruise identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647799.rdf
Name: cast
Units: unitless
Description: <p>Cast number. TMR = Trace Metal Rosette. CTD = Ship's CTD.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647800.rdf
Name: station
Units: unitless
Description: <p>Station number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647801.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude east.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647802.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude north.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647803.rdf
Name: depth
Units: meters (m)
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647804.rdf
Name: bottle
Units: unitless
Description: <p>Incubation bottle number (1,2 = experimental bottles; 3 = no addition control)</p>
http://lod.bco-dmo.org/id/dataset-parameter/647805.rdf
Name: nitr_rate
Units: nanomoles per liter per day (nmol L-1 d-1)
Description: <p>Nitrification rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/647806.rdf
Name: nitr_rate_SE
Units: nanomoles per liter per day (nmol L-1 d-1)
Description: <p>Standard error of the rate fit.</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
1555
https://datadocs.bco-dmo.org/file/p99nDrXsy28o0x/nitrification.csv
nitrification.csv
Primary data file for dataset ID 647792
download
https://osprey.bco-dmo.org/dataset/647792/data/download
download
onLine
dataset
<p>Nitrification rate incubations were conducted at Stations 1, 3, and 5 at four depths and followed procedures described in Santoro et al. 2010, Environ. Micro. Timecourse samples of d15NNOx were analyzed by isotope ratio mass spectrometer using the ‘denitrifier method.’&nbsp; Complete methods specific to the MetZyme cruise dataset deposited here are described in Santoro et al., submitted to L&amp;O.</p>
<p>Rates for Station 1 were initiated from the ship’s rosette; Stations 3 and 5 used a trace metal clean rosette.</p>
Specified by the Principal Investigator(s)
<p>The MATLAB script ‘metzyme_rates.m’ was used with the raw data files ('initials...' and ‘data...'). Compiled rates were deposited in a tab-delimited text file.</p>
<p>MATLAB scripts: (click to view files or right-click to save)<br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/metzyme_rates.m" target="_blank">metzyme_rates.m</a><br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/nitr_rate_rev.m" target="_blank">nitr_rate_rev.m</a></p>
<p>Raw data:&nbsp;(click to view files or right-click to save)<br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/initials_mzst1.csv" target="_blank">initials_mzst1.csv</a><br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/initials_mzst3.csv" target="_blank">initials_mzst3.csv</a><br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/initials_mzst5.csv" target="_blank">initials_mzst5.csv</a><br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/data_mzst1.csv" target="_blank">data_mzst1.csv</a><br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/data_mzst3.csv" target="_blank">data_mzst3.csv</a><br />
<a href="http://dmoserv3.whoi.edu/data/METZYME/data_mzst5.csv" target="_blank">data_mzst5.csv</a></p>
<p>BCO-DMO Processing:<br />
- Modified paramter names to conform with BCO-DMO naming conventions;<br />
- Added cruise ID.</p>
Specified by the Principal Investigator(s)
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
Cruise: KM1128
KM1128
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1128
Carl Lamborg
Woods Hole Oceanographic Institution
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel