http://lod.bco-dmo.org/id/dataset/4051
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
2013-10-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence accession numbers of 16S rRNA and hydrazine oxidoreductase genes (hzo) from the RRS James Cook cruise JC18 in the Montserrat, Caribbean, and from a UNCW 20-ft Center Console Boat in Cape Fear River Estuary, NC from 2007-2009
2013-10-08
publication
2013-10-08
revision
BCO-DMO Linked Data URI
2013-10-08
creation
http://lod.bco-dmo.org/id/dataset/4051
Bongkeun Song
Virginia Institute of Marine Science
principalInvestigator
Professor Gregory O'Mullan
Queens College
principalInvestigator
Craig Tobias
University of Connecticut
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: Song, B., O'Mullan, G., Tobias, C. (2013) Sequence accession numbers of 16S rRNA and hydrazine oxidoreductase genes (hzo) from the RRS James Cook cruise JC18 in the Montserrat, Caribbean, and from a UNCW 20-ft Center Console Boat in Cape Fear River Estuary, NC from 2007-2009. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 08 Oct 2013) Version Date 2013-10-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/4051 [access date]
Sequence accession numbers of 16S rRNA and hydrazine oxidoreductase genes (hzo) from Cape Fear River Estuary. Dataset Description: <p>Links are provided to GenBank for 16S rRNA and hzo genes from samples collected at the Cape Fear River Estuary.</p>
<p>Related publications:<br />
Hirsch, M.D., Long, Z.T, and Song, B. 2011. Anammox Bacterial Diversity in Various Aquatic Ecosystems Based on the Detection of Hydrazine Oxidase Genes (hzoA/hzoB). Environmental Microbiology 61:264-276. DOI:&nbsp;<a href="http://dx.doi.org/10.1007/s00248-010-9743-1" target="_blank">10.1007/s00248-010-9743-1</a></p> Methods and Sampling: <p>Sampling for the Cape Fear River Estuary was conducted using 20-foot center console boats at UNCW. Sediment sampling around the Montserrat Island was done during a cruise of R.R.S. James Cook (JC18).</p>
<p>Sampling locations:<br />
Cape Fear River Estuary located at the southeast of North Carolina (34 N 78 W depth range 1 to 20 m), and <br />
Montserrat Island sites (16 N 62 W depth range 787 to 1133 m).</p>
<p>Sediment samples from the Cape Fear River Estuary were collected using a petite Ponar grab sampler, while the Montserrat sediments were collected using SMBA box and Bowers and Connelly Mega Corer sampling devices. DNA extraction and PCR of 16S rRNA and hzo genes in anammox bacterial communities were conducted as reported in Hirsh et al. (2011).&nbsp;</p>
<p>For detailed methods, see Hirsch et al. (2011) including the supplementary material (DOI: <a href="http://dx.doi.org/10.1007/s00248-010-9743-1" target="_blank">10.1007/s00248-010-9743-1</a>)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0851435 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0851435
completed
Bongkeun Song
Virginia Institute of Marine Science
804-684-7411
P.O Box 1346
Gloucester Point
VA
23692
USA
songb@vims.edu
pointOfContact
Professor Gregory O'Mullan
Queens College
718-997-3452
65-30 Kissena Blvd Science Building, Room D206
Queens
NY
11367-1575
USA
gregory.omullan@qc.cuny.edu
pointOfContact
Craig Tobias
University of Connecticut
860-405-9140
1080 Shennecossett Rd.
Groton
CT
06340
USA
craig.tobias@uconn.edu
pointOfContact
asNeeded
Dataset Version: 08 Oct 2013
Unknown
description
taxon
sample_name
accession_number_link
Bottom Sediment Grab Samplers
Box Corer
Multi Corer
theme
None, User defined
sample type
taxon
sample identification
accession number
featureType
BCO-DMO Standard Parameters
Bottom Sediment Grab Samplers
Box Corer
Multi Corer
instrument
BCO-DMO Standard Instruments
JC18
CFRE_Song_2009
service
Deployment Activity
Montserrat, Caribbean
Cape Fear River Estuary, North Carolina
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.
Emerging Topics in Biogeochemical Cycles
http://www.nsf.gov/pubs/2007/nsf07049/nsf07049.jsp
Emerging Topics in Biogeochemical Cycles
The original call for proposals for Emerging Topics in Biogeochemical Cycles (ETBC) was issued in September 2007 by the US NSF Directorate for Geosciences (NSF 07-049).
The Geosciences Directorate (GEO) is substantially augmenting our past funding sources to explicitly support emerging areas of interdisciplinary research. We seek to foster transformational advances in our quantitative or mechanistic understanding of biogeochemical cycles that integrate physical-chemical-biological processes over the range of temporal and/or spatial scales in Earth’s environments. We encourage submission of proposals that address emerging topics in biogeochemical cycles, the water cycle or their coupling, across the interfaces of atmosphere, land, and oceans. Proposals must cross the disciplinary boundaries of two or more divisions in Geosciences (e.g. ATM, EAR, OCE) or of at least one division in Geosciences and a division in another NSF directorate.
Although funding programmatic disciplines continues to provide a robust and adaptable framework to build our understanding of the geosciences and the earth as a system, there are classes of emerging and challenging problems that require integration of concepts and observations across diverse fields. Our goal is to enhance such integration. Successful proposals need to develop intellectual excitement in the participating disciplinary communities. Also encouraged are proposals that have broader educational, diversity, societal, or infrastructure impacts that capitalize on this interdisciplinary opportunity.
ETBC
largerWorkCitation
program
Implication of ANAMMOX community structure and microbial interactions in estuarine N removal processes
https://osprey.bco-dmo.org/project/2285
Implication of ANAMMOX community structure and microbial interactions in estuarine N removal processes
<p><i>From NSF Award Abstract:</i></p>
<p>This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).</p>
<p>Estuaries, connecting the freshwater and marine environment, are among the most dynamic and the productive ecosystems on Earth. However, they are under threat from anthropogenic N loading, resulting in various symptoms of eutrophication. The intensity and duration of estuarine eutrophication and the rate of estuarine recovery strongly depend on microbial N removal processes (anaerobic ammonium oxidation (ANAMMOX) and denitrification). Denitrification has been intensively studied in various estuaries, while ANAMMOX as a recently discovered N removal pathway is much less studied in estuarine ecosystems. Existing studies indicate that ANAMMOX rates and its contribution to total N2 production (ANAMMOX significance) are system specific and controlled in part by reaction-scale substrate limitations and by environmental parameters. However, community structure (abundance and composition) of ANAMMOX bacteria have not been linked to their activities along environmental gradients. In addition, ANAMMOX community interactions with aerobic ammonia oxidizers and denitrifyers have not been adequately studied in estuarine and coastal environments.</p>
<p>The investigators will examine the importance of ANAMMOX community structure on their activities along estuarine gradients at the CFRE. In addition, microbial interactions among ANAMMOX, denitrifying and aerobic ammonia oxidizing (AAO) communities will be examined to gain a better understanding of sedimentary N cycles in the estuary. They will address the hypothesis that the total abundance of ANAMMOX bacteria will be linearly correlated to their activities, and that members of ANAMMOX communities are influenced differently by environmental parameters present along the estuarine gradients. Depending on the community structure of ANAMMOX bacteria, temporal and spatial variations of the ANAMMOX rates and its significance to N loss will be observed along the estuary. In addition, they will explore functional linkages among ANAMMOX, denitrifying and AAO communities in estuarine sediments that will alter the pathway of N loss. In order to test the proposed hypotheses, the investigators will conduct interdisciplinary and collaborative research by integrating molecular microbial techniques, 15N isotope tracer methods and multivariate statistic analyses. Thus, this project will address key gaps in our understanding of ANAMMOX ecology by understanding how the community structure of ANAMMOX bacteria influences their activities, and lead to a more complete understanding of estuarine N loss.</p>
Estuarine ANAMMOX
largerWorkCitation
project
eng; USA
oceans
Montserrat, Caribbean; Cape Fear River Estuary, North Carolina
2013-10-08
0
BCO-DMO catalogue of parameters from Sequence accession numbers of 16S rRNA and hydrazine oxidoreductase genes (hzo) from the RRS James Cook cruise JC18 in the Montserrat, Caribbean, and from a UNCW 20-ft Center Console Boat in Cape Fear River Estuary, NC from 2007-2009
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/36749.rdf
Name: description
Units: text
Description: <p>Description of the sequence type (16S rRNA or hzo).</p>
http://lod.bco-dmo.org/id/dataset-parameter/36750.rdf
Name: taxon
Units: text
Description: <p>The source organism.</p>
http://lod.bco-dmo.org/id/dataset-parameter/36751.rdf
Name: sample_name
Units: text
Description: <p>The clone identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/36752.rdf
Name: accession_number_link
Units: text
Description: <p>Unique sequence accession number and link out to GenBank.</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
87813
https://datadocs.bco-dmo.org/file/m77kzrnSREqA3/16SrRNA_and_hzo_accessions.csv
16SrRNA_and_hzo_accessions.csv
Primary data file for dataset ID 4051
download
https://osprey.bco-dmo.org/dataset/4051/data/download
download
onLine
dataset
<p>Sampling for the Cape Fear River Estuary was conducted using 20-foot center console boats at UNCW. Sediment sampling around the Montserrat Island was done during a cruise of R.R.S. James Cook (JC18).</p>
<p>Sampling locations:<br />
Cape Fear River Estuary located at the southeast of North Carolina (34 N 78 W depth range 1 to 20 m), and <br />
Montserrat Island sites (16 N 62 W depth range 787 to 1133 m).</p>
<p>Sediment samples from the Cape Fear River Estuary were collected using a petite Ponar grab sampler, while the Montserrat sediments were collected using SMBA box and Bowers and Connelly Mega Corer sampling devices. DNA extraction and PCR of 16S rRNA and hzo genes in anammox bacterial communities were conducted as reported in Hirsh et al. (2011).&nbsp;</p>
<p>For detailed methods, see Hirsch et al. (2011) including the supplementary material (DOI: <a href="http://dx.doi.org/10.1007/s00248-010-9743-1" target="_blank">10.1007/s00248-010-9743-1</a>)</p>
Specified by the Principal Investigator(s)
<p>DNA sequences were examined and edited using SeqMan Program (DNASTAR, Inc., Madison, WI). Both 16S rDNA and hzo gene sequences were aligned using ClustalW (<a href="http://www.ebi.ac.uk/Tools/clustalw2/index.html" target="_blank">http://www.ebi.ac.uk/Tools/clustalw2/index.html</a>). Phylogenetic analyses were conducted using the MEGA program. The sequences of 16S rRNA and hzo genes were deposited and available at the Genbank. The accession numbers are HM851535 to HM852029.</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
Bottom Sediment Grab Samplers
Bottom Sediment Grab Samplers
PI Supplied Instrument Name: Bottom Sediment Grab Samplers PI Supplied Instrument Description:A petite Ponar grab sampler was used to collect samples from the Cape Fear River Estuary. Instrument Name: Bottom Sediment Grab Samplers Instrument Short Name:BSGS Instrument Description: These samplers are designed to collect an accurate representative sample of the sediment bottom. The bite of the sampler should be deep enough so all depths are sampled equally. The closing mechanism is required to completely close and hold the sample as well as prevent wash-out during retrieval. Likewise, during descent the sampler should be designed to minimize disturbance of the topmost sediment by the pressure wave as it is lowered to the bottom. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/50/
Box Corer
Box Corer
PI Supplied Instrument Name: Box Corer PI Supplied Instrument Description:Sediments were collected at Montserrat using SMBA box corers. Instrument Name: Box Corer Instrument Short Name:Box Corer Instrument Description: General description of a box corer:
A box corer is a marine geological tool that recovers undisturbed soft surface sediments. It is designed for minimum disturbance of the sediment surface by bow wave effects. Traditionally, it consists of a weighted stem fitted to a square sampling box. The corer is lowered vertically until it impacts with the seabed. At this point the instrument is triggered by a trip as the main coring stem passes through its frame. While pulling the corer out of the sediment a spade swings underneath the sample to prevent loss. When hauled back on board, the spade is under the box. (definition from the SeaVox Device Catalog)
Box corers are one of the simplest and most commonly used types of sediment corers. The stainless steel sampling box can contain a surface sediment block as large as 50cm x 50cm x 75cm with negligible disturbance. Once the sediment is recovered onboard, the sediment box can be detached from the frame and taken to a laboratory for subsampling and further analysis. The core sample size is controlled by the speed at which the corer is lowered into the ocean bottom. When the bottom is firm, a higher speed is required to obtain a complete sample. A depth pinger or other depth indicator is generally used to determine when the box is completely filled with sediment. Once the core box is filled with sediment, the sample is secured by moving the spade-closing lever arm to lower the cutting edge of the spade into the sediment, until the spade completely covers the bottom of the sediment box. (definition from Woods Hole Oceanographic Institution). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Multi Corer
Multi Corer
PI Supplied Instrument Name: Multi Corer PI Supplied Instrument Description:Bowers and Connelly Mega Corer sampling devices were used to collect sediments at Montserrat island. Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Cruise: JC18
JC18
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel
JC18
Martin Palmer
University of Southampton
http://dmoserv3.whoi.edu/data_docs/Estuarine_ANAMMOX/jc018_cruise_report.pdf
Report describing JC18
Cruise: CFRE_Song_2009
CFRE_Song_2009
UNCW 20-ft Center Console Boat
vessel
CFRE_Song_2009
Bongkeun Song
Virginia Institute of Marine Science
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel
UNCW 20-ft Center Console Boat
vessel