http://lod.bco-dmo.org/id/dataset/672336
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
2017-01-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Amplicon sequencing of ammonia oxidizing archaea amoA gene from R/V Kilo Moana KM1314 in the North Pacific Ocean, Aug-Sept 2013 (Nitrification and Planktonic Biodiversity project)
2017-01-04
publication
2017-01-04
revision
BCO-DMO Linked Data URI
2017-01-04
creation
http://lod.bco-dmo.org/id/dataset/672336
Dr David A. Stahl
University of Washington
principalInvestigator
E. Virginia Armbrust
University of Washington
principalInvestigator
Allan Devol
University of Washington
principalInvestigator
Anitra E. Ingalls
University of Washington
principalInvestigator
James W. Moffett
University of Southern California
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: Stahl, D. A., Devol, A., Moffett, J. W., Ingalls, A. E., Armbrust, E. (2017) Amplicon sequencing of ammonia oxidizing archaea amoA gene from R/V Kilo Moana KM1314 in the North Pacific Ocean, Aug-Sept 2013 (Nitrification and Planktonic Biodiversity project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-01-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/672336 [access date]
Amplicon sequencing of ammonia oxidizing archaea amoA gene from cruise KM1314, Aug. 8 - Sept. 4, 2013 in the northern Pacific Dataset Description: <p>Amplicon sequencing of ammonia oxidizing archaea amoA gene data&nbsp; from R/V Kilo Moana KM1314 in the&nbsp;North Pacific Ocean (Seattle to Honolulu, including Line P, Station ALOHA).</p>
<p><strong>Related Datasets:</strong>&nbsp;<br />
<a href="https://www.bco-dmo.org/dataset/672310">Ammonia oxidation rate profiles</a><br />
<a href="https://www.bco-dmo.org/dataset/672363">Particulate vitamin B12 profiles</a></p>
<p>&nbsp;</p> Methods and Sampling: <p>We determined the community diversity for nitrite max samples at stations 1, 3, 5, 10, 11, 13, 14, 15, and 16 and chlorophyll max samples at station 8 (55 m). Marine AOA amoA genes were amplified from template DNA (~20 ng/uL) using a two-step enrichment procedure for target amplification and sample barcoding on a Fluidigm Access Array (Fluidigm Inc., San Francisco CA). Gene targets were amplified using primer pairs ArchAmoA_1F and ArchAmoA1R and sample specific Golay primers (Francis et al. 2005). Amplified products were analyzed by gel electrophoresis to ensure the correct amplicon size, quantified using pico-green, pooled to an equal molar concentration and sequenced in pair-end 300 bp mode using the Illumina HiSeq Platform. Resulting sequences were assessed for quality using fastq_eestats and trimmed at the 5’ (5bp) and 3’ (225bp) ends (Edgar 2010). Trimmed reads were then quality filtered in QIIME using the recommendations described by Bokulich et al. (2013). The resulting reads were then analyzed using the UPARSE pipeline with an OTU clustering identity of 95% (Edgar 2013). Representative OTU sequences were analyzed against a reference database of AOA amoA genes in the ARB software using the parsimony tool for insertion (Ludwig et al. 2004; Pester et al. 2012). Sample-OTU matrices from UPARSE were converted to biom format and rarified to 1000 reads per sample using the single_rarfy.py script in QIIME. The resulting output file was then used for calculation of Bray-Curtis similarity values between samples and hierarchical clustering using the package vegan in R.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046017 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046017
completed
Dr David A. Stahl
University of Washington
206-685-6657
Department of Civil and Environmental Engineering 302 More Hall, Box 352700
Seattle
WA
98195-2700
USA
dastahl@uw.edu
pointOfContact
E. Virginia Armbrust
University of Washington
206-543-4043
School of Oceanography Box 355351
Seattle
WA
98195-9472
USA
armbrust@uw.edu
pointOfContact
Allan Devol
University of Washington
206-543-1292
School of Oceanography University of Washington, Box 355351
Seattle
WA
98195
USA
devol@u.washington.edu
pointOfContact
Anitra E. Ingalls
University of Washington
206-221-6748
School of Oceanography Box 355351 4333 Brooklyn Ave NE
Seattle
WA
98195
USA
aingalls@u.washington.edu
pointOfContact
James W. Moffett
University of Southern California
213-740-5626
Biological Sciences, Earth Sciences, and Civil and Environmental Engineering 3616 Trousdale Pkwy
Los Angeles
CA
90089
USA
jmoffett@usc.edu
pointOfContact
asNeeded
Unknown
cruise_id
sta
depth
lat
lon
Arch_OTU95_1_reads
Arch_OTU95_2_reads
Arch_OTU95_5_reads
Arch_OTU95_29_reads
Arch_OTU95_34_reads
Arch_OTU95_38_reads
Illumina HiSeq Platform
theme
None, User defined
Cruise identfier
station number
depth
latitude
longitude
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
KM1314
service
Deployment Activity
The North Pacific Ocean (Cruise from Seattle to Honolulu, including Line P, Station ALOHA)
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Significance of nitrification in shaping planktonic biodiversity in the ocean
https://osprey.bco-dmo.org/project/2228
Significance of nitrification in shaping planktonic biodiversity in the ocean
<p>Microorganisms sustain the biogeochemical cycling of nitrogen, one of the most important nutrient cycles on earth. A key step in this cycle, the oxidation of ammonia to nitrite by autotrophic microorganisms, was for a century thought mediated by a few restricted bacterial genera. Significant ammonia oxidation, perhaps most, is now attributed to a previously enigmatic group of Archaea - the ammonia-oxidizing archaea (AOA) - of high abundance in both marine and terrestrial environments. The investigators prior physiological and environmental analyses, the foundation for this proposal, have shown that AOA are active within the marine photic zone and that their competitive fitness in the marine environment is at least in part attributable to an extremely high affinity for ammonia, growing at near maximum growth rates at concentrations of ammonia that would not sustain known bacterial ammonia oxidizers, and an unusual copper-based respiratory system that may render them more competitive in iron limited environments. The compelling inference from these prior analyses is that AOA alter and possibly control the forms of fixed nitrogen available to other microbial assemblages within the photic zone by converting ammonia, a nearly universally available form of nitrogen, into nitrite, a form only available to nitrite oxidizing bacteria and some phytoplankton. If correct, this has a significant impact on biodiversity.</p>
<p>The PIs will use the most recent technological advances in protein and high throughput sequencing to evaluate the significance of nitrification in shaping biodiversity (genomic and metagenomics), activity (transcriptome, proteome and stable isotope probing), and in controlling availability of an important trace element (copper). In turn, by resolving the environmental and biotic variables that influence the diversity, distribution and activity of AOA, they will advance general understanding of their taxonomy. More directly, functional knowledge of the contribution of AOA to regenerated nitrate will improve estimates of new ocean production ("biological pump") based on nitrate assimilation, which in the past has mostly neglected the importance of nitrification as a major source of nitrate. Together these studies will transform understanding of the marine nitrogen cycle, estimates of new production, and will ultimately provide a better understanding of the impact of human activity on this critical nutrient cycle.</p>
<p>The nitrogen cycle has been profoundly affected by anthropogenic inputs of reactive nitrogen into terrestrial, marine, and atmospheric systems having, or predicted to have, major impacts on marine biological production, increased N20 emissions, nitrogen pollution, and eutrophication. Likewise, there is a poor understanding of the relationship between nitrogen cycling and productivity in marine ecosystems. Marine systems are increasingly affected by ocean acidification and by atmospheric inputs of reactive nitrogen. Since both changes greatly alter nitrogen available to microorganisms, the characterization of the response of these environmentally relevant AOA is of tremendous relevance to understanding the affect of acidification and anthropogenic nitrogen inputs on major ocean processes.</p>
<p>The proposed project encompasses and integrates the three dimensions (functional genetic, and taxonomic) of biodiversity. First, the project is framed by function: microbial control of one of the most important nutrient cycles on earth, the nitrogen-cycle. Second, it is motivated by recent genetic analyses that associate activities of a novel clade of Archaea (provisionally assigned to a new kingdom within the Archaea, the Thaumarchaeota) with control of ammonia oxidation in the ocean. Third, it is built upon a compelling synthesis of physiological and environmental data that lead to its central hypothesis that by altering and possibly controlling the form of nitrogen, the AOA also alter biodiversity and ecological function in one of the most productive environments on earth. It identifies a specific taxonomic imperative. The tremendous genetic diversity among the globally abundant AOA catalogued almost exclusively by gene sequencing surveys and therefore lacking formal description makes it essential to resolve membership into ecologically relevant groups or clades as a prelude to developing a formal taxonomy. The investigators have assembled a group of researchers with specific expertise in each of dimension and uniquely qualified to address the research objectives outlined in an integrative way.</p>
Nitrification and Marine Planktonic Biodiversity
largerWorkCitation
project
eng; USA
oceans
The North Pacific Ocean (Cruise from Seattle to Honolulu, including Line P, Station ALOHA)
2017-01-04
0
BCO-DMO catalogue of parameters from Amplicon sequencing of ammonia oxidizing archaea amoA gene from R/V Kilo Moana KM1314 in the North Pacific Ocean, Aug-Sept 2013 (Nitrification and Planktonic Biodiversity 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
http://lod.bco-dmo.org/id/dataset-parameter/672352.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/672353.rdf
Name: sta
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/672354.rdf
Name: depth
Units: meters
Description: <p>sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/672355.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/672356.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/672357.rdf
Name: Arch_OTU95_1_reads
Units: amplicon reads
Description: <p>amplicon sequencing reads of AOA amoA gene (encoding alpha unit of ammonia monooxygenase) for OTU (operational taxonomic unit) 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/672358.rdf
Name: Arch_OTU95_2_reads
Units: amplicon reads
Description: <p>amplicon sequencing reads of AOA amoA gene (encoding alpha unit of ammonia monooxygenase) for OTU 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/672359.rdf
Name: Arch_OTU95_5_reads
Units: amplicon reads
Description: <p>amplicon sequencing reads of AOA amoA gene (encoding alpha unit of ammonia monooxygenase) for OTU 5</p>
http://lod.bco-dmo.org/id/dataset-parameter/672360.rdf
Name: Arch_OTU95_29_reads
Units: amplicon reads
Description: <p>amplicon sequencing reads of AOA amoA gene (encoding alpha unit of ammonia monooxygenase) for OTU 29</p>
http://lod.bco-dmo.org/id/dataset-parameter/672361.rdf
Name: Arch_OTU95_34_reads
Units: amplicon reads
Description: <p>amplicon sequencing reads of AOA amoA gene (encoding alpha unit of ammonia monooxygenase) for OTU 34</p>
http://lod.bco-dmo.org/id/dataset-parameter/672362.rdf
Name: Arch_OTU95_38_reads
Units: amplicon reads
Description: <p>amplicon sequencing reads of AOA amoA gene (encoding alpha unit of ammonia monooxygenase) for OUT 38</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
735
https://datadocs.bco-dmo.org/file/k66gkRyskGGo41/amoA_reads.csv
amoA_reads.csv
Primary data file for dataset ID 672336
download
https://osprey.bco-dmo.org/dataset/672336/data/download
download
onLine
dataset
<p>We determined the community diversity for nitrite max samples at stations 1, 3, 5, 10, 11, 13, 14, 15, and 16 and chlorophyll max samples at station 8 (55 m). Marine AOA amoA genes were amplified from template DNA (~20 ng/uL) using a two-step enrichment procedure for target amplification and sample barcoding on a Fluidigm Access Array (Fluidigm Inc., San Francisco CA). Gene targets were amplified using primer pairs ArchAmoA_1F and ArchAmoA1R and sample specific Golay primers (Francis et al. 2005). Amplified products were analyzed by gel electrophoresis to ensure the correct amplicon size, quantified using pico-green, pooled to an equal molar concentration and sequenced in pair-end 300 bp mode using the Illumina HiSeq Platform. Resulting sequences were assessed for quality using fastq_eestats and trimmed at the 5’ (5bp) and 3’ (225bp) ends (Edgar 2010). Trimmed reads were then quality filtered in QIIME using the recommendations described by Bokulich et al. (2013). The resulting reads were then analyzed using the UPARSE pipeline with an OTU clustering identity of 95% (Edgar 2013). Representative OTU sequences were analyzed against a reference database of AOA amoA genes in the ARB software using the parsimony tool for insertion (Ludwig et al. 2004; Pester et al. 2012). Sample-OTU matrices from UPARSE were converted to biom format and rarified to 1000 reads per sample using the single_rarfy.py script in QIIME. The resulting output file was then used for calculation of Bray-Curtis similarity values between samples and hierarchical clustering using the package vegan in R.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
-&nbsp;converted lat and lon to decimal degrees</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
Illumina HiSeq Platform
Illumina HiSeq Platform
PI Supplied Instrument Name: Illumina HiSeq Platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: KM1314
KM1314
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1314
Anitra E. Ingalls
University of Washington
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel