http://lod.bco-dmo.org/id/dataset/512782
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
2014-04-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Paired metagenomic and metatranscriptomic data from R/V Atlantic Explorer AE1006, AE1024, Bermuda Atlantic Time Series Station (BATS), Sargasso Sea, Mar and Aug 2010 (Active bacteria in surface waters project)
2014-04-23
publication
2014-04-23
revision
BCO-DMO Linked Data URI
2014-04-23
creation
http://lod.bco-dmo.org/id/dataset/512782
Dr Barbara Campbell
Clemson University
principalInvestigator
Dr John Heidelberg
University of Southern California
principalInvestigator
David L. Kirchman
University of Delaware
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: Campbell, B., Heidelberg, J., Kirchman, D. L. (2014) Paired metagenomic and metatranscriptomic data from R/V Atlantic Explorer AE1006, AE1024, Bermuda Atlantic Time Series Station (BATS), Sargasso Sea, Mar and Aug 2010 (Active bacteria in surface waters project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2014-04-23) Version Date 2014-04-23 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/512782 [access date]
Paired metagenomic and metatranscriptomic data from 2 cruises in the spring of 2010 and the summer of 2010 in the Sargasso Sea Dataset Description: Methods and Sampling: <p>A combination of pyrosequencing and QPCR approaches were used to examine rRNA:rDNA ratios, BrdU incorporating cells, and transcript types and amounts in the metatranscriptome of Sargasso Sea surface water. The investigators also used&nbsp;Micro-FISH to examine incorporation of thymidine, leucine, and PO4. Samples were&nbsp;collected in 2010 during the spring phytoplankton bloom when heterotrophic bacterial production is lowest and during the peak of bacterial production in summer.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0825468 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0825468
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0824981 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0824981
onGoing
Dr Barbara Campbell
Clemson University
864-656-0559
Department of Biological Sciences 155B Life Science Facility, 190 Collings St.
Clemson
SC
29634
USA
bcampb7@clemson.edu
pointOfContact
Dr John Heidelberg
University of Southern California
213-740-5791
AHF 107 University Park
Los Angeles
CA
90089-0701
jheidelb@usc.edu
pointOfContact
David L. Kirchman
University of Delaware
302-645-4375
School of Marine Science and Policy 700 Pilottown Road
Lewes
DE
19958
USA
kirchman@udel.edu
pointOfContact
asNeeded
Dataset Version: 2014-04-23
Unknown
cruise_id
date
lat
lon
depth
accession_number
Niskin bottle
theme
None, User defined
Cruise identfier
date
latitude
longitude
depth
accession number
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
AE1006
AE1024
service
Deployment Activity
Bermuda AtlanticTime Series Station (BATS)
Sargasso Sea, BATS
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.
Are abundant bacteria more active than rare bacteria in the Sargasso Sea?
https://osprey.bco-dmo.org/project/2253
Are abundant bacteria more active than rare bacteria in the Sargasso Sea?
<p>Marine prokaryotic communities are now known to be highly diverse and may be carrying out new types of metabolisms that, if confirmed, could fundamentally alter models of energy and material flow through the oceans. These metabolisms include photoheterotrophic and chemolithotrophic pathways that are entirely novel or were not thought to be occurring in the surface layer of the oceans. The problem is, we do not know which fraction of this diverse community is actually active in biogeochemical processes and whether the metabolic functions, especially the new ones suggested by genomic data, are actually being carried out by marine prokaryotic communities.</p>
<p>This project will address the following questions and hypotheses:</p>
<p>1. What bacteria are most active in open oceanic environments like the Sargasso Sea? The investigators hypothesize that the most abundant bacterioplankton groups are also the most active whereas the rare groups will be less active. This hypothesis will be explored using four indices of activity: i) levels of 16S rRNA vs. 16S rRNA genes; ii) replicating cells as measured by the incorporation of the thymidine analog, BrdU; iii) incorporation of key dissolved compounds by abundant bacterial groups as revealed by microautoradiography combined with fluorescence in situ hybridization (Micro-FISH), and iv) transcript levels of growth-dependent phylogenetic markers other than 16S rRNA (e.g. tuf, rpoB and dnaE). The investigators are especially interested in whether rare bacteria are inactive and are potentially part of a 'seed bank' that serves as the inoculum for future communities.</p>
<p>2. What metabolic processes are represented by the most commonly expressed genes? The investigators hypothesize that the most commonly expressed genes will be those associated with the processing of dissolved organic matter rather than other energy generating mechanisms, including photoheterotrophy and chemolithotrophy. Expression will be examined by pyrosequencing mRNA (metatranscriptome) from the Sargasso Sea. We will map the metatranscriptome onto metagenomic assemblies from the Sargasso Sea and explore which genes called in metagenomic studies are real rather than bioinformatic artifacts.</p>
<p>The project will use a combination of pyrosequencing and QPCR approaches to examine rRNA:rDNA ratios, BrdU incorporating cells, and transcript types and amounts in the metatranscriptome of Sargasso Sea surface water. Pyrosequencing (454) avoids amplification and cloning artifacts and it is cost effective. Preliminary analyses indicate that the sequence length of 454 reads and the proposed number of sequences are ideal for addressing the questions raised here. The investigators will also use Micro-FISH to examine incorporation of thymidine, leucine, and PO4. Samples will be collected twice yearly during the spring phytoplankton bloom when heterotrophic bacterial production is lowest and during the peak of bacterial production in summer.</p>
<p>This project will do much to alter our perception of microbial processes in the oligotrophic ocean by providing answers to long-standing questions about activity and standing stocks of bacterial populations and by linking metabolic processes to the extensive environmental genomic data now becoming available.</p>
<p>The project will support a graduate student and involve underrepresented undergraduates in summer research projects, including at sea field work. The results from this project will be incorporated into an environmental genomics web site and used in courses taught by Kirchman. The Kirchman and Heidelberg labs are featured in lab tours open to the public (~ 1000 visitors per year) and Campbell and Kirchman are also involved in Coast Day, an annual open house that attracts about 10,000 visitors. Finally, the PIs will be involved in K-12 teacher training workshops and other Delaware Center for Critical Zone Research outreach activities</p>
<p>The project is affiliated with the Bermuda Atlantic Time-Series Study (BATS), <a href="http://bats.bios.edu/">http://bats.bios.edu</a>.</p>
Active bacteria in surface waters
largerWorkCitation
project
eng; USA
oceans
Bermuda AtlanticTime Series Station (BATS); Sargasso Sea, BATS
2014-04-23
Coastal Delaware, Delaware Bay, Sargasso Sea
0
BCO-DMO catalogue of parameters from Paired metagenomic and metatranscriptomic data from R/V Atlantic Explorer AE1006, AE1024, Bermuda Atlantic Time Series Station (BATS), Sargasso Sea, Mar and Aug 2010 (Active bacteria in surface waters 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/512808.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification; AE is Atlantic Explorer</p>
http://lod.bco-dmo.org/id/dataset-parameter/512809.rdf
Name: date
Units: mm/dd/yyyy
Description: <p>date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/512810.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/512811.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/512812.rdf
Name: depth
Units: meters
Description: <p>depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/512813.rdf
Name: accession_number
Units: unitless
Description: <p>NCBI accession number</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
1575
https://datadocs.bco-dmo.org/file/4WW2r1PT7OqAO/bact_accessions.csv
bact_accessions.csv
Primary data file for dataset ID 512782
download
https://osprey.bco-dmo.org/dataset/512782/data/download
download
onLine
dataset
<p>A combination of pyrosequencing and QPCR approaches were used to examine rRNA:rDNA ratios, BrdU incorporating cells, and transcript types and amounts in the metatranscriptome of Sargasso Sea surface water. The investigators also used&nbsp;Micro-FISH to examine incorporation of thymidine, leucine, and PO4. Samples were&nbsp;collected in 2010 during the spring phytoplankton bloom when heterotrophic bacterial production is lowest and during the peak of bacterial production in summer.</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
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: AE1006
AE1006
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1006
Lilia Jackman
Bermuda Biological Station for Research
Cruise: AE1024
AE1024
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1024
Steven Bell
Bermuda Institute of Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel