http://lod.bco-dmo.org/id/dataset/641358
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
2016-03-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Quantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project)
2016-03-25
publication
2016-03-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2016-11-15
publication
https://doi.org/10.1575/1912/bco-dmo.664686
Karen G. Lloyd
University of Tennessee Knoxville
principalInvestigator
Andrew Steen
University of Tennessee Knoxville
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: Lloyd, K., Steen, A. (2016) Quantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 25 March 2016) Version Date 2016-03-25 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.664686 [access date]
Quantitative PCR data from sediment samples Dataset Description: <p>Quantitative PCR data from sediment samples</p>
<p><strong>Locations:</strong><br />
Site 59C (Little Belt); Site 60B (Anholt Loch); 63E (Landsort Deep); 65C (Bornholm Basin).<br />
Subsurface samples as deep as 85 meters below the Baltic Sea floor.</p> Methods and Sampling: <p><strong>Sampling and Analytical Methodology:</strong><br />
Genomic DNA was extracted from Baltic Sea Basin sediments using FastDNA® Spin Kit for Soil<br />
(MP Biomedicals). 16S rRNA gene copy numbers of targets were quantified with qPCR using the<br />
primers in the table in datasheet. Results of qPCR were rejected if the R2 of the standard curve was<br />
below 0.95, or if the melt curve showed evidence of primer dimers. SYBR green chemistry was used<br />
for all reactions, and Invitrogen mastermix was used for DNA copy number measurement on a<br />
BioRad iQ5 (Applied Biosystems, Foster City, California). Serial dilutions of full-length 16S rRNA<br />
gene PCR products from plasmids containing amplified partial 16S genes were used as standards.</p>
<p>&nbsp;</p>
<p><strong>Primers Used:</strong></p>
<pre>
Primer name Sequence (5' - 3') Target Reference
Bac340f TCCTACGGGAGGCAGCAGT Bacteria Nadkarni et al., 2002
Bac 515r CGTATTACCGCGGCTGCTGGCAC Bacteria Nadkarni et al., 2002
Arch915f GTGCTCCCCCGCCAATTCCT Archaea Kubo et al., 2012
Arch1059r GCCATGCACCWCCTCT Archaea Kubo et al., 2012
ANME1-628f GCT TTC AGG GAA TAC TGC ANME-1 Lloyd et al., 2011
ANME1-830r TCG CAG TAA TGC CAA CAC ANME-1 Lloyd et al., 2011
MCG528f CGGTAATACCAGCTCTCCGAG Kubo et al., 2012
MCG732r CGCGTTCTAGCCGACAGC Kubo et al., 2012
</pre>
<p>&nbsp;</p>
<p><strong>Primers used from the following publications:</strong><br />
<a href="http://dmoserv3.whoi.edu/data_docs/IODP_347/Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments.pdf" target="_blank">Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments</a></p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/IODP_347/Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set.pdf" target="_blank">Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set</a></p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/IODP_347/Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea.pdf" target="_blank">Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1431598 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1431598
completed
Karen G. Lloyd
University of Tennessee Knoxville
865-974-3441
M409 Walters Life Sciences Building 1414 West Cumberland Avenue
Knoxville
TN
37996-0845
USA
lloydk@usc.edu
pointOfContact
Andrew Steen
University of Tennessee Knoxville
865-456 0851
Department of Earth and Planetary Sciences 1412 Circle Drive
Knoxville
TN
37996-1410
USA
asteen1@utk.edu
pointOfContact
asNeeded
Dataset Version: 25 March 2016
Unknown
Identifier
Latitude
Longitude
Depth
Archaea_replicate_1
Archaea_replicate_2
Bacteria_replicate_1
Bacteria_replicate_2
ANME1_replicate_1
ANME1_replicate_2
MCG_replicate_1
MCG_replicate_2
BioRad iQ5
FastDNA® Spin Kit for Soil
theme
None, User defined
sample identification
latitude
longitude
depth core
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Thermal Cycler
Thermal Cycler
instrument
BCO-DMO Standard Instruments
IODP-347
service
Deployment Activity
Baltic Sea
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
International Ocean Discovery Program
http://www.iodp.org/index.php
International Ocean Discovery Program
The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans.
IODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards.
IODP's three platform providers include:
The U.S. National Science Foundation (NSF)
Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT)
The European Consortium for Ocean Research Drilling (ECORD)
More information on IODP, including the Science Plan and Policies/Procedures, can be found on their website at http://www.iodp.org/program-documents.
A summary table with links to IODP datasets currently hosted on Zenodo (https://zenodo.org/communities/iodp) can be accessed using the following link: https://iodp.tamu.edu/database/zenodo.html
IODP
largerWorkCitation
program
Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea
https://osprey.bco-dmo.org/project/639417
Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea
<p>Marine sediments contain a microbial population large enough to rival that of Earth's oceans, but much about this vast community is unknown. Innovations in total cell counting methods have refined estimates of cell concentrations, but tell us nothing about specific taxa. Isotopic data provides evidence that a majority of subsurface microorganisms survive by breaking down organic matter, yet measurable links between specific microbial taxa and their organic matter substrates are untested. The proposed work overcomes these limitations, with a particular focus on the degradation of proteins and carbohydrates, which comprise the bulk of classifiable sedimentary organic matter. The project will link specific taxa to potential extracellular enzyme activity in the genomes of single microbial cells, apply newly-identified, optimal methods for counting viable cells belonging to specific taxa using catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH), and measure the potential activity of their enzymes in situ. The resulting data will provide key evidence about the strategies subsurface life uses to overcome extreme energy limitation and contribute to the long-term carbon cycle.</p>
<p>The Principal Investigators are employing novel,improved methods to quantify cells of specific taxa in the marine subsurface and to determine the biogeochemical functions of those uncultured taxa, including:<br />
1) Determine the pathway of organic carbon degradation in single cell genomes of uncultured, numerically dominant subsurface microorganisms.<br />
2) Quantify viable bacteria and archaea in the deep subsurface using an improvement on the existing technology of CARD-FISH.<br />
3 )Measure the potential activities (Vmax values) of enzymes in deep Baltic Sea sediments, and use the abundances of enzyme-producing microorganisms to calculate depth profiles of cell-specific Vmax values.</p>
<p>The project combines these methods in order to identify and quantify the cells capable of degrading organic matter in deep sediments of the Baltic Sea, obtained from Integrated Ocean Drilling Program (IODP) expedition 347. These results will greatly expand our knowledge of the function and activity of uncultured microorganisms in the deep subsurface.</p>
<p>This project is associated with C-DEBI account number 157595.</p>
IODP-347 Microbial Quantification
largerWorkCitation
project
eng; USA
oceans
Baltic Sea
18.254
58.622167
10.107828
55.00483
2013-09-13
2013-10-30
Baltic Sea
0
BCO-DMO catalogue of parameters from Quantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification 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/641462.rdf
Name: Identifier
Units: text
Description: <p>Sample Identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/641463.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Site Latitude (South is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641464.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Site Longitude (West is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641465.rdf
Name: Depth
Units: meters
Description: <p>Depth of sample in core</p>
http://lod.bco-dmo.org/id/dataset-parameter/641466.rdf
Name: Archaea_replicate_1
Units: copies/uL
Description: <p>Archaea replicate 1 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641467.rdf
Name: Archaea_replicate_2
Units: copies/uL
Description: <p>Archaea replicate 2 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641468.rdf
Name: Bacteria_replicate_1
Units: copies/uL
Description: <p>Bacteria replicate 1 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641469.rdf
Name: Bacteria_replicate_2
Units: copies/uL
Description: <p>Bacteria replicate 2 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641470.rdf
Name: ANME1_replicate_1
Units: copies/uL
Description: <p>ANME1 replicate 1 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641471.rdf
Name: ANME1_replicate_2
Units: copies/uL
Description: <p>ANME1 replicate 2 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641472.rdf
Name: MCG_replicate_1
Units: copies/uL
Description: <p>MCG replicate 1 (Units are copies of target DNA per microliter of DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641473.rdf
Name: MCG_replicate_2
Units: copies/uL
Description: <p>MCG replicate 2 (Units are copies of target DNA per microliter of DNA)</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
3081
https://darchive.mblwhoilibrary.org/bitstream/1912/8515/1/data_qpcr.tsv
download
https://doi.org/10.1575/1912/bco-dmo.664686
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology:</strong><br />
Genomic DNA was extracted from Baltic Sea Basin sediments using FastDNA® Spin Kit for Soil<br />
(MP Biomedicals). 16S rRNA gene copy numbers of targets were quantified with qPCR using the<br />
primers in the table in datasheet. Results of qPCR were rejected if the R2 of the standard curve was<br />
below 0.95, or if the melt curve showed evidence of primer dimers. SYBR green chemistry was used<br />
for all reactions, and Invitrogen mastermix was used for DNA copy number measurement on a<br />
BioRad iQ5 (Applied Biosystems, Foster City, California). Serial dilutions of full-length 16S rRNA<br />
gene PCR products from plasmids containing amplified partial 16S genes were used as standards.</p>
<p>&nbsp;</p>
<p><strong>Primers Used:</strong></p>
<pre>
Primer name Sequence (5' - 3') Target Reference
Bac340f TCCTACGGGAGGCAGCAGT Bacteria Nadkarni et al., 2002
Bac 515r CGTATTACCGCGGCTGCTGGCAC Bacteria Nadkarni et al., 2002
Arch915f GTGCTCCCCCGCCAATTCCT Archaea Kubo et al., 2012
Arch1059r GCCATGCACCWCCTCT Archaea Kubo et al., 2012
ANME1-628f GCT TTC AGG GAA TAC TGC ANME-1 Lloyd et al., 2011
ANME1-830r TCG CAG TAA TGC CAA CAC ANME-1 Lloyd et al., 2011
MCG528f CGGTAATACCAGCTCTCCGAG Kubo et al., 2012
MCG732r CGCGTTCTAGCCGACAGC Kubo et al., 2012
</pre>
<p>&nbsp;</p>
<p><strong>Primers used from the following publications:</strong><br />
<a href="http://dmoserv3.whoi.edu/data_docs/IODP_347/Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments.pdf" target="_blank">Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments</a></p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/IODP_347/Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set.pdf" target="_blank">Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set</a></p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/IODP_347/Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea.pdf" target="_blank">Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea</a></p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Absolute quantification was calculated by converting Ct values of samples into copy numbers per<br />
microliter of DNA with the linear equation produced by the standard curve with R2 greater than 0.95.<br />
The quantification limit was defined as having fluorescence threshold cycle numbers (Ct) well within<br />
those of the simultaneously-run standard curve and being at least 3 Ct below the non-template control<br />
Ct.</p>
<p><strong>BCO-DMO Processing Notes</strong><br />
- Generated from original file "qPCR Exp IODP 347.xlsx, sheet: qPCR" contributed by Joy Buongiorno<br />
- Parameter names edited to conform to BCO-DMO naming convention found at <a href="http://usjgofs.whoi.edu/naming-guidelines.html" target="_blank">Choosing Parameter Name</a><br />
- Latitude and Longitude for sample inserted from Sites data<br />
- "nd" (no data) inserted into blank cells</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
BioRad iQ5
BioRad iQ5
PI Supplied Instrument Name: BioRad iQ5 PI Supplied Instrument Description:Genomic DNA was extracted from Baltic Sea Basin sediments using FastDNA® Spin Kit for Soil
(MP Biomedicals). 16S rRNA gene copy numbers of targets were quantified with qPCR using the
primers in the table in datasheet. Results of qPCR were rejected if the R2 of the standard curve was
below 0.95, or if the melt curve showed evidence of primer dimers. SYBR green chemistry was used
for all reactions, and Invitrogen mastermix was used for DNA copy number measurement on a
BioRad iQ5 (Applied Biosystems, Foster City, California). Serial dilutions of full-length 16S rRNA
gene PCR products from plasmids containing amplified partial 16S genes were used as standards.
BioRad iQ5 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)
FastDNA® Spin Kit for Soil
FastDNA® Spin Kit for Soil
PI Supplied Instrument Name: FastDNA® Spin Kit for Soil PI Supplied Instrument Description:Genomic DNA was extracted from Baltic Sea Basin sediments using FastDNA® Spin Kit for Soil
(MP Biomedicals). 16S rRNA gene copy numbers of targets were quantified with qPCR using the
primers in the table in datasheet. Results of qPCR were rejected if the R2 of the standard curve was
below 0.95, or if the melt curve showed evidence of primer dimers. SYBR green chemistry was used
for all reactions, and Invitrogen mastermix was used for DNA copy number measurement on a
BioRad iQ5 (Applied Biosystems, Foster City, California). Serial dilutions of full-length 16S rRNA
gene PCR products from plasmids containing amplified partial 16S genes were used as standards.
FastDNA® Spin Kit for Soil 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: IODP-347
IODP-347
MPSV GREATSHIP MANISHA
MPSV GREATSHIP MANISHA
vessel
IODP-347
Dr Thomas Andrén
Södertörn University
http://publications.iodp.org/preliminary_report/347/
Report describing IODP-347
MPSV GREATSHIP MANISHA
MPSV GREATSHIP MANISHA
vessel