http://lod.bco-dmo.org/id/dataset/686389
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
2017-03-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014
2017-03-28
publication
2017-03-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-12-27
publication
https://doi.org/10.26008/1912/bco-dmo.686389.1
Eric S. Boyd
Montana State University
principalInvestigator
Maximiliano J. Amenabar
Montana State University
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: Boyd, E. S., Amenabar, M. J. (2021) North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-03-28 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.686389.1 [access date]
North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 Dataset Description: <p>North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014.</p> Methods and Sampling: <p>All samples used in this work were collected as part of the North Atlantic long-coring expedition in Oct.-Dec. 2014 (R/V Knorr, Cruise KN223); this project focuses on sediments from 4 sites (2, 3, 11, 12) exhibiting variations in the depth to which oxygen penetrates. The sediment subsamples were collected from long piston cores or shorter gravity cores. While oxygen penetrates through the full long core depth at sites 11 and 12, oxygen was consumed in the sediment column at site 3 and especially at site 2. All samples were collected anaerobically in order to perform on-board culture enrichments via the most probable number (MPN) method. Sediments were placed in sterile serum vials, capped with butyl rubber stoppers and flushed with N2 for 2 min and maintained at 4 degrees C for immediate shipboard MPN inoculation work (this dataset). Parallel samples were similarly collected from these and additional core sections and maintained at 4 degrees C for later determination of microbial production rates (see <a href="https://www.bco-dmo.org/dataset/685944" target="_blank">microbial production dataset</a>).</p>
<p>Twenty ml of anaerobic saline media was added to the 30 ml sediment within each serum vial and mixed to create a sediment slurry. MPN assays were initiated on-board and were designed to quantify the abundance of viable microbial cells with specified metabolisms. Hungate tubes with synthetic marine base salts media were amended with various combinations of electron donors (acetate, peptone) and acceptors (oxygen, nitrate, and manganese(IV) oxide):</p>
<p><img alt="table of electron donors and acceptors used in this study" src="https://datadocs.bco-dmo.org/d3/data_docs/C-DEBI/boyd/electron_donors_acceptors.PNG" />Saline basal medium was composed of (g/L): 0.2 NH4Cl, 30 NaCl, 2.8 MgCl2, 0.33 KCl, 0.3 CaCl2, 0.3 KH2PO4, 0.01 NaBr, 0.015 H3BO3, 0.02 SrCl2, 0.02 KI, 0.02 FeCl3, 0.0075 MnSO4, 0.0045 Na2WO4.2H2O, 0.003 NiCl2, 0.02 CoSO4, 0.0015 ZnSO4, 0.002 CuSO4, and 0.0015 Na2MoO4. pH was adjusted to 6.2.</p>
<p>In the case of anaerobic MPN assays, Hungate tubes and their contents were boiled and purged with high purity N2 for 30 min. Aerobic assay tubes were prepared in air and were not purged. MPN assays were inoculated with 1 ml of sediment slurry and were diluted using 10-fold dilutions. MPN assays were incubated for 6-12 months at room temperature and were then assayed for activity/growth. Activity in MPN assays was evaluated by determining the headspace concentration of CO2 using an infrared gas detector. Additionally, colorimetric approaches specific to each anaerobic metabolism were used: the azo dye method (Strickland and Parsons 1968, Bull Fish Res Board Can 167:71) to detect the reduction of nitrate to nitrite and the T(4-CP)P method (Madison et al. 2011, Talanta, 84:374) to quantify production of Mn(II) from Mn(IV). Blank tubes were similarly prepared but not inoculated; these were analyzed to establish background levels of metabolites.</p>
<p>MPN assays were successful for all incubations using oxygen, Mn(IV) or nitrate as electron acceptors. However, the Mn(II) assay suffered from unidentified interferences in many cases. Growth as identified by CO2 accumulation was used where results of the Mn(II) assay were ambiguous. MPN results were converted to estimates of viable cell concentrations as follows. The highest dilution exhibiting evidence of growth was multiplied by the initial 1.6667-fold dilution used to make the sediment slurry. This count was considered the minimum MPN; the next higher dilution was considered the maximum MPN. For example, an assay exhibiting growth at 10^3 dilution but not at 10^4 dilution was considered to have a viable cell concentration of between 1,667-16,667 cells per cm^3 of sediment. For any subsequent calculations, such as cell turnover, the geometric mean of these values was used; e.g., 52,705 cells per cm^3 in this example case. In cases where no growth occurred at the lowest dilution or positive growth occurred at the highest dilution, MPN can only be constrained to be lower or higher than these estimates, respectively, and the MPN column is left blank.</p>
<p>For each electron acceptor/donor combination from each core section, the highest dilution MPN tube exhibiting growth was targeted for further culture transfers and eventual microbial identification/isolation. We have noted where PCR products were successfully obtained from these tubes, providing additional validation of the corresponding MPN result.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Eric S. Boyd
Montana State University
(406) 994-7046
Department of Microbiology and Immunology, 109 Lewis Hall PO Box 173520
Bozeman
MT
59717
USA
eboyd@montana.edu
pointOfContact
Maximiliano J. Amenabar
Montana State University
(406) 595-1968
Department of Microbiology and Immunology, 109 Lewis Hall PO Box 173520
Bozeman
MT
59717
United States
maximiliano.amenabar@msu.montana.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
site
lat
lon
depth_w
sed_thickness
basement_age
date_coring
cruise_id
platform
core
core_section
depth_mbsf
electron_donor
electron_acceptor
MPN_min
MPN_max
notes
PCR_products
infrared gas detector
gravity core
long piston core
theme
None, User defined
site
latitude
longitude
depth_w
sed_thickness
No BCO-DMO term
date
cruise_id
ship
core id
sample identification
meters below seafloor
cell_concentration
featureType
BCO-DMO Standard Parameters
Gas Analyzer
Gravity Corer
Piston Corer
instrument
BCO-DMO Standard Instruments
KN223
service
Deployment Activity
North and West Atlantic Ocean
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
Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities
http://www.darkenergybiosphere.org/award/defining-the-interplay-between-oxygen-organic-carbon-and-metabolism-in-subseafloor-sediment-communities/
Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities
<p>Abstract from C-DEBI:</p>
<p>Deep marine sediments harbor an abundance of microbial cells that, if active, are likely to exert a strong influence on element biogeochemical cycling. Despite decades of study, our understanding of the fraction of cells that are active in situ and the metabolic processes that sustain them remain under-explored. We propose an integrated set of analyses aimed at unraveling the links between geochemical heterogeneity, cellular viability and synthesis, and metabolism along a vertical depth profile in four sediment cores collected during the North Atlantic long coring expedition. These sediment columns exhibit varying levels of organic carbon and differences in the degree of oxygen penetration along the depth profile which we hypothesize exert strong influence on the extent and nature of microbial life. Most probable number assays containing nine different selective enrichment conditions were initiated using subsamples from these cores in Nov. 2014. Separate subsamples were preserved for use in measuring rates of secondary production. Multivariate modeling tools will be applied to integrate these measurements with co-registered geochemical measurements, cell counts, and molecular data provided by collaborators. This work will provide new insight into the dynamic interplay between O2 and organic carbon and microbial activity, viability, and productivity in deep marine sediments.</p>
<p>NOTE: This project follows the C-DEBI program <a href="http://www.darkenergybiosphere.org/internal/docs/C-DEBIDataManagementPlan_2015.pdf" target="_blank">Data Management Plan (PDF)</a>.</p>
Subseafloor metabolisms
largerWorkCitation
project
eng; USA
oceans
North and West Atlantic Ocean
-58.3283
-50.6203
14.4
29.6767
2014-11-03
2014-11-21
SW North Atlantic sediments (13-42° N, 48-71° W)
0
BCO-DMO catalogue of parameters from North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014
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/686400.rdf
Name: site
Units: unitless
Description: <p>Site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/686401.rdf
Name: lat
Units: decimal degrees
Description: <p>Site latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/686402.rdf
Name: lon
Units: decimal degrees
Description: <p>Site longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/686403.rdf
Name: depth_w
Units: meters (m)
Description: <p>Water depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/686404.rdf
Name: sed_thickness
Units: meters (m)
Description: <p>Sediment thickness</p>
http://lod.bco-dmo.org/id/dataset-parameter/686405.rdf
Name: basement_age
Units: millions of years ago (Ma)
Description: <p>Basement age</p>
http://lod.bco-dmo.org/id/dataset-parameter/686406.rdf
Name: date_coring
Units: unitless
Description: <p>Date of coring in yyyy-mm-dd format</p>
http://lod.bco-dmo.org/id/dataset-parameter/686407.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/686408.rdf
Name: platform
Units: unitless
Description: <p>Platform (e.g. vessel) name</p>
http://lod.bco-dmo.org/id/dataset-parameter/686409.rdf
Name: core
Units: unitless
Description: <p>Core identifier. LC = long core; GC = gravity core.</p>
http://lod.bco-dmo.org/id/dataset-parameter/686410.rdf
Name: core_section
Units: unitless
Description: <p>Core section</p>
http://lod.bco-dmo.org/id/dataset-parameter/686411.rdf
Name: depth_mbsf
Units: meters below sea floor (mbsf)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/686412.rdf
Name: electron_donor
Units: unitless
Description: <p>Organic compound added as an electron donor (acetate or peptone)</p>
http://lod.bco-dmo.org/id/dataset-parameter/686413.rdf
Name: electron_acceptor
Units: unitless
Description: <p>Inorganic addition serving as an electron acceptor (nitrate, oxygen, or manganese(IV) oxide)</p>
http://lod.bco-dmo.org/id/dataset-parameter/686414.rdf
Name: MPN_min
Units: viable cells per milliliter (cells/mL)
Description: <p>Minimum MPN; true viable (under these culture conditions) cell concentration is likely to be greater than or equal to this figure.</p>
http://lod.bco-dmo.org/id/dataset-parameter/686415.rdf
Name: MPN_max
Units: viable cells per milliliter (cells/mL)
Description: <p>Maxiumum MPN; True viable (under these culture conditions) cell concentration is likely to be less than or equal to this figure.</p>
http://lod.bco-dmo.org/id/dataset-parameter/686416.rdf
Name: notes
Units: unitless
Description: <p>Indicates samples for which no growth was noted at the lowest dilution tested as well as samples for which positive growth was detected at the highest dilution tested.</p>
http://lod.bco-dmo.org/id/dataset-parameter/686417.rdf
Name: PCR_products
Units: unitless
Description: <p>PCR products obtained? Yes = highest dilution exhibiting growth yielded PCR products; No = highest dilution exhibiting growth did not yield PCR products; N/A = not applicable because no growth was noted at any dilution and therefore no attempt was made to extract DNA for PCR amplification.</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
11886
https://darchive.mblwhoilibrary.org/bitstream/1912/27862/1/dataset-686389_sediment-microbial-mpns__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.686389.1
download
onLine
dataset
<p>All samples used in this work were collected as part of the North Atlantic long-coring expedition in Oct.-Dec. 2014 (R/V Knorr, Cruise KN223); this project focuses on sediments from 4 sites (2, 3, 11, 12) exhibiting variations in the depth to which oxygen penetrates. The sediment subsamples were collected from long piston cores or shorter gravity cores. While oxygen penetrates through the full long core depth at sites 11 and 12, oxygen was consumed in the sediment column at site 3 and especially at site 2. All samples were collected anaerobically in order to perform on-board culture enrichments via the most probable number (MPN) method. Sediments were placed in sterile serum vials, capped with butyl rubber stoppers and flushed with N2 for 2 min and maintained at 4 degrees C for immediate shipboard MPN inoculation work (this dataset). Parallel samples were similarly collected from these and additional core sections and maintained at 4 degrees C for later determination of microbial production rates (see <a href="https://www.bco-dmo.org/dataset/685944" target="_blank">microbial production dataset</a>).</p>
<p>Twenty ml of anaerobic saline media was added to the 30 ml sediment within each serum vial and mixed to create a sediment slurry. MPN assays were initiated on-board and were designed to quantify the abundance of viable microbial cells with specified metabolisms. Hungate tubes with synthetic marine base salts media were amended with various combinations of electron donors (acetate, peptone) and acceptors (oxygen, nitrate, and manganese(IV) oxide):</p>
<p><img alt="table of electron donors and acceptors used in this study" src="https://datadocs.bco-dmo.org/d3/data_docs/C-DEBI/boyd/electron_donors_acceptors.PNG" />Saline basal medium was composed of (g/L): 0.2 NH4Cl, 30 NaCl, 2.8 MgCl2, 0.33 KCl, 0.3 CaCl2, 0.3 KH2PO4, 0.01 NaBr, 0.015 H3BO3, 0.02 SrCl2, 0.02 KI, 0.02 FeCl3, 0.0075 MnSO4, 0.0045 Na2WO4.2H2O, 0.003 NiCl2, 0.02 CoSO4, 0.0015 ZnSO4, 0.002 CuSO4, and 0.0015 Na2MoO4. pH was adjusted to 6.2.</p>
<p>In the case of anaerobic MPN assays, Hungate tubes and their contents were boiled and purged with high purity N2 for 30 min. Aerobic assay tubes were prepared in air and were not purged. MPN assays were inoculated with 1 ml of sediment slurry and were diluted using 10-fold dilutions. MPN assays were incubated for 6-12 months at room temperature and were then assayed for activity/growth. Activity in MPN assays was evaluated by determining the headspace concentration of CO2 using an infrared gas detector. Additionally, colorimetric approaches specific to each anaerobic metabolism were used: the azo dye method (Strickland and Parsons 1968, Bull Fish Res Board Can 167:71) to detect the reduction of nitrate to nitrite and the T(4-CP)P method (Madison et al. 2011, Talanta, 84:374) to quantify production of Mn(II) from Mn(IV). Blank tubes were similarly prepared but not inoculated; these were analyzed to establish background levels of metabolites.</p>
<p>MPN assays were successful for all incubations using oxygen, Mn(IV) or nitrate as electron acceptors. However, the Mn(II) assay suffered from unidentified interferences in many cases. Growth as identified by CO2 accumulation was used where results of the Mn(II) assay were ambiguous. MPN results were converted to estimates of viable cell concentrations as follows. The highest dilution exhibiting evidence of growth was multiplied by the initial 1.6667-fold dilution used to make the sediment slurry. This count was considered the minimum MPN; the next higher dilution was considered the maximum MPN. For example, an assay exhibiting growth at 10^3 dilution but not at 10^4 dilution was considered to have a viable cell concentration of between 1,667-16,667 cells per cm^3 of sediment. For any subsequent calculations, such as cell turnover, the geometric mean of these values was used; e.g., 52,705 cells per cm^3 in this example case. In cases where no growth occurred at the lowest dilution or positive growth occurred at the highest dilution, MPN can only be constrained to be lower or higher than these estimates, respectively, and the MPN column is left blank.</p>
<p>For each electron acceptor/donor combination from each core section, the highest dilution MPN tube exhibiting growth was targeted for further culture transfers and eventual microbial identification/isolation. We have noted where PCR products were successfully obtained from these tubes, providing additional validation of the corresponding MPN result.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- re-formatted date to yyyy-mm-dd;<br />
- replaced missing data with "nd";<br />
- replaced "R/V Knorr" with "RV_Knorr" in data.</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
infrared gas detector
infrared gas detector
PI Supplied Instrument Name: infrared gas detector PI Supplied Instrument Description:Activity in MPN assays was evaluated by determining the headspace concentration of CO2 using an infrared gas detector. Instrument Name: Gas Analyzer Instrument Short Name:Gas Analyzer Instrument Description: Gas Analyzers - Instruments for determining the qualitative and quantitative composition of gas mixtures.
gravity core
gravity core
PI Supplied Instrument Name: gravity core PI Supplied Instrument Description:The sediment subsamples were collected from long piston cores or shorter gravity cores. Instrument Name: Gravity Corer Instrument Short Name:Gravity Corer Instrument Description: The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
long piston core
long piston core
PI Supplied Instrument Name: long piston core PI Supplied Instrument Description:The sediment subsamples were collected from long piston cores or shorter gravity cores. Instrument Name: Piston Corer Instrument Short Name:Piston Corer Instrument Description: The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Cruise: KN223
KN223
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN223
Richard W Murray
Boston University
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel