The sediment subsamples were collected from long piston cores or shorter gravity cores.
URL | https://www.bco-dmo.org/dataset/685944 |
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Download URL | https://www.bco-dmo.org/dataset/685944/data/download |
Media Type | text/tab-separated-values |
Created | March 27, 2017 |
Modified | October 2, 2017 |
State | Final no updates expected |
Brief Description | 3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 |
Acquisition Description
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 (see MPN 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 (this dataset).
We assessed microbial production on selected core sections at sites 11 and 12 using proxies for DNA synthesis (incorporation of methyl-3H thymidine) and protein synthesis (incorporation of 4,5-3H leucine). Core material was retained at 4 degrees C under an N2 atmosphere prior to slurry preparation. Aerobic slurry was prepared 1:1 by volume with 0.2 um-filtered deep seawater and incubations began immediately thereafter. Incubations (n=4 live treatments, n=4 TCA-killed controls) of 0.5 ml slurry each were conducted in sterile microfuge tubes for each label addition. Seawater-only blanks incubated and processed along with samples exhibited near background levels of activity. 50 ul of working 3H-Thy or 3H-Leu stock was added at time zero. This equates to 3.75 uCi Leu or 4.4375 uCi Thy per sample at concentrations of appx. 114 nmol label compound per liter slurry final. Incubations were carried out at 4 degrees C in the dark.
Incubations were terminated at 18-24 hr; a time-course experiment confirmed linearity of incorporation out to at least 24 hr. Live incubations were terminated with TCA and an extraction protocol modified from Dixon & Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation; the DNA fraction alone was isolated and similarly analyzed for 3H-Thy incorporation. Rates are reported as pmol leucine or thymidine incorporated per ml of sediment per day (based on mean treatment minus mean control). Errors were calculated by propagating the standard deviations of treatments and controls.
Processing Description
These data represent short-term rates of label incorporation at the stated levels of addition. No corrections for potential isotope dilution were attempted, given the overall low metabolic rates of the system. Rates are reported as determined; therefore, where mean controls exceeded mean treatments, negative rates are reported.
BCO-DMO Processing:
– modified parameter names to conform with BCO-DMO naming conventions;
– re-formatted date to yyyy-mm-dd;
– replaced “R/V Knorr” with “RV_Knorr” in data.
Instruments
The sediment subsamples were collected from long piston cores or shorter gravity cores.
Live incubations were terminated with TCA and an extraction protocol modified from Dixon & Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation.
Parameters
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Sediment thickness
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
name of the ship or vessel (See also platform.)
Core identification number or label; often used with ice, rock, sediment, or coral cores.
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
Sample depth
Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.
heterotrophic bacteria; leucine incorporation rate
standard deviation of leucine incorporation rates
thymidine incorporation rate; file dependent
Dataset Maintainers
Name | Affiliation | Contact |
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Eric Boyd | Montana State University | |
Maximiliano J. Amenabar | Montana State University | |
John E. Dore | Montana State University | |
Shannon Rauch | Montana State University | |
Shannon Rauch | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
BCO-DMO Project Info
Project Title | Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities |
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Acronym | Subseafloor metabolisms |
URL | https://www.bco-dmo.org/project/676615 |
Created | January 27, 2017 |
Modified | February 13, 2017 |
Project Description
Abstract from C-DEBI:
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.
NOTE: This project follows the C-DEBI program Data Management Plan (PDF).
Data Project Maintainers
Name | Affiliation | Role |
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Maximiliano J. Amenabar | Montana State University | http://ocean-data.org/schema/Co-ChiefScientistRole |
Eric Boyd | Montana State University | Lead Principal Investigator |
John E. Dore | Montana State University | Contact |