Download URLhttps://www.bco-dmo.org/dataset/685944/data/download
Media Typetext/tab-separated-values
CreatedMarch 27, 2017
ModifiedOctober 2, 2017
StateFinal no updates expected
Brief Description3H-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.


long piston core [Piston Corer]
Instance Description (long piston core)

The sediment subsamples were collected from long piston cores or shorter gravity cores.

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.
gravity core [Gravity Corer]
Instance Description (gravity core)

The sediment subsamples were collected from long piston cores or shorter gravity cores.

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).
liquid scintillation counting [Liquid Scintillation Counter]
Instance Description (liquid scintillation counting)

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.

Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.


site [site]

Site name

Sampling site identification.
lat [latitude]
Site latitude

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Site longitude

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

depth_w [depth_w]
Water depth

water depth, in meters

sed_thickness [sed_thickness]
Sediment thickness

Sediment thickness

basement_age [unknown]
Basement age
association with a community-wide standard parameter is not yet defined
date_coring [date]
Date of coring in yyyy-mm-dd format

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)

cruise_id [cruise_id]
Cruise identifier
cruise designation; name
platform [ship]
Platform (e.g. vessel) name

name of the ship or vessel (See also platform.)

core [core_id]
Core identifier. LC = long core; GC = gravity core.

core number/identification, to be used with ice, rock and sediment cores

core_section [sample]
Core section

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.

leucine_incorp [leuc_incorp]
Leucine incorporation; mean rate of incorporation of leucine based on mean live treatment (n=4) minus mean killed control (n=4).

heterotrophic bacteria; leucine incorporation rate

leu_sd [leuc_sd]
Standard deviation of rate of leucine incorporation based on propagation of sd of treatments and sd of controls.

standard deviation of leucine incorporation rates

thymidine_incorp [thy_incorp]
Thymidine incorporation; mean rate of incorporation of thymidine based on mean live treatment (n=4) minus mean killed control (n=4).

thymidine incorporation rate; file dependent

thy_sd [thy_sd]
Standard deviation of rate of thymidine incorporation based on propagation of sd of treatments and sd of controls.

standard deviation of thymidine incorporation rates

Dataset Maintainers

Eric BoydMontana State University
Maximiliano J. AmenabarMontana State University
John E. DoreMontana State University
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleDefining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities
AcronymSubseafloor metabolisms
CreatedJanuary 27, 2017
ModifiedFebruary 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).

Project Maintainers
Maximiliano J. AmenabarMontana State Universityhttp://ocean-data.org/schema/Co-ChiefScientistRole
Eric BoydMontana State UniversityLead Principal Investigator
John E. DoreMontana State UniversityContact