Download URLhttps://www.bco-dmo.org/dataset/649751/data/download
Media Type text/tab-separated-values
Created June 20, 2016
Modified August 19, 2016
State Final no updates expected
Brief Description

Methane and sulfate concentration profiles - sediment cores from White Oak River estuary Station H, October 2012

Acquisition Description

The cores were sequentially cut into 3 cm section from the topmost to bottommost depth. For methane measurements, 3 ml of sediments were taken via cut-off syringe immediately after each section was sliced and quickly added to 60 ml serum vials containing 1 ml of 0.1 M KOH, which were stoppered and crimp-sealed with butyl rubber stoppers to minimize gas loss. After being shaken for 1 min to release methane from sediments (> 99.5% of the methane equilibrated in the headspace), a 5 ml headspace aliquot was displaced with an equal volume of anaerobic distilled water, injected into a 1 ml sample loop, and then analyzed on an Agilent 7890a gas chromatograph  equipped with flame ionization detector. For sulfate measurements, plastic 15 ml tubes filled completely with sediment were centrifuged and the resulting porewater was filtered at 0.2 µm, acidified with 10% HCl and measured using a 2010i Dionex ion chromatograph.

Processing Description

Methane concentrations (mmol per litre of porewater) were calculated using the following equation:
[CH4] = (ρ(CH4)Vheadspace)/(RTφVsed1000)
where p(CH4) is the partial pressure of methane (in ppmv), Vheadspace is the volume of the serum vial headspace (ml) after the sediment and KOH are added, R is the universal gas constant, T is the temperature at time of measurement in Kelvin and Vsed is the volume (ml) of whole sediment added to the serum vial.

Porosity, φ, was calculated using the formula:
φ = (mw/ ρw)/(mww+((md-S*mw/1000)/ρds))
where mw is the mass of the water lost on drying, md is the mass of the dried sediment, ρw is the density of pure water, ρds is the density of dry sediment (assumed to be 2.5 g cm−3), and S is salinity in grams per kilogram (assumed to be 19 grams per kilogram for all samples).

Standards at sulfate concentrations 0, 0.1, 0.5, 1, 5, 10 mM measure prior to samples from each core and sample peak areas were converted to sulfate concentrations using the standard curves after accounting for the dilution ((peak area * slope + intercept) * 0.7 / 0.6) by the 10% HCl.

No samples have been flagged as below the detection limit.

BCO-DMO Processing:

– added conventional header with dataset name, PI name, version date
– renamed parameters to BCO-DMO and BODC standards
– replaced NaN with nd
– removed CH4_mod data


Instance Description

Agilent 7890a gas chromatograph equipped with flame ionization detector

Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)
Instance Description

2010i Dionex ion chromatograph

Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)


site [site]

site identification

Sampling site identification.
lat [latitude]
latitude; north is positive

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

lon [longitude]
longitude; east is positive

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

depth [depth]

depth of core sample

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

CH4 [unknown]

methane concentration in porewater

association with a community-wide standard parameter is not yet defined
SO4 [SO4]
sulfate concentration in porewater

Concentration of sulfate (SO4) per unit volume

core [sample]
core identification

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

CH4_mod [unknown]

???methane concentration in porewater - modified in some way???

association with a community-wide standard parameter is not yet defined
porosity [porosity]
measure of the void (i.e. "empty") spaces in wet sediment volume that evaporated after few weeks at 80ºC (i.e the water) in VV/VT
porosity in sediments

Dataset Maintainers

Karen G. LloydUniversity of Tennessee
Jordan T. BirdUniversity of Tennessee
Nancy CopleyUniversity of Tennessee Knoxville (UTK)
Nancy CopleyUniversity of Tennessee Knoxville (UTK)
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea
Acronym IODP-347 Microbial Quantification
Created February 29, 2016
Modified December 6, 2017
Project Description

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.

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:
1) Determine the pathway of organic carbon degradation in single cell genomes of uncultured, numerically dominant subsurface microorganisms.
2) Quantify viable bacteria and archaea in the deep subsurface using an improvement on the existing technology of CARD-FISH.
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.

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.

This project is associated with C-DEBI account number 157595.

Data Project Maintainers
Karen G. LloydUniversity of Tennessee Knoxville (UTK)Principal Investigator
Andrew D. SteenUniversity of Tennessee Knoxville (UTK)Co-Principal Investigator