URLhttps://www.bco-dmo.org/dataset/640333
Download URLhttps://www.bco-dmo.org/dataset/640333/data/download
Media Type text/tab-separated-values
Created March 11, 2016
Modified August 19, 2016
State Preliminary and in progress
Brief Description

Porewater geochemistry (sulfate, methane, and DIC) from sediments of the White Oak River (WOR), NC, Station H.

Acquisition Description

Three sediment pushcores were collected manually from the White Oak River, Station H. Cores were transported to the Institute of Marine Sciences in Morehead City, NC, and sectioned at 3 cm intervals. Porewater was preserved for methane, sulfate, DIC, and cell count measurements as described in Lloyd et al (2011) Environmental Microbiology 13(9) 2548-2564.

Briefly, for cell counts: sediments were fixed with 3% formaldehyde for 4-5 hours at 2 degrees C, washed twice with PBS and stored at -20 degrees C in 1:1 PBS:ethanol for approximately two weeks before counting. For sulfate, 15-ml tubes filled with sediment were centrifuged. The resulting porewater was filtered at 0.2 um, acidified with 10% HCl, and sulfate was measured by ion chromatograph. For methane measurements, 3 ml of sediment was sampled immediately after sectioning using a cutoff syringe into the side of the core, and quickly added to 60 ml serum vials which had been preloaded with 1 ml 0.1 M KOH. These were immediately stoppered and crimp-sealed with butyl rubber stoppers and then shaken vigorously to equilibrate methane into the headspace. Headspace methane was then measured by gas chromatography. Porewater for DIC was preserved in sealed glass vials and measured by ion chromatography.

Processing Description

All porewater geochemical measurements were calibrated to known standards. Cell counts were calculated using standard formulas to account for the volume of sediment filtered, the area of the filter, and the area of the gridded field.

BCO-DMO processing:
– modified parameter names to conform with BCO-DMO naming conventions;
– replaced blanks (missing data) and “not measured” with “nd” (no data);
– added site name, lat, lon, and date from metadata form;
– converted original lat and lon provided to decimal degrees.

Instruments

Details
Instance Description

Three sediment pushcores were collected manually from the White Oak River, Station H. Cores were transported to the Institute of Marine Sciences in Morehead City, NC, and sectioned at 3 cm intervals. 

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/

ion chromatograph [Ion Chromatograph]
Details
Instance Description (ion chromatograph)

Sulfate was measured by ion chromatograph. Porewater for DIC was preserved in sealed glass vials and measured by ion chromatography.

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)

gas chromatograph [Gas Chromatograph]
Details
Instance Description (gas chromatograph)

Headspace methane was measured by gas chromatography.

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)

Parameters

site [site]
Details
site
Name of sampling site.
Sampling site identification.
lat [latitude]
Details
lat
Latitude of sampling site.

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

lon [longitude]
Details
lon
Longitude of sampling site.

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

year [year]
Details
year
4-digit year of sampling.

year, reported as YYYY, e.g. 1995

month [month]
Details
month

2-digit month of sampling.

Month of year; numeric 1 to 12.

day [day]
Details
day
2-digit day of month.
day of month; numeric 1 to 31
core [unknown]
Details
core

Core identifier.

association with a community-wide standard parameter is not yet defined
depth_cmbsf [unknown]
Details
depth_cmbsf

Core depth.

association with a community-wide standard parameter is not yet defined
porosity [porosity]
Details
porosity
Porosity.
porosity in sediments
CH4 [unknown]
Details
CH4
Methane (CH4)
association with a community-wide standard parameter is not yet defined
SO4 [SO4]
Details
SO4
Sulfate (SO4--)

Concentration of sulfate (SO4) per unit volume

DIC [DIC]
Details
DIC
Dissolved inorganic carbon (DIC)

Dissolved Inorganic Carbon

cells [unknown]
Details
cells
Cell count
association with a community-wide standard parameter is not yet defined
cells_sd [unknown]
Details
cells_sd
Standard deviation of cells.
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Andrew D. SteenUniversity of Tennessee Knoxville (UTK)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Novel peptidases in subsurface sediments: Activities and substrate specificities
Acronym SEDpep
URLhttps://www.bco-dmo.org/project/636401
Created January 25, 2016
Modified January 25, 2016
Project Description

Description from C-DEBI:
The goal of this project was to explore the mechanisms of subsurface organoheterotrophy by identifying the range of extracellular peptidases present in sediments of the White Oak River, NC, consistent with C-DEBI Research Theme 1, Activity in the Deep Subseafloor Biosphere: function & rates of global biogeochemical processes. This grant funded two sampling expeditions to the White Oak River as well as extensive laboratory work with a purified peptidase that was supplied by collaborators Andrzej Joachimiak and Karolina Michalska of Argonne National Laboratory and preparatory work on peptidases of the Tennessee River. So far this dataset has led to the submission of two manuscripts, with one more manuscript in preparation. The White Oak River work showed that a wide range of peptidases are present in depths up to 80 cm in the White Oak River, which is deeper than the zone of methanogenesis. Although absolute peptidase activities declined with depth, activities normalized to cell abundance were roughly constant, and activities normalized to organic carbon oxidation rates increased nearly two orders of magnitude relative to the surface, indicating that extracellular peptidases were important to the subsurface ecosystem. Biochemical analysis of a purified peptidase that was expressed by the Argonne group showed it to be a novel aminopeptidase with specificity for N-terminal cysteine, a function not previously observed in peptidses. In summary, in situ and in vitro studies of subsurface peptidases revealed that they are ecologically important and may contain novel properties.

Data Project Maintainers
NameAffiliationRole
Andrew D. SteenUniversity of Tennessee Knoxville (UTK)Principal Investigator
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