URLhttps://www.bco-dmo.org/dataset/640372
Download URLhttps://www.bco-dmo.org/dataset/640372/data/download
Media Type text/tab-separated-values
Created March 14, 2016
Modified August 19, 2016
State Preliminary and in progress
Brief Description

Activities of extracellular peptidases at Station H of the White Oak River (WOR).

Acquisition Description

Sediment pushers were collected manually from the White Oak River, Station H. The core was transported to the Institute of Marine Sciences at Morehead City, NC, and sectioned at 3-cm intervals. Intervals are named for the center of the interval (i.e., depth=1.5 cm refers to the interval from 0 to 3 cm). Substrates were brought up in an anoxic slurry of buffered artificial seawater at an approximate ratio of 0.5 g sediment to 4 ml medium and transferred into 5 ml serum vials, which were briefly purged with N2 to preserve anoxia. Immediately after mixing and again three times over the course of about 4 hours, approximately 1 ml of sediment was removed, centrifuged briefly, and fluorescence of the supernatant was measured using a Promega Quantifluor ST fluorescence detector set to UV (ex ca. 350 nm, em ca 450 nm). Separately, the sediments were standardized using AMC, and a 6-hour incubation with AMC showed that sorption of AMC to sediments was negligible.

Processing Description

Activities were calculated as the rate of fluorescence production per gram sediment, calibrated with AMC standards.

BCO-DMO processing:
– modified parameter names to conform with BCO-DMO naming conventions;
– replaced “NA” 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

Sediment pushers were collected manually from the White Oak River, Station H. 

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/

centrifuge [Centrifuge]
Details

A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.

Promega Quantifluor ST fluorescence detector [Fluorometer]
Details

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

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

depth [depth]
Details
depth

Depth in centimeters below sediment-water interface.

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.

substrate [unknown]
Details
substrate

Name of fluorogenic substrate used:
Arg-AMC = Arginyl-aminomethylcoumarin (AMC),
Gly-AMC = glycyl-AMC,
Leu-AMC = Leucyl-AMC,
GlyGlyArg-AMC = glycyl-glycyl-arginyl-AMC,
BocValPro-Arg-AMC = tert-butyoxycarbonyl-AMC

association with a community-wide standard parameter is not yet defined
conc [unknown]
Details
conc
Concentration
association with a community-wide standard parameter is not yet defined
v0 [unknown]
Details
v0

V0

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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