URLhttps://www.bco-dmo.org/dataset/668648
Download URLhttps://www.bco-dmo.org/dataset/668648/data/download
Media Typetext/tab-separated-values
CreatedDecember 6, 2016
ModifiedJanuary 21, 2020
StateFinal no updates expected
Brief DescriptionPolysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments

Acquisition Description

In the Marmara Sea, surficial sediments were collected by multicorer, and deeper sediments from 570-585 cm and 520-530 cm were collected by gravity corer. Eastern Mediterranean sediments were collected by gravity corer. Guaymas Basin sediments were collected by push core.

Sediment incubations with fluorescently labeled organic substrates were set up with three live incubations, a kill control, and one live blank. Incubations were subsampled over time, and each subsample was centrifuged and syringe filtered through a 0.2 um GF filter. Porewater containing partially hydrolyzed fluorescent substrate products were processed using gel permeation chromatography with fluorescence detection. Standards of fluorescent substrates of known molecular weight were also run for the purpose of rate calculations.

GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector.

Instruments

Instance Description

Eastern Mediterranean sediments were collected by gravity corer. In the Marmara Sea, deeper sediments (from 570-585 cm and 520-530 cm) were collected by gravity corer.

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).
Instance Description

In the Marmara Sea, surficial sediments were collected by multicorer.

The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408.
Details
Instance Description

Guaymas Basin sediments were collected by push core.

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/

Shimadzu liquid chromatography system [Gel Permeation Chromatograph]
Details
Instance Description (Shimadzu liquid chromatography system)

GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector.

Instruments that separate components in aqueous or organic solution based on molecular size generally for molecular weight determination. Gel permeation chromatography (GPC) is a type of size exclusion chromatography (SEC), that separates analytes on the basis of size.

Parameters

description [unknown]
Details
description
Maximum potential hydrolysis rates of six polysaccharides measured in sediment incubations
association with a community-wide standard parameter is not yet defined
sample [sample]
Details
sample
Sample identifier

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

kcrate_1_nM_hr [unknown]
Details
kcrate_1_nM_hr
kill-corrected hydrolysis rate of experimental replicate 1, in nM/hr
association with a community-wide standard parameter is not yet defined
kcrate_2_nM_hr [unknown]
Details
kcrate_2_nM_hr
kill-corrected hydrolysis rate of experimental replicate 2, in nM/hr
association with a community-wide standard parameter is not yet defined
kcrate_3_nM_hr [unknown]
Details
kcrate_3_nM_hr
kill-corrected hydrolysis rate of experimental replicate 3, in nM/hr
association with a community-wide standard parameter is not yet defined
kcrate_live_nM_hr [unknown]
Details
kcrate_live_nM_hr
mean hydrolysis rate before kill correction
association with a community-wide standard parameter is not yet defined
mean_kcrate_nM_hr [unknown]
Details
mean_kcrate_nM_hr
mean kill-corrected hydrolysis rate of all replicates
association with a community-wide standard parameter is not yet defined
sd_kcrate_nM_hr [unknown]
Details
sd_kcrate_nM_hr
Standard deviation
association with a community-wide standard parameter is not yet defined
location [unknown]
Details
location
Location source of the sediment sample
association with a community-wide standard parameter is not yet defined
core [unknown]
Details
core
Identifier for the sediment core
association with a community-wide standard parameter is not yet defined
seddepth_cm [unknown]
Details
seddepth_cm
Sediment depth within the core
association with a community-wide standard parameter is not yet defined
core_depth [unknown]
Details
core_depth
Core + sediment depth
association with a community-wide standard parameter is not yet defined
treatment [treatment]
Details
treatment
Experimental treatment of sediment incubation

Experimental conditions applied to experimental units.  In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.

substrate [unknown]
Details
substrate
Polysaccharide substrate for which hydrolysis rates were measured
association with a community-wide standard parameter is not yet defined
timepoint [unknown]
Details
timepoint
Timepoint label of sample
association with a community-wide standard parameter is not yet defined
elapsedtime [unknown]
Details
elapsedtime
Time since incubation start time
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Adrienne HoarfrostUniversity of North Carolina at Chapel Hill (UNC-Chapel Hill)
Carol ArnostiUniversity of North Carolina at Chapel Hill (UNC-Chapel Hill)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleInvestigating microbial activities driving organic matter transformations in the deep subsurface
AcronymSedS
URLhttps://www.bco-dmo.org/project/662055
CreatedOctober 20, 2016
ModifiedOctober 20, 2016
Project Description

Project description from C-DEBI:
Heterotrophic organisms are central to subsurface microbial communities and play an important role in carbon cycling. Most approaches to measuring enzymatic activities rely on the addition of a fluorescently labeled substrate to a sediment incubation. However, quantifying rates of extracellular enzymatic hydrolysis of organic matter is often problematic due to the tendency for a fluorescently labeled organic substrate to sorb to the sediment matrix. This results in lower fluorescence intensities and distorted, inaccurate hydrolysis rate calculations. In this project, a desorption treatment was developed to counteract the adverse effects of sorption on enzymatic activity measurements. Upon subsampling a sediment incubation amended with a fluorescently labeled substrate, the subsample is treated with a concentrated solution of unlabeled substrate, along with 0.2% sodium dodecyl sulfate (SDS), in order to competitively desorb the adsorbed, fluorescent substrate target. This treatment improves measured fluorescence intensities by a median of 62.5%, and is particularly effective at desorbing high molecular weight substrate products, resulting in debiased hydrolysis rates that are 14.75 nM/hr lower on average. Competitive desorption treatment was demonstrated to be effective for multiple substrates and in a broad range of sediments from diverse geological and geochemical contexts. Future applications of this method will result in more quantitative and comparable hydrolysis rates in subsurface sediments, will enable enzymatic activity measurements in problematic sediments that were previously infeasible, and will facilitate physiological characterization of microbial communities and model organisms in order to better understand heterotrophic carbon cycling in the subsurface environment.

This project was funded by a C-DEBI Graduate Fellowship.

Project Maintainers
NameAffiliationRoleContact
Adrienne HoarfrostUniversity of North Carolina at Chapel Hill (UNC-Chapel Hill)Principal Investigator
Carol ArnostiUniversity of North Carolina at Chapel Hill (UNC-Chapel Hill)Co-Principal Investigator
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