Dataset: Polysaccharide Hydrolysis Rates
Deployment: M84-1

Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments

Principal Investigator:

Adrienne Hoarfrost (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

Co-Principal Investigator:

Carol Arnosti (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Investigating microbial activities driving organic matter transformations in the deep subsurface (SedS)

Current State:

Final no updates expected

Version:

09 December 2016

Deployment Synonyms:

DARC-SEAS

Version Date:

2016-12-09

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/669449/data

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Description

Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments. The polysaccharide hydrolysis rates for Marmara Sea sediment were generated during methods development experiments.

This dataset contains the final hydrolysis rates. Raw data are also available for download in a 20.5 MB .zip file.
The .zip file contains GPC chromatographic output for incubations with sediment from Guaymas Basin and the Eastern Mediterranean, used for hydrolysis rate calculations (CoreComparison folder). The "MarmaraMethods" folder contains GPC output for methods development experiments conducted using mud from the Marmara Sea. The "stds" folders contain GPC output for a set of standards of known molecular weight, which are necessary for rate calculations (each folder is a different run – depending on when a sample is run on the GPC, the standards run most recently are used as reference for rate calculations). Each file is raw chromatographic output is in fluorescence units (mV) over time for a 75-minute run.

The associated processing an analysis scripts are available through GitHub: https://github.com/ahoarfrost/SedS

Methods & Sampling

Dataset 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.

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0939564	NSF Division of Ocean Sciences

Instruments

Gel Permeation Chromatograph

Supplied Name: Shimadzu liquid chromatography system

Supplied Description:

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

Instrument Type

Generic Name: Gel Permeation Chromatograph

Acronym: GPC

Generic Description:

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.

Gravity Corer

Supplied Name:

Supplied 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.

Instrument Type

Generic Name: Gravity Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

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).

Multi Corer

Supplied Name:

Supplied Description:

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

Instrument Type

Generic Name: Multi Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

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.

Push Corer

Supplied Name:

Supplied Description:

Guaymas Basin sediments were collected by push core.

Instrument Type

Generic Name: Push Corer

Generic Description:

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/

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
description	Maximum potential hydrolysis rates of six polysaccharides measured in sediment incubations	unitless	no_bcodmo_term
sample	Sample identifier	unitless	sample
kcrate_1_nM_hr	kill-corrected hydrolysis rate of experimental replicate 1, in nM/hr	nM/hr	no_bcodmo_term
kcrate_2_nM_hr	kill-corrected hydrolysis rate of experimental replicate 2, in nM/hr	nM/hr	no_bcodmo_term
kcrate_3_nM_hr	kill-corrected hydrolysis rate of experimental replicate 3, in nM/hr	nM/hr	no_bcodmo_term
kcrate_live_nM_hr	mean hydrolysis rate before kill correction	nM/hr	no_bcodmo_term
mean_kcrate_nM_hr	mean kill-corrected hydrolysis rate of all replicates	nM/hr	no_bcodmo_term
sd_kcrate_nM_hr	Standard deviation	nM/hr	no_bcodmo_term
location	Location source of the sediment sample	unitless	no_bcodmo_term
core	Identifier for the sediment core	unitless	no_bcodmo_term
seddepth_cm	Sediment depth within the core	centimeter (cm)	no_bcodmo_term
core_depth	Core + sediment depth	centimeter (cm)	no_bcodmo_term
treatment	Experimental treatment of sediment incubation	unitless	treatment
substrate	Polysaccharide substrate for which hydrolysis rates were measured	unitless	no_bcodmo_term
timepoint	Timepoint label of sample	unitless	no_bcodmo_term
elapsedtime	Time since incubation start time	hours (hr)	no_bcodmo_term

Database

Contribute Data

Dataset: Polysaccharide Hydrolysis Rates
Deployment: M84-1

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Polysaccharide Hydrolysis RatesDeployment: M84-1

Dataset acquisition description

Dataset Processing Description

Dataset: Polysaccharide Hydrolysis Rates
Deployment: M84-1