Dataset: In situ sediment oxygen demand and infauna

Name: Processed dissolved oxygen and infauna of experimental chambers and ambient sensors acquired in the shallow subtidal shore-accessible site in Bon Secour Bay, Mobile Bay, Alabama, USA between August 7-12, 2021
Published: 2024-10-21
Keywords: sediment, dissolved oxygen, macrofauna, oceans

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Spatial Extent: N:30.239478 E:-87.894094 S:30.239478 W:-87.894094

SShallow subtidal shore-accessible site in Bon Secour Bay, Mobile Bay, AL, USA

Temporal Extent: 2021-08-07 - 2021-08-12

Project:

CAREER: Mechanisms of bioturbation and ecosystem engineering by benthic infauna (Bioturbation and Ecosystem Engineering)

Student:

Kara Gadeken (University of South Alabama; and Dauphin Island Sea Lab, USA-DISL)

Contact:

Kara Gadeken (University of South Alabama; and Dauphin Island Sea Lab, USA-DISL)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-10-21

Restricted:

Validated:

Current State:

Data not available

Processed dissolved oxygen and infauna of experimental chambers and ambient sensors acquired in the shallow subtidal shore-accessible site in Bon Secour Bay, Mobile Bay, Alabama, USA between August 7-12, 2021

Abstract:

This data set includes data and scripts from a field study examining the effect of diel oxygen cycling on faunal activity, and in turn sediment oxygen demand. The field experiment used in situ flow-through benthic chambers to measure oxygen consumption, as described in the methods paper Gadeken et al 2023 in L&O:Methods. The chambers were deployed and retrieved in three ~24 hour deployments in a shallow subtidal area of Bon Secour Bay in Mobile Bay, AL, in August 2021. Included in this data set are the raw data files of oxygen and temperature measurements from Onset HOBO DO loggers integrated into the benthic chamber system, annotated MATLAB scripts and workspaces detailing data processing and analysis, and faunal community data from the benthic chambers.

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Description

Five matlab script files (.m) are added as supplemental files to this dataset. They are for the data analysis and results/figures of the results paper. Some of these are run step-wise. Note that because Chamber 1 malfunctioned in all three deployments, the scripts regularly exclude that chamber in data processing and analyses. Users replicating these methods who have better luck with their chamber 1 will want to add in code modified from analysis of the other chambers to analyze those data.

Methods & Sampling

In brief, a custom field deployable benthic chamber system was used to collect sediment oxygen demand (SOD) data in situ from small replicate patches of sediment throughout a diel oxygen cycle. Chambers were "batch" style incubation chambers that periodically flushed the overlying water with water from the external environment to start another incubation, and SOD could be calculated from the slopes of each incubation. Upon completion of the 24 hour deployment, the chambers were extracted, oxygen data offloaded from the chamber loggers, and the faunal community in each chamber identified and counted (1mm sieve).

Problems/Issues

* The flush mechanism for chamber 1 malfunctioned during all three deployments of the system. This is evident by the lack of the expected sawtooth pattern in the data but worth noting here. The scripts regularly exclude that chamber in data processing and analyses. Users replicating these methods who have better luck with their chamber 1 will want to add in code modified from analysis of the other chambers to analyze those data.

Data Processing Description

The data file s the compiled data for every high-quality chamber incubation among all three deployments, the product of data processing, filtration, and consolidation done in MATLAB scripts 2, 3 and 4. This sheet is used in MATLAB script 5 for data analysis. It contains the start date and time of the incubation, the elapsed time since the start of the deployment (dayfrac), the chamber number out of 5 replicate chambers, the SOD (sediment oxygen demand) in mmol m-2 d-1, the Initial DO (dissolved oxygen) of that incubation in mg L-1, the total biomass of fauna within the chamber in grams, the deployment number, and the overall study sample number.

DO data processing involved manual selection of oxygen slopes from raw oxygen data for each deployment to generate a data set of sediment oxygen demand (SOD) values. Data were compiled into a master data sheet which was then used to compare SOD with the dissolved oxygen levels at the time of the slope and the faunal community in the particular chamber.

BCO-DMO Processing

* Added Matlab script files as supplemental files

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1844910

Deployments

None available yet

Instruments

benthic incubation chamber

Supplied Name:

Supplied Description:

This project used a custom built field deployable benthic chamber system. Construction and functioning of the system are outlined in Gadeken et al 2023 L&O:Methods.

Instrument Type

Generic Name: benthic incubation chamber

Generic Description:

A device that isolates a portion of seabed plus overlying water from its surroundings. Either returns the entire system to the surface or incorporates sampling devices and/or in-situ sensors.

Onset HOBO U26-001 Dissolved Oxygen Data Logger

Supplied Name: Onset HOBO DO loggers (U26-001)

Supplied Description:

Instrument Type

Generic Name: Onset HOBO U26-001 Dissolved Oxygen Data Logger

Acronym: HOBO DO logger (U26-001)

Generic Description:

A dissolved oxygen sensor, temperature sensor, and integrated data logger. The HOBO U26-001 can be used in freshwater and saltwater conditions, and outputs dissolved oxygen (mg/L) and temperature (degC) measurements.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Latitude	Latitude of approximate sampling location, south is negative	decimal degrees	lat
Longitude	Longitude of approximate sampling location, west is negative	decimal degrees	lon
StartTime	StartTime of incubation in Central Standard Time (CST) Format: %Y-%m-%dT%H:%M:%S	unitless	time_begin
dayfrac	Proportion of a day after start of deployment at which that data point was collected. Start was 11AM for all three deployments.	unitless	sample_descrip
Chamber	Number of chamber in the deployment, out of 5 replicate chambers	unitless	sample_descrip
SOD	Sediment Oxygen Demand, the rate of oxygen flux across the sediment-water interface	millimoles per square meter per day (mmol m-2 d-1)	O2
InitialDO	Dissolved oxygen concentration at the beginning of the incubation	milligrams per liter (mg L-1)	O2
biomass	Biomass for the chamber area of 0.17 per square meters (not yet standardized to m-2)	grams (g)	weight_g
deployment	Deployment number (1-3)	unitless	deployno
sample	Replicate sample out of all chambers in all deployments, numbered in ascending deployment and chamber order	unitless	sample_descrip

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Dataset: In situ sediment oxygen demand and infauna