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Short Citation:
Office for Coastal Management, 2023: Evaluating Whether Oyster Aquaculture Can Help Restore Water Quality - NERRS/NSC(NERRS Science Collaborative),

Item Identification

Title: Evaluating Whether Oyster Aquaculture Can Help Restore Water Quality - NERRS/NSC(NERRS Science Collaborative)
Status: Completed
Creation Date: 2020-12

The project team established an experiment that mimicked commercial aquaculture practices and allowed for a robust comparison of nitrogen removal rates from three commonly used gear types: floating bags of oysters, oyster condos suspended in midwater, and bottom cages of oysters. All gear was deployed in the same environmental setting (Waquoit Bay, Falmouth, MA) and maintained by the Town of Falmouth in a manner that a typical grower would follow. The growing systems were maintained for two full growing seasons (2018 and 2019) and compared to a nearby control site. Every two weeks during the growing season, the team conducted a series of measurements to provide a robust estimate of nitrogen fluxes and microbial activity below each of the aquaculture operations. Measurements included: (1) nutrient analyses of sediment, porewater and bottom water samples, (2) genetic sequencing of RNA and DNA extracted from sediment samples to determine the presence and activity level of certain bacteria; and 3) measurements of N2 fluxes from sediment cores placed in flux chambers to measure N2 production rates. All three oyster growing methods enhanced nitrogen removal relative to the control site. However, gene expression data indicate that nitrogen retention may be induced under some gear, particularly after the end of July under bottom cages, and to a lesser extent other gear types.


Towns along Cape Cod are under pressure to reduce and mitigate nitrogen inputs to improve coastal water quality. Many towns are exploring the use of various shellfish aquaculture systems as a cost effective way to remediate water quality. This project addressed a critical information gap identified by water quality managers and regulators, specifically: how much nitrogen is removed from coastal waters by common oyster aquaculture methods, and what culturing practices should be adopted to maximize benefits for water quality? This information is helping regulators decide how much credit they can give towns for installing shellfish aquaculture as part of their water quality improvement plan, and provide guidance to towns and growers on best practices to maximize water quality benefits.

Supplemental Information:

==Project lead and contact information:

Dan Rogers, Assistant Professor

Department of Chemistry, Stonehill College


==List of Project Datasets

Five related datasets are described in this document

1. Microbial community structure data - iTag Amplicon library

2. Microbial processes data - RNA-Seq Metatranscriptomic sequences

3. Bottom water, porewater and sediment chemistry

4. Gene expression (RT-qPCR) and nitrogen flux measurements

5. Oyster weight data


Theme Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Science Keywords
None 16S hypervariable
None Ammonia
None aquaculture
None Crassostrea virginica
None Denitrification
None Eastern oysters
None gene expression
None Illumina pair-end
None iTag
None lux chambers
None Metatranscription
None N2 production
None Nitrate, Ammonia, Sedimentary Carbon and Nitrogen
None oyster farms
None RNA-seq
None RT-qPCR
None Sedimentary Carbon and Nitrogen
None shellfish

Spatial Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Location Keywords
None Waquoit Bay NERR, MA

Data Set Information

Data Set Scope Code: Data Set
Maintenance Frequency: None Planned
Distribution Liability:

The distributor does not assume liability.

Support Roles

Data Steward

CC ID: 1065216
Date Effective From: 2015
Date Effective To:
Contact (Organization): Office for Coastal Management (OCM)
Address: 2234 South Hobson Avenue
Charleston, SC 29405-2413


CC ID: 1065217
Date Effective From: 2015
Date Effective To:
Contact (Organization): Office for Coastal Management (OCM)
Address: 2234 South Hobson Avenue
Charleston, SC 29405-2413

Metadata Contact

CC ID: 795447
Date Effective From: 2017-10-31
Date Effective To:
Contact (Person): Cothran, Jeremy
Email Address:


CC ID: 795448
Date Effective From: 2017-11
Date Effective To:
Contact (Person): Rogers, Daniel
Email Address:


Currentness Reference: Ground Condition

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 795445
W° Bound: -70.555
E° Bound: -70.482
N° Bound: 41.64
S° Bound: 41.544

Waquoit Bay, MA NERR

Extent Group 1 / Time Frame 1

CC ID: 795444
Time Frame Type: Range
Start: 2017-11
End: 2020-12

Access Information

Security Class: Unclassified
Data Access Constraints:


Data Use Constraints:

Cite this dataset when used as a source: NOAA retains the right to analyze, synthesize and publish summaries of the NERRS/NSC data. The NERRS/NSC retains the right to be fully credited for having collected and process the data. Following academic courtesy standards, the NERR site where the data were collected should be contacted and fully acknowledged in any subsequent publications in which any part of the data are used. The data enclosed within this package/transmission are only as accurate as the quality assurance and quality control procedures that are described in the associated metadata reporting statement allow. The user bears all responsibility for its subsequent use/misuse in any further analyses or comparisons. The Federal government does not assume liability to the Recipient or third persons, nor will the Federal government reimburse or indemnify the Recipient for its liability due to any losses resulting in any way from the use of this data. Requested citation format: NOAA National Estuarine Research Reserve System (NERRS) Science Collaborative(NSC).

Distribution Information

Distribution 1

CC ID: 1065218
Download URL:
Distributor: Office for Coastal Management (OCM) (2015 - Present)
File Name: Rogers17
File Type: Multiple formats



CC ID: 795450
URL Type:
Online Resource

This site provides a project overview and links to all associated products, including data.


CC ID: 1065215
URL Type:
Online Resource

Online article describing the project.

Data Quality



Quality Control Procedures Employed:

This information is detailed within the project links.


Lineage Statement:

This information is detailed within the project links.



CC ID: 1065220

Process Steps

Process Step 1

CC ID: 1065221


Process Contact: Office for Coastal Management (OCM)

Catalog Details

Catalog Item ID: 54578
GUID: gov.noaa.nmfs.inport:54578
Metadata Record Created By: Jeremy Cothran
Metadata Record Created: 2018-11-01 11:23+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-08-09 17:11+0000
Metadata Record Published: 2019-11-08
Owner Org: OCM
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2019-11-08
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2020-11-08