Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01–1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.

Cite this data as: Lisa A. Johnson, Suzanne C. Dufour, Derek D.N. Smith, Anthony J. Manning, Bulbul Ahmed, Sherry Binette, Dounia Hamoutene. Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. Ecotoxicology and Environmental Safety. Volume 268. 2023. 115683. ISSN 0147-6513. https://doi.org/10.1016/j.ecoenv.2023.115683

Datasets available for download

• Raw DNA sequencesHTML
  To Download

  • More information
  • Go to resource
• Values of the family-level 16S rRNA gene...CSV
  To Download

  • More information
  • Go to resource
• Values of the family-level 16S rRNA gene...XLSX
  To Download

  • More information
  • Go to resource
• Values of the family-level 16S rRNA gene...CSV
  To Download

  • More information
  • Go to resource
• Values of the family-level 16S rRNA gene...XLSX
  To Download

  • More information
  • Go to resource
• Data dictionaryCSV
  To Download

  • More information
  • Go to resource

• Genomics Research...
• Nature and Environment
• RNA-sequencing
• Science and Technology

Additional Info

• Maturity Level 1 (54%)
• Maturity Level 2 (31%)
• Maturity Level 3 (0%)
• Maturity Level 4 (0%)
• Maturity Level 5 (0%)
• Maturity Level 6 (0%)

Field	Value
Last Updated	October 20, 2025, 02:49 (UTC)
Created	October 20, 2025, 02:49 (UTC)
Domain / Topic Domain or topic of the dataset being cataloged.	Biota, Environment, Oceans
Title Title for the Dataset.	Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline
Description A description of the dataset.	In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01–1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria. Cite this data as: Lisa A. Johnson, Suzanne C. Dufour, Derek D.N. Smith, Anthony J. Manning, Bulbul Ahmed, Sherry Binette, Dounia Hamoutene. Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. Ecotoxicology and Environmental Safety. Volume 268. 2023. 115683. ISSN 0147-6513. https://doi.org/10.1016/j.ecoenv.2023.115683
Tags / Keywords Keywords/tags categorizing the dataset.	Genomics Research... Nature and Environment RNA-sequencing Science and Technology
Format (CSV, XLS, TXT, PDF, etc) File format of the dataset.
Dataset Size Dataset size in megabytes.
Metadata Identifier Metadata identifier – can be used as the unique identifier for catalogue entry
Published Date Published date of the dataset.	2024-12-30
Time Period Data Span (start date) Start date of the data in the dataset.
Time Period Data Span (end date) End date of time data in the dataset.
GeoSpatial Area Data Span A spatial region or named place the dataset covers.

Field	Value
Access category Type of access granted for the dataset (open, closed, service, etc).
License License used to access the dataset.	Open Government Licence - Canada
Limits on use Limits on use of data.
Location Location of the dataset.	https://open.canada.ca/data/en/dataset/519f52ef-100b-4a0e-addb-ce0b78b8e4ac
Data Service Data service for accessing a dataset.
Owner Owner of the dataset.	Fisheries and Oceans Canada | Pêches et Océans Canada
Contact Point Who to contact regarding access?
Contact Point Email The email to contact regarding access?
Publisher Publisher of the dataset.
Publisher Email Email of the publisher.	[email protected]
Author Author of the dataset.
Author Email Email of the author.
Accessed At Date the data and metadata was accessed.

Field	Value
Identifier Unique identifier for the dataset.
Language Language(s) of the dataset
Link to dataset description A URL to an external document describing the dataset.
Persistent Identifier Data is identified by a persistent identifier.
Globally Unique Identifier Data is identified by a persistent and globally unique identifier.
Contains data about individuals Does the data hold data about individuals?
Contains data about identifiable individuals Does the data hold identifiable data about individual?
Contains Indigenous Data Does the data hold data about Indigenous communities?
Portal Type Platform type of the source portal.

Field	Value
Version Version of the datatset	None
Source Source of the dataset.	None
Version notes Version notes about the dataset.
Is version of another dataset Link to dataset that it is a version of.
Other versions Link to datasets that are versions of it.
Provenance Text Provenance Text of the data.
Provenance URL Provenance URL of the data.
Temporal resolution Describes how granular the date/time data in the dataset is.
GeoSpatial resolution in meters Describes how granular (in meters) geospatial data is in the dataset.
GeoSpatial resolution (in regions) Describes how granular (in regions) geospatial data is in the dataset.

Field	Value
Indigenous Community Permission Who holds the Indigenous Community Permission. Who to contact regarding access to a dataset that has data about Indigenous communities.
Community Permission Community permission (who gave permission).
The Indigenous communities the dataset is about Indigenous communities from which data is derived.

Field	Value
Number of data rows If tabular dataset, total number of rows.
Number of data columns If tabular dataset, total number of unique columns.
Number of data cells If tabular dataset, total number of cells with data.
Number of data relations If RDF dataset, total number of triples.
Number of entities If RDF dataset, total number of entities.
Number of data properties If RDF dataset, total number of unique properties used by the triples.
Data quality Describes the quality of the data in the dataset.
Metric for data quality A metric used to measure the quality of the data, such as missing values or invalid formats.

Please login or register to comment.