A comparison of visual and molecular methods for inferring biological communities in aquaculture enriched sediments - Impact assessment and cost-benefit analysis
Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visua...
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| Published in: | Marine pollution bulletin Vol. 209; no. Pt A; p. 117172 |
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| Main Authors: | , , , , , |
| Format: | Journal Article |
| Language: | English |
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Elsevier Ltd
01-12-2024
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| Abstract | Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples.
•16S and 18S rRNA metabarcoding both detect aquaculture derived organic enrichment.•Sediment metazoan communities derived from metabarcoding and visual methods differ.•Metabarcoding was faster than visual identification for 14 or more samples.•Metabarcoding was cheaper than visual identification for 96 or more samples. |
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| AbstractList | Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples.
•16S and 18S rRNA metabarcoding both detect aquaculture derived organic enrichment.•Sediment metazoan communities derived from metabarcoding and visual methods differ.•Metabarcoding was faster than visual identification for 14 or more samples.•Metabarcoding was cheaper than visual identification for 96 or more samples. Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples.Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples. Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples. |
| ArticleNumber | 117172 |
| Author | Coutts, Alexander Zimmermann, Danielle Strain, Elisabeth M.A. Bowman, John P. Ross, Donald J. Davey, Adam |
| Author_xml | – sequence: 1 givenname: Alexander surname: Coutts fullname: Coutts, Alexander email: alexander.coutts@utas.edu.au organization: Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia – sequence: 2 givenname: Danielle surname: Zimmermann fullname: Zimmermann, Danielle organization: Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia – sequence: 3 givenname: Adam surname: Davey fullname: Davey, Adam organization: Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia – sequence: 4 givenname: John P. surname: Bowman fullname: Bowman, John P. organization: Tasmanian Institute for Agriculture, University of Tasmania, Hobart, Tasmania, Australia – sequence: 5 givenname: Donald J. surname: Ross fullname: Ross, Donald J. organization: Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia – sequence: 6 givenname: Elisabeth M.A. surname: Strain fullname: Strain, Elisabeth M.A. organization: Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39454403$$D View this record in MEDLINE/PubMed |
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| Copyright | 2024 University of Tasmania Copyright © 2024 University of Tasmania. Published by Elsevier Ltd.. All rights reserved. |
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| Issue | Pt A |
| Keywords | Soft sediment eDNA metabarcoding Environmental monitoring Macrofauna Aquaculture |
| Language | English |
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