Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding.
Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities.
Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand. Electronic address: xavier.pochon@cawthron.org.nz.
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Pochon
Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
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Wood
Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Research, PO Box 1870, Bergen 5817, Norway.
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Keeley
Department of Genetics and Evolution, University of Geneva, Switzerland.
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Lejzerowicz
Department of Genetics and Evolution, University of Geneva, Switzerland; IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France.
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Esling
Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand.
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Drew
Department of Genetics and Evolution, University of Geneva, Switzerland.
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Pawlowski
D000818:Animals; D017756:Aquaculture; D044822:Biodiversity; D017753:Ecosystem; D004784:Environmental Monitoring / Q000379:methods*; D056908:Foraminifera / Q000145:classification / Q000235:genetics*; D019015:Geologic Sediments / Q000737:chemistry*; D059014:High-Throughput Nucleotide Sequencing; D015999:Multivariate Analysis; D009520:New Zealand; D012474:Salmon
Aquaculture; Benthic ecology; Biomonitoring; Foraminifera; High-throughput sequencing; Metabarcoding