title: Assessing the effects of salmon farming seabed enrichment using bacterial community diversity and high-throughput sequencing.
abstract: Aquaculture is an extremely valuable and rapidly expanding sector of the seafood industry. The sediment below active aquaculture farms receives inputs of organic matter from uneaten food and faecal material and this has led to concerns related to environmental sustainability. The impacts of organic enrichment on macrobenthic infauna are well characterized; however, much less is known about effect on bacterial communities. In this study, sediment, macrobenthic infauna samples and environmental data were collected along an enrichment gradient radiating out from a Chinook salmon (Oncorhynchus tshawytscha) farm (Marlborough Sounds; New Zealand). DNA and RNA were extracted and 16S rRNA metabarcodes from bacterial communities characterized using high-throughput sequencing. Desulfobacterales dominated at the cage (DNA and RNA), and at sites 50 m (DNA and RNA) and 150 m (RNA) from the farm. In contrast, unclassified bacteria from the class Gammaproteobacteria were the most abundant taxa at control sites (625 and 4000 m). Pronounced differences among DNA and RNA samples occurred at the cage site where Desulfobacterales abundance was markedly higher in RNA samples. There were strong correlations between shifts in bacterial communities and total organic matter and redox. This suggests that bacterial composition is strongly influenced by organic enrichment, a trait that may make them useful for assessing impacts associated with aquaculture farms.
authors.affiliation: Coastal and Freshwater Group, Cawthron Institute, 7010 Nelson, New Zealand.
authors.forename: Eddy
authors.initials: E
authors.lastname: Dowle
authors.affiliation: Coastal and Freshwater Group, Cawthron Institute, 7010 Nelson, New Zealand Institute of Marine Science, University of Auckland, 1142 Auckland, New Zealand.
authors.forename: Xavier
authors.initials: X
authors.lastname: Pochon
authors.affiliation: Coastal and Freshwater Group, Cawthron Institute, 7010 Nelson, New Zealand.
authors.forename: Nigel
authors.initials: N
authors.lastname: Keeley
authors.affiliation: Coastal and Freshwater Group, Cawthron Institute, 7010 Nelson, New Zealand School of Biological Science, University of Waikato, 3240 Hamilton, New Zealand susie.wood@cawthron.org.nz.
authors.forename: Susanna A
authors.initials: SA
authors.lastname: Wood
mesh_terms: D000818:Animals; D017756:Aquaculture / Q000379:methods; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D045858:Desulfitobacterium / Q000235:genetics / Q000302:isolation & purification; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D019015:Geologic Sediments / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D059013:Microbial Consortia; D009520:New Zealand; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012474:Salmon / Q000382:microbiology*; D017747:Seafood / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: aquaculture; bacterial diveristy; high-throughput sequencing; salmon farming