Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
Highlights
The aquaculture industry is becoming a major food production sector to satisfy the increasing global demand for fish and seafood, the Western world is still developing its potential (FAO, 2020)
5,326,942 high-quality reads were obtained after sequencing, quality filtering, and taxonomic assignment, which were used for downstream analyses. These sequences clustered into 125,749 amplicon sequence variants (ASVs), 2,536 (1.8%) of which could not be assigned to a phylum and were termed “unclassified bacteria.”
Because the aim of our study was to link the ecological properties of bacterial taxon groups to the degree of aquaculture impact on the benthic environment, we have refrained from analyzing individual bacterial ASVs in detail but instead considered ecologically informative taxon ranks
Summary
The aquaculture industry is becoming a major food production sector to satisfy the increasing global demand for fish and seafood, the Western world is still developing its potential (FAO, 2020). The vast majority of studies dedicated to the environmental impacts of coastal aquafarming analyzed either changes in benthic macrofaunal communities in the vicinity of salmon farms (Carroll et al, 2003; Macleod and Forbes, 2004; Porrello et al, 2005; Hall-Spencer et al, 2006) or the echoes of bacterial action through geochemical signals such as changes in oxygen and sulfide concentrations or in redox potential (Hargrave, 2010; Cranford et al, 2020) Such studies showed a succession of macrofaunal communities along organic enrichment gradients, generally following the traditional pattern described by Pearson and Rosenberg (1978): With increasing aquafarm-related benthic disturbance, benthic organisms that are less resistant to environmental change are replaced by fewer, more tolerant or opportunistic species. Regulatory environmental compliance monitoring programs take advantage of macroinvertebrates as bioindicators to assess the environmental quality of the seafloor in the vicinity of salmon farms (Black and Paterson, 1998; Borja et al, 2009; Sany et al, 2014)
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