Abstract
Coastal aquaculture has experienced substantial growth in the last few decades and associated impacts on natural environments are of increasing importance. Understanding both the effects of aquaculture on marine ecosystems and the processes of recovery during fallowing periods is crucial for the development of a more environmentally sustainable industry. Because bacteria are sensitive to environmental change, surveying fluctuations in bacterial communities is a promising tool for monitoring the status of benthic environments. Here, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in flocculent matter samples collected over a period of 3 years and at various distances from cages (0–200 meters) at production and fallow (3–35 months) salmon aquaculture sites in southern Newfoundland to evaluate the environmental impact of aquaculture on predominantly hard-bottom substrates. Bacterial composition analysis revealed four clusters, three of which (defined as “recently disturbed,” “intermediate impact,” and “high impact”) differed markedly from a fourth “low impact” cluster that contained far-field samples collected >500 m from cages. Samples within the high impact group were most often collected directly under cages, whereas those in the intermediate impact group were mainly sampled from 20 to 40 m from cages. Large scale phylum shifts (increases of Bacteroidetes, Firmicutes, Spirochaetes, and decreases in Proteobacteria and Epsilonbacteraeota) and a decline in bacterial diversity were observed in the high impact cluster, indicating significant ecological change. Samples from sites of different fallow duration were found in the high impact cluster, indicating a lack of recovery, even after 35 months of fallowing. Finally, we identified 28 genera as bacterial biomarkers, specific to one or more clusters, including genera associated with organically enriched environments and previously reported in the context of aquaculture impacts. Tracking the relative abundance of biomarkers in relation to different lengths of fallowing in the three more impacted clusters showed that these markers remained significantly above low impact cluster levels at all times, further pointing toward incomplete recovery. Our results suggest that coastal aquaculture on hard-bottom substrates is prone to long lasting impacts on bacterial communities, especially below cages, and that effects can be accurately tracked using bacterial community profiles or specific biomarkers.
Highlights
Aquaculture is a rapidly growing industry, contributing nearly 50% of the fish consumed on a global scale (FAO, 2016)
Using unsupervised clustering of 16S rRNA bacterial community compositions, we revealed samples clustered in specific groups (Figure 1)
Based on sample metadata as well as bacterial taxonomic composition and diversity, we suggest that these clusters of samples reflect the benthic bacterial community response to varying degrees of impact that aquaculture operations exert on the benthic environment
Summary
Aquaculture is a rapidly growing industry, contributing nearly 50% of the fish consumed on a global scale (FAO, 2016). Salmon are kept in suspended net pens over water depths greater than 30 m throughout a 1 to 2-year growth period and are fed fish pellets until harvesting (Hamoutene et al, 2013, 2015; Hamoutene, 2014), at which point a fallow period may be implemented (Fisheries and Oceans Canada, 2015). The seafloor within the vicinity of cages at salmon aquaculture sites may receive substantial inputs of particulate matter (Carroll et al, 2003; Jusup et al, 2009). This particulate matter consists mostly of decaying fish-feed pellets, fish fecal matter, microbes and other organic matter. In aquaculture impact studies (and ) this material is referred to as flocculent matter (DFO, 2014; Salvo et al, 2015; Hamoutene et al, 2016; Verhoeven et al, 2016) due to its characteristic flocculent appearance when it deposits and remains on the benthic surface (Yokoyama et al, 2006), where it can drive significant benthic community changes (Ye et al, 1991)
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