Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

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.

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

“…These bacteria have been reported as microbes related to aquaculture operations. For instance, sulphate-reducing bacteria such as members of the family Desulfovibrionaceae have been found to be enriched in sediments by aquaculture activity (Blancheton et al, 2013; Aranda et al, 2015; Frühe et al, 2021). Sulphate reducing bacteria can be enriched by high levels of organic matter relying on, for instance, fermented to acidic end products (i.e., by Psychromonadaceae, Vibrionaceae , and other marine (facultatively) anaerobic chemoorganotrophs), leading to the increased production of H 2 S (Barton and Hamilton, 2007; Kwon et al, 2016).…”

“…These include members of the taxa Psychromonadaceae ( Psychromonas ), Fusobacteriales (Fusobacteriaceae), Vibrionaceae, Desulfovibrionaceae (Desulfovibrio), Sulfurimonadaceae (Sulfurimonas), Sulfurovaceae (Sulfurovum), Fusibacteraceae (Fusibacter), Rhizobiales , and Sphingomonadaceae . Various microbial groups have been associated with marine environments receiving high level of nutrients and some have been reported as potential aquaculture impact biomarkers in the past (Blancheton et al, 2013; Kandel et al, 2014; Rasigraf et al, 2017; Verhoeven et al, 2018; Yang et al, 2019; Haro-Moreno et al, 2020; Zhang et al, 2020; Aalto et al, 2021; Dully et al, 2021; Frühe et al, 2021; Mahmoud and Magdy, 2021; Pan et al, 2021). According to these studies, such taxa are usually found in high abundance in near-cages sites, including Sulfurovum, Vibrionaceae, Desulfovibrionaceae, Methylotenera, Hyphomonadaceae, Spirosomaceae and Fusibacter, Flavobacteriaceae (NS3a marine group) and Bacteriovoracaceae .…”

“…According to these studies, such taxa are usually found in high abundance in near-cages sites, including Sulfurovum, Vibrionaceae, Desulfovibrionaceae, Methylotenera, Hyphomonadaceae, Spirosomaceae and Fusibacter, Flavobacteriaceae (NS3a marine group) and Bacteriovoracaceae . Moreover, Psychromonadaceae ( Psychromonas ), Fusobacteriales (Fusobacteriaceae) and Vibrionaceae have been also reported as members of the fish gut microbiome(Verhoeven et al, 2018; Frühe et al, 2021; Pan et al, 2021).…”

“…Spirochaetaceae ASVs are capable of anaerobic carbohydrate metabolism commonly found in the salmon gut microbiome (Fogarty et al, 2019). Members of this genus are often found in aquaculture impacted sites (Verhoeven et al, 2016; Kolda et al, 2020; Frühe et al, 2021). Another potential pathogen potentially present in the gut of fish (and with aquaculture systems in general) are the members of Arcobacteraceae .…”

“…These bacteria have been reported as microbes related to aquaculture operations. For instance, sulphate-reducing bacteria such as members of the family Desulfovibrionaceae have been found to be enriched in sediments by aquaculture activity (Blancheton et al, 2013;Aranda et al, 2015;Frühe et al, 2021).…”