Taxonomy and diversity of bacterial communities associated with marine sediments from Chilean salmonid farms

Abstract

A marine sediment survey beneath four salmon farms in southern Chile was conducted. 16S rRNA pyrosequencing‐based analysis was used to study the taxonomy and diversity of bacterial communities in sediments. Samples were taken under farm cages (study site) and reference (control) sites at different seasons and productive periods. Families associated with phyla Proteobacteria and Bacteroidetes were the most abundant, representing on average 50.7% of the total bacterial community. Flavobacteriaceae was the single family observed in all samples and also the most abundant. Bacterial diversity and richness indices (Chao1, Shannon and PD) at the study sites during productive periods showed a broader range of values than those measured in control or resting stage samples. Also, a very low number of shared families (2/54), compared with those taken at control (13/31) and resting stages (13/45), was observed. Bray–Curtis clustering of libraries resulted in two main clades, one mainly represented by samples of the study site and productive states, dominated by Sulfurovum with low values for bacterial diversity and richness indices and a community structure related to sulphidic sediments, while the other clades, mainly composed by control and resting samples, resulted dominated by Flavobacteriaceae and exhibited higher values of diversity and richness.

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline

“…The reconstruction of metagenome-assembled genomes in the microbial-mediated sulfur cycle determined that Sedimenticolaceae possess near-complete, encoded pathways for denitrification ( Vavourakis et al, 2019 ). Indeed, along with Desulfobulbaceae , Sedimenticolaceae was the most abundant family reported in association with marine sediments from Chilean salmonid farms ( Miranda et al, 2020 ). Furthermore, some of these families including Desulfobacteraceae were observed in the permanent anoxic/hypoxic sediment in the deepest part of the Baltic Sea, which highlighted active functional traits related to OM degradation, reduction of sulfate, and methanogenesis ( Broman et al, 2017 ).…”

“…High abundance, diversity, and activity of microorganisms in marine sediments play vital roles in global biogeochemical cycles ( Prokopenko et al, 2013 ; Hoshino et al, 2020 ), partially because they are involved in the transforming and degrading organic matter ( Koho et al, 2013 ), these processes, release nitrogen and phosphorus nutrients into the water column, thus facilitating the growth of primary producers and contributing to climate regulation ( Cavicchioli et al, 2019 ). However, most previous studies that consider the composition and spatial distribution of microbial communities in coastal areas both worldwide ( Jayakumar et al, 2012 ; Glass et al, 2015 ) and in Chile have focused on the water column (e.g., Molina et al, 2010 , 2020 , 2021 ; Stewart et al, 2012 ; Ulloa et al, 2012 ) and little is known about benthic microbial structure, activity and interactions in marine sediments that experience fluctuating redox conditions due to the oxygen-depleted waters and trace metal (TM) gradients ( Farías et al, 2004 ; Broman et al, 2017 ; Rasigraf et al, 2017 ; Miranda et al, 2020 ).…”

Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria

“…All three genera grow (micro)aerobically and oxidize reduced sulfur compounds (sulfide, thiosulfate, tetrathionate and elemental sulfur) in marine environments ( Campbell et al, 2006 ; Takai et al, 2006 ; Park et al, 2011 ; Williams et al, 2012 ; Kojima et al, 2017 ). In particular, sulfidic fish farm sediments are well-known for an increased presence of Campylobacterota ( Sulfurovum or Sulfurimonas ) during the production cycle and fallowing periods ( Aranda et al, 2015 ; Verhoeven et al, 2018 ; Kolda et al, 2020 ; Miranda et al, 2020 ; Quero et al, 2020 ). Thick mats of filamentous microbes from the Thiotrichaceae family performing sulfide oxidation are also commonly found in sediments near cages ( Aranda et al, 2015 ; Miranda et al, 2020 ).…”

“…In particular, sulfidic fish farm sediments are well-known for an increased presence of Campylobacterota ( Sulfurovum or Sulfurimonas ) during the production cycle and fallowing periods ( Aranda et al, 2015 ; Verhoeven et al, 2018 ; Kolda et al, 2020 ; Miranda et al, 2020 ; Quero et al, 2020 ). Thick mats of filamentous microbes from the Thiotrichaceae family performing sulfide oxidation are also commonly found in sediments near cages ( Aranda et al, 2015 ; Miranda et al, 2020 ). However, such microbial mats were not observed at the SPP and LPP field sites upon retrieval of the sediment and taxa assigned to this family contributed less than 0.01% of the 16S rRNA gene sequences.…”

“…A sizeable fraction of this fish farming (33.1 million tons) occurs in marine waters ( FAO, 2022 ). This intensive aquaculture practice generates large quantities of organic waste that predominantly sinks to the seafloor, which includes both waste products (feces) and undigested fish food ( Quiñones et al, 2019 ; Miranda et al, 2020 ). The enrichment of organic matter in sediments underneath fish cages promotes anaerobic mineralization, and particularly stimulates sulfate reduction, which generates high concentrations of sulfide in sediments ( Holmer and Kristensen, 1996 ).…”