Abstract

This study investigates prokaryotic communities within sub-Antarctic marine sediments impacted by salmonid aquaculture in southern Chile, employing 16S rRNA gene sequencing to assess alpha and beta diversity, as well as the inferred functional roles of prokaryotes in sediment biogeochemistry, with particular emphasis on rocky seabeds exhibiting varying degrees of giant sulphur-oxidising bacteria (GSOB) mat coverage. Candidatus Isobeggiatoa was identified as the predominant member of the Beggiatoaceae GSOB, consistent with its established ecological role in sulphide-rich marine environments. A novel U-shaped pattern in prokaryotic alpha diversity was observed along the GSOB coverage gradient, characterised by a decline of up to 30 % in transitional zones followed by partial recovery in areas of extensive GSOB mat coverage; beta diversity analysis reflected this trend, confirming significant shifts in community structure across the gradient. Changes in community composition were primarily attributable to fluctuations in the relative abundance of key bacterial taxa, notably Sulfurovum and Sulfurimonas, which predominated in transitional zones but diminished at sites with extensive GSOB coverage. The partial recovery of alpha diversity in highly impacted sites with greater GSOB coverage was accompanied by an increase in anaerobic chemolithotrophic and fermentative groups, indicative of a successional dynamic. Collectively, these findings elucidate a clear relationship between GSOB mat coverage and prokaryotic community composition in aquaculture-affected sediments and support the recommendation of a standardised GSOB coverage scale as a bioindicator for the management of vulnerable sub-Antarctic marine ecosystems.