Oyster aquaculture enhances sediment microbial diversity: insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter-feeding, possibly leading to changes in the structure and function of sediment microbial communities. Further, oysters can initiate changes in sediment elemental concentrations, several of which are important mediators of microbial metabolism. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 yr of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA gene amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration, suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes observed here provides important insights for establishing best practices for sustainable farming in these areas.