Coastal anoxic sediment microbial community response to varying nutrient loading and salinity increase

Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently experience these fluctuations. This study investigates how the sediment microbial community coped with such changes by simulating coastal conditions in two methane-saturated, sulfidic anoxic bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) but under eutrophic (high) or, oligotrophic (low) conditions, and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium (DNRA) dominated under oligotrophic conditions. Methane oxidation was driven by canonical Methylobacter and Methylomonas species in eutrophic conditions, whereas a more diverse methane-oxidizing microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and a representative of gammaproteobacterial MBAE14. Novel putative copper-containing methane monooxygenases (CuMMOs) were identified in MBAE14 and co-enriched Rugosibacter genome, suggesting the need for further physiological and genetic characterization. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel biochemical pathways crucial for ecosystem functioning.