Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments

Abstract

Abstract Estuaries are highly productive ecosystems where sediment microbes mediate carbon and nutrient cycling. Our understanding of estuarine microbial communities is limited by a lack of system level characterizations. Here we obtained 639 novel metagenome-assembled genomes (MAGs) from four seasons across San Francisco Bay (SFB), the largest estuary on the West Coast of the United States. In shallow sediments, we observed a broad diversity of uncultured prokaryotes with distinct pathways for nitrogen and sulfur cycling. This includes 12 Nitrospira capable of complete nitrification (comammox) and 5 Bacteroidota and Gammaproteobacteria with pathways for complete denitrification. We also identified abundant sulfur oxidizing and reducing organisms, including rdsr-encoding Spirochaetota. We observe phylum-level shifts in community composition across sites, yet key nitrogen and sulfur metabolisms are maintained throughout the estuary. This functional redundancy is important to consider for understanding microbial community responses to climate change and human activity in estuarine ecosystems.