Bacterial abundance and aerobic microbial activity across natural and oyster aquaculture habitats during summer conditions in a northeastern Pacific estuary

We measured sediment properties and the abundance and aerobic metabolism of microbes in Willapa Bay, Washington, USA, to test the response of sediment microbes to oyster aquaculture. Sites spanned the estuary gradient (practical salinity units ranged from 24 to 30 under seasonally low river flows) and six different low-intertidal habitat types: eelgrass (Zostera marina), unstructured tideflat, oyster hummocks (reefs of Crassostrea gigas), longline oyster aquaculture, hand-picked on-bottom oyster aquaculture, and dredged on-bottom oyster aquaculture. Aerobic metabolism was assessed by sole-source carbon use (SSCU) of 31 carbon sources on Biolog plates. Sediments generally became siltier and more organically enriched into the estuary, but no consistent differences in sediment properties occurred across habitat types. Bacterial cell density tracked organic content. Across the estuary gradient, overall aerobic SSCU increased less steeply than bacterial cell density, possibly as anaerobic metabolism became more important. Across habitats, aerobic SSCU differed significantly in both overall metabolism and diversity of carbon sources. Aerobic metabolism was generally lower for sediment microbes from intertidal on-bottom oyster aquaculture than from eelgrass. Humans indirectly alter microbial activity through biogenic habitats created during aquaculture, but, as has been shown for bivalves more generally, these changes were relatively small, particularly in comparison to sediment changes along estuarine gradients.