eDNA and GeoChip: New Tools Linking Microbial Communities to Biogeochemical Functions in Eutrophic Estuarine Sediment

Estuaries are productive and diverse ecosystems that are important for humans, birds, and numerous marine species. Estuaries can be greatly affected by anthropogenic disturbances, and particularly local California estuaries that are shallow with tightly linked water-sediment interfaces. Many anthropogenic stressors contribute to dramatic changes in the ecological structure of these environments, especially enhanced supplies of nutrients that cause macroalgal blooms. We conducted seasonal field surveys to further explore human impacts on local California estuaries focusing on the sediment microbial community and subsequent biogeochemical changes paired with standard water quality measurements (e.g., pH). We used estuarine sediment environmental DNA (eDNA) to access the microbial community composition via 16S amplicon sequencing and functional analysis using the microarray, GeoChip 5.0. We found areas with poor water quality (i.e., acidic) were not only enhanced with specific microbial communities but also functional genes indicative of microbial processes that have the potential to cause poor water quality (i.e., acidification). As expected, poor water quality was a feature experienced only in the summer following large macroalgal blooms, but we were able to link these processes with the microbial functions that cause them. Our results suggest that both eDNA and GeoChip are valuable tools that can be used to further explore ecological questions in estuarine environments globally.