Interception of River Sediment in Estuaries Revealed by Microbial Community Source Tracking

The time lag between river-borne sediment input to estuaries and its subsequent effects on estuarine ecosystems is difficult to measure but is a conceptually important time scale that influences managed interventions at watershed scales. This study investigated high-throughput sequencing of microbial fingerprinting as a novel method for tracking fluvial sediment movement through estuaries during the days and weeks following river floods. Bioassay incubation experiments in the Choptank and Pocomoke Rivers, Maryland, U.S.A. revealed that microbial communities in river and tidal waters were more similar to each other than to those in saline waters. Although microbial community composition shifted over time, distinct fingerprints remained identifiable for over 15 days. In tidal water treatments, introduced microbial fingerprints from river and saline sources persisted, while in saline treatments, microbial fingerprints from introduced river and tidal communities faded—highlighting the selective influence of ambient water chemistry and salinity on microbial survival and composition. Applying these methods during storm events, we found that riverine microbial fingerprints were rapidly diluted: 50% of riverine sediment was deposited within the upper 10 km of the estuary and less than 30% of the sediment in the mesohaline estuary was attributable to river sediment inputs during the event. These are the first such measurements of deposition and dilution of river sediment that estuarine models and other approaches might only predict or imply. The results also demonstrate the broader viability of microbial fingerprinting as a tool for tracing short-term sediment dynamics and source contributions in estuarine environments.