Spatio-temporal fish gill microbiota analysis as indicators in estuarine fish health monitoring

Coastal marine and estuarine systems are subject to enormous endogenous and exogenous pressures, particularly climate change, while at the same time being highly productive sources and nurseries for fish populations. Interactions between host and microbiome are increasingly recognized for their importance for fish health, with growing evidence indicating that the abundance and virulence of pathogenic bacteria are rapidly increasing. The microbial composition of the gill mucus reflects environmental conditions and represents a major entry route for pathogens into the fish body. High-throughput sequencing of prokaryotic populations from 250 samples of two fish species with highly different habitat preferences, as well as seasonal and spatial distributions in the Elbe estuary system, allowed us to describe the variation of the microbiota along a salinity gradient and under fluctuating environmental conditions. The analysis of estuarine fish core microbiota in relation to variable bacterial components indicated dysbiotic states under sustained hypoxia and high nutrient loads largely driven by the takeover of opportunistic pathogens ( Acinetobacter , Shewanella , Aeromonas ). By correlating bacterial abundances with environmental and physiological parameters in a co-occurrence network approach, we describe plasticity in microbiota composition, identify biomarkers of fish health and reconstruct movement patterns of the fish. Our results will help to shape future non-invasive and cost-effective monitoring programs, and identify factors that might be controlled in the estuary to promote fish and stock health.