Summer warming and deoxygenation shape estuarine microbial plankton across domains of life

Abstract Microbial plankton have complex relationships with interacting coastal changes, including warming, eutrophication, and deoxygenation. At intra-annual scales, these changes can be tracked during the summer progression of warming and deoxygenation in eutrophic, seasonally hypoxic coasts. To study these dynamics, we combined flow cytometry (prokaryote biomass), microscopy (biomass of consumer protists and micrometazoans), and DNA metabarcoding (diversity of prokaryotes and microbial eukaryotes) in a harbour of the Long Island Sound estuary (New York, USA) over two summers. We found that biomass values remained relatively stable, whereas alpha- and beta-diversity differed significantly between pre-hypoxic and hypoxic periods. Among more than 10 abiotic and biotic variables analysed, temperature emerged as the most significant predictor of prokaryote biomass, and both prokaryote and microeukaryote alpha- and beta-diversity. Yet shifts in taxonomic profiles, with higher proportions of prokaryote N- and S-cyclers and protistan parasites during hypoxia, suggest functional changes more strongly linked to lower dissolved oxygen (DO) than to higher temperatures. Overall, we revealed that summer warming has a stronger influence on microbial biomass and diversity than deoxygenation, while the latter covaries with taxa that have specific biogeochemical roles (e.g. ammonia oxidation with consequent DO consumption) or biological interactions (e.g. parasitism). These findings underscore the importance of temperature and DO in structuring microbial plankton across domains of life and provide insight into potential microbial responses (or contributions) to environmental stress.