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A growing body of literature has highlighted the importance of phytoplankton-bacterial associations to marine and estuarine ecological and biogeochemical function, but their population linkages remain sparsely characterized within urban estuaries. Since many developed coastlines are heavily impacted by anthropogenic nutrient inputs, elucidating their phytoplankton-bacterial dynamics provides insight into nutrient cycling, productivity, and can help inform water quality management. This study compared surface (0.5 m depth) physical water quality, cell abundances of major phytoplankton taxa and bacteria, as well as concentrations of chlorophylla(chla) and dissolved organic matter (DOM) in the nitrogen (N)-enriched Western Long Island Sound (WLIS), USA, between mid-channel and shore sites (in 2020 and 2021). Shore bacterial and phytoplankton abundances as well as DOM concentrations (primarily dissolved organic N and carbon [DOC]), were significantly higher than mid-channel, especially during summer, indicative of terrestrial loading influencing microbial assemblages as well as N and C cycling. Abundances of key phytoplankton taxa were better indicators of bacterial abundances than chla, as bacterial abundances positively and significantly correlated with those of dinoflagellates, especially the most common generaProrocentrum(mid-channel, shore) andHeterocapsa(shore only), but not with diatoms. However, pennate diatom abundances negatively and significantly correlated with DOC concentrations in the mid-channel. Results highlight the impact of terrestrial inputs on WLIS microbial assemblage dynamics, presumably by favoring bacteria and dinoflagellate population coupling, as well as shed new ecological insight into how phytoplankton and bacterial communities respond to nutrient loadings in urban estuaries. 

Eutrophication and hypoxia markedly alter trophic dynamics and nutrient cycling in estuarine water columns, but little is known about the microbial communities that drive and interact with these changes. Here we studied microbial plankton (bacteria, archaea, protists and micro-metazoans) in a large temperate estuary where bottom hypoxia occurs every summer due to warmer temperatures, stratification, and oxidation of organic matter fueled by nutrient enrichment. We used high-throughput sequencing of the 16S and 18S rRNA genes (V4 region) and quantified multiple abiotic and biotic factors in surface and bottom waters during the summer of 2019. The conditions associated with the intensification of hypoxia in bottom waters as the summer progressed were linked to significant changes in the diversity, community structure and potential functioning of microbial communities. Under maximum hypoxia (dissolved oxygen concentration: 0.9-3.1 mg l -1 ), there were increased proportions of ammonia-oxidizing archaea (AOA), bacterivorous and parasitic protists, and copepod nauplii. Sequence proportions of AOA ( Nitrosopumilus) and nitrite-oxidizing bacteria ( Nitrospinaceae) were significantly correlated with the concentration of oxidized N species (nitrite plus nitrate, which peaked at 14.4 µM) and the proportions of nauplii DNA sequences and biomass. Our data support a tight coupling of biogeochemical and food web processes, with rapid oxidation of ammonia and accumulation of oxidized N species as hypoxia intensifies during the summer.