Microbial communities (bacteria, archaea and eukaryotes) in a temperate estuary during seasonal hypoxia

Abstract

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.

Protists in hypoxic waters of Jinhae Bay and Masan Bay, Korea, based on metabarcoding analyses: emphasizing surviving dinoflagellates

“…In the present study, the heterotrophic dinoflagellate Gyrodinium dominans was consistently present in all samples from both surface and bottom waters of Jinhae and Masan Bays in both hypoxic and non-hypoxic periods. Similarly, Santoferrara et al (2022) also reported a wide distribution of G. dominans in both the surface and bottom waters during hypoxic and non-hypoxic periods in Long Island Sound, USA. In addition, Eom et al (2024) reported that G. dominans grew in hypoxic waters by feeding on algal prey in laboratory experiments, which supports our field observations.…”

“…Among the phyla that are ASV-assigned in the present study, the phylum Dinoflagellata exhibited the highest relative read abundance in both non-hypoxic surface and hypoxic bottom waters during the hypoxic period. Similarly, Santoferrara et al (2022) reported that the relative read abundance of the phylum Dinoflagellata in the hypoxic water (<2 mg L -1 ) of Long Island Sound, USA, was the highest among the protistan phyla. Additionally, Rocke et al (2016) reported that the relative read abundances of the phylum Dinoflagellata in the hypoxic water of Tolo Harbor, Hong Kong, were the highest and second highest.…”

“…. (2013),Rocke et al (2016),Lee et al (2020),Rajan et al (2021),Ok et al (2021a),Santoferrara et al (2022),Scully et al (2022) This study Numbers in parentheses represent the number of species in the list. The dinoflagellate species in the list were identified based on the amplicon sequence variant data.…”

“…Molecular sequencing is one such useful tool for characterizing protistan community structures, which identifies numerous protist taxa in target environments with high sensitivity and taxonomic resolution (Santoferrara et al 2020, Jang et al 2022. Protist community structures and some species surviving in hypoxic waters have been investigated using molecular sequencing in limited regions such as Long Island Sound, USA and Tolo Harbor, Hong Kong (Rocke et al 2016, Santoferrara et al 2022. To better understand protist species that can thrive in hypoxic waters and to comprehensively characterize protist community structures in various marine environments, it is essential to conduct DNA sequencing analyses across a broader range of countries and regions.…”

Transitions in nitrogen and organic matter form and concentration correspond to bacterial population dynamics in a hypoxic urban estuary

“…Similarly, outputs from a coupled physical-biogeochemical model showed that WLIS simulated bacterial biomass density (per unit volume) begins to increase during Apr, fluctuates late spring-early summer, reaching 2.75 mmol N m −3 in Jul and 2 mmol N m −3 in Aug before decreasing during the fall (Liu et al 2015 ). While less is known about WLIS microbial diversity, high-throughput sequencing using 16S rRNA genes revealed that spatial and temporal trends in dominant taxa coincided with bottom-water hypoxia during 2019 (Santoferrara et al 2022 ).

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