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Aquatic Microbial Ecology


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AME 88:61-79 (2022)  -  DOI: https://doi.org/10.3354/ame01982

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

Luciana F. Santoferrara1,2,5,*, George B. McManus2, Dianne I. Greenfield3,4, Susan A. Smith2

1Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
2Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
3Advanced Science Research Center at the Graduate Center, City University of New York, New York, NY 10031, USA
4School of Earth and Environmental Sciences, Queens College, Flushing, NY 11367, USA
5Present address: Department of Biology, Hofstra University, Hempstead, NY 11549, USA
*Corresponding author:

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.


KEY WORDS: Microbial plankton · Prokaryotes · Protists · DNA · Deoxygenation · Eutrophication · Long Island Sound


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Cite this article as: Santoferrara LF, McManus GB, Greenfield DI, Smith SA (2022) Microbial communities (bacteria, archaea and eukaryotes) in a temperate estuary during seasonal hypoxia. Aquat Microb Ecol 88:61-79. https://doi.org/10.3354/ame01982

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