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Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of... Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd 1-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Microbial Ecology Springer Journals

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance

Lee, Jessica; Francis, Christopher
Microbial Ecology , Volume 73 (2) – Oct 5, 2016
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References (67)

Publisher
Springer Journals
Copyright
Copyright © 2016 by Springer Science+Business Media New York
Subject
Life Sciences; Microbiology; Ecology; Microbial Ecology; Geoecology/Natural Processes; Nature Conservation; Water Quality/Water Pollution
ISSN
0095-3628
eISSN
1432-184X
DOI
10.1007/s00248-016-0865-y
pmid
27709247
Publisher site
See Article on Publisher Site

Abstract

Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd 1-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.

Journal

Microbial Ecology – Springer Journals

Published: Oct 5, 2016

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