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

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.

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Acknowledgments

This work was supported by NSF CAREER Grant OCE-0847266 (to C.A.F.) and by a Stanford Graduate Fellowship (from William R. and Sara Hart Kimball) and a Marshall-EPA Fellowship (to J.A.L.). We thank Julian Damashek for his extensive help with a great many aspects of this work, from assisting with sample collection to providing feedback on data presentation, and especially for carrying out the chemical analysis of the bottom-water samples. Arushi Atluri provided invaluable assistance with acquisition and processing of the nirK sequences. Finally, also owe extensive thanks to Jim Cloern, Jessica Dyke, Amy Kleckner, Jan Thompson, and the other USGS scientists and staff who made our work on the R/V Polaris possible.

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Correspondence to Christopher A. Francis.

Additional information

The nucleotide sequences reported in this study have been deposited in GenBank under accession nos. KR060094—KR060621 (for nirK) and KR060622—KR061281 (for nirS).

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Lee, J.A., Francis, C.A. Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance. Microb Ecol 73, 271–284 (2017). https://doi.org/10.1007/s00248-016-0865-y

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Keywords

  • Nitrogen cycle
  • Denitrification
  • nirK
  • nirS
  • Estuarine sediment
  • San Francisco Bay