Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium"

Sarah Zecchin, Ralf C. Mueller, Jana Seifert, Ulrich Stingl, Karthik Anantharaman, Martin von Bergen, Lucia Cavalca, Michael Pester

Research output: Contribution to journalArticlepeer-review

38 Scopus citations

Abstract

Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4·2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA), with expression of its first step being detected in bulk soil without gypsum amendment. The relative abundances of Nbg-4 were similar under both treatments, indicating that Nbg-4 maintained stable populations while shifting its energy metabolism. Whether Nbg-4 is a strict sulfate reducer or can couple sulfur oxidation to DNRA by operating the pathway of dissimilatory sulfate reduction in reverse could not be resolved. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as an electron donor; the Wood-Ljungdahl pathway was expressed under both treatments. Comparison to publicly available Nitrospirae genome bins revealed the pathway for dissimilatory sulfate reduction also in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the name “Candidatus Sulfobium mesophilum,” gen. nov., sp. nov.
Original languageEnglish (US)
JournalAPPLIED AND ENVIRONMENTAL MICROBIOLOGY
Volume84
Issue number5
DOIs
StatePublished - Feb 14 2018
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2022-06-03
Acknowledgements: This research was financed by the German Research Foundation (DFG) (PE 2147/1-1, to M.P.) and the European Union (FP7-People-2013-CIG, grant PCIG14-GA-2013-630188, to M.P.). This research was also supported by the Ph.D. Program in Food Systems at the University of Milan, as well as by an Erasmus+ placement studentship, both awarded to S.Z. Funding for U.S. was provided through baseline funds from KAUST and through the USDA National Institute of Food and Agriculture, Hatch project FLA-FTL-005631.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Ecology
  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology

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