Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium
Mueller, Ralf C.
van Bergen, Martin
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AbstractNitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. However, little is known about their genetic make-up and physiology. Here, we present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and analyzed its in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The genome of Nbg-4 was assembled from replicated metagenomes of rice paddy soil that was used to grow rice plants in the presence and absence of gypsum (CaSO4x2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression thereof 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, which was expressed in bulk soil without gypsum amendment. The relative abundance of Nbg-4-related metagenome reads was similar under both treatments indicating that it maintained stable populations while shifting its energy metabolism. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as electron donor, with the Wood-Ljungdahl pathway being expressed under both conditions. Comparison to publicly available Nitrospirae genome bins confirmed that the pathway for dissimilatory sulfate reduction is also present in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the phylum 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., spec. nov.
CitationZecchin S, Mueller RC, Seifert J, Stingl U, Anantharaman K, et al. (2017) Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium. Available: http://dx.doi.org/10.1101/196774.
SponsorsThis research was financed by the German Research Foundation (DFG, PE 2147/1-1 to MP) and the European Union (FP7-People-2013-CIG, Grant No PCIG14-GA-2013-630188 to MP). Furthermore, this research was supported by the PhD School in Food Systems from the University of Milano as well as by an ERASMUS+ placement studentship, both awarded to SZ. Funding for US was provided through baseline funds from KAUST and through the USDA National Institute of Food and Agriculture, Hatch project FLA-FTL-005631. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. The authors declare no conflict of interests.
PublisherCold Spring Harbor Laboratory