title: Genetic basis for nitrate resistance in Desulfovibrio strains.
abstract: Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance.
authors.affiliation: Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA.
authors.forename: Hannah L
authors.initials: HL
authors.lastname: Korte
authors.affiliation: Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA.
authors.forename: Samuel R
authors.initials: SR
authors.lastname: Fels
authors.affiliation: Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA.
authors.forename: Geoff A
authors.initials: GA
authors.lastname: Christensen
authors.affiliation: Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Morgan N
authors.initials: MN
authors.lastname: Price
authors.affiliation: Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Jennifer V
authors.initials: JV
authors.lastname: Kuehl
authors.affiliation: Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA.
authors.forename: Grant M
authors.initials: GM
authors.lastname: Zane
authors.affiliation: Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Deutschbauer
authors.affiliation: Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.affiliation: Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA.
authors.forename: Judy D
authors.initials: JD
authors.lastname: Wall
keywords: Desulfovibrio; fitness profiling; functional genomics; nitrate inhibition; nitrite; stress response; sulfate-reducing bacteria; sulfide control