title: Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism.
abstract: Desulfovibrio vulgaris is a metabolically flexible micro-organism. It can use sulfate as an electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with a hydrogen-scavenging partner to relieve inhibition by hydrogen. These alternative metabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntrophic in a lactate-oxidizing dual-culture with Methanosarcina barkeri to a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 h after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Upregulation was observed for genes encoding ATPase and the membrane-integrated energy-conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipoproteins and membrane-bound proteins was downregulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologues found only in another syntrophic bacterium, Syntrophobacter fumaroxidans, and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome-encoding genes, which may be involved in the sulfidogenic metabolism.
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Caroline M
authors.initials: CM
authors.lastname: Plugge
authors.affiliation: Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA.
authors.forename: Johannes C M
authors.initials: JCM
authors.lastname: Scholten
authors.affiliation: Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Culley
authors.affiliation: Department of Biostatistics, Biomathematics, and Bioinformatics, Georgetown University, Washington DC, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Nie
authors.affiliation: Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA.
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Brockman
authors.affiliation: Center for Ecogenomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.|Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA.
authors.forename: Weiwen
authors.initials: W
authors.lastname: Zhang
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D016969:Desulfovibrio vulgaris / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D007773:Lactates / Q000378:metabolism; D017021:Methanosarcina barkeri / Q000235:genetics / Q000378:metabolism*; D013431:Sulfates / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D007773:Lactates; D013431:Sulfates