Project description:Desulfovibrio aespoeensis Aspo-2, DSM 10631(T), is a mesophilic, hydrogenotrophic sulfate-reducing bacterium sampled from a 600-m-deep subsurface aquifer in hard rock under the island of Äspö in southeastern Sweden. We report the genome sequence of this bacterium, which is a 3,629,109-bp chromosome; plasmids were not found.
Project description:Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.
Project description:We report the complete genome sequence of the anaerobic, sulfonate-respiring, sulfate-reducing bacterium Desulfovibrio desulfuricans IC1. The genome was assembled into a single 3.25-Mb circular chromosome with 2,680 protein-coding genes identified. Sequencing of sulfonate-metabolizing anaerobes is key for understanding sulfonate degradation and its role in the sulfur cycle.
Project description:Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.
Project description:Microorganisms are key players in the transformation of mercury into neurotoxic methylmercury (MeHg). Nevertheless, this mechanism and the opposite MeHg demethylation remain poorly understood. Here, we explored the impact of inorganic mercury (IHg) and MeHg concentrations from 0.05 to 50 ?M on the production and degradation of MeHg in two sulfate-reducing bacteria, Pseudodesulfovibrio hydrargyri BerOc1 able to methylate and demethylate mercury and Desulfovibrio desulfuricans G200 only able to demethylate MeHg. MeHg produced by BerOc1 increased with increasing IHg concentration with a maximum attained for 5 ?M, and suggested a saturation of the process. MeHg was mainly found in the supernatant suggesting its export from the cell. Hg L3-edge High- Energy-Resolution-Fluorescence-Detected-X-ray-Absorption-Near-Edge-Structure spectroscopy (HERFD-XANES) identified MeHg produced by BerOc1 as MeHg-cysteine2 form. A dominant tetracoordinated ?HgS form was detected for BerOc1 exposed to the lowest IHg concentrations where methylation was detected. In contrast, at the highest exposure (50 ?M) where Hg methylation was abolished, Hg species drastically changed suggesting a role of Hg speciation in the production of MeHg. The tetracoordinated ?HgS was likely present as nano-particles as suggested by transmission electron microscopy combined to X-ray energy dispersive spectroscopy (TEM-X-EDS) and nano-X ray fluorescence (nano-XRF). When exposed to MeHg, the production of IHg, on the contrary, increased with the increase of MeHg exposure until 50 ?M for both BerOc1 and G200 strains, suggesting that demethylation did not require intact biological activity. The formed IHg species were identified as various tetracoordinated Hg-S forms. These results highlight the important role of thiol ligands and Hg coordination in Hg methylation and demethylation processes.
Project description:Whole-genome fitness analysis in microbes that uses saturating transposon mutagenesis combined with massively parallel sequencing (Tn-seq) is providing a measure of the contribution of each gene to a given growth condition. With this technique, gene fitness profiles and essential genes are discovered by simultaneous analyses of whether the absence of each gene product alters the growth kinetics of the bacterium. Here we modify the standard Tn-seq procedure to simplify and shorten the process by including delivery of the transposon through conjugation and liquid culture enrichment of the mutant pool, creating transposon liquid enrichment sequencing (TnLE-seq). To illustrate the success of these modifications and the robustness of the procedure, analyses of gene fitness of two cultures of the strictly anaerobic bacterium Desulfovibrio vulgaris Hildenborough were performed, with growth on lactate as the electron donor and sulfate as the electron acceptor. These data demonstrate reproducibility and provide a base condition for analysis of fitness changes in deletion mutants and in various growth conditions. The procedural modifications will facilitate the application of this powerful genetic analysis to microbes lacking a facile genetic system. Pilot studies produced 2.5×10(5) and 3.4×10(5) unique insertion mutants in the anaerobe Desulfovibrio vulgaris Hildenborough grown under typical laboratory conditions in rich medium. These analyses provided two similar high-resolution maps of gene fitness across the genome, and the method was also applied to growth in minimal medium. These results were also compared to the coverage obtained with a ca. 13,000-member cataloged transposon library constructed by sequencing transposon insertion sites in individual mutants.
Project description:The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, 'Candidatus Endomicrobium trichonymphae' and 'Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of 'Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of 'Ca. Desulfovibrio trichonymphae'. The genome is small (1?410?056?bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of 'Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, 'Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, 'Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and 'Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut.