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1. The complete genome sequence for putative H2- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome 
Handley, Kim M., Bartels, Daniela, O'Loughlin, Edward J., Williams, Kenneth H., Trimble, William L., Skinner, Kelly, Gilbert, Jack A., Desai, Narayan, Glass, Elizabeth M., Paczian, Tobias, Wilke, Andreas, Antonopoulos, Dionysios, Kemner, Kenneth M., and Meyer, Folker
- Environmental Microbiology. Nov 2014, Vol. 16 Issue 11, p3443, 20 p.
Transfer RNA -- Physiological aspects, Transfer RNA -- Analysis, Nitric oxide -- Physiological aspects, Nitric oxide -- Analysis, Genomes -- Physiological aspects, Genomes -- Analysis, Sulfites -- Physiological aspects, Sulfites -- Analysis, Aquifers -- Physiological aspects, Aquifers -- Analysis, Genetic research -- Physiological aspects, Genetic research -- Analysis, Phylogeny -- Physiological aspects, Phylogeny -- Analysis, Sulfides -- Physiological aspects, Sulfides -- Analysis, Genomics -- Physiological aspects, and Genomics -- Analysis
Byline: Kim M. Handley, Daniela Bartels, Edward J. O'Loughlin, Kenneth H. Williams, William L. Trimble, Kelly Skinner, Jack A. Gilbert, Narayan Desai, Elizabeth M. Glass, Tobias Paczian, Andreas Wilke, Dionysios Antonopoulos, Kenneth M. Kemner, Folker Meyer Summary We reconstructed the complete 2.4Mb-long genome of a previously uncultivated epsilonproteobacterium, Candidatus Sulfuricurvum sp. RIFRC-1, via assembly of short-read shotgun metagenomic data using a complexity reduction approach. Genome-based comparisons indicate the bacterium is a novel species within the Sulfuricurvum genus, which contains one cultivated representative, S.kujiense. Divergence between the species appears due in part to extensive genomic rearrangements, gene loss and chromosomal versus plasmid encoding of certain (respiratory) genes by RIFRC-1. Deoxyribonucleic acid for the genome was obtained from terrestrial aquifer sediment, in which RIFRC-1 comprised a1/447% of the bacterial community. Genomic evidence suggests RIFRC-1 is a chemolithoautotrophic diazotroph capable of deriving energy for growth by microaerobic or nitrate-/nitric oxide-dependent oxidation of S.sub.0, sulfide or sulfite or H.sub.2 oxidation. Carbon may be fixed via the reductive tricarboxylic acid cycle. Consistent with these physiological attributes, the local aquifer was microoxic with small concentrations of available nitrate, small but elevated concentrations of reduced sulfur and NH.sub.4.sub.+/NH.sub.3-limited. Additionally, various mechanisms for heavy metal and metalloid tolerance and virulence point to a lifestyle well-adapted for metal(loid)-rich environments and a shared evolutionary past with pathogenic Epsilonproteobacteria. Results expand upon recent findings highlighting the potential importance of sulfur and hydrogen metabolism in the terrestrial subsurface. CAPTION(S): Fig.S1. (a) Graph showing the output from the assembly of Ca. Sulfuricurvum genome contigs based on different quantities of metagenomic input reads. (b) Graph of the genome assembly output based on the number of input reads and the number of mismatches to the genome. (c) Graph of the assembly output based on different relative proportions of Ca. Sulfuricurvum-like reads in the metagenome. Fig.S2. Circular genome plots of (a) strain RIFRC-1 and (b) the closest relative S.kujiense. Tracks 1 and 2 (outermost) are forward and reverse protein coding regions respectively, coloured by Seed subsystem categories; track 3 shows rRNA; track 4 shows tRNA and putative insertion sequences associated with annotated transposases; track 5 shows genomic islands predicted using the EGID method (Che etal., 2011); track 7 shows genes associated with hydrogen, nitrogen and sulfur utilization, nitrogen-fixation and metal(loid) detoxification; and tracks 8 and 9 show GC content and skew respectively. Fig.S3. Sqr and Fcc predicted protein unrooted maximum-likelihood tree. Bootstrap values from 1000 replicates of a[yen]50 are shown. GenBank accession numbers are given in parentheses. The scale bar represents the number of substitutions per site. Fig.S4. Hydrogenase predicted protein unrooted maximum-likelihood tree. Bootstrap values from 1000 replicates of a[yen]50 are shown. GenBank accession numbers are given in parentheses. The scale bar represents the number of substitutions per site. Bolded cluster designations A-D equate to the hydrogenase gene map designations in Fig.4. Unbolded cluster designations denote Escherichia coli hydrogenases 1-4, HupV and EchE hydrogenases, and in grey hydrogenase phylogenetic groupings designated by Vignais etal. (2001) and Vignais and Colbeau (2004). Fig.S5. ArsC and ArsR predicted protein unrooted maximum-likelihood tree. Branch colours denote phyla. Scale bars represent the number of substitutions per site. TableS1. Geochemistry of groundwater monitoring well LR-MLS-21. TableS2. Comparison of S-oxidizing Epsilonproteobacteria. Abbreviations: Uncultured (Uncl.); Aerobic (Aer.); Anaerobic (Anaer.); oxidation (ox.); reduction (red.); fixation (fix.); References (Ref.); Yes (Y); No (N); Genes present (G). TableS3. Location of key predicted proteins associated with S, N and H utilization, metal(loid) tolerance, toxin-antitoxin systems, virulence and the reductive tricarboxylic acid (rTCA) cycle. TableS4. Genomic positions of predicted insertion sequences (IS) and genomic islands. TableS5. Summary of community genomic shotgun and amplicon sequence data.
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