Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11T (= DSM 44721T)

Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated from soil based on its ability to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria. It displays tolerance to salts (up to 8%) and is related to Corynebacterium variabile involved in cheese ripening. As this is a type strain of Corynebacterium, this project describing the 2.75 Mbp long chromosome with its 2,369 protein-coding and 72 RNA genes will aid the Genomic Encyclopedia of Bacteria and Archaea project.     

Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1T (= DSM 45190T)

Corynebacterium maris Coryn-1^T Ben-Dov et al. 2009 is a member of the genus Corynebacterium which contains Gram-positive, non-spore forming bacteria with a high G+C content. C. maris was isolated from the mucus of the Scleractinian coral Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It displays tolerance to salts (up to 10%) and is related to the soil bacterium Corynebacterium halotolerans. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project, describing the 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584 protein-coding and 67 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.     

Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain CrmT (= DSM 23852T)

Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain Crm^T and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.     

Mechanism of delta pH maintenance in active and inactive cells of an obligately acidophilic bacterium.

The acidophilic bacterium PW2 possessed a delta pH of ca. 1.9 and a delta psi of 0 mV, corresponding to a proton motive force (delta p) of--114 mV. Protonophore-treated cells possessed little delta p but a delta pH of ca. 1.5, as measured by salicylic acid distribution or pH measurement of cell lysates. Starving PW2 cells continued to possess a delta pH of ca. 1.7, but exhibited converse changes in delta psi and delta p, with the former rising to +80 to +100 mV and the latter dropping essentially to 0; progressive loss of respiration, cellular ATP, and culture viability accompanied these changes. Thus, the protonophore-treated or starving PW2 cells attained an H+ electrochemical equilibrium. Net H+ influx resulting from declining respiration probably accounted for the increased delta psi in these cells; indeed, when respiration was progressively inhibited in active cells, there was increasing transient H+ influx and a proportional increase in delta psi. This transient H+ influx was sufficient to lethally acidify the cytoplasm, but for a buffering capacity of 85 nmol of H+/mg of protein per pH unit. Thus, the linkage of the transient H+ influx with the rise in the delta psi and the cytoplasmic buffering capacity play central roles in acidophilism, and it is conceivable that the same impermeant cellular macromolecule(s) accounts for both. If so, the delta psi would be a Donnan potential that in active cells is offset by energy-dependent H+ extrusion.     

High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China

Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169^T was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169^T is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169^T, together with the complete genome sequence and annotation from a culture of DSM 21076^T. The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.     

"Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum

From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum."     

Complete genome sequence of Desulfurispirillum indicum strain S5(T)

Desulfurispirillum indicum strain S5(T) is a strictly anaerobic bacterium isolated from river sediment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysiogenetes, which currently only includes three other cultured species. Strain S5(T) is the type strain of the species and it is capable of growth using selenate, selenite, arsenate, nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619 proteins and 49 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of arsenic and selenium, in addition to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.     

Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T)

Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).     

Inhibition of respiratory oxidation of elemental sulfur (S0) and thiosulfate in Thiobacillus versutus and another sulfur-oxidizing bacterium

Abstract The rates of thiosulfate, elemental sulfur (S⁰) and sulfite oxidation were measured respirometrically with an oxygen electrode using young cells of Thiobacillus versutus growing chemolithoautotrophically on thiosulfate under normal air pressure. Myxothiazol, an inhibitor of the cytochrome b−c₁ segment, and HQNO (2-N-heptyl-4-hydroxyquiniline N-oxide), acting in the quinone-cytochrome b region, both significantly inhibited the thiosulfate oxidation rate. The effect on the oxidation rate of S⁰ was even stronger. The oxidation of sulfite or ascorbate + TMPD (N,N,N',N'-tetramethyl-p-phenylenediamine) (substrates releasing electrons at the level of cytochrome c) was not inhibited by myxothiazol and HQNO. Thiosulfate, S⁰, sulfite and ascorbate + TMPD oxidations were strongly inhibited by KCN. These respiratory activities were almost completely eliminated by cell breakage. The reduction of b-type cytochrome was observed in thiosulfate-reduced minus sulfite-reduced difference spectra. This study confirms that S⁰ is an important intermediate of thiosulfate oxidation in Thiobacillus versutus , and that electrons released by S⁰ oxidation enter the respiratory chain in the quinone-cytochrome b region. This would allow an increased gain of energy, while less energy would probably be required for pyridine-nucleotide reduction.     

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment,and emendation of Phaeobacter daeponensis

TF-218^T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218^T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218^T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.     

Evidence for two pathways of thiosulfate oxidation in Starkeya novella (formerly Thiobacillus novellus)

The pathway of thiosulfate oxidation in the facultatively chemolithotrophic, sulfur-oxidizing bacterium Starkeya novella (formerly Thiobacillus novellus) has not been established beyond doubt. Recently, isolation of the sorAB genes, which encode a soluble sulfite:cytochrome c oxidoreductase, has been reported, indicating that a thiosulfate-oxidizing pathway not involving a multienzyme complex may exist in this organism. Here we report the cloning and sequencing of the soxBCD genes from S. novella, which are closely related to the corresponding genes encoding the thiosulfate-oxidizing multienzyme complex from Paracoccus pantotrophus. These findings suggest two distinct pathways for thiosulfate oxidation in S. novella. The expression of sorAB and soxC in cells grown on thiosulfate- and/or glucose-containing media was studied by Western blot analysis. The results showed that the SorAB protein is synthesized in the presence of thiosulfate irrespective of the presence of glucose. In contrast, the SoxC protein is subject to repression by glucose; the repression, however, appears to be dependent on the relative amounts of glucose and thiosulfate present. The regulatory effects observed for the expression of sorAB are likely to be mediated by an extracytoplasmic function sigma factor encoded by the sigE gene identified upstream of sorAB.     

Indirect oxidation of Co(II) in the presence of the marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1

Cobalt(II) oxidation in aquatic environments has been shown to be linked to Mn(II) oxidation, a process primarily mediated by bacteria. This work examines the oxidation of Co(II) by the spore-forming marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1, which enzymatically catalyzes the formation of reactive nanoparticulate Mn(IV) oxides. Preparations of these spores were incubated with radiotracers and various amounts of Co(II) and Mn(II), and the rates of Mn(II) and Co(II) oxidation were measured. Inhibition of Mn(II) oxidation by Co(II) and inhibition of Co(II) oxidation by Mn(II) were both found to be competitive. However, from both radiotracer experiments and X-ray spectroscopic measurements, no Co(II) oxidation occurred in the complete absence of Mn(II), suggesting that the Co(II) oxidation observed in these cultures is indirect and that a previous report of enzymatic Co(II) oxidation may have been due to very low levels of contaminating Mn. Our results indicate that the mechanism by which SG-1 oxidizes Co(II) is through the production of the reactive nanoparticulate Mn oxide.     

A Novel function of cytochrome C (555, Chlorobium thiosulfatophilum) in oxidation of thiosulfate

Thiosulfate-cytochrome c-551 reductase derived from $\text{Chlorobium}\text{thiosulfatophilum}$ has been highly purified. The enzyme reduces cytochrome $\text{c}\text{-551 of}\text{C}\text{.}\text{thiosulfatophilum}$ in the presence of thiosulfate while cytochrome $\text{c}$-555 of the organism is not reduced by the enzyme. Cytochrome $\text{c}$-555 reacts with the enzyme at an appreciable rate only in the presence of cytochrome $\text{c}$-551. However, the reduction rate of cytochrome $\text{c}$-551 by the enzyme is greatly enhanced on addition of a catalytic amount of cytochrome $\text{c}$-555. Therefore, cytochrome $\text{c}$-555 seems to function as an effector on thiosulfate-cytochrome $\text{c}$-551 reductase as well as it acts as the electron donor to the light-excited chlorobium chlorophylls.     

Evidence suggesting energy-dependent formaldehyde transport in an RuMP-type methylotroph (T15)

Formaldehyde accumulation ratios ([¹⁴CH₂O]_i/[¹⁴CH₂O]_o) as high as 12-fold were measured in anaerobic, CH₃OH-energized, whole cell suspensions of the ribulose monophosphate (RuMP)-type methylotrophic strain T15. Uptake kinetics were extremely rapid, enabling the attainment of equilibrium in only 10–30 s. Transport appears to be energy-dependent and associated with the protonmotive force (pmf). Anaerobic incubation with 5 M carbonyl p-(trifluoromethoxy)-phenylhydrazone (FCCP) led to 70%–90% reduction of the accumulation ratio. Though not as pronounced, diminished uptake was also observed in the presence of 140 M nigericin, 161 M valinomycin and 90 mM KSCN, commensurate with their effects on pmf. Accumulation of CH₂O as a function of external pH followed a trend more similar to that of pmf than either pH or . Preventing energization by incubation with 100 M N,N-dicyclohexylcarbodiimide (DCCD) led to nearly 80% inhibition of CH₂O transport. Over short time periods it was possible to chase accumulated ¹⁴CH₂O from previously loaded cells by collapsing pmf; however, this technique also indicated that significant ¹⁴CH₂O incorporation began to occur within 3 min.Abbreviations FCCP Carbonyl cyanide p-(trifluoromethyoxy)-phenylhydrazone - DCCD N,N-dicyclohexylcarbodiimide - RuMP ribulose monophosphate - TPP⁺ tetra[U-¹⁴C]phenylphosphonium - pmf protonmotive force     

H2 oxidation in the presence of thiosulfate, by a Thermoanaerobacter strain isolated from an oil-producing well

Abstract A thermophilic rod (strain SEBR 5268), isolated from an oil-producing well, was identified as a Thermoanaerobacter strain that was phenotypically related to T. finnii . Both SEBR 5268 and T. finnii oxidized H₂ by reducing thiosulfate to sulfide using yeast extract as growth substrate. H₂ oxidation in the presence of thiosulfate was significant at the end of the exponential growth of SEBR 5268 and was maintained during the lysis phase. In the absence of thiosulfate, H₂ was inhibitory for both strains. The role of H₂ consumption by these bacteria is discussed with regard to their metabolism on organic compounds.