Hymenobacter nivis sp nov., isolated from red snow in Antarctica

A novel aerobic bacterial strain, P3(T), was isolated from a red snow obtained from Antarctica. Cells of strain P3(T) were rod-shaped, non-motile, catalase-negative, oxidase-positive and Gramstain-negative. Growth was observed at temperatures ranging from 0 to 25 degrees C, with optimum growth at 15 degrees C. The pH range for growth was pH 5.3-7.8. The G+C content of the genomic DNA was 55.0 mol%. The major components in the fatty acid profile were iso-C-15: 0, summed feature 4 (iso-C-17:1 I and/or anteiso-C-17:1 B), anteiso-C-15:0 and summed feature 3 (isoC(16:1)omega 7c and/or iso-C(16:1 omega)6c). The predominant isoprenoid quinone was MK-7. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel isolate was a member of the genus Hymenobacter, and the strain showed highest sequence similarity (94 %) with Hymenpbacter glaciei VUG-A130(T), Hymenobacter soli PB17(T) and Hymenobacter antarcticus VUG-A42aa(T). On the basis of phylogenetic and phenotypic properties strain P3(T) represents a novel species of the genus Hymenobacter (for which the name Hymenobacter nivis sp. nov. is proposed. The types strain is P3(T) (= DSM 101755(T) = NBRC 111535(T))

Arsenite Oxidation by a Newly Isolated Betaproteobacterium Possessing arx Genes and Diversity of the arx Gene Cluster in Bacterial Genomes

Microbes play essential roles in arsenic transformation in the environment. Microbial arsenite oxidation is catalyzed by either of two distantly related arsenite oxidases, referred to as AIO and ARX. The arx genes encoding ARX and its regulatory proteins were originally defined in the genomes of gammaproteobacteria isolated from an alkaline soda lake. The arx gene cluster has been identified in a limited number of bacteria, predominantly in gammaproteobacteria isolated from lakes characterized by high pH and high salinity. In the present study, a novel arsenite-oxidizing betaproteobacterium, strain M52, was isolated from a hot spring microbial mat. The strain oxidized arsenite under both microaerophilic and nitrate-reducing conditions at nearly neutral pH. Genome analysis revealed that the strain possesses the arx gene cluster in its genome and lacks genes encoding AIO. Inspection of the bacterial genomes available in the GenBank database revealed that the presence of this gene cluster is restricted to genomes of Proteobacteria, mainly in the classes Gammaproteobacteria and Betaproteobacteria. In these genomes, the structure of the gene cluster was generally well-conserved, but genes for regulatory proteins were lacking in genomes of strains belonging to a specific lineage. Phylogenetic analysis suggested that ARX encoded in the genomes can be divided into three groups, and strain M52 belongs to a group specific for organisms living in low-salt environments. The ArxA protein encoded in the genome of strain M52 was characterized by the presence of a long insertion, which was specifically observed in the same group of ARX. In clone library analyses with a newly designed primer pair, a diverse ArxA sequence with a long insertion was detected in samples of lake water and hot spring microbial mat, characterized by low salinity and a nearly neutral pH. Among the isolated bacterial strains whose arsenite oxidation has been demonstrated, strain M52 is the first betaproteobacterium that possesses the arx genes, the first strain encoding ARX of the group specific for low-salt environments, and the first organism possessing the gene encoding ArxA with a long insertion

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘Sulfuricellaceae’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences

Induction of Tumor-specific T Cell Immunity by Anti-DR5 Antibody Therapy

Because tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) preferentially induces apoptosis in tumor cells and plays a critical role in tumor surveillance, its receptor is an attractive target for antibody-mediated tumor therapy. Here we report that a monoclonal antibody (mAb) against the mouse TRAIL receptor, DR5, exhibited potent antitumor effects against TRAIL-sensitive tumor cells in vivo by recruiting Fc receptor–expressing innate immune cells, with no apparent systemic toxicity. Administration of the agonistic anti-DR5 mAb also significantly inhibited experimental and spontaneous tumor metastases. Notably, the anti-DR5 mAb-mediated tumor rejection by innate immune cells efficiently evoked tumor-specific T cell immunity that could also eradicate TRAIL-resistant variants. These results suggested that the antibody-based therapy targeting DR5 is an efficient strategy not only to eliminate TRAIL-sensitive tumor cells, but also to induce tumor-specific T cell memory that affords a long-term protection from tumor recurrence

Sulfuriflexus mobilis gen. nov., sp nov., a sulfur-oxidizing bacterium isolated from a brackish lake sediment

A chemolithotrophic sulfur-oxidizing bacterium, strain aks1(T), was isolated from sediment of a brackish lake in Japan. The cells were curved rod-shaped and Gram-stain-negative. The G+C content of the genomic DNA was 53 mol%. The major components in the cellular fatty acid profile were C-16:0 and summed feature 3 (C-16 (: 1)omega 7c and/or C-16 (: 1)omega 6c). As electron donor for chemolithoautotrophic growth, strain aks1(T) oxidized thiosulfate, sulfide, and elemental sulfur. The strain could utilize oxygen and nitrate as an electron acceptor for thiosulfate oxidation. Growth was observed at a temperature range of 5-34 degrees C, with optimum growth at 30-32 degrees C. Growth of the strain was observed at a pH range of 6.4-8.7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is related to members of the family Granulosicoccaceae within the order Chromatiales, with sequence similarities around 92%. On the basis of phylogenetic and phenotypic properties, strain aks1(T) represents a novel species of a new genus, for which the name Sulfuriflexus mobilis gen. nov., sp. nov. is proposed. The type strain of the type species is aks1(T) (=DSM 102939(T) =NBRC 111889(T))

Methyloradius palustris gen. nov., sp. nov., a methanol-oxidizing bacterium isolated from snow

A novel methylotrophic bacterium, strain Zm11(T), was isolated from reddish brown snow collected in a moor in Japan. Cells of the isolate were Gram-stain-negative, motile, and rod-shaped (0.6-0.7 x 1.2-2.7 mu m). Growth was observed at 5-32 degrees C with an optimum growth temperature of 25-28 degrees C. The pH range for growth was 5.4-7.8 with an optimum pH of 6.8. The strain utilized only methanol as carbon and energy sources for aerobic growth. The major cellular fatty acids (> 40% of total) were summed feature 3 (C-16:1 omega 7c and/or C-16:1 omega 6c) and C-16: 0. The predominant quinone was Q-8, and major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The complete genome of strain Zm11(T) is composed of a circular chromosome (2,800,413 bp), with G + C content of 46.4 mol%. Phylogenetic analyses were conducted based on the 16S rRNA gene sequence and conserved proteins encoded in the genome. The results of analyses indicate that strain Zm11(T) is a member of the family Methylophilaceae but does not belong to any existing genus. On the basis of its genomic and phenotypic properties, strain Zm11(T) (= DSM111909(T) = NBRC114766(T)) is proposed as the type strain of a new species in a new genus, Methyloradius palustris gen. nov., sp. nov

Vertical distribution of major sulfate-reducing bacteria in a shallow eutrophic meromictic lake

The vertical distribution of sulfate-reducing bacteria was investigated in a shallow, eutrophic, meromictic lake, Lake Harutori, located in a residential area of Kushiro, Japan. A steep chemocline, characterized by gradients of oxygen, sulfide and salinity, was found at a depth of 3.5-4.0 m. The sulfide concentration at the bottom of the lake was high (up to a concentration of 10.7 mM). Clone libraries were constructed using the aprA gene, which encodes adenosine-5'-phosphosulfate reductase subunit A, in order to monitor sulfate-reducing bacteria. In the aprA clone libraries, the most abundant sequences were those from the Desulfosarcina-Desulfococcus (DSS) group. A primer set for a DSS group-specific 16S rRNA gene was used to construct another clone library, analysis of which revealed that the uncultured group of sulfate-reducing bacteria, SEEP SRB-1, accounted for nearly half of the obtained sequences. Quantification of the major bacterial groups by catalyzed reporter deposition-fluorescence in situ hybridization demonstrated that the DSS group accounted for 3.2-4.8% of the total bacterial community below the chemocline. The results suggested that the DSS group was one of the major groups of sulfate-reducing bacteria and that these presumably metabolically versatile bacteria might play an important role in sulfur cycling in Lake Harutori. (C) 2014 Elsevier GmbH. All rights reserved

Thiosulfativibrio zosteraegen. nov., sp. nov., andThiosulfatimonas sediminisgen. nov., sp. nov.

Aerobic, Gram-stain-negative, obligately chemolithoautotrophic thiosulfate-oxidizing bacteria, strains AkT22(T)and aks77(T)were isolated from a brackish lake in Japan. Strains AkT22(T)and aks77(T)were isolated from samples of eelgrass and sediment, respectively. Growth on sulfide, tetrathionate, elemental sulfur, and organic substrates was not observed for both strains. Growth of the strains was observed at 5 degrees C or higher temperature, with optimum growth at 22 degrees C. Strain AkT22(T)grew at a pH range of 5.8-8.0, with optimum growth at pH 6.7-7.8. Strain aks77(T)grew at a pH range of 5.8-8.5, with optimum growth at pH 7.0-7.9. Major cellular fatty acids (> 10% of total) of strain AkT22(T)were C-16:1, C-18:1, and C-16:0. The sole respiratory quinone was ubiquinone-8 in both strains. The genome of strain AkT22(T)consisted of a circular chromosome, with size of approximately 2.6 Mbp and G + C content of 43.2%. Those values of the genome of strain aks77(T)were ca. 2.7 Mbp and 45.5%, respectively. Among cultured bacteria,Thiomicrorhabdus aquaedulcisHaS4(T)showed the highest sequence identities of the 16S rRNA gene, to strains AkT22(T)(94%) and aks77(T)(95%). On the basis of these results,Thiosulfativibrio zosteraegen. nov., sp. nov. andThiosulfatimonas sediminisgen. nov., sp. nov. are proposed, with type strains of AkT22(T)(= BCRC 81184(T) = NBRC 114012(T) = DSM 109948(T)) and aks77(T)(= BCRC 81183(T) = NBRC 114013(T)), respectively

Seasonal Changes in Organic Matter Mineralization in a Sublittoral Sediment and Temperature-Driven Decoupling of Key Processes

Seasonal changes in the mineralization of organic compounds in sediments were investigated in temperate, sublittoral zone sediments (Tokyo Bay, Japan). The total mineralization rate and sulfate reduction rate showed large seasonal variations over the year, and although the fluctuations in both rates correlated with temperature, the latter was irregularly high in May. The concentration of organic carbon dissolved in interstitial water was specifically high in April. A culture-based experiment was also conducted under temperatures corresponding to the seasonal changes. In the culture incubated at a temperature corresponding to April (13℃), hydrolysis and fermentation proceeded, but terminal oxidation was hindered, thereby resulting in acetate accumulation. At a temperature corresponding to May (22℃), acetate oxidation coupled with sulfate reduction was observed. The temperature-related differences were also reflected in the bacterial community structure in the cultures analyzed by DGGE. In the culture incubated at the lower temperature, sulfate-reducing bacteria of incomplete oxidizers was detected, while sequence found in the culture incubated at the higher temperature was related to complete oxidizers. These results suggest that complete and incomplete oxidizing sulfate-reducing bacteria act as distinct functional groups, responding to temperature in different ways, particularly in environments characterized by large temperature fluctuations