Nine thermophilic denitrification bacteria were isolated from field soil, mud, and spa samples. The alignment of 16S rDNA showed that all were identical to the genus Geobacillus. Two of the bacteria produced N2O and N2 gas and the other seven strains produced N2 gas from nitrate. We examined the growth substrates for Geobacillus TDN01 and determined that sodium succinate, pyruvate, formate, acetate, glycerol, glucose, sucrose, and cellobiose well supported growth of the isolate. Growth occurred under the following concentration of NO3- and phosphate: 10-60 mmol/L, and 0.1-50 mmol/L, respectively. Thermophilic TDN01 grown on sodium succinate accumulated nitrite. A time course of denitrification by Geobacillus TDN01 in a jar fermentor revealed that maintaining a pH of around 7 is important for denitrification without accumulating NO2. The NO3- and NO2- consumption ratios of Geobacillus were 44-75 and 9-41 times higher, respectively, than those of Pseudomonas stutzeri JCM 5965T.
The thermophilic denitrifying bacterium Geobacillus sp. strain TDN01 was examined to determine the effects of nitrogen and carbon sources and nitrate and nitrite concentrations on denitrification in a batch culture. The specific nitrate removal rate was 12 times higher with ammonia than without ammonia. The consumption rates of nitrate and succinate were proportional. Furthermore, the growth rates with 120 and 150 mM nitrate were only slightly lower than those with 60 mM and did not cause notable growth inhibition. Denitrification ability in continuous culture was analyzed based on the data for batch culture. The maximum specific growth rate μmax and substrate saturation constant KS in the Monod equation were determined by gradually changing the dilution rate. The maximum denitrification rate was six times higher than that of mesophilic bacteria.
Seven yeast strains isolated from natural substrates of Thailand were found to represent two novel species of Candida, an ascomycetous anamorphic genus. Three strains, ST-233, ST-259 and ST-260, isolated from insect frass and plant leaves were found to represent a single novel species related to Metschnikowia agaves in a tree based on the D1/D2 domain sequences of the 26S rRNA genes. This species is clearly discriminated from M. agaves by the carbon assimilation patterns and required vitamins. The remaining four strains, ST-18, ST-261, ST-606 and ST-658, isolated from the fruit body of a mushroom, insect frass, decayed jack fruit and an unidentified flower, were found to represent a single species which is related to Candida corydali, a recently described insect-associated species, in a neighbor-joining tree based on the D1/D2 sequences. This species is clearly discriminated from C. corydali by the ability to assimilate propane-1,2-diol and the inability to assimilate glucono-δ-lactone. They are described as Candida wancherniae sp. nov. and Candida morakotiae sp. nov., respectively.
MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase, was investigated for acetic acid bacteria, and growth on methanol was examined for the bacteria by using various media. Of 21 strains of acetic acid bacteria studied, Acidomonas methanolica strains showed the presence of mxaF gene exclusively, and grew on a defined medium containing methanol. Further, none of the strains tested of which the growth on methanol had been previously reported, except for Acidomonas methanolica, showed the presence of mxaF gene or the growth on methanol. Precautions were taken against false growth on compounds used for identification of bacteria.
The highly conserved organization of microcystin biosynthesis (mcy) gene clusters, which includes nonribosomal peptide synthetase (NRPS) genes, polyketide synthase (PKS) genes, and fused NRPS-PKS genes, has been characterized in the genus Microcystis. In this study, a total of 135 cyanobacterial strains from four different geographical locations in Japan were isolated. Fourteen mcy-possessing (mcy+) strains were identified according to PCR amplification between two genes from domestic mcy+ strains and the mcy gene’s organization was classified into five types. Phylogenetic relationships of the 16S-23S internal transcribed spacer region indicated that the five types of mcy gene cluster structure classified into two groups of the genus Microcystis. HPLC of the isolated mcy+ strain containing a partial deletion of mcyI (ΔmcyI) revealed that microcystin production disappeared. A transcriptional analysis of the Δ mcyI-strain and an assay of recombinant McyI dehydrogenase activity showed that McyI is responsible for microcystin biosynthesis. Based on patterns of the PCR amplicons and analyses of nucleotide sequences in the mcy gene cluster of Microcystis, we confirmed the presence of inserts at three specific loci, between mcyA and mcyD, and downstream of mcyC and mcyJ. Our study is the first investigation of the mcy gene cluster structure in the genus Microcystis from environmental samples.
A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (MSL79T) isolated from an estuarine sediment in the Sea of Japan of the Japanese islands was characterized phenotypically and phylogenetically. Cells were Gram-negative, motile with a polar flagellum, non-spore-forming, curved rods. Cells had desulfoviridin and c-type cytochrome. Catalase and oxidase activities were not detected. The optimum NaCl concentration for growth was 2.0% (wt/vol). The optimum temperature was 35°C and the optimum pH was 6.5. Strain MSL79T utilized H2, formate, pyruvate, lactate, fumarate, malate, succinate, ethanol, propanol and butanol as electron donors for sulfate reduction. The organic electron donors were incompletely oxidized to mainly acetate. Sulfite and thiosulfate were used as electron acceptors with lactate as an electron donor. Without electron acceptors, pyruvate, fumarate and malate supported the growth. The genomic DNA G + C content was 62.1 mol%. Menaquinone MK-6(H2) was the major respiratory quinone. Major cellular fatty acids were C16:0, iso-C15:0, anteiso-C15:0, iso-C17:0, anteiso-C17:0 and iso-C17:1ω9. Phylogenetic analysis based on the 16S rRNA gene sequence as well as the α-subunit of dissimilatory sulfite reductase gene sequence assigned the strain to the family Desulfovibrionaceae within the class Deltaproteobacteria. The closest validly described species based on the 16S rRNA gene sequences were Desulfovibrio aespoeensis (sequence similarity; 95.0%) and Desulfovibrio profundus (94.3%). On the basis of the significant differences in the 16S rRNA gene sequences and the phenotypic characteristics between strain MSL79T and each of the most closely related species, Desulfovibrio portus sp. nov. is proposed. The type strain is MSL79T (= JCM 14722T= DSM 19338T).
We investigated the biochemical properties of the enzymes involved in trehalose metabolism in the cyanobacterium Nostoc punctiforme strain IAM M-15 to elucidate the mechanism of trehalose accumulation in response to desiccation and salt stress. There was no detectable trehalose in fully hydrated N. punctiforme cells; however, these cells accumulated trehalose upon desiccation. Moreover, NaCl treatment also induced trehalose accumulation. The three genes for trehalose metabolism, treZ (maltooligosyltrehalose trehalohydrolase, Mth), treY (maltooligosyltrehalose synthase, Mts), and treH (trehalase), were found as a gene cluster, and the mRNAs for these genes were detectable at similar levels during desiccation. Trehalase of N. punctiforme was heterologously expressed in E. coli cells in an active form with a molecular mass of 52 kDa. Trehalase activity was strongly inhibited in the presence of 10 mM NaCl while trehalose synthesis activity remained active in the presence of salt. These data suggest that the rate of trehalose production exceeds that of trehalose hydrolysis under water-stress conditions characterized by increased cellular solute concentrations. In the proposed mechanism, control of trehalase plays an important role in trehalose accumulation in terrestrial cyanobacteria under conditions of extreme desiccation.
A bacterial strain capable of degrading chitin, strain SAY3T, was isolated from moat water of Ueda Castle in Nagano Prefecture, Japan. The strain was gram-negative, curved rod-shaped, facultatively anaerobic, and motile with a single polar flagellum. It grew well with chitin as a sole carbon source. The cellular fatty acids profiles showed the presence of C16:1 ω7c and C16:0 as the major components. The G+C content of DNA was 67.6 mol% and Q-8 was the major respiratory quinone. A 16S rRNA gene sequence-based phylogenetic analysis showed the strain belonged to the family Neisseriaceae but was distantly related (＜94% identity) to any previously known species. Since the strain was clearly distinct from closely related genera in phenotypic and chemotaxonomic characteristics, it should be classified under a new genus and a new species. We propose the name Chitiniphilus shinanonensis gen. nov., sp. nov. The type strain is SAY3T (=NBRC 104970T=NICMB 14509T).
Amphibacillus is a genus for Gram-positive, spore-forming, rod-shaped, facultatively anaerobic bacteria with low-G+C content of DNA, established by Niimura et al. in 1990. Amphibacillus xylanus, the type species of the genus, grows well under both strictly anaerobic and aerobic conditions in spite of lacking any isoprenoid quinones, cytochromes, and catalase. Amphibacillus fermentum and Amphibacillus tropicus were later proposed by Zhilina et al. in 2001 for the isolates from a soda lake. In this paper, we revealed the latter two species also lacked isoprenoid quinones, cytochrome and catalase, and that they grew well under strictly anaerobic and aerobic conditions. The consistent growth of A. xylanus under both conditions is due to the presence of anaerobic and aerobic pathways for glucose metabolism in the organism. Although A. fermentum and A. tropicus are supposed to have a side enzymatic pyruvate pathway to produce lactate under both conditions, the two species have two major pyruvate metabolic pathways as observed in A. xylanus. Analysis data indicated that NADH formed both by the aerobic pyruvate pathway and by the glycolytic pathway was re-oxidized by the NADH oxidase in A. fermentum and A. tropicus as well as A. xylanus, and furthermore that the NADH oxidase-Prx (AhpC) system, i.e., NADH oxidase scavenging hydrogen peroxide with Prx, also functions in A. tropicus as observed with A. xylanus. Not only the taxonomical character of the genus Amphibacillus but also the growth characterization based on the two metabolic pathways and unique oxygen metabolism are distinctive in those traits from other facultative anaerobes.
A green sulfur bacterium, strain JAGS6T was isolated from a marine aquaculture pond located near Kakinada on the east coast of India. Cells of strain JAGS6T were Gram-negative, non-motile, coccoid, 1-1.2 µm in diameter, with prosthecae. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JAGS6T clusters with members of the genus Prosthecochloris and the sequence similarity with the nearest relative, Prosthecochloris vibrioformis, is 96.7%. Cultures of strain JAGS6T are green in color and the cells contain bacteriochlorophyll c and most likely carotenoids of the chlorobactene series as photosynthetic pigments. Strain JAGS6T is mesophilic, halotolerant (up to 7% NaCl) and is obligately phototrophic, utilizing sulfide but not thiosulfate as a photosynthetic electron donor. Sulfur globules are deposited outside the cells during oxidation of sulfide. On the basis of 16S rRNA gene sequence analysis and its morphological and physiological characteristics, strain JAGS6T is distinct from described species of the genus Prosthecochloris and we propose to describe it as a new species, Prosthecochloris indica, sp. nov. The type strain is JAGS6T (= JCM 13299T = ATCC BAA1214T).