A strictly anaerobic bacterial strain (WN081T) was isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. Cells were Gram-staining negative, non-motile, non-spore-forming straight rods. The strain grew rather well on PY agar slants supplemented with a B-vitamin mixture as well as sugars (PYV4S medium) and made translucent and glossy colonies. Growth in liquid medium with the same composition, however, was scanty, and growth was not improved in spite of various additives to the medium. Strain WN081T produced small amounts of acetate, propionate, isobutyrate, butyrate, isovalerate and H2 from PYV liquid medium. The strain did not use carbohydrates or organic acids. The pH range for growth was narrow (pH 6.8−8.2), having a pH optimum at 6.8−7.5. The temperature range for growth was 10−37°C, the optimum being 25−30°C. The strain was sensitive to bile, and did not have catalase or oxidase activities. Hydrogen sulfide was produced from L-cysteine and L-methionine as well as peptone. Indole was produced from L-tryptophan and peptone. The strain had iso-C15:0 as the exclusively predominant cellular fatty acid (70%) together with some branched chain components (such as iso-C15:0 DMA, iso-C17:0 3-OH and iso-C15:0 aldehyde) as minor components. The genomic DNA G+C content was 32.3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain WN081T in the phylum Bacteroidetes with rather low sequence similarities with the related species such as Rikenella microfusus (85.7% sequence similarity), Alistipes putredinis (85.5%) and Alistipes finegoldii (85.5%) in the family Rikenellaceae. Based on the phylogenetic, physiological and chemotaxonomic analyses, the novel genus and species Anaerocella delicata gen. nov., sp. nov. is proposed to accommodate the strain. The type strain is WN081T (= JCM 17049T = DSM 23595T).
Bacterial strains capable of degrading trichlorophenol (2,4,6-TCP) were isolated from the secondary sludge of a pulp and paper mill and were characterized. These isolates were identified as Planococcus rifietoensis (CL4) and Bacillus pumilus (CL5), based on their 16S rRNA sequence analysis. These isolates were able to grow and utilize 2,4,6-TCP as their source of carbon as well as energy. HPLC analysis and stoichometric release of chloride in the medium confirmed the degradation ability of these isolates. Removal efficiency of 2,4,6-TCP by these isolates was discovered to be high. They were able to remove 90% of 2,4,6-TCP when grown at a concentration of 600 mg L−1. Inoculation of these bacteria completely removed 2,4,6-TCP within 2 weeks from the sludge of the pulp and paper mill when supplemented at the rate of 100 mg L−1. Absorbable Organic Halogen (AOX) and Extractable Organic Halogen (EOX) were significantly reduced by 63% and 70% respectively from the sludge due to inoculation of these bacteria. These isolates have high potential to remove 2,4,6-TCP and may be used for removal of 2,4,6-TCP from pulp paper mill waste.
A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile bacteriun, designated DCY58T, was isolated from a ginseng field in Pocheon Province, South Korea. Colonies of strain DCY58T were circular, 0.5−1.5 mm in diameter, yellow, and convex on an R2A agar plate after 2 days. The 16S rRNA gene sequence analysis revealed that strain DCY58T belongs to the family of the Sphingomonadaceae and is most closely related to the species of genus Sphingomonas with similarity levels of 95.7−96.4%. Strain DCY58T contained Q-10 as the predominant ubiquinone. The major cellular fatty acids included Summed Feature 8 (containing C18:1ω6c and/or C18:1ω7c), C14:0 2-OH and C16:0. The DNA G+C content was 65.1 mol%. Furthermore, strain DCY58T differed from other related Sphingomonas species by a number of phenotypic characteristics. On the basis of the evidence presented in this study, strain DCY58T is described as a novel species of genus Sphingomonas, for which the name Sphingomonas ginsengisoli sp. nov., is proposed. The type strain is DCY58T (=KCTC 23762T =JCM 18016T).
Sporocytophaga sp. JL-01 is a sliding cellulose degrading bacterium that can decompose filter paper (FP), carboxymethyl cellulose (CMC) and cellulose CF11. In this paper, the morphological characteristics of S. sp. JL-01 growing in FP liquid medium was studied by Scanning Electron Microscope (SEM), and one of the FPase components of this bacterium was analyzed. The results showed that the cell shapes were variable during the process of filter paper cellulose decomposition and the rod shape might be connected with filter paper decomposing. After incubating for 120 h, the filter paper was decomposed significantly, and it was degraded absolutely within 144 h. An FPase1 was purified from the supernatant and its characteristics were analyzed. The molecular weight of the FPase1 was 55 kDa. The optimum pH was pH 7.2 and optimum temperature was 50°C under experiment conditions. Zn2+ and Co2+ enhanced the enzyme activity, but Fe3+ inhibited it.
A new thermophilic spore-forming strain Ge1T was isolated from the Guclukonak hot spring in Sırnak, Turkey. The strain was identified by using a polyphasic taxonomic approach. Strain Ge1T was Gram-positive, spore-forming, alkaliphilic rod-shaped, motile, occurring in pairs or filamentous. Growth was observed between 30 and 65°C (optimum 60°C) and at pH 5.5−10.0 (optimum pH 9.0). It was capable of utilizing starch, growth was observed at 0−3% NaCl (w/v) and was positive for catalase and urease. The major cellular fatty acids were iso-C15:0 and iso-C17:0, and the predominant lipoquinone found was menaquinone MK7 type. The DNA G+C content of the genomic DNA of strain Ge1T was 52.0%. Comparative 16S rRNA gene sequence studies showed that the isolate belonged to the genus Geobacillus. The DNA-DNA hybridization mean values between the representative strain Ge1T and the closely related species G. subterraneus, G. thermodenitrificans, G. thermocatenulatus, G. vulcani and G. thermoleovorans were 69.3%, 57%, 37%, 27% and 26%, respectively. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Ge1T. Based on these results, we propose assigning a novel subspecies of Geobacillus subterraneus, to be named as Geobacillus subterraneus subsp. aromaticivorans subsp. nov. with the type strain Ge1T (DSM 23066 T= CIP 110341T).
Sea cucumbers play an important role in nutrient cycling of marine ecosystems by consuming sediments and moving sand, thus occupying a similar niche to earthworms in terrestrial ecosystems. However, our understanding of microbial diversity and functions associated with sea cucumbers is meager. Here, we isolated 141 bacterial strains under aerobic conditions using various media from the intestine of Holothuria leucospilota, a common sea cucumber in Japanese warm waters. By partial 16S rRNA gene sequences of the isolates, the isolates were tentatively affiliated with 55 described species. Among them, 23 species were common between 2 individuals of H. leucospilota. High diversity was observed in the genera Bacillus and Vibrio, which are often found in marine sediments, marine animals and other various environments. Most isolates showed various polysaccharide degradation activities and were able to grow under or were tolerant of anaerobic condition. We suggest that these aerobically isolated bacteria can play a role in digestion of detritus in aerobic and/or anaerobic regions of the intestine.
Group C Streptococcus dysgalactiae (GCSD) is a pathogen of farmed fish. Almost all GCSD isolates from Asian countries, including Japan, Taiwan, Malaysia, and China, have a serum opacity factor (SOF-FD). Although the SOF-FD sequences in different GCSD isolates are identical, different opacification activities are observed. Three types of variations were observed in the upstream sequence of the sof-FD gene in GCSD isolates with different SOF-FD activities. Type 1 was characterized by insertion of an IS981-like element into the upstream region of the sof-FD gene. In Type 2, an IS981-like element was inserted into the upstream region in a direction opposite to that in Type 1. In Type 3, no IS element was inserted. Type 1 was predominant among Japanese isolates (129 of 133). Isolates from other Asian countries were generally Type 3 (13 of 16). Except for 1 strain, Type 1 strains exhibited opacification activities with optical densities (ODs)>0.6, while Type 2 and Type 3 strains have low opacification activities (ODs >0.2). Only Type 1 strains have putative −10 and −35 promoter regions upstream of the sof-FD gene, and the expression level of the sof-FD gene was higher in Type 1 strains than in Type 2 and Type 3 strains.
Because archaea possess many respiratory enzymes or radical scavengers with catalytic domains that contain iron, the expression of the genes encoding these enzymes might be regulated by iron acquisition. The genome of an archaeon, Thermoplasma volcanium contains a gene that encodes Fur (TVN0292). The fur gene of T. volcanium was amplified by PCR, and cloned into plasmid pET28a. TvFur (T. volcanium Fur protein) was expressed in E. coli cells and then purified. EMSA revealed that TvFur binds to its own promoter DNA. The binding to its own promoter was in an Mn2+-, Zn2+-, and Ni2+-dependent manner. DNase I footprinting analysis revealed that the binding sequence of tvfur promoter was 5′-G TTATTAT G TTTATAT A TTAATTA G-3′. An analysis utilizing oligonucleotides in TvFur-binding sequences revealed that TvFur binds to the TATA-box or regions in the vicinity of the TATA-box in the promoter. These results indicated that TvFur regulates transcription depending on the availability of environmental divalent cations.