The Journal of General and Applied Microbiology (J GEN APPL MICROBIOL )

Publisher: Tōkyō Daigaku. Ōyō Biseibutsu Kenkyūjo


The Journal of General and Applied Microbiology is issued bimonthly, one volume a year, by The Microbiology Research Foundation. The journal is devoted to the publication of original papers pertaining to general and applied microbiology.

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    Journal of general and applied microbiology
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Publications in this journal

  • The Journal of General and Applied Microbiology 06/2014; 60:89-93.
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    ABSTRACT: The carbon storage regulator (Csr) global regulatory system is conserved in many eubacteria and coordinates the expression of various genes that facilitate adaptation during the major physiological growth phase. The Csr system in Escherichia coli comprises an RNA-binding protein, CsrA; small non-coding RNAs, CsrB and CsrC; and a decay factor for small RNAs, CsrD. In this study, we identified the Csr system in Serratia marcescens 2170. S. marcescens CsrA was 97% identical to E. coli CsrA. CsrB and CsrC RNAs had typical stem-loop structures, including a GGA motif that is the CsrA binding site. CsrD was composed of N-terminal two times transmembrane region and HAMP-like, GGDEF, and EAL domains. Overexpression of S. marcescens csr genes complemented the phenotype of E. coli csr mutants. S. marcescens CsrD affected the decay of CsrB and CsrC RNAs in E. coli. These resultssuggest that the Csr system in S. marcescens is composed of an RNA-binding protein, two Csr small RNAs, and a decay factor for Csr small RNAs.
    The Journal of General and Applied Microbiology 01/2014; 60(2):79-88.
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    ABSTRACT: The intracellular trehalose levels in Shirakami kodama yeast, a strain of Saccharomyces cerevisiae, isolated in 1997 from leaf mold in the Shirakami Mountains and since used as a commercial baker's yeast, are remarkably high, which presumably is related to its tolerance of freezing and drought conditions. We isolated a spore clone from Shirakami kodama yeast with about 1.7-fold higher intracellular trehalose levels than the parental strain and set out to elucidate how this spore clone can accumulate intracellular trehalose to such a high concentration. The gene for trehalose 6-phosphate synthase, TPS1, was duplicated in this spore clone. Both TPS1 genes contributed to the high level of intracellular trehalose as a 3.4-fold decrease resulted from the disruption of one of the two TPS1 genes. Both Msn2 and Msn4, which bind to stress responsive elements in the promoter region of TPS1, were required for production of high levels of trehalose. Furthermore, the neutral trehalase activity of this spore clone is about 3-fold less than that of the laboratory strain although the gene for neutral trehalase, NTH1, functioned normally. These findings indicate that two TPS1 genes and the low trehalase activity are associated with high trehalose accumulation in this spore clone. The wide range of stresses of which we found the spore clone to be tolerant makes this yeast very attractive for commercial application and for further research into the mechanisms underlying stress responses and trehalose metabolism.
    The Journal of General and Applied Microbiology 01/2014; 60(4):147-55.
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    ABSTRACT: Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo.
    The Journal of General and Applied Microbiology 01/2014; 60(2):65-74.
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    ABSTRACT: The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DCY69(T) is JX233806. A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile strain, designated strain DCY69(T), was isolated from the soil of a ginseng field in the Republic of Korea. Colonies of strain DCY69(T) were circular, 0.5-1.5 mm diameter, yellow, and convex on an R2A agar plate after 2 days. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DCY69(T) belonged to the genus Flavobacterium with 90.5-98.3% gene sequence similarity. The major predominant quinone was MK-6. The major cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and unidentified polar lipids (L1, L2). The genomic DNA G+C content of strain DCY69(T) was 35.0mol%. The strain DCY69(T) transformed ginsenoside Rb1 into Rd and F2. Based on the polyphasic taxonomic data, strain DCY69(T) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium panaciterrae sp. nov. is proposed. The type strain is DCY69(T)(= KCTC 32392(T) = JCM 19161(T)), isolated from the soil of a ginseng field in the Republic of Korea.
    The Journal of General and Applied Microbiology 01/2014; 60(2):59-64.
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    ABSTRACT: This paper is concerned with optimization of fermentation conditions for lipstatin production with Streptomyces toxytricini zjut011 by the single factor and orthogonal tests. Five single factors of important effects on lipstatin production were explored. L-Leucine was identified to be the most suitable precursor for lipstatin biosynthesis and for the first time the divalent cations Mg(2+), Co(2+) and Zn(2+) were found to have significant effect on enhancing lipstatin fermentation titer. The effects of the additives on the lipstatin production were in the order of L-leucine > Mg(2+) > Co(2+) > Zn(2+) > octanoic acid. The optimized conditions for lipstatin production were determined as 45.72 mmol/L of L-leucine (added on the 4 th day), 31.1985 mmol/L of octanoic acid (added on the 6th day), 12 mmol/L of Mg(2+), 1 mmol/L of Co(2+) and 0.25 mmol/L of Zn(2+). Under these conditions, a maximum lipstatin of 4.208 g/ml was achieved in verification experiments in 500 ml shake flasks.
    The Journal of General and Applied Microbiology 01/2014; 60(3):106-11.
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    ABSTRACT: Bacterial tail-specific proteases (Tsps) have been attributed a wide variety of functions including intracellular virulence, cell wall morphology, proteolytic signal cascades and stress response. This study tested the hypothesis that Tsp has a key function for the transmissive form of Legionella pneumophila. A tsp mutant was generated in Legionella pneumophila 130b and the characteristics of this strain and the isogenic wild-type were examined using a range of growth and proteomic analyses. Recombinant Tsp protein was also produced and analyzed. The L. pneumophila tsp mutant showed no defect in growth on rich media or during thermo-osmotic stress conditions. In addition, no defects in cellular morphology were observed when the cells were examined using transmission electron microscopy. Purified recombinant Tsp was found to be an active protease with a narrow substrate range. Proteome analysis using iTRAQ (5% coverage of the proteome) found that, of those proteins detected, only 5 had different levels in the tsp mutant compared to the wild type. ACP (Acyl Carrier Protein), which has a key role for Legionella differentiation to the infectious form, was reduced in the tsp mutant; however, tsp(-) was able to infect and replicate inside macrophages to the same extent as the wild type. Combined, these data demonstrate that Tsp is a protease but is not essential for Legionella growth or cell infection. Thus, Tsp may have functional redundancy in Legionella.
    The Journal of General and Applied Microbiology 01/2014; 60(3):95-100.
  • The Journal of General and Applied Microbiology 01/2014; 60(4):156-9.
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    ABSTRACT: The bacterial flagellar motor is mainly energized by either a proton (H(+)) or sodium ion (Na(+)) motive force and the motor torque is generated by interaction at the rotor-stator interface. MotA/MotB-type stators use H(+) as the coupling ion, whereas MotP/MotS- and PomA/PomB-type stators use Na(+). Bacillus subtilis employs both H(+)-coupled MotA/MotB and Na(+)-coupled MotP/MotS stators, which contribute to the torque required for flagellar rotation. In Escherichia coli, there is a universally conserved Asp-32 residue of MotB that is critical for motility and is a predicted H(+)-binding site. In B. subtilis, the conserved aspartic acid residue corresponds to Asp-24 of MotB (MotB-D24) and Asp-30 of MotS (MotS-D30). Here we report the isolation of two mutants, MotB-D24E and MotS-D30E, which showed a non-motile and poorly motile phenotype, respectively. Up-motile mutants were spontaneously isolated from each mutant. We identified a suppressor mutation at MotB-T181A and MotP-L172P, respectively. Mutants MotB-T181A and MotP-L172P showed about 50% motility and a poorly motile phenotype compared to each wild type strain. These suppressor sites were suggested to indirectly affect the structure of the ion influx pathway.
    The Journal of General and Applied Microbiology 01/2014; 60(4):131-9.
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    ABSTRACT: Some microorganisms, such as Escherichia coli, harbor transhydrogenases that catalyze the interconversion between NADPH and NADH. However, such transhydrogenase genes have not been found in the genome of a glutamic acid-producing bacterium Corynebacterium glutamicum. In this study, the E. coli transhydrogenase genes udhA and pntAB were introduced into the C. glutamicum wild-type strain ATCC 13032, and the metabolic characteristics of the recombinant strains under aerobic and microaerobic conditions were examined. No major metabolic changes were observed following the introduction of the E. coli transhydrogenase genes under aerobic conditions. Under microaerobic conditions, significant metabolic change was not observed following the introduction of the udhA gene. However, the specific production rates of lactic acid, acetic acid, and succinic acid, and the overall production levels of acetic acid and succinic acid were increased by introducing the E. coli pntAB gene. Moreover, the NADH/NAD(+) ratio was increased by introduction of pntAB. Our results suggest that the E. coli PntAB transhydrogenase enhances the conversion of NADPH to NADH in C. glutamicum under microaerobic conditions, and the increased NADH/NAD(+) ratio results in increased succinic acid production. In addition, acetic acid production might be enhanced to supply ATP to the anaplerotic reaction catalyzed by pyruvate carboxylase.
    The Journal of General and Applied Microbiology 01/2014; 60(3):112-8.
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    ABSTRACT: A moderately halophilic bacterium, strain HNA-14(T), was isolated from a saline-alkali soil sample collected in Shache County, Xinjiang Province. On the basis of the polyphasic taxonomic data, the isolate was considered to be a member of the genus Bacillus. The organism grew optimally at 30°C and pH 8.0. It was moderately halophilic and its optimum growth occurred at 5-10% NaCl. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 48.6 mol%. Strain HNA-14(T) exhibited a low 16S rRNA gene sequence similarity of 96% with its nearest neighbors [Bacillus clausii KSM-K16 (96.5%), Bacillus xiaoxiensis DSM 21943(T)(96.2%), Bacillus clausii DSM 8716(T) (96.1%), Bacillus patagoniensis PAT05(T) (96.1%), Bacillus lehensis MLB-2(T) (96.0%), Bacillus oshimensis K11(T) (95.9%) and Bacillus hunanensis DSM 23008(T) (95.8%)] and the phenotypic characteristics indicate that strain HNA-14(T) can be distinguished from them. Therefore, a novel species of the genus Bacillus, Bacillus shacheensis sp. nov. (type strain, HNA-14(T)=KCTC 33145=DSM 26902) is proposed.
    The Journal of General and Applied Microbiology 01/2014; 60(3):101-5.
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    ABSTRACT: We compared pairs of 1,226 bacterial strains with whole genome sequences and calculated their average nucleotide identity (ANI) between genomes to determine whether whole genome comparison can be directly used for bacterial species definition. We found that genome comparisons of two bacterial strains from the same species (SGC) have a significantly higher ANI than those of two strains from different species (DGC), and that the ANI between the query and the reference genomes can be used to determine whether two genomes come from the same species. Bacterial species definition based on ANI with a cut-off value of 0.92 matched well (81.5%) with the current bacterial species definition. The ANI value was shown to be consistent with the standard for traditional bacterial species definition, and it could be used in bacterial taxonomy for species definition. A new bioinformatics program (ANItools) was also provided in this study for users to obtain the ANI value of any two bacterial genome pairs ( This program can match a query strain to all bacterial genomes, and identify the highest ANI value of the strain at the species, genus and family levels respectively, providing valuable insights for species definition.
    The Journal of General and Applied Microbiology 01/2014; 60(2):75-8.
  • The Journal of General and Applied Microbiology 01/2014; 60(4):160-2.
  • The Journal of General and Applied Microbiology 01/2014; 60(3):119-21.
  • The Journal of General and Applied Microbiology 01/2013;
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    ABSTRACT: 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 identifi ed as Planococcus rifi etoensis (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 confi rmed the degradation ability of these isolates. Removal effi ciency 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 signifi cantly 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.
    The Journal of General and Applied Microbiology 01/2012; 58:413-420.
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    ABSTRACT: Sulfobacillus sp. TPY is a moderately thermophilic and acidophilic bacterium found in hydrothermal vents in the Pacific Ocean. This bacterium can oxidize ferrous sulfate (Fe(2+)) and elemental sulfur (S(0)) under separate conditions. We used random arbitrarily primed polymerase chain reaction (RAP-PCR) to screen and identify differentially expressed genes from bacteria grown on Fe(2+) or S(0) as the energy source. Fifty-five differential cDNA fragments were isolated and subjected to single-pass sequencing. Thirty-five fragments were identified as orthologs of known genes in the GenBank databases, of which 19 were confirmed to be differentially expressed at the transcriptional level by Northern blot analysis. Among these 19 genes, 14 genes, including isocitrate dehydrogenase, formyltetrahydrofolate deformylase, 3-hydroxybutyryl-CoA dehydrogenase, and GTP-binding protein, were upregulated in TPY grown on Fe(2+) or downregulated in TPY grown on S(0), while five genes such as the outer membrane adhesion-like protein, phosphomannomutase, and cysteine desulfurase sufS were upregulated in TPY strain grown on S(0) or downregulated in TPY grown on Fe(2+). These altered genes are involved in metabolism, osmotic stress, cell membrane alterations, oxidative stress, and the regulatory adaptive response. These results will aid our understanding of the molecular basis of Fe(2+) or S(0) oxidation by the moderately thermophilic and acidophilic bacteria.
    The Journal of General and Applied Microbiology 10/2010; 56(5):389-97.
  • The Journal of General and Applied Microbiology 10/2010; 56(5):413-8.