Microbes and Environments (MICROBES ENVIRON )

Publisher: Nihon Biseibutsu Seitai Gakkai


Microbes and Environments is the publication of the Japanese Society of Microbial Ecology. The Journal is issued four times per year.

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    Microbes and environments (Online)
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Enrichment cultures of anaerobic ammonium oxidation (anammox) bacteria as planktonic cell suspensions are essential for studying their ecophysiology and biochemistry, while their cultivation is still laborious work. The present study aimed to cultivate two phylogenetically distinct anammox bacteria, “Candidatus Brocadia sinica” and “Ca. Scalindua sp.” in the form of planktonic cells by using membrane bioreactors (MBRs). The MBRs were continuously operated for more than 250 d with nitrogen loading rates of 0.48-1.02 and 0.004-0.09 kgN m-3 d-1 for “Ca. Brocadia sinica” and “Ca. Scalindua sp.”, respectively. Planktonic anammox bacterial cells were successfully enriched (>90%) in the MBRs, which were confirmed by fluorescence in-situ hybridization and 16S rRNA gene sequencing analysis. Decay rate and half-saturation constant for NO2- of “Ca. Brocadia sinica” were determined to be 0.0029-0.0081 d-1 and 0.47 mgN L-1, respectively by using the enriched planktonic cells. The present study demonstrated that MBR enables to culture planktonic anammox bacterial cells, which are suitable for studying their ecophysiology and biochemistry.
    Microbes and Environments 08/2013;
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    ABSTRACT: The present study describes the occurrence of a unique archaeal ammonia monooxygenase alpha subunit (amoA) gene in nitrifying acid-sulfate soil microcosms at pH 3.5. The soil was collected from an abandoned paddy field in Thailand. Microcosms were incubated in the dark at 30°C for 372 days with the following three treatments: addition of ammonium sulfate solution once a month (I) or once a week (II), and addition of only sterilized water (III). A quantitative PCR analysis revealed an increase in abundance of the archaeal amoA gene in microcosm soils in which nitrate concentrations increased after incubation. A phylogenetic analysis indicated a predominance of the novel gene, and a predominance of a betaproteobacterial amoA gene affiliated with the genus Nitrosospira. A 16S rRNA gene-based PCR assay revealed that crenarchaeotic Group I.1d was predominant among the Crenarchaeota in microcosms. These results suggest the presence of ammonia-oxidizing archaea corresponding to the unique amoA lineage in nitrifying acid-sulfate soil microcosms at pH 3.5.
    Microbes and Environments 01/2009; 24(2):168-74.
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    ABSTRACT: The amount of trehalose in cells of the cyanobacterium Spirulina (Arthrospira) platensis increased rapidly when a high concentration of NaCl was added to the culture medium. Inhibition of sodium ion transport by amiloride and monensin significantly decreased the amount of cellular trehalose, suggesting that the influx of sodium ions into the cells is coupled with the accumulation of trehalose. The amount of maltooligosyl trehalose hydrolase (Mth) which produces trehalose from maltooligosyl trehalose increased gradually after the increase in cellular trehalose. The gene for Mth was cloned and identified by Southern blot analysis. Real time RT-PCR analysis revealed that the expression of mth was enhanced by the addition of NaCl to the culture medium. It was concluded that both catalytic activity of Mth and the synthesis of Mth protein were enhanced by the addition of NaCl to the cells.
    Microbes and Environments 01/2009; 24(1):52-6.
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    ABSTRACT: The splicing of a bacterial group II subclass B intron B.me.I1 from Bacillus megaterium chromosomes was investigated. RT-PCR and nucleic acid hybridization methods were used to understand the role of the intron-encoded protein (IEP) in the splicing of B.me.I1. An in vivo assay showed that the splicing occurred in the absence of IEP. An in vitro assay showed that B.me.I1 was spliced under conditions similar to those of the intracellular environment with no help from other biological molecules. Because all group II introns previously reported needed IEPs for their splicing in vivo, our results suggest that B.me.I1 is an "actual" self-splicing group II intron. This is also the first report to recognize the existence of group II introns that independently splice mRNA in vivo. The self-splicing of a bacterial intron may support that eukaryotic spliceosomal introns originated in bacterial genomes.
    Microbes and Environments 01/2009; 24(1):28-32.
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    ABSTRACT: Four hundred and fifty nine isolates of fluorescent pseudomonads were obtained from the leaves and roots of potato plants. Of these, 20 leaf isolates and 28 root isolates induced violacein production in two N-acylhomoserine lactone (AHL)-reporter strains-Chromobacterium violaceum CV026 and VIR24. VIR24 is a new reporter strain for long N-acyl-chain-homoserine lactones, which can not be detected by CV026. Thin-layer chromatography revealed that the isolates produced multiple AHL molecules. We compared the 16S rRNA gene sequences of these isolates with sequences from a known database, and examined phylogenetic relationships. The AHL-producing isolates generally separated into three groups. Group I was mostly composed of leaf isolates, and group III, root isolates. Group II comprised both leaf and root isolates. There was a correlation between the phylogenetic cluster and the AHL molecules produced and some phenotypic characteristics. Our study confirmed that AHL-producing fluorescent pseudomonads could be distinguished in the phyllosphere and rhizosphere of potato plants.
    Microbes and Environments 01/2009; 24(4):305-14.
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    ABSTRACT: Clone libraries were used to evaluate the effects of 2,4-dinitroanisole (DNAN) and n-methyl-4-nitroaniline (MNA) on bacterial populations within three anaerobic bioreactors. Prior to the addition of DNAN and MNA greater than 69% of the clones in each reactor were identified as a single Desulfuromonales species. However, after 60 days of treatment the Desulfuromonales distribution decreased to less than 13% of the distribution and a clone identified as a Levilinea sp. became the dominant organism at greater than 27% of the clone distribution in each reactor suggesting the species may play an important roll in the reduction of DNAN and MNA.
    Microbes and Environments 01/2009; 24(1):72-5.
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    ABSTRACT: The nutrient ion concentrations in the interstitial waters of biofilms (BFs) formed on reed and stone surfaces were investigated in the northern and southern basins of Lake Biwa over several years. The following were observed for both types of BF: 1) Concentrations of ammonium, nitrate, nitrite, and phosphate ions were much (hundreds to thousands of times) higher in the BFs than in the surrounding lake water; 2) the concentration of ions, especially nitrate ions, in the BFs changed seasonally, being higher from winter to spring and lower from summer to autumn, synchronizing with the changes in the lake water; 3) dissolved-form N:P ratios were higher in the lake water than BFs; and 4) the bacterial flora of the BFs differed from that of the lake water, with smaller seasonal variations. The present study reveals for the first time that the inside of BFs in a natural environment is rich in nutrient ions and shows similar seasonal changes as the lake water. The BFs in an aquatic environment provide a microenvironment capable of sustaining a specific bacterial flora different from that in the surrounding lake water.
    Microbes and Environments 01/2009; 24(1):43-51.
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    ABSTRACT: Among the fundamental questions in marine microbial ecology are which taxa or phylogenetic groups account for total bacterial productivity and what is the relative contribution of each. We combined bromodeoxyuridine (BrdU) immunocytochemistry and fluorescence in situ hybridization (BIC-FISH) to examine phylotype-specific contributions to total bacterial productivity in eutrophic seawater. We also examined year-round changes in phylotype-specific contributions and explored the factors controlling these changes. Monitoring by BIC-FISH throughout the year revealed the importance of the Roseobacter/Rhodobacter group as a constantly proliferating basic population (27% of all BrdU-positive cells), although their contribution was not significantly correlated with water temperature or with chlorophyll a or organic matter concentration. The Bacteroidetes were another important group, as they greatly increased in abundance after the end of phytoplankton blooms. Two other phylotypes tested, the SAR86 and Vibrio groups, changed their contributions to bacterial productivity with changes in water temperature. To our knowledge, this study was the first to estimate the yearly contribution of major subgroups of marine bacteria to total bacterial productivity in a seawater environment.
    Microbes and Environments 01/2009; 24(4):315-21.
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    ABSTRACT: The nucleotide sequences of two endopolygalacturonase genes (pg1 and pg5) and two exopolygalacturonase genes (pgx1 and pgx4), which encode members of a major family of secreted cell-wall-degrading enzymes (CWDEs), were compared to detect the extent of genetic variation among isolates of Fusarium oxysporum. The nucleotide variation rate in exons was 0.23-0.93%, higher than that in introns (0.01-0.64%) and untranslated regions (UTRs) (0.07-0.25%), resulting in 0.05-0.31% variation in amino acids. pgx1 exhibited the most genetic diversity. Phylogenetic analysis of the four genes, which reside on different chromosomes, revealed different evolutionary patterns for each. Our results suggest a biased evolution of the polygalacturonase genes of F. oxysporum, or alternatively, that the genes were acquired at different times during evolution.
    Microbes and Environments 01/2009; 24(2):113-20.
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    ABSTRACT: In the model leguminous plant Lotus japonicus, the reception of a symbiotic signal called Nod factor (NF), which is secreted by the symbiont bacterium Mesorhizobium loti, induces wavy shaped root hairs. This is called root hair deformation. To dissect the root hair deformation process, we studied symbiosis- deficient mutants of L. japonicus, castor, nup85, ccamk and nsp2. The CASTOR, NUP85, and CCaMK genes are also required for mycorrhizal infection and thus called common symbiotic genes. On the global application of NF, all the mutants except nsp2 exhibited extensive branching of root hairs. The actin cytoskeleton was also observed as a marker for NF-dependent responses in mutant root hairs. At 2 hours of NF treatment, the ccamk mutant showed exaggerated swelling compared with the other mutants, indicating CCaMK to be required to terminate the swelling. In the nsp2 mutant, two hours of NF treatment remarkably induced swelling at root hair tips, although root hair deformation was not apparent at 24 hours of NF treatment. These results showed that common symbiotic components are involved in root hair deformation, which is regulated by a fine tuning mechanism early in the symbiosis between leguminous plants and rhizobia.
    Microbes and Environments 01/2009; 24(2):128-34.
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    ABSTRACT: Environmental isolates of Salmonella enterica serover Enteritidis (S. Enteritidis) clones were grown to the logarithmic phase, washed and re-suspended in saline or Luria-Bertani (LB) medium, and then 10-µL aliquots of the suspensions were dried overnight at room temperature. The dried bacteria were mixed with 1 mL of ice-cold PBS, suspended and examined for colony-forming activity. All of the pathogenic clones with high levels of SEp22, identical to Salmonella Dps, maintained good viability if suspended in LB medium prior to drying. However, none of the non-virulent strains, exhibiting low levels of SEp22, survived. Similar results were obtained with sep22-knocked out mutants, suggesting that SEp22 is important for the acquisition of dry-resistance. Nutritional factors, such as LB medium, cabbage extracts, and egg yolk but not egg white, were shown to be necessary for the acquisition of dry-resistance, because none of the clones remained viable irrespective of SEp22 expression if suspended in saline. Scanning electron micrograms also supported the importance of nutrition, showing re-growth of the bacteria after drying in LB but not in saline. These results suggest the importance of both SEp22 expression and nutrients for the acquisition of dry-resistance by S. Enteritidis.
    Microbes and Environments 01/2009; 24(2):121-7.