Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 25 , Issue 3
Showing 1-13 articles out of 13 articles from the selected issue
Minireview
  • Souichiro Kato, Kazuya Watanabe
    2010 Volume 25 Issue 3 Pages 145-151
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: July 13, 2010
    JOURNALS FREE ACCESS
    In natural and engineered ecosystems, diverse species of microbes coexist and interact, resulting in the emergence of community functions. Since microbes have evolved under such circumstances, it is reasonable to deduce that they have acquired strategies for specific interspecies interactions in complex microbial communities. In this review, we discuss the ecological and evolutionary interactions in syntrophic methanogenic consortia comprised of organic acid-oxidizing bacteria and methanogenic archaea. These microbes are known to exhibit mutual interactions (syntrophy), although the molecular mechanisms underlying these sophisticated partnerships have only just been discovered. In addition, recent genomic studies have provided insights into evolutionary interactions among members of methanogenic consortia, from which a novel concept termed "niche-associated evolution" has been proposed for interpreting how specialists evolve in a biological community. We suggest that microbial interspecies interactions are much more complex and sophisticated than hitherto realized and pivotal to the development and functioning of microbial communities.
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Regular Papers
  • Hitomi Kajiwara, Munetoyo Toda, Toshiki Mine, Hiroshi Nakada, Hiroyuki ...
    2010 Volume 25 Issue 3 Pages 152-155
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: May 13, 2010
    JOURNALS FREE ACCESS
    Oligosaccharides containing N-acetylneuraminic acid on the cell surface of some pathogenic bacteria are important for host-microbe interactions. N-acetylneuraminic acid (Neu5Ac) plays a major role in the pathogenicity of bacterial pathogens. For example, cell surface sialyloligosaccharide moieties of the human pathogen Haemophilus influenzae are involved in virulence and adhesion to host cells. In this study, we have established a method of visualizing Neu5Ac linked to a glycoconjugate on the bacterial cell surface based on lectin staining. Photobacterium damselae strain JT0160, known to produce a-2,6-sialyltransferase, was revealed to possess Neu5Ac by HPLC. Using the strain, a strong Sambucus sieboldiana lectin-binding signal was detected. The bacteria producing α-2,6-sialyltransferases could be divided into two groups: those with a lot of α-2,6-linked Neu5Ac on the cell surface and those with a little. In the present study, we developed a useful method for evaluating the relationship between Neu5Ac expression on the cell surface and the degree of virulence of marine bacteria.
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  • Daisuke Mayumi, Takuya Yoshimoto, Hiroo Uchiyama, Nobuhiko Nomura, Tos ...
    2010 Volume 25 Issue 3 Pages 156-163
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: May 15, 2010
    JOURNALS FREE ACCESS
    The community structure of methane-oxidizing bacteria (methanotrophs) is affected by concentrations of methane and oxygen. In rice fields, concentrations of both gases differ significantly between the flooded and drained seasons. We investigated the active methanotrophic community structures in flooded and drained soils by DNA-based stable isotope probing. Active methanotrophic diversity was assessed with clone library-based analyses of the 16S rRNA gene and the particulate methane monooxygenase gene (pmoA). The active methanotrophic populations were also estimated by group-specific quantitative real-time PCR assays targeting the 16S rRNA gene and the pmoA gene in 13C-labeled DNA. These molecular biological analyses showed that the flooded rice field soil was dominated by Type II methanotrophs closely related to the genera Methylocystis and Methylosinus, whereas the drained rice field soil was dominated by Type I methanotrophs closely related to the genera Methylomonas, Methylosarcina, and Methylomicrobium. The alternating conditions in a rice field select for methanotrophs adapted to each environment, resulting in a dramatic change in methanotrophic community structure from one season to another.
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  • Shinya Matsumoto, Daisuke Ishikawa, Goro Saeki, Yoshiteru Aoi, Satoshi ...
    2010 Volume 25 Issue 3 Pages 164-170
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: June 08, 2010
    JOURNALS FREE ACCESS
    Microbial population dynamics were investigated during the formation of nitrifying granules in an aerobic upflow fluidized bed (AUFB) reactor fed ammonia as a sole energy source. Analyses of clone libraries of 16S rRNA gene and the ammonia monooxygenase subunit A gene (amoA) revealed that although the clones obtained from the seed sludge were widely distributed among the ammonia-oxidizing bacteria (AOB) isolates, the community structure of AOB shifted towards the Nitrosomonas mobilis lineage as granulation proceeded. Quantitative fluorescence in situ hybridization showed that changes in the bacterial population occurred concomitantly with changes in nitrification performance and the size of granules. AOB associated with the N. mobilis lineage were predominant in the early stages as nitrifying granules formed (average diameter, 126 mm). In mature granules (average diameter, 270 mm), at least three types of AOB, N. mobilis, Nitrosomonas oligotropha, and Nitrosomonas europaea, formed different niches and coexisted. Nitrite-oxidizing bacteria (NOB) affiliated with Nitrospira spp. were detected in the start-up period, but were replaced by NOB affiliated with Nitrobacter spp. after granules formed.
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  • Takahiro Segawa, Nozomu Takeuchi, Kazunari Ushida, Hiroshi Kanda, Shir ...
    2010 Volume 25 Issue 3 Pages 171-182
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: June 17, 2010
    JOURNALS FREE ACCESS
    To clarify altitudinal changes in the bacterial community on Gulkana Glacier in Alaska, we analyzed bacterial 16S rRNA gene by low-cycle PCR amplification, denaturing gradient gel electrophoresis (DGGE), and culturing in a snowmelt medium at 4°C. Low-cycle PCR-based cloning revealed the presence of 100 bacterial OTUs; however, 41 OTUs were identified only in a single clone, suggesting that their abundance was limited because of difficulty in predominating on the glacier. In contrast, 17 major OTUs accounted for 57–87% of the clone library at each site, suggesting that they accounted for the major part of the bacteria on the glacier. In addition, five of the 17 OTUs were included in the 21 OTUs cultured in the snowmelt medium. Based on the dominant phylotypes and DGGE results, the bacterial community on the glacier could be divided into three types, corresponding to the snow-covered, snow- and ice-covered, and bare-ice areas of the glacier. Our results suggest that a relatively limited number of bacteria predominate and that each phylotype is adapted to a distinct set of conditions on the glacier.
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  • Yuta Murakami, Shigeto Otsuka, Keishi Senoo
    2010 Volume 25 Issue 3 Pages 183-189
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: June 19, 2010
    JOURNALS FREE ACCESS
    We examined the abundance and community structure of sphingomonads in the decaying leaf residues of eight plant species as well as the nearby soil, by 16S rRNA gene-based real-time PCR and denaturing gradient gel electrophoresis. In the leaf residues, the sphingomonads generally accumulated to high levels, comprising approximately 15% of the total bacteria, and formed a community structure related to sampling locations. At least within the time period studied, their abundance in leaf residues changed, but their community structure was basically maintained. In soil, sphingomonads made up only 1.7% of total bacteria on average. The community structure of sphingomonads differed between the leaf residues and bulk soil, among plant plots, and among samples collected at different times. The results show that particular sphingomonad populations accumulate in leaf residues compared to the surrounding bulk soil under field conditions.
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  • Yumi Mori, Kevin J. Purdy, Brian B. Oakley, Ryuji Kondo
    2010 Volume 25 Issue 3 Pages 190-196
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: July 03, 2010
    JOURNALS FREE ACCESS
    A new set of primers for the detection of phototrophic sulfur bacteria in natural environments is described. The primers target the α-subunit of the reverse dissimilatory sulfite reductase gene (dsrA). PCR-amplification resulted in products of the expected size from all the phototrophic strains tested, including purple sulfur and green sulfur bacteria. Seventy-nine clones obtained from environmental DNA using the primers were sequenced and all found to be closely related to the dsrA of purple sulfur bacteria and green sulfur bacteria. This newly developed PCR assay targeting dsrA is rapid and simple for the detection of phototrophic sulfur bacteria in situ and superior to the use of culture-dependent techniques.
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  • Kana Yamamoto, Satoshi D. Ohdachi, Yasuhiro Kasahara
    2010 Volume 25 Issue 3 Pages 197-203
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: June 30, 2010
    JOURNALS FREE ACCESS
    Soil bacteria play important roles as litter decomposers in most terrestrial ecosystems and microbial activity is affected by activities of soil invertebrates. In soil ecosystems of forests in Hokkaido, the long-clawed shrew is an important predator whose preying on soil invertebrates may indirectly affect soil bacterial communities. To estimate indirect top-down effects of shrews on the soil bacterial community, field experiments were conducted using enclosures in which shrews were introduced and removed, and changes in bacterial community composition, species richness, diversity, and evenness were observed using automated ribosomal intergenic spacer analysis (ARISA). Abiotic environmental conditions (ambient temperature, soil temperature, soil moisture content and soil pH) were also considered. Bacterial community structure was significantly affected by soil moisture content and soil temperature. The significant causes of the change in bacterial species richness, diversity, and evenness varied among experimental treatments; however, soil moisture tended to have significantly negative effects on these indices in all cases. In the present study, effects of shrews on the bacterial community were not detected.
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  • Tomoyasu Nishizawa, Zhaorigetu , Masakazu Komatsuzaki, Yoshinori Sato, ...
    2010 Volume 25 Issue 3 Pages 204-210
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: July 13, 2010
    JOURNALS FREE ACCESS
    This study aimed to characterize soil fungal communities in upland rice fields managed with tillage/non-tillage and winter cover-cropping (hairy vetch and cereal rye) practices, using PCR-based molecular methods. The study plots were maintained as upland fields for 5 years and the soils sampled in the second and fifth years were analyzed using T-RFLP (terminal restriction fragment length polymorphism) profiling and clone libraries with the internal transcribed spacer (ITS) region and domain 1 (D1) of the fungal large-subunit (fLSU) rRNA (D1fLSU) as the target DNA sequence. From the 2nd-year-sample, 372 cloned sequences of fungal ITS-D1fLSU were obtained and clustered into 80 nonredundant fungal OTUs (operational taxonomic units) in 4 fungal phyla. The T-RFLP profiling was performed with the 2nd- and 5th-year-samples and the major T-RFs (terminal restriction fragments) were identified using a theoretical fragment analysis of the ITS-D1fLSU clones. These molecular analyses showed that the fungal community was influenced more strongly by the cover-cropping than tillage practices. Moreover, the non-tilled, cover-cropped soil was characterized by a predominance of Cryptococcus sp. in the phylum Basidiomycota. We provided a genetic database of the fungal ITS-D1fLSUs in the differently managed soils of upland rice fields.
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  • Mitsuhiro Yoshida, Takashi Yoshida, Yukari Yoshida-Takashima, Aki Kash ...
    2010 Volume 25 Issue 3 Pages 211-215
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: July 24, 2010
    JOURNALS FREE ACCESS
    The aim of this study was to develop a quantitative real-time reverse transcription-PCR (real-time RT-PCR) assay to detect and quantify mRNA of cyanophages within infected Microcystis aeruginosa cells in a freshwater pond. Laboratory-based data showed that the relative abundance of the cyanophage g91 mRNA within host cells increased before cyanophage numbers increased in culture. This transcriptional pattern indicated the kinetics of the viral infection suggesting the real-time RT-PCR method to be a potential tool for environmental monitoring of cyanophage infections. In this field survey, the numbers of infected M. aeruginosa cell populations estimated from cyanophage numbers were low at 0.01–2.9 cells mL−1. The highest relative abundance of phage g91 RNA (10−2 per rnpB transcript) was at about the same levels of expression as laboratory-based growth data for Ma-LMM01 (estimated density of infected host cells: 105 cells mL−1); and was observed when cyanophage numbers rapidly increased (as well as a decrease in host cell numbers). Quantification of cyanophage numbers is important to understand ecological relationships between the phage and its hosts. Our data suggest the quantification of phage gene transcripts within a natural host cell population to be a strong tool for investigating the quantitative effects of phage lysis during infection of the host population.
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Short Communications
  • Ousmane Diene, Takuya Takahashi, Akane Yonekura, Youji Nitta, Kazuhiko ...
    2010 Volume 25 Issue 3 Pages 216-219
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: May 11, 2010
    JOURNALS FREE ACCESS
    A new fungal isolate that grows endophytically in sweet sorghum was identified as Helminthosporium velutinum Link ex Ficinus & Schubert. Light-microscopy of cross-sections of colonized sweet sorghum roots showed that the intercellular, pigmented hyphae of the fungus was mostly limited to the epidermal layer and formed outer mantle-like structures. This endophyte has the ability to significantly increase sweet sorghum biomass. This is the first report of Helminthosporium as an endophyte and could help realize sustainable the biomass production for biofuel purposes.
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  • Sachiko Masuda, Shima Eda, Chiaki Sugawara, Hisayuki Mitsui, Kiwamu Mi ...
    2010 Volume 25 Issue 3 Pages 220-223
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: May 14, 2010
    JOURNALS FREE ACCESS
    Bradyrhizobium japonicum is a facultative chemolithoautotroph capable of using thiosulfate and H2 as an electron donor and CO2 as a carbon source. In B. japonicum USDA110, the mutant of cbbL gene encoding a large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was unable to grow using thiosulfate and H2 as an electron donor. The cbbL deletion mutant was able to grow and oxidize thiosulfate in the presence of succinate. These results showed that the major route of CO2 fixation for thiosulfate-dependent chemoautotrophic growth is the Calvin-Benson-Bassham cycle involving RuBisCO in B. japonicum.
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  • Thanwalee Sooksa-Nguan, Phrek Gypmantasiri, Nantakorn Boonkerd, Janice ...
    2010 Volume 25 Issue 3 Pages 224-227
    Published: 2010
    Released: September 03, 2010
    [Advance publication] Released: June 07, 2010
    JOURNALS FREE ACCESS
    The factors of alternating flooding and draining during the vegetative growth phase and applying compost to investigate changes in bacterial community composition between the system of rice intensification (SRI) and conventionally managed rice were investigated. 16S rRNA gene T-RFLP analysis showed the major changes in the bacterial communities from the beginning of cultivation to vegetative phase, at which time the groups formed remained consistent until the end of cropping season. Significant and consistent separations of microbial communities between the two systems were revealed. These results suggested that the differences in rice cultivation practice can cause the changes in microbial communities.
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