Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 28 , Issue 4
Showing 1-14 articles out of 14 articles from the selected issue
Research Highlight
Regular Papers
  • Satoshi Kawaichi, Norihiro Ito, Takashi Yoshida, Yoshihiko Sako
    2013 Volume 28 Issue 4 Pages 405-413
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 21, 2013
    JOURNALS FREE ACCESS
    Physicochemical characteristics and archaeal and bacterial community structures in an iron-rich coastal hydrothermal field, where the temperature of the most active hot spot reaches above 100°C, were investigated to obtain fundamental information on microbes inhabiting a coastal hydrothermal field. The environmental settings of the coastal hydrothermal field were similar in some degree to those of deep-sea hydrothermal environments because of its emission of H2, CO2, and sulfide from the bottom of the hot spot. The results of clone analyses based on the 16S rRNA gene led us to speculate the presence of a chemo-synthetic microbial ecosystem, where chemolithoautotrophic thermophiles, primarily the bacterial order Aquificales, function as primary producers using H2 or sulfur compounds as their energy source and CO2 as their carbon source, and the organic compounds synthesized by them support the growth of chemoheterotrophic thermophiles, such as members of the order Thermales and the family Desulfurococcaceae. In addition, the dominance of members of the bacterial genus Herbaspirillum in the high temperature bottom layer led us to speculate the temporal formation of mesophilic zones where they can also function as primary producing or nitrogen-fixing bacteria.
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  • Keisuke Takeshima, Tatsuo Hidaka, Min Wei, Tadashi Yokoyama, Kiwamu Mi ...
    2013 Volume 28 Issue 4 Pages 414-421
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 13, 2013
    JOURNALS FREE ACCESS
    The early molecular dialogue between soybean and the bacterium Bradyrhizobium japonicum is crucial for triggering their symbiotic interaction. Here we found a single large genomic locus that is widely separated from the symbiosis island and was conspicuously induced within minutes after the addition of genistein. This locus (named BjG30) contains genes for the multidrug efflux pump, TetR family transcriptional regulator, and polyhydroxybutyrate (PHB) metabolism. The induction of BjG30 by genistein was competitively inhibited by daidzein, although both genistein and daidzein are soybean-derived inducers of nodulation (nod) genes. Such a differential expression pattern is also observed in some legume-derived flavonoids, which structurally differ in the hydroxy/deoxy group at the 5-position. In addition, not only did the induction start far in advance of nodW and nodD1 after the addition of genistein, but the levels showed distinct concentration dependence, indicating that the induction pattern of BjG30 is completely different from that of nod genes. The deletion of genes encoding either the multidrug efflux pump or PHB metabolism, especially the former, resulted in defective nodulation performance and nitrogen-fixing capability. Taken together, these results indicate that BjG30, and especially its multidrug efflux pump, may play a key role in the early stage of symbiosis by balancing the dual functions of genistein as both a nod gene inducer and toxicant.
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  • Asako Kusumi, Xianshu Li, Yu Osuga, Arata Kawashima, Ji-Dong Gu, Masao ...
    2013 Volume 28 Issue 4 Pages 422-431
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: December 13, 2013
    JOURNALS FREE ACCESS
    The Bayon temple in Angkor Thom, Cambodia has shown serious deterioration and is subject to the formation of various pigmented biofilms. Because biofilms are damaging the bas-reliefs, low reliefs engraved on the surface of sandstone, information about the microbial community within them is indispensable to control biofilm colonization. PCR-denaturing gradient gel electrophoresis (DGGE) analysis of biofilm samples from the pigmented sandstone surfaces showed that the bacterial community members in the biofilms differed clearly from those in the air and had low sequence similarity to database sequences. Non-destructive sampling of biofilm revealed novel bacterial groups of predominantly Rubrobacter in salmon pink biofilm, Cyanobacteria in chrome green biofilm, Cyanobacteria and Chloroflexi in signal violet biofilm, Chloroflexi in black gray biofilm, and Deinococcus-Thermus, Cyanobacteria, and Rubrobacter in blue green biofilm. Serial peeling-off of a thick biofilm by layers with adhesive sheets revealed a stratified structure: the blue–green biofilm, around which there was serious deterioration, was very rich in Cyanobacteria near the surface and Chloroflexi in deep layer below. Nitrate ion concentrations were high in the blue–green biofilm. The characteristic distribution of bacteria at different biofilm depths provides valuable information on not only the biofilm formation process but also the sandstone weathering process in the tropics.
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  • Yoshikane Itoh, Keiko Sakagami, Yoshihito Uchino, Chanita Boonmak, Tet ...
    2013 Volume 28 Issue 4 Pages 432-435
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 19, 2013
    JOURNALS FREE ACCESS
    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48°C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL-1. This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C.
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  • Mamoru Oshiki, Takanori Awata, Tomonori Kindaichi, Hisashi Satoh, Sato ...
    2013 Volume 28 Issue 4 Pages 436-443
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 08, 2013
    JOURNALS FREE ACCESS
    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. The present study aimed to cultivate two phylogenetically distinct anammox bacteria, “Candidatus Brocadia sinica” and “Ca. Scalindua sp.” in the form of planktonic cells 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 was confirmed by fluorescence in-situ hybridization and 16S rRNA gene sequencing analysis. The 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, using enriched planktonic cells. The present study demonstrated that MBR enables the culture of planktonic anammox bacterial cells, which are suitable for studying their ecophysiology and biochemistry.
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  • Takashi Furukawa, Yoshihiro Suzuki
    2013 Volume 28 Issue 4 Pages 444-449
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 19, 2013
    JOURNALS FREE ACCESS
    This study aimed to identify specific river sources of fecal contamination by applying pulsed-field gel electrophoresis (PFGE) to environmental water samples from a recreational beach in Japan. The genotypes of all Enterococcus faecium and Enterococcus faecalis strains used as indicators of fecal pollution on the recreational beach and rivers were analyzed by PFGE, and the PFGE profiles of the strains were classified at a 0.9 similarity level using dendrogram analysis. PFGE types of E. faecium isolated from Sakai River or urban drainage were classified in the same cluster. Therefore, the probable sources of fecal pollution on the recreational beach were Sakai River and urban drainage. The approaches for microbial source tracking employed in this study used PFGE with Enterococcus species as an indicator can be a potential tool to specify the source(s) of fecal pollution and contribute to improved public health in coastal environments.
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  • Keqiang Shao, Guang Gao, Xiangming Tang, Yongping Wang, Lei Zhang, Boq ...
    2013 Volume 28 Issue 4 Pages 450-456
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: December 13, 2013
    JOURNALS FREE ACCESS
    The most common natural disturbances in shallow lakes are wind-induced waves, which cause catastrophic changes in the aquatic fauna of lakes. Recovery from these changes is always prolonged. The objective of this study was to understand the resilience and recovery of the particle-attached bacterial community composition (PABCC) after frequent wind-wave disturbance in a large shallow eutrophic lake. To accomplish this, we designed a mesocosm experiment including an undisturbed control, and a physically disturbed treatment that stimulated the superposition of two different intensities of wind-induced waves in the large shallow eutrophic Lake Taihu, China. The PABCC was determined by denaturing gradient gel electrophoresis, following by cloning and sequencing of the selected samples. We observed that the most marked change of the PABCC occurred in the disturbed treatment, in which the concentrations of suspended solids (SS) and the water turbidity varied strongly. However, we observed low recovery of the PABCC within 4 days post-disturbance when the investigated environmental factors had also recovered. Our results indicated that the resistance of the PABCC is low, and resilience is also low following frequent disturbance by wind-waves in a large shallow eutrophic lake.
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  • Wei Sun, Chunyu Xia, Meiying Xu, Jun Guo, Aijie Wang, Guoping Sun
    2013 Volume 28 Issue 4 Pages 457-465
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 19, 2013
    JOURNALS FREE ACCESS
    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b- and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg-1 sediment, NH4+-N >144 mg kg-1 sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg-1 sediment, NH4+-N <93 mg kg-1 sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.
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  • Hideaki Sasaki, Susumu Shirato, Tomoya Tahara, Kenji Sato, Hiroyuki Ta ...
    2013 Volume 28 Issue 4 Pages 466-469
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 19, 2013
    JOURNALS FREE ACCESS
    The Fukushima Daiichi Nuclear Power Plant accident released large amounts of radioactive substances into the environment and contaminated the soil of Tohoku and Kanto districts in Japan. Removal of radioactive material from the environment is an urgent problem, and soil purification using plants is being considered. In this study, we investigated the ability of 12 seed plant species and a cyanobacterium to accumulate radioactive material. The plants did not accumulate radioactive material at high levels, but high accumulation was observed in the terrestrial cyanobacterium Nostoc commune. In Nihonmatsu City, Fukushima Prefecture, N. commune accumulated 415,000 Bq/kg dry weight 134Cs and 607,000 Bq kg-1 dry weight 137Cs. The concentration of cesium in N. commune tended to be high in areas where soil radioactivity was high. A cultivation experiment confirmed that N. commune absorbed radioactive cesium from polluted soil. These data demonstrated that radiological absorption using N. commune might be suitable for decontaminating polluted soil.
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  • Yuichi Saeki, Sokichi Shiro, Toshiyuki Tajima, Akihiro Yamamoto, Reiko ...
    2013 Volume 28 Issue 4 Pages 470-478
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 16, 2013
    JOURNALS FREE ACCESS
    We characterized the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia from weakly acidic soils in Japan and their geographical distribution in an ecological study of indigenous soybean rhizobia. We isolated bradyrhizobia from three kinds of Rj-genotype soybeans. Their genetic diversity and community structure were analyzed by PCR-RFLP analysis of the 16S–23S rRNA gene internal transcribed spacer (ITS) region with 11 Bradyrhizobium USDA strains as references. We used data from the present study and previous studies to carry out mathematical ecological analyses, multidimensional scaling analysis with the Bray-Curtis index, polar ordination analysis, and multiple regression analyses to characterize the relationship between soybean-nodulating bradyrhizobial community structures and their geographical distribution. The mathematical ecological approaches used in this study demonstrated the presence of ecological niches and suggested the geographical distribution of soybean-nodulating bradyrhizobia to be a function of latitude and the related climate, with clusters in the order Bj123, Bj110, Bj6, and Be76 from north to south in Japan.
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  • Qian Yin, Dongmei Yue, Yuke Peng, Ying Liu, Lin Xiao
    2013 Volume 28 Issue 4 Pages 479-486
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 16, 2013
    JOURNALS FREE ACCESS
    The overuse of antibiotics has accelerated antibiotic resistance in the natural environment, especially fresh water, generating a potential risk for public health around the world. In this study, antibiotic resistance in Lake Taihu was investigated and this was the first thorough data obtained through culture-dependent methods. High percentages of resistance to streptomycin and ampicillin among bacterial isolates were detected, followed by tetracycline and chloramphenicol. Especially high levels of ampicillin resistance in the western and northern regions were illustrated. Bacterial identification of the isolates selected for further study indicated the prevalence of some opportunistic pathogens and 62.0% of the 78 isolates exhibited multiple antibiotic resistance. The presence of ESBLs genes was in the following sequence: blaTEM > blaSHV > blaCTMX and 38.5% of the isolates had a class I integrase gene. Of all tested strains, 80.8% were able to transfer antibiotic resistance through conjugation. We also concluded that some new families of human-associated ESBLs and AmpC genes can be found in natural environmental isolates. The prevalence of antibiotic resistance and the dissemination of transferable antibiotic resistance in bacterial isolates (especially in opportunistic pathogens) was alarming and clearly indicated the urgency of realizing the health risks of antibiotic resistance to human and animal populations who are dependent on Lake Taihu for water consumption.
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Short Communications
  • Zhihua Bao, Kazuhiro Sasaki, Takashi Okubo, Seishi Ikeda, Mizue Anda, ...
    2013 Volume 28 Issue 4 Pages 487-490
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 19, 2013
    JOURNALS FREE ACCESS
    Rice seedlings were inoculated with Azospirillum sp. B510 and transplanted into a paddy field. Growth in terms of tiller numbers and shoot length was significantly increased by inoculation. Principal-coordinates analysis of rice bacterial communities using the 16S rRNA gene showed no overall change from B510 inoculation. However, the abundance of Veillonellaceae and Aurantimonas significantly increased in the base and shoots, respectively, of B510-inoculated plants. The abundance of Azospirillum did not differ between B510-inoculated and uninoculated plants (0.02–0.50%). These results indicate that the application of Azospirillum sp. B510 not only enhanced rice growth, but also affected minor rice-associated bacteria.
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  • Hao Zheng, Dylan Bodington, Chong Zhang, Kazuhiko Miyanaga, Yasunori T ...
    2013 Volume 28 Issue 4 Pages 491-494
    Published: 2013
    Released: December 20, 2013
    [Advance publication] Released: November 15, 2013
    JOURNALS FREE ACCESS
    Phylogenetic diversity of [FeFe]-hydrogenase (HydA) in termite guts was assessed by pyrosequencing PCR amplicons obtained using newly designed primers. Of 8,066 reads, 776 hydA phylotypes, defined with 97% nucleotide sequence identity, were recovered from the gut homogenates of three termite species, Hodotermopsis sjoestedti, Reticulitermes speratus, and Nasutitermes takasagoensis. The phylotype coverage was 92–98%, and the majority shared only low identity with database sequences. It was estimated that 194–745 hydA phylotypes existed in the gut of each termite species. Our results demonstrate that hydA gene diversity in the termite gut microbiota is much higher than previously estimated.
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