Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 29 , Issue 4
Showing 1-17 articles out of 17 articles from the selected issue
Research Highlight
Regular Papers
  • Anja Klančnik, Darinka Vučković, Polona Jamnik, Maja Abram, Sonja Smol ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 338-345
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: October 02, 2014
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    Thermotolerant Campylobacter spp. frequently cause bacterial gastroenteritis in humans commonly infected through the consumption of undercooked poultry meat. We examined Campylobacter jejuni heat-stress responses in vitro after exposure to 48°C and 55°C. The in vivo modulation of its pathogenicity was also investigated using BALB/c mice intravenously infected with stressed C. jejuni. Regardless of the bacterial growth phase, the culturability and viability of C. jejuni in vitro was reduced after exposure to 55°C. This correlated with the altered protein profile and decreased virulence properties observed in vivo. Heat stress at 48°C elicited the transition to more resistant bacterial forms, independent of morphological changes or the appearance of shorter spiral and coccoid cells. This treatment did not cause marked changes in bacterial virulence properties in vivo. These results indicated that the characteristics and pathogenicity of C. jejuni in response to heat stress are temperature dependent. Further studies on the responses of C. jejuni to stresses used during food processing, as well as the modulation of its virulence, are important for a better understanding of its contamination and infective cycle, and will, thus, contribute to improved safety in the food production chain.
  • Hayato Takihara, Jun Ogihara, Takao Yoshida, Shujiro Okuda, Mutsuyasu ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 346-352
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: October 11, 2014
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    We previously reported that R. erythropolis PR4 translocated from the aqueous to the alkane phase, and then grew in two phase cultures to which long-chain alkanes had been added. This was considered to be beneficial for bioremediation. In the present study, we investigated the proteins involved in the translocation of R. erythropolis PR4. The results of our proteogenomic analysis suggested that GroEL2 was upregulated more in cells that translocated inside of the pristane (C19) phase than in those located at the aqueous-alkane interface attached to the n-dodecane (C12) surface. PR4 (pK4-EL2-1) and PR4 (pK4-ΔEL2-1) strains were constructed to confirm the effects of the upregulation of GroEL2 in translocated cells. The expression of GroEL2 in PR4 (pK4-EL2-1) was 15.5-fold higher than that in PR4 (pK4-ΔEL2-1) in two phase cultures containing C12. The growth and cell surface lipophilicity of PR4 were enhanced by the introduction of pK4-EL2-1. These results suggested that the plasmid overexpression of groEL2 in PR4 (pK4-EL2-1) led to changes in cell localization, enhanced growth, and increased cell surface lipophilicity. Thus, we concluded that the overexpression of GroEL2 may play an important role in increasing the organic solvent tolerance of R. erythropolis PR4 in aqueous-alkane two phase cultures.
  • Akiko Hanada, Takashi Kurogi, Nguyen Minh Giang, Takeshi Yamada, Yuki ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 353-362
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: September 20, 2014
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    Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear.
  • Clemens Karwautz, Tillmann Lueders
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 363-369
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: October 02, 2014
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    The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impede well clogging by fine sediments and also biofilms. In the present study, bacterial communities were investigated in a drinking water production system before, during, and after hydraulic purging. Variations were observed in bacterial communities between different wells of the same production system before maintenance, despite them having practically identical water chemistries. This may have reflected the distinct usage practices of the different wells, and also local aquifer heterogeneity. Hydraulic jetting of one well preferentially purged a subset of the dominating taxa, including lineages related to Diaphorobacter, Nitrospira, Sphingobium, Ralstonia, Alkanindiges, Janthinobacterium, and Pseudomonas spp, suggesting their tendency for growth in well-associated biofilms. Lineages of potential drinking water concern (i.e. Legionellaceae, Pseudomonadaceae, and Acinetobacter spp.) reacted distinctly to hydraulic jetting. Bacterial diversity was markedly reduced in drinking water 2 weeks after the cleaning procedure. The results of the present study provide a better understanding of drinking water wells as a microbial habitat, as well as their role in the microbiology of drinking water systems.
  • Kamonluck Teamtisong, Pongpan Songwattana, Rujirek Noisangiam, Pongdet ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 370-376
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: October 04, 2014
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    Bradyrhizobium sp. DOA9, a non-photosynthetic bacterial strain originally isolated from the root nodules of the legume Aeschynomene americana, is a divergent nod-containing strain. It exhibits a broad host range, being able to colonize and efficiently nodulate the roots of most plants from the Dalbergioid, Millettioid, and Robinioid tribes (7 species of Papilionoideae). In all cases, nodulation was determinate. The morphology and size of DOA9 bacteroids isolated from the nodules of various species of Papilionoideae were indistinguishable from the free-living form. However, they were spherical in Arachis hypogaea nodules. GusA-tagged DOA9 also colonized rice roots as endophytes. Since broad-host-range legume symbionts often carry multiple replicons in their genome, we analyzed the replicons for symbiosis genes by electrophoresis. DOA9 carried two replicons, a chromosome (cDOA9) and single megaplasmid (pDOA9) larger than 352 kb. The genes for nodulation (nodA, B, C) and nitrogen fixation (nifH) were localized on the megaplasmid. Southern blot hybridization revealed two copies of nodA on the megaplasmid, single copies of nodB and C on the megaplasmid, and one copy each of nifH on the chromosome and megaplasmid. These results suggested that Bradyrhizobium sp. DOA9 may have the unusual combination of a broad host range, bacteroid differentiation, and symbiosis-mediating replicons.
  • Ting-Wen Cheng, Li-Hung Lin, Yue-Ting Lin, Sheng-Rong Song, Pei-Ling W ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 377-387
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: October 02, 2014
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    Terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. The exact community compositions responsible for carbon cycling beneath these surface features remain obscure. As sulfate reduction represents an essential process for anoxic organic mineralization, this study collected muddy fluids from a high-temperature hydrocarbon seep in Taiwan and analyzed community structures of sulfate-supplemented sediment slurries incubated anoxically at elevated temperatures. The results obtained demonstrated that sulfate consumption occurred between 40°C and 80°C. Dominant potential sulfate reducers included Desulfovibrio spp., Desulfonatronum spp., Desulforhabdus spp., and Desulfotomaculum spp. at 40°C, Thermodesulfovibrio spp. at 50°C, Thermodesulfovibrio spp. and Thermacetogenium spp. at 60°C, Thermacetogenium spp. and Archaeoglobus spp. at 70°C, and Archaeoglobus spp. at 80°C. None of these potential sulfate reducers exceeded 7% of the community in the untreated sample. Since no exogenous electron donor was provided during incubation, these sulfate reducers appeared to rely on the degradation of organic matter inherited from porewater and sediments. Aqueous chemistry indicated that fluids discharged in the region represented a mixture of saline formation water and low-salinity surface water; therefore, these lines of evidence suggest that deeply-sourced, thermophilic and surface-input, mesophilic sulfate-reducing populations entrapped along the subsurface fluid transport could respond rapidly once the ambient temperature is adjusted to a range close to their individual optima.
  • Fang-Fang Xu, Tomohiro Morohoshi, Wen-Zhao Wang, Yuka Yamaguchi, Yan L ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 388-392
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: November 08, 2014
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    Concern regarding household biofilms has grown due to their widespread existence and potential to threaten human health by serving as pathogen reservoirs. Previous studies identified Methylobacterium as one of the dominant genera found in household biofilms. In the present study, we examined the mechanisms underlying biofilm formation by using the bacterial consortium found in household pink slime. A clone library analysis revealed that Methylobacterium was the predominant genus in household pink slime. In addition, 16 out of 21 pink-pigmented bacterial isolates were assigned to the genus Methylobacterium. Although all of the Methylobacterium isolates formed low-level biofilms, the amount of the biofilms formed by Methylobacterium sp. P-1M and P-18S was significantly increased by co-culturing with other Methylobacterium strains that belonged to a specific phylogenetic group. The single-species biofilm was easily washed from the glass surface, whereas the dual-species biofilm strongly adhered after washing. A confocal laser scanning microscopy analysis showed that the dual-species biofilms were significantly thicker and tighter than the single-species biofilms.
  • Wei-Yu Chen, Jer-Horng Wu, Juu-En Chang
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 393-400
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: December 10, 2014
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    A deeper understanding of the microbial community structure is very important in bioremediation for polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs). However, this has been insufficiently addressed in previous studies. To obtain more information, we pyrosequenced the V4/V5 regions of the 16S rRNA genes of bacterial communities transited from polluted soil to batch microcosms that rapidly degraded high concentrations of octachlorodibenzofuran (OCDF). The analysis results contained an average of 11,842 reads per sample, providing the first detailed description of bacterial communities associated with PCDD/Fs. The community composition markedly changed to be concomitant with the degradation of OCDF, indicating that a distinctive population structure developed rapidly in the microcosm. Although oxygen gas was provided weekly to the microcosm, the growth of potential degraders, Sphingomonas, Pseudomonas, Rhodococcus, and Clostridium, was observed, but in consistently low quantities. While anaerobic Sedimentibacter initially emerged as an abundant pioneer, several aerobic participants, such as the genera Brevundimonas, Pseudoxanthomonas, and Lysobacter, exhibited a large increase in their 16S rRNA gene copies within the timeframe, which showed a temporal population dynamic, and indicated their collaborative contributions to the degradation of OCDF under hypoxic conditions. These results have provided a deeper insight into the microbial community structure and population dynamics of the OCDF-degrading microcosm.
  • Kengo Matsunaga, Kengo Kubota, Hideki Harada
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 401-407
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: December 10, 2014
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    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4–8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes.
  • Swan Firquet, Sophie Beaujard, Pierre-Emmanuel Lobert, Famara Sané, De ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 408-412
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: December 03, 2014
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    Heat inactivation of viruses was reported, however, the thermal resistance of viruses in droplets has not been studied. The aim of this study was to evaluate the pattern of heat resistance of minute virus of mice (MVM), coxsackievirus B4 (CVB4), influenza A virus (H1N1), and herpes simplex virus type 1 (HSV1) contained in droplets. Four μL droplets containing viruses (> 104.5 TCID50) were applied onto warmed surface obtained by using a self-made heating device. Viral suspensions were exposed to temperatures ranging from 70 to 130°C for 0 to 90 min depending on the virus, and then the recovered viral preparations were tittered. Inactivation rates were calculated from curves that were analysed according to the first order kinetics model. Full inactivation was obtained for MVM in 90 min at 80°C and in 2 s at 130°C, for H1N1 in 14 s at 70°C and in 1 s at 110°C, for CVB4 and HSV-1 in 5 s and 7 s respectively at 70°C and in 1 s at 100°C. Clearly, MVM was more resistant than H1N1 that was more resistant than HSV-1 and CVB4, which was reflected by increasing inactivation rates. The impact of short time exposure to heat onto the infectivity of viruses contained in a small volume of suspension has been determined. For the first time, the inactivation of viral particles contained in drops exposed to temperatures higher than 100°C has been investigated. It appears that heating can have an unexpected faster virucidal effect than previously described.
  • Shota Oku, Ayaka Komatsu, Yutaka Nakashimada, Takahisa Tajima, Junichi ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 413-419
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: December 10, 2014
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    Pseudomonas fluorescens Pf0-1 exhibited chemotactic responses to l-malate, succinate, and fumarate. We constructed a plasmid library of 37 methyl-accepting chemotaxis protein (MCP) genes of P. fluorescens Pf0-1. To identify a MCP for l-malate, the plasmid library was screened using the PA2652 mutant of Pseudomonas aeruginosa PAO1, a mutant defective in chemotaxis to l-malate. The introduction of Pfl01_0728 and Pfl01_3768 genes restored the ability of the PA2652 mutant to respond to l-malate. The Pfl01_0728 and Pfl01_3768 double mutant of P. fluorescens Pf0-1 showed no response to l-malate or succinate, while the Pfl01_0728 single mutant did not respond to fumarate. These results indicated that Pfl01_0728 and Pfl01_3768 were the major MCPs for l-malate and succinate, and Pfl01_0728 was also a major MCP for fumarate. The Pfl01_0728 and Pfl01_3768 double mutant unexpectedly exhibited stronger responses toward the tomato root exudate and amino acids such as proline, asparagine, methionine, and phenylalanine than those of the wild-type strain. The ctaA, ctaB, ctaC (genes of the major MCPs for amino acids), Pfl01_0728, and Pfl01_3768 quintuple mutant of P. fluorescens Pf0-1 was less competitive than the ctaA ctaB ctaC triple mutant in competitive root colonization, suggesting that chemotaxis to l-malate, succinate, and/or fumarate was involved in tomato root colonization by P. fluorescens Pf0-1.
  • Yoko Shiina, Manabu Itakura, Hyunseok Choi, Yuichi Saeki, Masahito Hay ...
    Type: Regular Papers
    2014 Volume 29 Issue 4 Pages 420-426
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: December 03, 2014
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    Bradyrhizobium japonicum strains that have the nosZ gene, which encodes N2O reductase, are able to mitigate N2O emissions from soils (15). To examine the distribution of nosZ genotypes among Japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosZ and nodC genotypes. The 1556 resultant isolates were classified into the nosZ+/nodC+ genotype (855 isolates) and nosZ−/nodC+ genotype (701 isolates). The 11 soil samples in which nosZ− isolates significantly dominated (P < 0.05; the χ2 test) were all Andosols (a volcanic ash soil prevalent in agricultural fields in Japan), whereas the 17 soil samples in which nosZ+ isolates significantly dominated were mainly alluvial soils (non-volcanic ash soils). This result was supported by a principal component analysis of environmental factors: the dominance of the nosZ− genotype was positively correlated with total N, total C, and the phosphate absorption coefficient in the soils, which are soil properties typical of Andosols. Internal transcribed spacer sequencing of representative isolates showed that the nosZ+ and nosZ− isolates of B. japonicum fell mainly into the USDA110 (BJ1) and USDA6 (BJ2) groups, respectively. These results demonstrated that the group lacking nosZ was dominant in Andosols, which can be a target soil type for an N2O mitigation strategy in soybean fields. We herein discussed how the nosZ genotypes of soybean bradyrhizobia depended on soil types in terms of N2O respiration selection and genomic determinants for soil adaptation.
Short Communications
  • Keishi Kameyama, Kikuji Itoh
    Type: Short Communication
    2014 Volume 29 Issue 4 Pages 427-430
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: October 04, 2014
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    The aim of the present study was to identify bacteria that may contribute to the onset of metabolic dysfunctions. We isolated and identified a candidate bacterium belonging to Lachnospiraceae (strain AJ110941) in the feces of hyperglycemic obese mice. The colonization of germ-free ob/ob mice by AJ110941 induced significant increases in fasting blood glucose levels as well as liver and mesenteric adipose tissue weights, and decreases in plasma insulin levels and HOMA-β values. These results indicated that the specific gut commensal bacterium AJ110941 influenced the development of obesity and diabetes in ob/ob mice with genetic susceptibility for obesity.
  • Hayato Takihara, Chiaki Matsuura, Jun Ogihara, Noriyuki Iwabuchi, Mich ...
    Type: Short Communication
    2014 Volume 29 Issue 4 Pages 431-433
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: December 10, 2014
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    We recently reported that the overexpression of GroEL2 played an important role in increasing the alkane tolerance of Rhodococcus erythropolis PR4. In the present study, we examined the effects of the introduction of groEL2 on the alkane tolerance of other Rhodococcus strains. The introduction of groEL2 into Rhodococcus strains led to increased alkane tolerance. The translocation of R. rhodochrous ATCC12674 cells to and survival in the n-octane (C8) phase in two phase culture were significantly enhanced by the introduction of groEL2 derived from strain PR4, suggesting that engineering cells to overexpress GroEL2 represents an effective strategy for enhancing organic solvent tolerance in Rhodococcus.
  • Kanako Tago, Hideomi Itoh, Yoshitomo Kikuchi, Tomoyuki Hori, Yuya Sato ...
    Type: Short Communication
    2014 Volume 29 Issue 4 Pages 434-437
    Published: 2014
    Released: December 19, 2014
    [Advance publication] Released: November 20, 2014
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    The diversity and abundance of Burkholderia species in sugarcane field soils were investigated by a 16S rRNA gene-based approach using genus-specific primers. A total of 365,721 sequences generated by the Illumina MiSeq platform were assigned to the genus Burkholderia. Nearly 58% of these sequences were placed in a previously defined cluster, including stinkbug symbionts. Quantitative PCR analysis revealed a consistent number of 16S rRNA gene copies for Burkholderia species (107 g−1 soil) across the sampled fields. C/N, pH, and nitrate concentrations were important factors shaping the Burkholderia community structure; however, their impacts were not significant considering the overall genus size.
Author's Correction
  • Xiao-Mei Lv, Ming-Fei Shao, Chao-Lin Li, Ji Li, Xin-lei Gao, Fei-Yun S ...
    Type: Author’s Correction
    2014 Volume 29 Issue 4 Pages 438
    Published: 2014
    Released: December 19, 2014
    JOURNALS FREE ACCESS
    Volume 29, No. 3, Page 261–268, 2014

    Incorrect:
    Xiao-Mei Lv1,2, Ming-Fei Shao1,2,3, Chao-Lin Li12, Ji Li1,2,3*, Xin-lei Gao1,2, and Fei-Yun Sun1,2,3
    * Corresponding author. E-mail: liji98@tsinghua.org.cn;
    Tel: +86–0755–2603–2692; Fax: +86–0755–2670–3651.

    Correct:
    Xiao-Mei Lv1,2, Ming-Fei Shao1,2,3*, Chao-Lin Li1,2, Ji Li1,2,3**, Xin-lei Gao1,2, and Fei-Yun Sun1,2,3
    * Corresponding author. E-mail: mfshao@hitsz.edu.cn
    Tel: +86–0755–2603–2692; Fax: +86–0755–2670–3651.
    ** Corresponding author. E-mail: liji98@tsinghua.org.cn;
    Tel: +86–0755–2603–2692; Fax: +86–0755–2670–3651.

    This correction has been completed on the electronic file of the present paper available at J-STAGE.
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