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Behera SS, Ray RC. Bioprospecting of cowdung microflora for sustainable agricultural, biotechnological and environmental applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100018. [PMID: 34841310 PMCID: PMC8610318 DOI: 10.1016/j.crmicr.2020.100018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/28/2022] Open
Abstract
The review aims at highlighting the manifold applications of cow dung (CD) and CD microflora covering agricultural, biotechnological and environmental applications. The update research on CD microflora and CD in agricultural domain such as biocontrol, growth promotion, organic fertilizer, sulfur oxidation, phosphorus solubilization, zinc mobilization and underlying mechanisms involved in these processes are discussed. The significance of CD applications in tropical agriculture in context to climate change is briefly emphasized. The advances on genomics and proteomics of CD microflora for enhanced yield of enzymes, organic acids, alternative fuels (biomethane and biohydrogen) and other biocommodities, and environmental applications in context to biosorption of heavy metals, biodegradation of xenobiotics, etc. have been given critical attention.
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Key Words
- AD, anaerobic digesters
- AP, apple pomace
- ARB, antibiotic-resistant bacteria
- ARGs, antibiotic-resistant genes
- BOD, biochemical oxygen demand
- Biocontrol
- Biodegradation
- Biogas
- Bioprocess
- Bioremediation
- Biosorption
- C/N, carbon nitrogen ratio
- CD, cow dung
- CDP, cow dung powder
- CEC, cation exchange capacity
- Cow dung
- DO, dissolved oxygen
- EC, electric conductivity
- IAA, indole-3-acetic acids
- NPK, nitrogen, phosphorus, and potassium
- NPP, net primary productivity
- OM, organic matter
- PGPR, plant growth promoting rhizobateria
- PSM, P-solubilizing microorganisms
- Panchagavya
- SGR, specific growth rate
- SSF, solid sate fermentation
- SmF, sub-merged fermentation
- TOC, total organic carbon
- TPPB, two phase partitioning bioreactor
- TS, total solids
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Affiliation(s)
- Sudhanshu S Behera
- Department of Biotechnology, National Institute of Technology, GE Road, Raipur 492010, India.,Department of Fisheries and Animal Resource Development, Government of Odisha, India
| | - Ramesh C Ray
- Centre for Food Biology and Environment Studies, Bhubaneswar 751019, India
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Matturro B, Rossetti S, Leitão P. CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) for Complex Environmental Samples. Methods Mol Biol 2021; 2246:129-140. [PMID: 33576987 DOI: 10.1007/978-1-0716-1115-9_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
CARD-FISH technique allows us to increase microbial cell detection compared to traditional FISH assays. Specific nonfluorescent oligonucleotide probes targeting 16S rRNA genes are employed and are chemically activated by the binding of tyramide molecules, with the latter able to generate a cascade of fluorescence signals, improving sensitivity and reducing background noise. The technique has been successfully applied for the detection of microorganisms in different environmental matrices and under different growth conditions (including those where cells are characterized by low physiological activity and low ribosome content). This chapter presents a straightforward procedure to execute CARD-FISH analysis, from sample preparation and fixation, to microscopic visualization, along with relevant technical notes.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo St. (RM), 00015, Italy.
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo St. (RM), 00015, Italy
| | - Patrícia Leitão
- Cento de Recursos Naturais e Ambiente (CERENA), Faculty of Engineering, University of Porto, Porto, Portugal
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Tashiro Y, Hasegawa Y, Shintani M, Takaki K, Ohkuma M, Kimbara K, Futamata H. Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells. Front Microbiol 2017; 8:571. [PMID: 28439261 PMCID: PMC5383704 DOI: 10.3389/fmicb.2017.00571] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/20/2017] [Indexed: 12/01/2022] Open
Abstract
Membrane vesicles (MVs) are secreted from a wide range of microbial species and transfer their content to other cells. Although MVs play critical roles in bacterial communication, whether MVs selectively interact with bacterial cells in microbial communities is unclear. In this study, we investigated the specificity of the MV-cell interactions and evaluated the potential of MVs to target bacterial cells for delivery. MV association with bacterial cells was examined using a fluorescent membrane dye to label MVs. MVs derived from the enterobacterium Buttiauxella agrestis specifically interacted with cells of the parent strain but interacted less specifically with those of other genera tested in this study. Electron microscopic analyses showed that MVs were not only attached on B. agrestis cells but also fused to them. The interaction energy, which was characterized by hydrodynamic diameter and zeta potential based on the Derjaguin–Landau–Verwey–Overbeek (DLVO) theory, was significant low between MVs and cells in B. agrestis, compared to those between B. agrestis MVs and cells of other genera. Similar specific interaction was also occurred between B. agrestis MVs and cells of six other species belonging to Buttiauxella spp. B. agrestis harboring plasmid pBBR1MCS-1 secreted plasmid-containing MVs (p-MVs), and plasmid DNA in p-MVs was transferred to the same species. Moreover, antibiotic-associated MVs enabled effective killing of target species; the survival rate of B. agrestis was lower than those of Escherichia coli and Pseudomonas aeruginosa in the presence of gentamicin-associated MVs derived from B. agrestis. Altogether, we provide the evidence that MVs selectively interact with target bacterial cells and offer a new avenue for controlling specific bacterial species using bacterial MVs in microbial communities.
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Affiliation(s)
- Yosuke Tashiro
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka UniversityHamamatsu, Japan
| | - Yusuke Hasegawa
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka UniversityHamamatsu, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka UniversityHamamatsu, Japan.,Graduate School of Science and Technology, Shizuoka UniversityHamamatsu, Japan.,Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Japan
| | - Kotaro Takaki
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka UniversityHamamatsu, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Japan
| | - Kazuhide Kimbara
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka UniversityHamamatsu, Japan.,Graduate School of Science and Technology, Shizuoka UniversityHamamatsu, Japan
| | - Hiroyuki Futamata
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka UniversityHamamatsu, Japan.,Graduate School of Science and Technology, Shizuoka UniversityHamamatsu, Japan.,Research Institute of Green Science and Technology, Shizuoka UniversityShizuoka, Japan
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Tsuchiya Y, Eda S, Kiriyama C, Asada T, Morisaki H. Analysis of Dissolved Organic Nutrients in the Interstitial Water of Natural Biofilms. MICROBIAL ECOLOGY 2016; 72:85-95. [PMID: 26961802 DOI: 10.1007/s00248-016-0749-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 02/28/2016] [Indexed: 06/05/2023]
Abstract
In biofilms, the matrix of extracellular polymeric substances (EPSs) retains water in the interstitial region of the EPS. This interstitial water is the ambient environment for microorganisms in the biofilms. The nutrient condition in the interstitial water may affect microbial activity in the biofilms. In the present study, we measured the concentrations of dissolved organic nutrients, i.e., saccharides and proteins, contained in the interstitial water of biofilms formed on the stones. We also analyzed the molecular weight distribution, chemical species, and availability to bacteria of some saccharides in the interstitial water. Colorimetric assays showed that the concentrations of saccharides and proteins in the biofilm interstitial water were significantly higher (ca. 750 times) than those in the surrounding lake waters (p < 0.05). Chromatographic analyses demonstrated that the saccharides in the interstitial waters were mainly of low molecular-weight saccharides such as glucose and maltose, while proteins in the interstitial water were high molecular-weight proteins (over 7000 Da). Bacterial growth and production of EPS occurred simultaneously with the decrease in the low molecular-weight saccharide concentrations when a small portion of biofilm suspension was inoculated to the collected interstitial water, suggesting that the dissolved saccharides in the interstitial water support bacterial growth and formation of biofilms.
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Affiliation(s)
- Yuki Tsuchiya
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Shima Eda
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Chiho Kiriyama
- Graduate School of Science and Engineering, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoya Asada
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hisao Morisaki
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan.
- Graduate School of Science and Engineering, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan.
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji Higashi, Kusatsu, Shiga, 525-8577, Japan.
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Shift of Propionate-Oxidizing Bacteria with HRT Decrease in an UASB Reactor Containing Propionate as a Sole Carbon Source. Appl Biochem Biotechnol 2014; 175:274-86. [DOI: 10.1007/s12010-014-1265-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/15/2014] [Indexed: 10/24/2022]
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Ban Q, Li J, Zhang L, Jha AK, Zhang Y. Quantitative analysis of previously identified propionate-oxidizing bacteria and methanogens at different temperatures in an UASB reactor containing propionate as a sole carbon source. Appl Biochem Biotechnol 2013; 171:2129-41. [PMID: 24026412 DOI: 10.1007/s12010-013-0465-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/22/2013] [Indexed: 10/26/2022]
Abstract
Propionate degradation is crucial for maintaining the efficiency and stability of an anaerobic reactor. However, there was little information about the effects of ecological factor on propionate-oxidizing bacteria (POB). In current research, quantitative real-time fluorescence polymerase chain reaction (QPCR) of some identified POB and methanogens with a decrease in temperature in an upflow anaerobic sludge bed (UASB) reactor containing propionate as sole carbon source was investigated. The results showed that there were at least four identified POB, including Pelotomaculum schinkii, Pelotomaculum propionicum, Syntrophobacter fumaroxidans, and Syntrophobacter sulfatireducens, observed in this UASB reactor. Among them, P. schinkii was dominated during the whole operational period. Its quantity was 1.2 × 10(4) 16S rRNA gene copies per nanogram of DNA at 35 °C. A decrease in temperature from 35 to 30 °C led to P. schinkii to be increased by 1.8 times and then it was gradually reduced with a decrease in temperature from 30 to 25, 20, and 18 °C stepwise. A decrease in temperature from 35 to 20 °C did not make the amount of methanogens markedly changed, but hydrogenotrophic methanogens (Methanospirillum) and acetotrophic methanogens (Methanosaeta) at 18 °C were increased by an order of magnitude and 1.0 time, respectively, compared with other experimental conditions.
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Affiliation(s)
- Qiaoying Ban
- College of Environment and Resource, Shanxi University, Taiyuan, Shanxi, 030006, People's Republic of China,
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7
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Haruta S, Yoshida T, Aoi Y, Kaneko K, Futamata H. Challenges for complex microbial ecosystems: combination of experimental approaches with mathematical modeling. Microbes Environ 2013; 28:285-94. [PMID: 23995424 PMCID: PMC4070964 DOI: 10.1264/jsme2.me13034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature.
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Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University
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8
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Yoshida N, Ye L, Liu F, Li Z, Katayama A. Evaluation of biodegradable plastics as solid hydrogen donors for the reductive dechlorination of fthalide by Dehalobacter species. BIORESOURCE TECHNOLOGY 2013; 130:478-485. [PMID: 23313696 DOI: 10.1016/j.biortech.2012.11.139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
Biodegradable plastics (BPs) were evaluated for their applicability as sustainable and solid H(2) donors for microbial reductive dechlorination of 4,5,6,7-tetrachlorophthalide (fthalide). After a screening test of several BPs, the starch-based plastic (SP) that produced the highest levels of H(2) was selected for its use as the sole H(2) donor in this reaction. Fthalide dechlorination was successfully accomplished by combining an H(2)-producing SP culture and a KFL culture containing Dehalobacter species, supplemented with 0.13% and 0.5% SP, respectively. The efficiency of H(2) use in dechlorination was evaluated in a combined culture containing the KFL culture and strain Clostridium sp. Ma13, a new isolate that produces H(2) from SP. Results obtained with this culture indicated increased H(2)-fraction for fthalide dechlorination much more in this culture than in compared with a KFL culture supplemented with 20mM lactate, which are 0.75 H(2)·glucose(-1) and 0.015 H(2)·lactate(-1) in mol ratio, respectively.
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Affiliation(s)
- Naoko Yoshida
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan.
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Tashiro Y, Yawata Y, Toyofuku M, Uchiyama H, Nomura N. Interspecies interaction between Pseudomonas aeruginosa and other microorganisms. Microbes Environ 2013; 28:13-24. [PMID: 23363620 PMCID: PMC4070684 DOI: 10.1264/jsme2.me12167] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Microbes interact with each other in multicellular communities and this interaction enables certain microorganisms to survive in various environments. Pseudomonas aeruginosa is a highly adaptable bacterium that ubiquitously inhabits diverse environments including soil, marine habitats, plants and animals. Behind this adaptivity, P. aeruginosa has abilities not only to outcompete others but also to communicate with each other to develop a multispecies community. In this review, we focus on how P. aeruginosa interacts with other microorganisms. P. aeruginosa secretes antimicrobial chemicals to compete and signal molecules to cooperate with other organisms. In other cases, it directly conveys antimicrobial enzymes to other bacteria using the Type VI secretion system (T6SS) or membrane vesicles (MVs). Quorum sensing is a central regulatory system used to exert their ability including antimicrobial effects and cooperation with other microbes. At least three quorum sensing systems are found in P. aeruginosa, Las, Rhl and Pseudomonas quinolone signal (PQS) systems. These quorum-sensing systems control the synthesis of extracellular antimicrobial chemicals as well as interaction with other organisms via T6SS or MVs. In addition, we explain the potential of microbial interaction analysis using several micro devices, which would bring fresh sensitivity to the study of interspecies interaction between P. aeruginosa and other organisms.
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Affiliation(s)
- Yosuke Tashiro
- Division of Environmental Engineering, Hokkaido University, Hokkaido, Japan
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Oshiki M, Onuki M, Satoh H, Mino T. Microbial community composition of polyhydroxyalkanoate-accumulating organisms in full-scale wastewater treatment plants operated in fully aerobic mode. Microbes Environ 2012; 28:96-104. [PMID: 23257912 PMCID: PMC4070681 DOI: 10.1264/jsme2.me12141] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Hokkaido University, Japan.
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Kaiya S, Utsunomiya S, Suzuki S, Yoshida N, Futamata H, Yamada T, Hiraishi A. Isolation and functional gene analyses of aromatic-hydrocarbon-degrading bacteria from a polychlorinated-dioxin-dechlorinating process. Microbes Environ 2012; 27:127-35. [PMID: 22791044 PMCID: PMC4036015 DOI: 10.1264/jsme2.me11283] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aerobic aromatic-hydrocarbon-degrading bacteria from a semi-anaerobic microbial microcosm that exhibited apparent complete dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were isolated through enrichment and plating culture procedures with dibenzofuran as the model substrate. By 16S rRNA gene sequence comparisons, these dibenzofuran-degrading isolates were identified as being members of the phyla Actinobacteria, Firmicutes, and Proteobacteria, among which those of the genera Paenibacillus and Rhizobium were most abundant. All of the isolates utilized naphthalene as the sole carbon and energy source and degraded dibenzofuran metabolically or co-metabolically; however, they hardly attacked monochlorinated dibenzofuran and dibenzo-p-dioxin. By PCR cloning and sequencing, genes predicted to encode aromatic-ring-hydroxylating dioxygenase (AhDO) were detected in all test isolates. Real-time quantitative PCR assays with specific primer sets detected approximately 10⁵ copies of the AhDO large subunit genes g⁻¹ wet wt in the microcosm from which the isolates were obtained. This order of the copy number corresponded to approximately 1% of the 16S rRNA gene copies from "Dehalococcoides" and its relatives present as potent dechlorinators. These results suggest that aerobic AhDO-containing bacteria co-exist and play a role in the oxidative degradation of less chlorinated and completely dechlorinated products in the PCDD/F-dechlorinating process, thereby achieving the apparent complete dechlorination of PCDD/Fs.
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Affiliation(s)
- Shinichi Kaiya
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi 441-8580, Japan
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Wang Y, Hayatsu M, Fujii T. Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 2012; 27:111-21. [PMID: 22791042 PMCID: PMC4036013 DOI: 10.1264/jsme2.me11304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.
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Affiliation(s)
- Yong Wang
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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Thong-On A, Suzuki K, Noda S, Inoue JI, Kajiwara S, Ohkuma M. Isolation and characterization of anaerobic bacteria for symbiotic recycling of uric acid nitrogen in the gut of various termites. Microbes Environ 2012; 27:186-92. [PMID: 22791052 PMCID: PMC4036019 DOI: 10.1264/jsme2.me11325] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recycling of the nitrogenous waste uric acid (UA) of wood-feeding termites by their gut bacteria is one of the significant aspects of symbiosis for the conservation of nitrogen sources. Diverse anaerobic UA-degrading bacteria comprising 16 species were isolated from the gut of eight termite species, and were assigned to Clostridia, Enterobacteriaceae, and low G+C Gram-positive cocci. UA-degrading Clostridia had never been isolated from termite guts. UA-degrading ability was sporadically distributed among phylogenetically various culturable anaerobic bacteria from termite guts. A strain of Clostridium sp., which was commonly isolated from three termite species and represented a probable new species in cluster XIVa of clostridia, utilized UA as a nitrogen source but not as a sole carbon and energy source. This feature is in clear contrast to that of well-studied purinolytic clostridia or previously isolated UA degraders from termite guts, which also utilize UA as a sole carbon and energy source. Ammonia is the major nitrogenous product of UA degradation. Various purines stimulated the growth of this strain when added to an otherwise growth-limiting, nitrogen poor medium. The bacterial species involved the recycling of UA nitrogen in the gut microbial community of termites are more diverse in terms of both taxonomy and nutritional physiology than previously recognized.
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Affiliation(s)
- Arunee Thong-On
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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Okubo T, Ikeda S, Yamashita A, Terasawa K, Minamisawa K. Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria. Microbes Environ 2012; 27:204-8. [PMID: 22791055 PMCID: PMC4036018 DOI: 10.1264/jsme2.me11258] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyrosequence targeting of the 16S rRNA gene has been adopted for microbial communities associated with field-grown plants. To examine phylogenetic drifts according to read length and bioinformatic tools, original and chopped sequences (250–570 bp) covering the V1–V4 regions of 16S rRNA genes were compared using pyrosequence and Sanger reads of rice root microbiomes. The phylogenetic assignment at genus level depended on read length, especially in the genus Bradyrhizobium, which is one of the ecologically important bacterial genera associated with plants. We discuss the methodology of phylogenetic assignments of plant-associated bacteria by 16S rRNA pyrosequence.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
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Ito T, Yoshiguchi K, Ariesyady HD, Okabe S. Identification and quantification of key microbial trophic groups of methanogenic glucose degradation in an anaerobic digester sludge. BIORESOURCE TECHNOLOGY 2012; 123:599-607. [PMID: 22944494 DOI: 10.1016/j.biortech.2012.07.108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/23/2012] [Accepted: 07/28/2012] [Indexed: 05/23/2023]
Abstract
We investigated the major phylogenetic groups and population size of glucose-, propionate-, and acetate-degrading bacteria in the glucose-degrading anaerobic digester sludge by stable-isotope probing analysis of 16S rRNA (RNA-SIP) with [(13)C(6)]glucose followed by time course analysis of microautoradiography combined with fluorescent in situ hybridization (MAR-FISH) with [U-(14)C]glucose. The results indicated that glucose was predominately degraded to CH(4) and CO(2) by glucose-degrading Propionibacterium and Olsenella that are belonging to the phylum Actinobacteria, propionate-degrading Smithella and Syntrophobacter, and acetate-degrading Methanosaeta and Synergistes group 4 in this anaerobic sludge. The population size of propionate degraders was the smallest among three trophic groups and the specific degradation rate of propionate was also low. The specific degradation rate of acetate was low even though their population size was comparable to the glucose degraders. These results could explain why the degradation of propionate and acetate was the rate-limiting step in methanogenic glucose degradation.
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Affiliation(s)
- Tsukasa Ito
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
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Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
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Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
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Puspita ID, Kamagata Y, Tanaka M, Asano K, Nakatsu CH. Are uncultivated bacteria really uncultivable? Microbes Environ 2012; 27:356-66. [PMID: 23059723 PMCID: PMC4103542 DOI: 10.1264/jsme2.me12092] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/20/2012] [Indexed: 11/16/2022] Open
Abstract
Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.
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Affiliation(s)
- Indun Dewi Puspita
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17 Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido 062–8517,
Japan
| | - Michiko Tanaka
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Kozo Asano
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Cindy H. Nakatsu
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907,
USA
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Inaba S, Ikenishi F, Itakura M, Kikuchi M, Eda S, Chiba N, Katsuyama C, Suwa Y, Mitsui H, Minamisawa K. N(2)O emission from degraded soybean nodules depends on denitrification by Bradyrhizobium japonicum and other microbes in the rhizosphere. Microbes Environ 2012; 27:470-6. [PMID: 23047151 PMCID: PMC4103556 DOI: 10.1264/jsme2.me12100] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 05/30/2012] [Indexed: 11/12/2022] Open
Abstract
A model system developed to produce N(2)O emissions from degrading soybean nodules in the laboratory was used to clarify the mechanism of N(2)O emission from soybean fields. Soybean plants inoculated with nosZ-defective strains of Bradyrhizobium japonicum USDA110 (ΔnosZ, lacking N(2)O reductase) were grown in aseptic jars. After 30 days, shoot decapitation (D, to promote nodule degradation), soil addition (S, to supply soil microbes), or both (DS) were applied. N(2)O was emitted only with DS treatment. Thus, both soil microbes and nodule degradation are required for the emission of N(2)O from the soybean rhizosphere. The N(2)O flux peaked 15 days after DS treatment. Nitrate addition markedly enhanced N(2)O emission. A (15)N tracer experiment indicated that N(2)O was derived from N fixed in the nodules. To evaluate the contribution of bradyrhizobia, N(2)O emission was compared between a nirK mutant (ΔnirKΔnosZ, lacking nitrite reductase) and ΔnosZ. The N(2)O flux from the ΔnirKΔnosZ rhizosphere was significantly lower than that from ΔnosZ, but was still 40% to 60% of that of ΔnosZ, suggesting that N(2)O emission is due to both B. japonicum and other soil microorganisms. Only nosZ-competent B. japonicum (nosZ+ strain) could take up N(2)O. Therefore, during nodule degradation, both B. japonicum and other soil microorganisms release N(2)O from nodule N via their denitrification processes (N(2)O source), whereas nosZ-competent B. japonicum exclusively takes up N(2)O (N(2)O sink). Net N(2)O flux from soybean rhizosphere is likely determined by the balance of N(2)O source and sink.
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Affiliation(s)
- Shoko Inaba
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Fumio Ikenishi
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Masakazu Kikuchi
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Shima Eda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Naohiko Chiba
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1–13–27 Kasuga, Bunkyo-ku, Tokyo 112–8551,
Japan
| | - Chie Katsuyama
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1–13–27 Kasuga, Bunkyo-ku, Tokyo 112–8551,
Japan
| | - Yuichi Suwa
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1–13–27 Kasuga, Bunkyo-ku, Tokyo 112–8551,
Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
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Kurniawan A, Yamamoto T, Tsuchiya Y, Morisaki H. Analysis of the ion adsorption-desorption characteristics of biofilm matrices. Microbes Environ 2012; 27:399-406. [PMID: 22673305 PMCID: PMC4103547 DOI: 10.1264/jsme2.me11339] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The characteristics of biofilm polymers formed on stone surfaces in Lake Biwa and ion adsorption and desorption to and from these biofilms were investigated. The results indicated that both positively and negatively charged sites exist in the biofilm polymer. A physicochemical interaction between these sites and ions in the surrounding water seems to promote the adsorption of ions to the biofilm through an attractive electrostatic interaction and an ion-exchange mechanism. The results also indicated that, in comparison with ion-exchange resins, ions were more loosely bound to and desorbed more easily from the biofilm polymer. This suggests that microbes in the biofilm can readily use these ions as nutrient ions. Our present findings indicate that the biofilm may play an important role in supplying nutrient ions to microbes in the biofilm and in the development of a nutrient-rich environment within the biofilm through both ion adsorption and desorption. This study shows for the first time that the inside of a biofilm can be a sustainable environment for microbes.
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Affiliation(s)
- Andi Kurniawan
- Graduate School of Science and Engineering, Ritsumeikan University, 1–1–1 Noji Higashi, Kusatsu, Shiga, 525–8577, Japan
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Everroad RC, Otaki H, Matsuura K, Haruta S. Diversification of bacterial community composition along a temperature gradient at a thermal spring. Microbes Environ 2012; 27:374-81. [PMID: 22673306 PMCID: PMC4103544 DOI: 10.1264/jsme2.me11350] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To better understand the biogeography and relationship between temperature and community structure within microbial mats, the bacterial diversity of mats at a slightly alkaline, sulfide-containing hot spring was explored. Microbial mats that developed at temperatures between 75-52°C were collected from an area of approximately 1 m(2) in Nakabusa, Nagano, Japan. Bacterial 16S rRNA genes from these samples were examined by terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis. T-RFLP profiles revealed 66 unique fragments (T-RFs). Based on total T-RFs observed in environmental profiles and clone libraries, a temperature effect on diversity was determined, with complexity in the community increasing as temperature decreased. The T-RF pattern indicated four distinct community assemblages related to temperature. Members of the Aquificales and particularly the sulfur-oxidizing bacterium Sulfurihydrogenibium were present at all temperatures and were the dominant component of mats taken at 75-67°C. Sulfide oxidation, which persisted throughout the temperature gradient, was the presumed dominant pathway of primary production above 67°C. As temperature decreased, successive additions of anoxygenic and oxygenic phototrophs increased primary productivity, allowing for diversification of the community.
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Affiliation(s)
- R Craig Everroad
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
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Narihiro T, Terada T, Ohashi A, Kamagata Y, Nakamura K, Sekiguchi Y. Quantitative detection of previously characterized syntrophic bacteria in anaerobic wastewater treatment systems by sequence-specific rRNA cleavage method. WATER RESEARCH 2012; 46:2167-75. [PMID: 22342314 DOI: 10.1016/j.watres.2012.01.034] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 05/12/2023]
Abstract
Quantitative monitoring method of two important trophic groups of bacteria in methanogenic communities was established and applied to six different anaerobic processes. The method we employed was based upon our previous sequence-specific rRNA cleavage method that allows quantification of rRNA of target groups so that the populations reflecting in situ activity could be determined. We constructed a set of scissor probes targeting the Chloroflexi group known as 'semi-syntrophic' heterotrophic bacteria and fatty acid-oxidizing syntrophs to determine their relative abundance in the processes. By using the method, we found that several reactors harbored a large amount of organisms belonging to the phylum Chloroflexi accounting for up to 20% of the total prokaryotic populations. Propionate-oxidizing syntrophs, Syntrophobacter, Smithella and Pelotomaculum were also found to be significant comprising up to 3.9% of the total populations, but their distribution is highly dependent on the process examined. This is the first clear, non-PCR based quantitative evidence that those organisms play active roles under in situ methanogenic conditions.
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Affiliation(s)
- Takashi Narihiro
- Bio-Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
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Arakawa Y, Akiyama Y, Furukawa H, Suda W, Amachi S. Growth stimulation of iodide-oxidizing α-Proteobacteria in iodide-rich environments. MICROBIAL ECOLOGY 2012; 63:522-531. [PMID: 22138964 DOI: 10.1007/s00248-011-9986-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/11/2011] [Indexed: 05/31/2023]
Abstract
α-Proteobacteria that can oxidize iodide (I(-)) to molecular iodine (I(2)) have only been isolated from iodide-rich natural and artificial environments, i.e., natural gas brine waters and seawaters supplemented with iodide, respectively. To understand the growth characteristics of such iodide-oxidizing bacteria (IOB) under iodide-rich environments, microcosms comprising natural seawater and 1 mM iodide were prepared, and the succession of microbial communities was monitored by culture-independent techniques. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis showed that bacteria closely related with known IOB were predominant in the microcosms after several weeks of incubation. Quantitative PCR analysis targeting specific 16S rRNA gene regions of IOB showed that the relative abundance of IOB in the microcosms was 6-76% of the total bacterial population, whereas that in natural seawater was less than 1%. When 10(3) cells mL(-1) of IOB were inoculated into natural seawater supplemented with 0.1-1 mM iodide, significant growth (cell densities, 10(5)-10(6) cells mL(-1)) and I(2) production (6-32 μM) were observed. Interestingly, similar growth stimulation occurred when 12-44 μM of I(2) was added to seawater, instead of iodide. IOB were found to be more I(2) tolerant than the other heterotrophic bacteria in seawater. These results suggest that I(2) plays a key role in the growth stimulation of IOB in seawater. IOB could potentially attack other bacteria with I(2) to occupy their ecological niche in iodide-rich environments.
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Affiliation(s)
- Yumi Arakawa
- Department of Applied Biosciences, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo City, Chiba, 271-8510, Japan
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Okubo T, Tsukui T, Maita H, Okamoto S, Oshima K, Fujisawa T, Saito A, Futamata H, Hattori R, Shimomura Y, Haruta S, Morimoto S, Wang Y, Sakai Y, Hattori M, Aizawa SI, Nagashima KVP, Masuda S, Hattori T, Yamashita A, Bao Z, Hayatsu M, Kajiya-Kanegae H, Yoshinaga I, Sakamoto K, Toyota K, Nakao M, Kohara M, Anda M, Niwa R, Jung-Hwan P, Sameshima-Saito R, Tokuda SI, Yamamoto S, Yamamoto S, Yokoyama T, Akutsu T, Nakamura Y, Nakahira-Yanaka Y, Hoshino YT, Hirakawa H, Mitsui H, Terasawa K, Itakura M, Sato S, Ikeda-Ohtsubo W, Sakakura N, Kaminuma E, Minamisawa K. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ 2012; 27:306-15. [PMID: 22452844 PMCID: PMC4036050 DOI: 10.1264/jsme2.me11321] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/28/2012] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Takahiro Tsukui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Hiroko Maita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Shinobu Okamoto
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Takatomo Fujisawa
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Akihiro Saito
- Department of Material and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology 2200–2 Toyosawa, Fukuroi, Shizuoka 437–8555, Japan
| | - Hiroyuki Futamata
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Reiko Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Yumi Shimomura
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yong Wang
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yoriko Sakai
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Shin-ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727–0023, Japan
| | - Kenji V. P. Nagashima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sachiko Masuda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Tsutomu Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Akifumi Yamashita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hiromi Kajiya-Kanegae
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Ikuo Yoshinaga
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Kazunori Sakamoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271–8510, Japan
| | - Koki Toyota
- Tokyo University of Agriculture and Technology, 2–24–16, Naka, Koganei, Tokyo 184–8588, Japan
| | - Mitsuteru Nakao
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Mitsuyo Kohara
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Mizue Anda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Rieko Niwa
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Park Jung-Hwan
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422–8529, Japan
| | - Shin-ichi Tokuda
- National Institute of Vegetable and Tea Sciences, National Agriculture and Food Research Organization, 3–1–1 Kannondai, Tsukuba, Ibaraki 305–8666, Japan
| | - Sumiko Yamamoto
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Syuji Yamamoto
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo university of Agriculture and Technology, 3–5–8 Saiwaicho, Fuchu, Tokyo 183–8509, Japan
| | - Tomoko Akutsu
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Yasukazu Nakamura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Yuka Nakahira-Yanaka
- Graduate School of Life and Environment Sciences, University of Tsukuba, 1–1–1 Ten-noudai, Tsukuba, Ibaraki 305–8572, Japan
| | - Yuko Takada Hoshino
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hideki Hirakawa
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Kimihiro Terasawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Wakako Ikeda-Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Natsuko Sakakura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Eli Kaminuma
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
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Okabe S, Nakamura Y, Satoh H. Community structure and in situ activity of nitrifying bacteria in Phragmites root-associated biofilms. Microbes Environ 2012; 27:242-9. [PMID: 22446303 PMCID: PMC4036055 DOI: 10.1264/jsme2.me11314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The amount of oxygen released by Phragmites roots and the community structure and in situ activity of nitrifying bacteria in the root biofilms were analyzed by the combined use of 16S rRNA gene-cloning analysis, quantitative PCR (qPCR) assay and microelectrodes. Axial and radial O₂ microprofiles were obtained for individual roots of Phragmites in a horizontal flow reactor fed with artificial medium continuously. Axial O₂ profiles revealed that O₂ was released at a rate of 0.21 μmol O₂ cm⁻² (root surface area) h⁻¹ only in the apical region (up to ca. 40 mm from the root apex), where there was a high abundance (10⁷ to 10⁸ copies g⁻¹ biomass) of Nitrosomonas-like AOB and Nitrospira-like NOB. This abundance, however, sharply declined to the detection limit at positions more basal than 80 mm. Phylogenetic analysis based on 16S rRNA gene identified strains related to Nitrosomonas oligotropha and Nitrosomonas cryotolerans as the predominant AOB and strains related to Nitrospira marina and Nitrospira moscoviensis as the predominant NOB in the root biofilms. Based on radial O₂ microprofiles, the oxic region only extended about 0.5 mm into the surrounding sediment due to a high rate of O₂ consumption in the rhizosphere. The net NH₄⁺ and O₂ consumption rates in the apical region were higher than those determined at the oxic sediment surface in which the abundance of AOB and NOB was one order of magnitude lower than in the rhizosphere. These results clearly indicated that Phragmites root biofilms played an important role in nitrification in the waterlogged anoxic sediment.
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Affiliation(s)
- Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo Hokkaido 060-8628, Japan.
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25
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Enomoto M, Nakagawa S, Sawabe T. Microbial communities associated with holothurians: presence of unique bacteria in the coelomic fluid. Microbes Environ 2012; 27:300-5. [PMID: 22446312 PMCID: PMC4036045 DOI: 10.1264/jsme2.me12020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Marine invertebrates interact with various microorganisms ranging from pathogens to symbionts. One-to-one symbiosis between a single microbial species and a single host animal has served as a model for the study of host-microbe interactions. In addition, increasing attention has recently been focused on the complex symbiotic associations, e.g., associations between sponges and their symbionts, due to their biotechnological potential; however, relatively little is known about the microbial diversity associated with members of the phylum Echinodermata. Here, for the first time, we investigated microbial communities associated with a commercially important holothurian species, Apostichopus japonicus, using culture-dependent and -independent methods. Diverse and abundant heterotrophs, mostly Gammaproteobacteria members, were cultured semi-quantitatively. Using the cloning and sequencing technique, different microbial communities were found in different holothurian tissues. In the holothurian coelomic fluid, potentially metabolically active and phylogenetically unique members of Epsilonproteobacteria and Rickettsiales were discovered. This study suggests that coelomic fluids of marine invertebrates, at least those inhabiting intertidal areas where physical and chemical conditions fluctuate, provide microbes with unique and stable habitats.
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Affiliation(s)
- Masaki Enomoto
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Japan
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26
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Hirayama J, Eda S, Mitsui H, Minamisawa K. Nitrate-dependent N₂O emission from intact soybean nodules via denitrification by Bradyrhizobium japonicum bacteroids. Appl Environ Microbiol 2011; 77:8787-90. [PMID: 22003029 PMCID: PMC3233077 DOI: 10.1128/aem.06262-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/10/2011] [Indexed: 11/20/2022] Open
Abstract
In the presence of nitrate, N₂O emission increased markedly from soybean roots inoculated with nosZ mutant of Bradyrhizobium japonicum, but not from soybean roots inoculated with a napA nosZ double mutant, indicating that B. japonicum bacteroids in soybean nodules are able to convert the exogenously supplied nitrate into N₂O via a denitrification pathway.
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Affiliation(s)
- Junta Hirayama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shima Eda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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27
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Ishii S, Ikeda S, Minamisawa K, Senoo K. Nitrogen cycling in rice paddy environments: past achievements and future challenges. Microbes Environ 2011; 26:282-92. [PMID: 22008507 DOI: 10.1264/jsme2.me11293] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitrogen is generally the most limiting nutrient for rice production. In rice paddy soils, various biochemical processes can occur regarding N cycling, including nitrification, denitrification, and nitrogen fixation. Since its discovery in the 1930s, the nitrification-denitrification process has been extensively studied in Japan. It may cause N loss from rice paddy soils, while it can also reduce environmental pollutions such as nitrate leaching and emission of nitrous oxide (N(2)O). In this review article, we first summarize the early and important findings regarding nitrification-denitrification in rice paddy soils, and then update recent findings regarding key players in denitrification and N(2)O reduction. In addition, we also discuss the potential occurrence of other newly found reactions in the N cycle, such as archaeal ammonia oxidization, fungal denitrification, anaerobic methane oxidation coupled with denitrification, and anaerobic ammonium oxidation.
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Affiliation(s)
- Satoshi Ishii
- Division of Environmental Engineering, Hokkaido University, Sapporo, Japan.
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28
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Taniguchi A, Tada Y, Hamasaki K. Seasonal variations in the community structure of actively growing bacteria in neritic waters of Hiroshima Bay, western Japan. Microbes Environ 2011; 26:339-46. [PMID: 21791885 DOI: 10.1264/jsme2.me11212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using bromodeoxyuridine (BrdU) magnetic beads immunocapture and a PCR-denaturing gradient gel electrophoresis (DGGE) technique (BUMP-DGGE), we determined seasonal variations in the community structures of actively growing bacteria in the neritic waters of Hiroshima Bay, western Japan. The community structures of actively growing bacteria were separated into two clusters, corresponding to the timing of phytoplankton blooms in the autumn-winter and spring-summer seasons. The trigger for changes in bacterial community structure was related to organic matter supply from phytoplankton blooms. We identified 23 phylotypes of actively growing bacteria, belonging to Alphaproteobacteria (Roseobacter group, 9 phylotypes), Gammaproteobacteria (2 phylotypes), Bacteroidetes (8 phylotypes), and Actinobacteria (4 phylotypes). The Roseobacter group and Bacteroidetes were dominant in actively growing bacterial communities every month, and together accounted for more than 70% of the total DGGE bands. We revealed that community structures of actively growing bacteria shifted markedly in the wake of phytoplankton blooms in the neritic waters of Hiroshima Bay.
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Affiliation(s)
- Akito Taniguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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29
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Ryuda N, Hashimoto T, Ueno D, Inoue K, Someya T. Visualization and direct counting of individual denitrifying bacterial cells in soil by nirK-targeted direct in situ PCR. Microbes Environ 2011; 26:74-80. [PMID: 21487206 DOI: 10.1264/jsme2.me10180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 10(8) to 2.6 × 10(9) cells g(-1) dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.
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Affiliation(s)
- Noriko Ryuda
- Division of Soil Science, Faculty of Agriculture, Saga University, Saga 840–8502, Japan
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30
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Mohanty SR, Kollah B, Brodie EL, Hazen TC, Roden EE. 16S rRNA gene microarray analysis of microbial communities in ethanol-stimulated subsurface sediment. Microbes Environ 2011; 26:261-5. [PMID: 21558677 DOI: 10.1264/jsme2.me11111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A high-density 16S rRNA gene microarray was used to analyze microbial communities in a slurry of ethanol-amended, uranium-contaminated subsurface sediment. Of specific interest was the extent to which the microarray could detect temporal patterns in the relative abundance of major metabolic groups (nitrate-reducing, metal-reducing, sulfate-reducing, and methanogenic taxa) that were stimulated by ethanol addition. The results show that the microarray, when used in conjunction with geochemical data and knowledge of the physiological properties of relevant taxa, provided accurate assessment of the response of key functional groups to biostimulation.
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Affiliation(s)
- Santosh R Mohanty
- Department of Geoscience, University of Wisconsin, Madison, 1215 W. Dayton St., WI 53706, USA
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31
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Anda M, Ikeda S, Eda S, Okubo T, Sato S, Tabata S, Mitsui H, Minamisawa K. Isolation and genetic characterization of Aurantimonas and Methylobacterium strains from stems of hypernodulated soybeans. Microbes Environ 2011; 26:172-80. [PMID: 21512309 DOI: 10.1264/jsme2.me10203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aims of this study were to isolate Aurantimonas and Methylobacterium strains that responded to soybean nodulation phenotypes and nitrogen fertilization rates in a previous culture-independent analysis (Ikeda et al. ISME J. 4:315-326, 2010). Two strategies were adopted for isolation from enriched bacterial cells prepared from stems of field-grown, hypernodulated soybeans: PCR-assisted isolation for Aurantimonas and selective cultivation for Methylobacterium. Thirteen of 768 isolates cultivated on Nutrient Agar medium were identified as Aurantimonas by colony PCR specific for Aurantimonas and 16S rRNA gene sequencing. Meanwhile, among 187 isolates on methanol-containing agar media, 126 were identified by 16S rRNA gene sequences as Methylobacterium. A clustering analysis (>99% identity) of the 16S rRNA gene sequences for the combined datasets of the present and previous studies revealed 4 and 8 operational taxonomic units (OTUs) for Aurantimonas and Methylobacterium, respectively, and showed the successful isolation of target bacteria for these two groups. ERIC- and BOX-PCR showed the genomic uniformity of the target isolates. In addition, phylogenetic analyses of Aurantimonas revealed a phyllosphere-specific cluster in the genus. The isolates obtained in the present study will be useful for revealing unknown legume-microbe interactions in relation to the autoregulation of nodulation.
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Affiliation(s)
- Mizue Anda
- Graduate School of Life Sciences, Tohoku University, Sendai 980–8577, Japan
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32
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Furukawa T, Takahashi H, Yoshida T, Suzuki Y. Genotypic analysis of Enterococci isolated from fecal-polluted water from different sources by pulsed-field gel electrophoresis (PFGE) for application to microbial source tracking. Microbes Environ 2011; 26:181-3. [PMID: 21502739 DOI: 10.1264/jsme2.me10174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
PFGE has potential applications in the source tracking of fecal pollution in aquatic environments. We tried to distinguish the genotypes of Enterococcus faecium collected from fecal-contaminated water using PFGE. Well identified 115 strains of E. faecium were classified into 25 PFGE patterns, and characteristics distinctive to each genotype were recognized. Analysis of the characteristics of genotypes using PFGE can be used to track source of fecal pollution.
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Affiliation(s)
- Takashi Furukawa
- Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki 889–2192, Japan
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33
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Liu GH, Nakamura T, Amemiya T, Rajendran N, Itoh K. Analysis of bacterial populations in the environment using two-dimensional gel electrophoresis of genomic DNA and complementary DNA. Microbes Environ 2011; 26:184-7. [PMID: 21502731 DOI: 10.1264/jsme2.me10161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.
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Affiliation(s)
- Guo-Hua Liu
- Graduate School of Engineering, Yokohama National University, Yokohama 240–8501, Japan
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34
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Baba T, Yamaguchi N, Tani K, Nasu M. Inactivation of bacteria in freshwater by momentary decompression following high pressurization. Microbes Environ 2011; 26:92-4. [PMID: 21487210 DOI: 10.1264/jsme2.me10175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rapid and continuous pressure treatment was realized using a hydraulic pump and the momentary decompression following high pressurization was used to inactivate bacteria. The number of colony-forming E. coli decreased to 1/1000 in response to 10 cycles of pressure treatment. In groundwater samples, repeated pressure treatment led to a two-log decrease in the number of colony-forming bacteria. These findings suggest that repeated cycles of momentary decompression following high pressurization enabled a marked decrease in bacterial growth activity. The results presented herein may contribute to microbiological quality control and the safety of freshwater.
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Affiliation(s)
- Takashi Baba
- Graduate School of Pharmaceutical Sciences, Osaka University, 1–6 Yamadaoka, Suita, Osaka 565–0871, Japan
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35
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Tsuchiya Y, Hiraki A, Kiriyama C, Arakawa T, Kusakabe R, Morisaki H. Seasonal change of bacterial community structure in a biofilm formed on the surface of the aquatic macrophyte Phragmites australis. Microbes Environ 2011; 26:113-9. [PMID: 21502742 DOI: 10.1264/jsme2.me10183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The seasonal change of bacterial community structure in biofilms on the surface of reed (Phragmites australis) was investigated for about three years (from 2005 June to 2008 March) in Lake Biwa by comparing it with that in surrounding lake water. The community structure in biofilms was different from that in the lake water throughout the seasons and years. The community structure in lake water was similar in the same seasons of different years, corresponding to similar environmental factors (i.e., temperature, dissolved oxygen, and light intensity) and nutrient ion concentrations at the same season. However, the community structure in the biofilms was not similar in the same season of different years. This seems to be due to the formation of new biofilms on sprouted reeds in every early summer and the high nutrient concentrations and bacterial density in subsequently formed biofilms. Although the community structure in the biofilms changed along with the seasonal change, the bacteria belonging to Bacillus and Paenibacillus were detected in any season. This study revealed the possibility that the bacterial community structure in the initial stage of the biofilm formation govern the subsequent seasonal change of the community structure in biofilms.
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Affiliation(s)
- Yuki Tsuchiya
- Graduate School of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525–8577, Japan
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36
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Borjigin N, Furukawa K, Shimoda Y, Tabata S, Sato S, Eda S, Minamisawa K, Mitsui H. Identification of Mesorhizobium loti Genes Relevant to Symbiosis by Using Signature-Tagged Mutants. Microbes Environ 2011; 26:165-71. [DOI: 10.1264/jsme2.me10213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | | | | | - Shima Eda
- Graduate School of Life Sciences, Tohoku University
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37
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Doughari HJ, Ndakidemi PA, Human IS, Benade S. The Ecology, Biology and Pathogenesis of Acinetobacter spp.: An Overview. Microbes Environ 2011; 26:101-12. [DOI: 10.1264/jsme2.me10179] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | - Spinney Benade
- Applied Sciences Faculty, Cape Peninsula University of Technology
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38
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Rashid R, Morohoshi T, Someya N, Ikeda T. Degradation of N-Acylhomoserine Lactone Quorum Sensing Signaling Molecules by Potato Root Surface-Associated Chryseobacterium Strains. Microbes Environ 2011; 26:144-8. [DOI: 10.1264/jsme2.me10207] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Rumana Rashid
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University
| | - Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University
| | - Nobutaka Someya
- National Agricultural Research Center for Hokkaido Region (NARCH), National Agricultural and Food Research Organization (NARO)
| | - Tsukasa Ikeda
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University
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39
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Kwon S, Moon E, Kim TS, Hong S, Park HD. Pyrosequencing Demonstrated Complex Microbial Communities in a Membrane Filtration System for a Drinking Water Treatment Plant. Microbes Environ 2011; 26:149-55. [DOI: 10.1264/jsme2.me10205] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Soondong Kwon
- School of Civil, Environmental and Architectural Engineering, Korea University
| | - Eunjeong Moon
- School of Civil, Environmental and Architectural Engineering, Korea University
| | - Taek-Seung Kim
- School of Civil, Environmental and Architectural Engineering, Korea University
| | - Seungkwan Hong
- School of Civil, Environmental and Architectural Engineering, Korea University
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University
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40
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Nakamura K, Tamaki H, Kang MS, Mochimaru H, Lee ST, Nakamura K, Kamagata Y. A Six-well Plate Method: Less Laborious and Effective Method for Cultivation of Obligate Anaerobic Microorganisms. Microbes Environ 2011; 26:301-6. [DOI: 10.1264/jsme2.me11120] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kohei Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Myung Suk Kang
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- National Institute of Biological Resources
| | - Hanako Mochimaru
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Sung-Taik Lee
- Department of Biological Sciences, KAIST (Korea Advanced Institute of Science and Technology)
| | - Kazunori Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Toyohira
- Research Faculty of Agriculture, Hokkaido University
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