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Yang S, Mahmood M, Baral R, Wu H, Almloff M, Stanton LE, Min D, Smiley BK, Iiams JC, Yu J, Im J. Forage conservation is a neglected nitrous oxide source. PNAS NEXUS 2024; 3:pgae373. [PMID: 39351542 PMCID: PMC11440176 DOI: 10.1093/pnasnexus/pgae373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/10/2024] [Indexed: 10/04/2024]
Abstract
Agricultural activities are the major anthropogenic source of nitrous oxide (N 2 O ), an important greenhouse gas and ozone-depleting substance. However, the role of forage conservation as a potential source ofN 2 O has rarely been studied. We investigatedN 2 O production from the simulated silage of the three major crops-maize, alfalfa, and sorghum-used for silage in the United States, which comprises over 90% of the total silage production. Our findings revealed that a substantialN 2 O could be generated, potentially placing forage conservation as the third largestN 2 O source in the agricultural sector. Notably, the application of chlorate as an additive significantly reducedN 2 O production, but neither acetylene nor intermittent exposure to oxygen showed any impact. Overall, the results highlight that denitrifiers, rather than nitrifiers, are responsible forN 2 O production from silage, which was confirmed by molecular analyses. Our study reveals a previously unexplored source ofN 2 O and provides a crucial mechanistic understanding for effective mitigation strategies.
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Affiliation(s)
- Seongmin Yang
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Maheen Mahmood
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Rudra Baral
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Hui Wu
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA
| | - Marc Almloff
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Lauren E Stanton
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Brenda K Smiley
- Corteva Agriscience, Forage Additive Research, Johnston, IA 50131, USA
| | - J Chris Iiams
- Corteva Agriscience, Forage Additive Research, Johnston, IA 50131, USA
| | - Jisang Yu
- Department of Agricultural Economics, Kansas State University, Manhattan, KS 66506, USA
| | - Jeongdae Im
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
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Roca-Couso R, Flores-Félix JD, Deb S, Giagnoni L, Tondello A, Stevanato P, Squartini A, García-Fraile P, Rivas R. Metataxonomic analysis of endophytic bacteria of blackberry (Rubus ulmifolius Schott) across tissues and environmental conditions. Sci Rep 2024; 14:13388. [PMID: 38862607 PMCID: PMC11166949 DOI: 10.1038/s41598-024-64248-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
(1) Background: Endophytic bacteria represent an important component of plant wellness. They have been widely studied for their involvement in plant development and enhancement of stress tolerance. In this work, the endophytic communities of roots, stems, and leaves of blackberry (Rubus ulmifolius Schott) were studied in three different niches: natural, riverside, and human-impacted niches. (2) Results: The microbiome composition revealed that Sphingomonadaceae was the most abundant family in all samples, accounting for 9.4-45.8%. In contrast, other families seem to be linked to a specific tissue or niche. Families Microbacteriaceae and Hymenobacteraceae increased their presence in stem and leaf samples, while Burkholderiaceae abundance was important in riverside samples. Alpha and beta diversity analyses showed that root samples were the most diverse, and they gathered together in the same cluster, apart from the rest of the samples. (3) Conclusions: The analysis of the microbiome of R. ulmifolius plants revealed that the composition was essentially the same in different niches; the differences were primarily influenced by plant tissue factors with a core genome dominated by Sphingomonadaceae. Additionally, it was observed that R. ulmifolius can select its own microbiome, and this remains constant in all tissues evaluated regardless the niche of sampling.
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Affiliation(s)
- Rocío Roca-Couso
- Department of Microbiology and Genetics, Biology Departmental Building, University of Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185, Salamanca, Spain
| | - José David Flores-Félix
- Department of Microbiology and Genetics, Biology Departmental Building, University of Salamanca, 37007, Salamanca, Spain.
- Institute for Agribiotechnology Research (CIALE), 37185, Salamanca, Spain.
| | - Saptarathi Deb
- Department of Agronomy, Animals, Food, Natural Resources, and Environment, DAFNAE University of Padova, 35020, Legnaro, PD, Italy
| | - Lucia Giagnoni
- Department of Agronomy, Animals, Food, Natural Resources, and Environment, DAFNAE University of Padova, 35020, Legnaro, PD, Italy
| | - Alessandra Tondello
- Department of Agronomy, Animals, Food, Natural Resources, and Environment, DAFNAE University of Padova, 35020, Legnaro, PD, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Animals, Food, Natural Resources, and Environment, DAFNAE University of Padova, 35020, Legnaro, PD, Italy
| | - Andrea Squartini
- Department of Agronomy, Animals, Food, Natural Resources, and Environment, DAFNAE University of Padova, 35020, Legnaro, PD, Italy
| | - Paula García-Fraile
- Department of Microbiology and Genetics, Biology Departmental Building, University of Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185, Salamanca, Spain
- Associated Unit, University of Salamanca-CSIC (IRNASA), 37008, Salamanca, Spain
| | - Raúl Rivas
- Department of Microbiology and Genetics, Biology Departmental Building, University of Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185, Salamanca, Spain
- Associated Unit, University of Salamanca-CSIC (IRNASA), 37008, Salamanca, Spain
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Yang S, Lee J, Mahmood M, Min D, Im J. Evaluation and optimization of lysis method for microbial DNA extraction from epiphytic phyllosphere samples. J Microbiol Methods 2023; 206:106677. [PMID: 36716930 DOI: 10.1016/j.mimet.2023.106677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
Analysis of microbial communities in the epiphytic phyllosphere can be challenging, especially when applying sequencing-based techniques, owing to the interference of plant-derived biomolecules such as nucleic acids. A review of recent studies on the epiphytic microbiome revealed that both mechanical and enzymatic lysis methods are widely used. Here, we evaluated the effects of the two lysis methods on DNA extraction yield, purity, integrity, and microbial 16S rRNA gene copy number per ng of template genomic DNA under different extraction conditions. Furthermore, the effect on bacterial community composition, diversity, and reproducibility was examined using 16S rRNA gene amplicon sequencing. The enzymatic lysis method yielded one to two orders of magnitude more DNA, but the DNA quality was suboptimal. Conversely, the samples prepared using the mechanical method showed high DNA purity albeit lower yield. Unexpectedly, mechanical lysis showed a higher DNA integrity number (DIN) than enzymatic lysis. The 16S rRNA amplicon sequencing results demonstrated that the samples prepared via mechanical disruption exhibited reproducibly similar microbial community compositions regardless of the extraction conditions. In contrast, the enzymatic lysis method resulted in inconsistent taxonomic compositions under different extraction conditions. This study demonstrates that mechanical DNA disruption is more suitable for epiphytic phyllosphere samples than enzymatic disruption.
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Affiliation(s)
- Seongmin Yang
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Jaejin Lee
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - Maheen Mahmood
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Jeongdae Im
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA.
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Farooq B, Nazir A, Anjum S, Farooq M, Farooq MU. Diversity of various symbiotic associations between microbes and host plants. RHIZOBIOME 2023:1-18. [DOI: 10.1016/b978-0-443-16030-1.00006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Ali M, Ali Q, Sohail MA, Ashraf MF, Saleem MH, Hussain S, Zhou L. Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective. Int J Mol Sci 2021; 22:ijms221810165. [PMID: 34576331 PMCID: PMC8465699 DOI: 10.3390/ijms221810165] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.
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Affiliation(s)
- Mohsin Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Q.A.); (L.Z.)
| | - Muhammad Aamir Sohail
- Center for Excellence in Molecular Plant Sciences, National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China;
| | | | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Punjab, Pakistan;
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Correspondence: (Q.A.); (L.Z.)
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6
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Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants. Microbiol Res 2019; 221:36-49. [DOI: 10.1016/j.micres.2019.02.001] [Citation(s) in RCA: 366] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/11/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022]
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8
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Kanno M, Constant P, Tamaki H, Kamagata Y. Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen. Environ Microbiol 2016; 18:2495-506. [PMID: 26636257 DOI: 10.1111/1462-2920.13162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/21/2015] [Accepted: 11/27/2015] [Indexed: 11/28/2022]
Abstract
High-affinity hydrogen (H2 )-oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric H2 uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, seven Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favourable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as atmospheric H2 sink.
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Affiliation(s)
- Manabu Kanno
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
| | - Philippe Constant
- Centre INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, QC, Canada, H7V 1B7
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
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Müller T, Ruppel S. Progress in cultivation-independent phyllosphere microbiology. FEMS Microbiol Ecol 2013; 87:2-17. [PMID: 24003903 PMCID: PMC3906827 DOI: 10.1111/1574-6941.12198] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/28/2022] Open
Abstract
Most microorganisms of the phyllosphere are nonculturable in commonly used media and culture conditions, as are those in other natural environments. This review queries the reasons for their ‘noncultivability’ and assesses developments in phyllospere microbiology that have been achieved cultivation independently over the last 4 years. Analyses of total microbial communities have revealed a comprehensive microbial diversity. 16S rRNA gene amplicon sequencing and metagenomic sequencing were applied to investigate plant species, location and season as variables affecting the composition of these communities. In continuation to culture-based enzymatic and metabolic studies with individual isolates, metaproteogenomic approaches reveal a great potential to study the physiology of microbial communities in situ. Culture-independent microbiological technologies as well advances in plant genetics and biochemistry provide methodological preconditions for exploring the interactions between plants and their microbiome in the phyllosphere. Improving and combining cultivation and culture-independent techniques can contribute to a better understanding of the phyllosphere ecology. This is essential, for example, to avoid human–pathogenic bacteria in plant food.
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Affiliation(s)
- Thomas Müller
- Leibniz-Centre for Agricultural Landscape Research, Müncheberg, Institute of Landscape Biogeochemistry, Müncheberg, Germany
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10
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Sasaki K, Ikeda S, Ohkubo T, Kisara C, Sato T, Minamisawa K. Effects of plant genotype and nitrogen level on bacterial communities in rice shoots and roots. Microbes Environ 2013; 28:391-5. [PMID: 23979487 PMCID: PMC4070954 DOI: 10.1264/jsme2.me12212] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
To examine whether microbial community structure differs across rice genotypes, automated ribosomal intergenic spacer analysis (ARISA) was conducted. Nine cultivars of Oryza sativa ssp. indica or japonica and seven lines of other Oryza species were grown in paddy fields with low, standard, and high levels of N fertilization. Multidimensional scaling plots of bacterial ARISA for aerial parts of rice (shoots) revealed that the structure of shoot bacterial communities was significantly affected by plant genotype (indica or japonica) based on similarity tests, whereas root microbiomes were largely affected by the N fertilization level.
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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: 1.0] [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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Dudeja SS, Giri R, Saini R, Suneja-Madan P, Kothe E. Interaction of endophytic microbes with legumes. J Basic Microbiol 2011; 52:248-60. [DOI: 10.1002/jobm.201100063] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 04/27/2011] [Indexed: 11/11/2022]
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Sato A, Watanabe T, Unno Y, Purnomo E, Osaki M, Shinano T. Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical Arbor, Melastoma malabathricum L. Microbes Environ 2011; 24:81-7. [PMID: 21566359 DOI: 10.1264/jsme2.me08565] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diversity of diazotrophic bacteria in the rhizosphere of Melastoma malabathricum L. was investigated by cloning-sequencing of the nifH gene directly amplified from DNA extracted from soil. Samples were obtained from the rhizosphere and bulk soil of M. malabathricum growing in three different soil types (acid sulfate, peat and sandy clay soils) located very close to each other in south Kalimantan, Indonesia. Six clone libraries were constructed, generated from bulk and rhizosphere soil samples, and 300 nifH clones were produced, then assembled into 29 operational taxonomic units (OTUs) based on percent identity values. Our results suggested that nifH gene diversity is mainly dependent on soil properties, and did not differ remarkably between the rhizosphere and bulk soil of M. malabathricum except in acid sulfate soil. In acid sulfate soil, as the Shannon diversity index was lower in rhizosphere than in bulk soil, it is suggested that particular bacterial species might accumulate in the rhizosphere.
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Affiliation(s)
- Atsuya Sato
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kitaku, Sapporo 060-8589, Japan
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Okabe S, Oshiki M, Kamagata Y, Yamaguchi N, Toyofuku M, Yawata Y, Tashiro Y, Nomura N, Ohta H, Ohkuma M, Hiraishi A, Minamisawa K. A great leap forward in microbial ecology. Microbes Environ 2011; 25:230-40. [PMID: 21576878 DOI: 10.1264/jsme2.me10178] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.
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Affiliation(s)
- Satoshi Okabe
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060–8628, Japan.
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Isawa T, Yasuda M, Awazaki H, Minamisawa K, Shinozaki S, Nakashita H. Azospirillum sp. strain B510 enhances rice growth and yield. Microbes Environ 2011; 25:58-61. [PMID: 21576855 DOI: 10.1264/jsme2.me09174] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inoculation experiments with the endophytic bacterium Azospirillum sp. strain B510, an isolate from surface-sterilized stems of field-grown rice, were conducted in pots in a greenhouse, and in paddy fields in Hokkaido, Japan. B510 significantly enhanced the growth of newly generated leaves and shoot biomass under greenhouse conditions. When rice seedlings were treated with 1×10(8) CFU ml(-1), then transplanted to paddy fields, tiller numbers and seed yield significantly increased. Azospirillum sp. strain B510 is a promising bacterial inoculant for plant growth promotion and agricultural practices.
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Affiliation(s)
- Tsuyoshi Isawa
- Research and Development Center, Mayekawa Mfg. Co., Ltd., 2000 Tatsuzawa, Moriya, Ibaraki, Japan
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Inaba S, Tanabe K, Eda S, Ikeda S, Higashitani A, Mitsui H, Minamisawa K. Nitrous oxide emission and microbial community in the rhizosphere of nodulated soybeans during the late growth period. Microbes Environ 2011; 24:64-7. [PMID: 21566356 DOI: 10.1264/jsme2.me08544] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examined N(2)O emissions from the rhizosphere of field-grown soybeans during the late growth stage (99-117 days after sowing). Marked emissions were detected from the nodulated root systems of field-grown soybeans, whereas a non-nodulating soybean mutant showed no emission. Degraded nodules exclusively generated the N(2)O. A culture-independent analysis of microbial communities showed Bradyrhizobium sp., Acidvorax facilis, Salmonella enterica, Xanthomonas sp., Enterobacter cloacae, Pseudomonas putida, Fusarium sp., nematodes, and other protozoans to be more abundant in the degraded nodules, suggesting that some of these organisms participate in the N(2)O emission process in the soybean rhizosphere.
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Affiliation(s)
- Shoko Inaba
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoboku, Sendai 980-8577, Japan
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The genotype of the calcium/calmodulin-dependent protein kinase gene (CCaMK) determines bacterial community diversity in rice roots under paddy and upland field conditions. Appl Environ Microbiol 2011; 77:4399-405. [PMID: 21551283 DOI: 10.1128/aem.00315-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of the Oryza sativa calcium/calmodulin-dependent protein kinase OsCCaMK genotype (dominant homozygous [D], heterozygous [H], recessive homozygous [R]) on rice root-associated bacteria, including endophytes and epiphytes, were examined by using a Tos17 rice mutant line under paddy and upland field conditions. Roots were sampled at the flowering stage and were subjected to clone library analyses. The relative abundance of Alphaproteobacteria was noticeably decreased in R plants under both paddy and upland conditions (0.8% and 3.0%, respectively) relative to those in D plants (10.3% and 17.4%, respectively). Population shifts of the Sphingomonadales and Rhizobiales were mainly responsible for this low abundance in R plants. The abundance of Anaerolineae (Chloroflexi) and Clostridia (Firmicutes) was increased in R plants under paddy conditions. The abundance of a subpopulation of Actinobacteria (Saccharothrix spp. and unclassified Actinosynnemataceae) was increased in R plants under upland conditions. Principal coordinate analysis revealed unidirectional community shifts in relation to OsCCaMK gene dosage under both conditions. In addition, shoot length, tiller number, and plant weight decreased as the OsCCaMK gene dosage decreased under upland conditions. These results suggest significant impacts of OsCCaMK on both the diversity of root-associated bacteria and rice plant growth under both paddy and upland field conditions.
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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: 1.1] [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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Ikeda S, Anda M, Inaba S, Eda S, Sato S, Sasaki K, Tabata S, Mitsui H, Sato T, Shinano T, Minamisawa K. Autoregulation of nodulation interferes with impacts of nitrogen fertilization levels on the leaf-associated bacterial community in soybeans. Appl Environ Microbiol 2011; 77:1973-80. [PMID: 21239540 PMCID: PMC3067336 DOI: 10.1128/aem.02567-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 01/07/2011] [Indexed: 11/20/2022] Open
Abstract
The diversities leaf-associated bacteria on nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans were evaluated by clone library analyses of the 16S rRNA gene. To analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (SN) (15 kg N ha(-1)) or heavy nitrogen (HN) (615 kg N ha(-1)) fertilization. Under SN fertilization, the relative abundance of Alphaproteobacteria was significantly higher in Nod(-) and Nod(++) soybeans (82% to 96%) than in Nod(+) soybeans (54%). The community structure of leaf-associated bacteria in Nod(+) soybeans was almost unaffected by the levels of nitrogen fertilization. However, differences were visible in Nod(-) and Nod(++) soybeans. HN fertilization drastically decreased the relative abundance of Alphaproteobacteria in Nod(-) and Nod(++) soybeans (46% to 76%) and, conversely, increased those of Gammaproteobacteria and Firmicutes in these mutant soybeans. In the Alphaproteobacteria, cluster analyses identified two operational taxonomic units (OTUs) (Aurantimonas sp. and Methylobacterium sp.) that were especially sensitive to nodulation phenotypes under SN fertilization and to nitrogen fertilization levels. Arbuscular mycorrhizal infection was not observed on the root tissues examined, presumably due to the rotation of paddy and upland fields. These results suggest that a subpopulation of leaf-associated bacteria in wild-type Nod(+) soybeans is controlled in similar ways through the systemic regulation of autoregulation of nodulation, which interferes with the impacts of N levels on the bacterial community of soybean leaves.
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Affiliation(s)
- Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Mizue Anda
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Shoko Inaba
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Shima Eda
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Kazuhiro Sasaki
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Satoshi Tabata
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Tadashi Sato
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Takuro Shinano
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan, Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
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Ikeda S, Okubo T, Anda M, Nakashita H, Yasuda M, Sato S, Kaneko T, Tabata S, Eda S, Momiyama A, Terasawa K, Mitsui H, Minamisawa K. Community- and genome-based views of plant-associated bacteria: plant-bacterial interactions in soybean and rice. PLANT & CELL PHYSIOLOGY 2010; 51:1398-410. [PMID: 20685969 DOI: 10.1093/pcp/pcq119] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Diverse microorganisms are living as endophytes in plant tissues and as epiphytes on plant surfaces in nature. Questions about driving forces shaping the microbial community associated with plants remain unanswered. Because legumes developed systems to attain endosymbioses with rhizobia as well as mycorrhizae during their evolution, the above questions can be addressed using legume mutants relevant to genes for symbiosis. Analytical methods for the microbial community have recently been advanced by enrichment procedures of plant-associated microbes and culture-independent analyses targeting the small subunit of rRNA in microbial ecology. In this review, we first deal with interdisciplinary works on the global diversity of bacteria associated with field-grown soybeans with different nodulation genotypes and nitrogen application. A subpopulation of Proteobacteria in aerial parts of soybean shoots was likely to be regulated through both the autoregulation system for plant-rhizobium symbiosis and the nitrogen signaling pathway, suggesting that legumes accommodate a taxonomically characteristic microbial community through unknown plant-microbe communications. In addition to the community views, we then show multiphasic analysis of a beneficial rice endophyte for comparative bacterial genomics and plant responses. The significance and perspectives of community- and genome-based approaches are discussed to achieve a better understanding of plant-microbe interactions.
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Affiliation(s)
- Seishi Ikeda
- Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido 082-0081, Japan
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Kawaguchi M, Minamisawa K. Plant-microbe communications for symbiosis. PLANT & CELL PHYSIOLOGY 2010; 51:1377-80. [PMID: 20841337 DOI: 10.1093/pcp/pcq125] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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Ikeda S, Okubo T, Kaneko T, Inaba S, Maekawa T, Eda S, Sato S, Tabata S, Mitsui H, Minamisawa K. Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels. THE ISME JOURNAL 2010; 4:315-26. [PMID: 19924157 DOI: 10.1038/ismej.2009.119] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The diversity of stem-associated bacteria of non-nodulated (Nod(-)), wild-type nodulated (Nod(+)) and hypernodulated (Nod(++)) soybeans were evaluated by clone library analyses of the 16S ribosomal RNA gene. Soybeans were dressed with standard nitrogen (SN) fertilization (15 kg N ha(-1)) and heavy nitrogen (HN) fertilization (615 kg N ha(-1)). The relative abundance of Alphaproteobacteria in Nod(+) soybeans (66%) was smaller than that in Nod(-) and Nod(++) soybeans (75-76%) under SN fertilization, whereas that of Gammaproteobacteria showed the opposite pattern (23% in Nod(+) and 12-16% in Nod(-) and Nod(++) soybeans). Principal coordinate analysis showed that the bacterial communities of Nod(-) and Nod(++) soybeans were more similar to each other than to that of Nod(+) soybeans under SN fertilization. HN fertilization increased the relative abundance of Gammaproteobacteria in all nodulation phenotypes (33-57%) and caused drastic shifts of the bacterial community. The clustering analyses identified a subset of operational taxonomic units (OTUs) at the species level in Alpha- and Gammaproteobacteria responding to both the nodulation phenotypes and nitrogen fertilization levels. Meanwhile, the abundance of Betaproteobacteria was relatively constant in all libraries constructed under these environmental conditions. The relative abundances of two OTUs in Alphaproteobacteria (Aurantimonas sp. and Methylobacterium sp.) were especially sensitive to nodulation phenotype and were drastically decreased under HN fertilization. These results suggested that a subpopulation of proteobacteria in soybeans is controlled in a similar manner through both the regulation systems of plant-rhizobia symbiosis and the nitrogen signaling pathway in plants.
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Affiliation(s)
- Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
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Kaneko T, Minamisawa K, Isawa T, Nakatsukasa H, Mitsui H, Kawaharada Y, Nakamura Y, Watanabe A, Kawashima K, Ono A, Shimizu Y, Takahashi C, Minami C, Fujishiro T, Kohara M, Katoh M, Nakazaki N, Nakayama S, Yamada M, Tabata S, Sato S. Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510. DNA Res 2010; 17:37-50. [PMID: 20047946 PMCID: PMC2818188 DOI: 10.1093/dnares/dsp026] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3 311 395 bp) and six plasmids, designated as pAB510a (1 455 109 bp), pAB510b (723 779 bp), pAB510c (681 723 bp), pAB510d (628 837 bp), pAB510e (537 299 bp), and pAB510f (261 596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N2 fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C4-dicarboxylate during its symbiotic relationship with the host plant.
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Ikeda S, Kaneko T, Okubo T, Rallos LEE, Eda S, Mitsui H, Sato S, Nakamura Y, Tabata S, Minamisawa K. Development of a bacterial cell enrichment method and its application to the community analysis in soybean stems. MICROBIAL ECOLOGY 2009; 58:703-14. [PMID: 19662454 DOI: 10.1007/s00248-009-9566-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Accepted: 07/06/2009] [Indexed: 05/06/2023]
Abstract
A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem homogenates were fractionated by a series of differential centrifugations followed by a Nycodenz density gradient centrifugation. The efficiency of bacterial cell enrichment was assessed by ribosomal intergenic spacer analysis (RISA). The intensity and the number of bacterial amplicons of RISA were markedly increased in the DNA extracted from the enriched bacterial cells compared to that in the DNA directly extracted from soybean stems. The phylogenetic diversity of the enriched bacterial cells was evaluated by analyzing a clone library of 16S rRNA gene in comparison with those of the culturable fractions of the enriched and non-enriched stem-associated bacteria, endophytic bacteria, and epiphytic bacteria. The results indicated that the method was able to enrich both endophytic and epiphytic bacteria from soybean stems, and was useful to assess the bacterial diversity based on a 16S rRNA gene clone library. When the sequence data from all clones (1,332 sequences) were combined, 72 operational taxonomic units were affiliated with Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes, which also provided the most comprehensive set of data on the bacterial diversity in the aerial parts of soybeans.
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Affiliation(s)
- Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
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Sudtachat N, Ito N, Itakura M, Masuda S, Eda S, Mitsui H, Kawaharada Y, Minamisawa K. Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum. Appl Environ Microbiol 2009; 75:5012-7. [PMID: 19502448 PMCID: PMC2725485 DOI: 10.1128/aem.00755-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 05/27/2009] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium japonicum, a symbiotic nitrogen-fixing soil bacterium, has multiple gene copies for aromatic degradation on the genome and is able to use low concentrations of vanillate, a methoxylated lignin monomer, as an energy source. A transcriptome analysis indicated that one set of vanA1B, pcaG1H1, and genes for C(1) compound catabolism was upregulated in B. japonicum USDA110 cells grown in vanillate (N. Ito, M. Itakura, S. Eda, K. Saeki, H. Oomori, T. Yokoyama, T. Kaneko, S. Tabata, T. Ohwada, S. Tajima, T. Uchiumi, E. Masai, M. Tsuda, H. Mitsui, and K. Minamisawa, Microbes Environ. 21:240-250, 2006). To examine the functions of these genes in vanillate degradation, we tested cell growth and substrate consumption in vanA1B, pcaG1H1, and mxaF mutants of USDA110. The vanA1B and pcaG1H1 mutants were unable to grow in minimal media containing 1 mM vanillate and protocatechuate, respectively, although wild-type USDA110 was able to grow in both media, indicating that the upregulated copies of vanA1B and pcaG1H1 are exclusively responsible for vanillate degradation. Mutating mxaF eliminated expression of gfa and flhA, which contribute to glutathione-dependent C(1) metabolism. The mxaF mutant had markedly lower cell growth in medium containing vanillate than the wild-type strain. In the presence of protocatechuate, there was no difference in cell growth between the mxaF mutant and the wild-type strain. These results suggest that the C(1) pathway genes are required for efficient vanillate catabolism. In addition, wild-type USDA110 oxidized methanol, whereas the mxaF mutant did not, suggesting that the metabolic capability of the C(1) pathway in B. japonicum extends to methanol oxidation. The mxaF mutant showed normal nodulation and N(2) fixation phenotypes with soybeans, which was not similar to symbiotic phenotypes of methylotrophic rhizobia.
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Ishii S, Kadota K, Senoo K. Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data. J Microbiol Methods 2009; 78:344-50. [PMID: 19616587 DOI: 10.1016/j.mimet.2009.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/08/2009] [Accepted: 07/08/2009] [Indexed: 11/29/2022]
Abstract
DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies.
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Affiliation(s)
- Satoshi Ishii
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
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Kaga H, Mano H, Tanaka F, Watanabe A, Kaneko S, Morisaki H. Rice Seeds as Sources of Endophytic Bacteria. Microbes Environ 2009; 24:154-62. [DOI: 10.1264/jsme2.me09113] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hiroko Kaga
- Kyoto Seika Girls' Junior / Senior High School
| | - Hironobu Mano
- Product Research & Development Dept., Pokka Corporation
| | - Fumiko Tanaka
- Kyoto Junior High School Attached to Kyoto University of Education
| | | | - Satoshi Kaneko
- Graduate School of Science and Engineering, Ritsumeikan University
| | - Hisao Morisaki
- Graduate School of Science and Engineering, Ritsumeikan University
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Okubo T, Ikeda S, Kaneko T, Eda S, Mitsui H, Sato S, Tabata S, Minamisawa K. Nodulation-Dependent Communities of Culturable Bacterial Endophytes from Stems of Field-Grown Soybeans. Microbes Environ 2009; 24:253-8. [DOI: 10.1264/jsme2.me09125] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University
| | | | - Shima Eda
- Graduate School of Life Sciences, Tohoku University
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Ikeda S, Rallos LEE, Okubo T, Eda S, Inaba S, Mitsui H, Minamisawa K. Microbial community analysis of field-grown soybeans with different nodulation phenotypes. Appl Environ Microbiol 2008; 74:5704-9. [PMID: 18658280 PMCID: PMC2547038 DOI: 10.1128/aem.00833-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 07/14/2008] [Indexed: 11/20/2022] Open
Abstract
Microorganisms associated with the stems and roots of nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod(+) soybean roots. Fusarium solani was stably associated with nodulated (Nod(+) and Nod(++)) roots and less abundant in Nod(-) soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod(-), Nod(+), or Nod(++)). The analysis of root samples indicated that the microbial community in Nod(-) soybeans was more similar to that in Nod(++) soybeans than to that in Nod(+) soybeans.
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Affiliation(s)
- Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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Saito A, Kawahara M, Ikeda S, Ishimine M, Akao S, Minamisawa K. Broad Distribution and Phylogeny of Anaerobic Endophytes of Cluster XIVa Clostridia in Plant Species Including Crops. Microbes Environ 2008; 23:73-80. [DOI: 10.1264/jsme2.23.73] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Asami Saito
- Graduate School of Life Sciences, Tohoku University
| | | | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University
| | - Masato Ishimine
- Miyako Branch, Okinawa Prefectural Agricultural Experiment Station
| | - Shoichiro Akao
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, Miyazaki University
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Huong NL, Itoh K, Suyama K. 2,4-Dichlorophenoxyacetic Acid (2,4-D)- and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacterial Community in Soil-Water Suspension during the Enrichment Process. Microbes Environ 2008; 23:142-8. [DOI: 10.1264/jsme2.23.142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Nguyen L. Huong
- Faculty of Life and Environmental Science, Shimane University
| | - Kazuhito Itoh
- Faculty of Life and Environmental Science, Shimane University
| | - Kousuke Suyama
- Faculty of Life and Environmental Science, Shimane University
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Suda W, Oto M, Amachi S, Shinoyama H, Shishido M. A Direct Method to Isolate DNA from Phyllosphere Microbial Communities without Disrupting Leaf Tissues. Microbes Environ 2008; 23:248-52. [DOI: 10.1264/jsme2.23.248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Wataru Suda
- Graduate School of Horticulture, Chiba University
| | - Michiei Oto
- Department of Biotechnology, Tokyo Technical College
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University
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