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Calatrava V, Hom EF, Guan Q, Llamas A, Fernández E, Galván A. Genetic evidence for algal auxin production in Chlamydomonas and its role in algal-bacterial mutualism. iScience 2024; 27:108762. [PMID: 38269098 PMCID: PMC10805672 DOI: 10.1016/j.isci.2023.108762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024] Open
Abstract
Interactions between algae and bacteria are ubiquitous and play fundamental roles in nutrient cycling and biomass production. Recent studies have shown that the plant auxin indole acetic acid (IAA) can mediate chemical crosstalk between algae and bacteria, resembling its role in plant-bacterial associations. Here, we report a mechanism for algal extracellular IAA production from L-tryptophan mediated by the enzyme L-amino acid oxidase (LAO1) in the model Chlamydomonas reinhardtii. High levels of IAA inhibit algal cell multiplication and chlorophyll degradation, and these inhibitory effects can be relieved by the presence of the plant-growth-promoting bacterium (PGPB) Methylobacterium aquaticum, whose growth is mutualistically enhanced by the presence of the alga. These findings reveal a complex interplay of microbial auxin production and degradation by algal-bacterial consortia and draws attention to potential ecophysiological roles of terrestrial microalgae and PGPB in association with land plants.
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Affiliation(s)
- Victoria Calatrava
- Departamento de Bioquímica y Biología Molecular. Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Erik F.Y. Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677-1848, USA
| | - Qijie Guan
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677-1848, USA
| | - Angel Llamas
- Departamento de Bioquímica y Biología Molecular. Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular. Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular. Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain
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Walitang DI, Roy Choudhury A, Subramanian P, Lee Y, Choi G, Cho K, Yun SH, Jamal AR, Woo SH, Sa T. Microbe-Responsive Proteomes During Plant-Microbe Interactions Between Rice Genotypes and the Multifunctional Methylobacterium oryzae CBMB20. RICE (NEW YORK, N.Y.) 2023; 16:23. [PMID: 37145322 PMCID: PMC10163190 DOI: 10.1186/s12284-023-00639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant-microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association. RESULTS In this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis-trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine-tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice. CONCLUSIONS Interaction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.
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Affiliation(s)
- Denver I Walitang
- Department of Environmental and Biological Chemistry, Chungbuk National University, 28644, Cheongju, Republic of Korea
- College of Agriculture, Fisheries and Forestry, Romblon State University, Romblon, Philippines
| | - Aritra Roy Choudhury
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Republic of Korea
- PG and Research Department of Biotechnology and Microbiology, National College, Tiruchirapalli, Tamilnadu, India
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, 28644, Cheongju, Republic of Korea
| | - Geon Choi
- Department of Environmental and Biological Chemistry, Chungbuk National University, 28644, Cheongju, Republic of Korea
| | - Kun Cho
- Bio-chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Sung Ho Yun
- Bio-chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Aysha Rizwana Jamal
- Department of Environmental and Biological Chemistry, Chungbuk National University, 28644, Cheongju, Republic of Korea
| | - Sun-Hee Woo
- Department of Agronomy, Chungbuk National University, Cheongju, Republic of Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, Chungbuk National University, 28644, Cheongju, Republic of Korea.
- The Korean Academy of Science and Technology, Seongnam, Republic of Korea.
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Sahu KP, Kumar A, Sakthivel K, Reddy B, Kumar M, Patel A, Sheoran N, Gopalakrishnan S, Prakash G, Rathour R, Gautam RK. Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease. ENVIRONMENTAL MICROBIOME 2022; 17:28. [PMID: 35619157 PMCID: PMC9134649 DOI: 10.1186/s40793-022-00421-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/09/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future. RESULTS The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings. CONCLUSIONS PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.
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Affiliation(s)
- Kuleshwar Prasad Sahu
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744101, India
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mukesh Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Asharani Patel
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, 176062, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744101, India
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Torres MJ, González-Ballester D, Gómez-Osuna A, Galván A, Fernández E, Dubini A. Chlamydomonas-Methylobacterium oryzae cooperation leads to increased biomass, nitrogen removal and hydrogen production. BIORESOURCE TECHNOLOGY 2022; 352:127088. [PMID: 35364237 DOI: 10.1016/j.biortech.2022.127088] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 05/27/2023]
Abstract
In the context of algal wastewater bioremediation, this study has identified a novel consortium formed by the bacterium Methylobacterium oryzae and the microalga Chlamydomonas reinhardtii that greatly increase biomass generation (1.22 g L-1·d-1), inorganic nitrogen removal (>99%), and hydrogen production (33 mL·L-1) when incubated in media containing ethanol and methanol. The key metabolic aspect of this relationship relied on the bacterial oxidation of ethanol to acetate, which supported heterotrophic algal growth. However, in the bacterial monocultures the acetate accumulation inhibited bacterial growth. Moreover, in the absence of methanol, ethanol was an unsuitable carbon source and its incomplete oxidation to acetaldehyde had a toxic effect on both the alga and the bacterium. In cocultures, both alcohols were used as carbon sources by the bacteria, the inhibitory effects were overcome and both microorganisms mutually benefited. Potential biotechnological applications in wastewater treatment, biomass generation and hydrogen production are discussed.
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Affiliation(s)
- María Jesús Torres
- Universidad de Córdoba, Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Ed. C6, Planta Baja, 14071 Córdoba, Spain.
| | - David González-Ballester
- Universidad de Córdoba, Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Ed. C6, Planta Baja, 14071 Córdoba, Spain.
| | - Aitor Gómez-Osuna
- Universidad de Córdoba, Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Ed. C6, Planta Baja, 14071 Córdoba, Spain.
| | - Aurora Galván
- Universidad de Córdoba, Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Ed. C6, Planta Baja, 14071 Córdoba, Spain.
| | - Emilio Fernández
- Universidad de Córdoba, Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Ed. C6, Planta Baja, 14071 Córdoba, Spain.
| | - Alexandra Dubini
- Universidad de Córdoba, Departamento de Bioquímica y Biología Molecular, Campus Universitario de Rabanales, Ed. C6, Planta Baja, 14071 Córdoba, Spain.
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Bajpai A, Mahawar H, Dubey G, Atoliya N, Parmar R, Devi MH, Kollah B, Mohanty SR. Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change. J Basic Microbiol 2022; 62:889-899. [DOI: 10.1002/jobm.202200087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Apekcha Bajpai
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- Department of Microbiology Barkatullah University Bhopal India
| | - Himanshu Mahawar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- ICAR‐Directorate of Weed Research Jabalpur India
| | - Garima Dubey
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Nagvanti Atoliya
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Rakesh Parmar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Mayanglambam H. Devi
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Bharati Kollah
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Santosh R. Mohanty
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
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Salt Stress Tolerance-Promoting Proteins and Metabolites under Plant-Bacteria-Salt Stress Tripartite Interactions. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The rapid increase in soil salinization has impacted agricultural output and poses a threat to food security. There is an urgent need to focus on improving soil fertility and agricultural yield, both of which are severely influenced by abiotic variables such as soil salinity and sodicity. Abiotic forces have rendered one-third of the overall land unproductive. Microbes are the primary answer to the majority of agricultural production’s above- and below-ground problems. In stressful conditions, proper communication between plants and beneficial microbes is critical for avoiding plant cell damage. Many chemical substances such as proteins and metabolites synthesized by bacteria and plants mediate communication and stress reduction. Metabolites such as amino acids, fatty acids, carbohydrates, vitamins, and lipids as well as proteins such as aquaporins and antioxidant enzymes play important roles in plant stress tolerance. Plant beneficial bacteria have an important role in stress reduction through protein and metabolite synthesis under salt stress. Proper genomic, proteomic and metabolomics characterization of proteins and metabolites’ roles in salt stress mitigation aids scientists in discovering a profitable avenue for increasing crop output. This review critically examines recent findings on proteins and metabolites produced during plant-bacteria interaction essential for the development of plant salt stress tolerance.
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Damo JLC, Ramirez MDA, Agake SI, Pedro M, Brown M, Sekimoto H, Yokoyama T, Sugihara S, Okazaki S, Ohkama-Ohtsu N. Isolation and Characterization of Phosphate Solubilizing Bacteria from Paddy Field Soils in Japan. Microbes Environ 2022; 37. [PMID: 35598988 PMCID: PMC9530731 DOI: 10.1264/jsme2.me21085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorus (P) is abundant in soil and is essential for plant growth and development; however, it is easily rendered insoluble in complexes of different types of phosphates, which may lead to P deficiency. Therefore, increases in the amount of P released from phosphate minerals using microbial inoculants is an important aspect of agriculture. The present study used inorganic phosphate solubilizing bacteria (iPSB) in paddy field soils to develop microbial inoculants. Soils planted with rice were collected from different regions of Japan. Soil P was sequentially fractionated using the Hedley method. iPSB were isolated using selective media supplemented with tricalcium phosphate (Ca-P), aluminum phosphate (Al-P), or iron phosphate (Fe-P). Representative isolates were selected based on the P solubilization index and soil sampling site. Identification was performed using 16S rRNA and rpoB gene sequencing. Effectiveness was screened based on rice cultivar Koshihikari growth supplemented with Ca-P, Al-P, or Fe-P as the sole P source. Despite the relatively homogenous soil pH of paddy field sources, three sets of iPSB were isolated, suggesting the influence of fertilizer management and soil types. Most isolates were categorized as β-Proteobacteria (43%). To the best of our knowledge, this is the first study to describe the genera Pleomorphomonas, Rhodanobacter, and Trinickia as iPSB. Acidovorax sp. JC5, Pseudomonas sp. JC11, Burkholderia sp. JA6 and JA10, Sphingomonas sp. JA11, Mycolicibacterium sp. JF5, and Variovorax sp. JF6 promoted plant growth in rice supplemented with an insoluble P source. The iPSBs obtained may be developed as microbial inoculants for various soil types with different P fixation capacities.
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Affiliation(s)
| | | | - Shin-ichiro Agake
- United Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Mannix Pedro
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños
| | - Marilyn Brown
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños
| | | | | | - Soh Sugihara
- Institute of Agriculture, Tokyo University of Agriculture and Technology
| | - Shin Okazaki
- Institute of Agriculture, Tokyo University of Agriculture and Technology
| | - Naoko Ohkama-Ohtsu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology
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Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A. Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species. Front Microbiol 2021; 12:740610. [PMID: 34737731 PMCID: PMC8561711 DOI: 10.3389/fmicb.2021.740610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/06/2021] [Indexed: 01/06/2023] Open
Abstract
The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.
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Affiliation(s)
- Ola Alessa
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Mugla, Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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9
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Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria. Curr Microbiol 2021; 78:2623-2630. [PMID: 33990868 DOI: 10.1007/s00284-021-02525-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the tree canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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Agarwal P, Giri BS, Rani R. Unravelling the Role of Rhizospheric Plant-Microbe Synergy in Phytoremediation: A Genomic Perspective. Curr Genomics 2020; 21:334-342. [PMID: 33093797 PMCID: PMC7536802 DOI: 10.2174/1389202921999200623133240] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 12/27/2022] Open
Abstract
Background Accretion of organic and inorganic contaminants in soil interferes in the food chain, thereby posing a serious threat to the ecosystem and adversely affecting crop productivity and human life. Both endophytic and rhizospheric microbial communities are responsible for the biodegradation of toxic organic compounds and have the capability to enhance the uptake of heavy metals by plants via phytoremediation approaches. The diverse set of metabolic genes encoding for the production of biosurfactants and biofilms, specific enzymes for degrading plant polymers, modification of cell surface hydrophobicity and various detoxification pathways for the organic pollutants, plays a significant role in bacterial driven bioremediation. Various genetic engineering approaches have been demonstrated to modulate the activity of specific microbial species in order to enhance their detoxification potential. Certain rhizospheric bacterial communities are genetically modified to produce specific enzymes that play a role in degrading toxic pollutants. Few studies suggest that the overexpression of extracellular enzymes secreted by plant, fungi or rhizospheric microbes can improve the degradation of specific organic pollutants in the soil. Plants and microbes dwell synergistically, where microbes draw benefit by nutrient acquisition from root exudates whereas they assist in plant growth and survival by producing certain plant growth promoting metabolites, nitrogen fixation, phosphate solubilization, auxin production, siderophore production, and inhibition or suppression of plant pathogens. Thus, the plant-microbe interaction establishes the foundation of the soil nutrient cycle as well as decreases soil toxicity by the removal of harmful pollutants. Conclusion The perspective of integrating genetic approach with bioremediation is crucial to evaluate connexions among microbial communities, plant communities and ecosystem processes with a focus on improving phytoremediation of contaminated sites.
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Affiliation(s)
- Priyanka Agarwal
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, Uttar Pradesh, India; 2Department of Chemical Engineering and Technology, Centre of Advanced Study, Indian Institute of Technology Banaras Hindu University, Varanasi221005, India
| | - Balendu Shekher Giri
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, Uttar Pradesh, India; 2Department of Chemical Engineering and Technology, Centre of Advanced Study, Indian Institute of Technology Banaras Hindu University, Varanasi221005, India
| | - Radha Rani
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, Uttar Pradesh, India; 2Department of Chemical Engineering and Technology, Centre of Advanced Study, Indian Institute of Technology Banaras Hindu University, Varanasi221005, India
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12
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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13
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Phenotypic diversity of Methylobacterium associated with rice landraces in North-East India. PLoS One 2020; 15:e0228550. [PMID: 32092057 PMCID: PMC7039438 DOI: 10.1371/journal.pone.0228550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/19/2020] [Indexed: 11/19/2022] Open
Abstract
The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.
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14
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Grossi CEM, Fantino E, Serral F, Zawoznik MS, Fernandez Do Porto DA, Ulloa RM. Methylobacterium sp. 2A Is a Plant Growth-Promoting Rhizobacteria That Has the Potential to Improve Potato Crop Yield Under Adverse Conditions. FRONTIERS IN PLANT SCIENCE 2020; 11:71. [PMID: 32127795 PMCID: PMC7038796 DOI: 10.3389/fpls.2020.00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/17/2020] [Indexed: 05/11/2023]
Abstract
A Gram-negative pink-pigmented bacillus (named 2A) was isolated from Solanum tuberosum L. cv. Desirée plants that were strikingly more developed, presented increased root hair density, and higher biomass than other potato lines of the same age. The 16S ribosomal DNA sequence, used for comparative gene sequence analysis, indicated that strain 2A belongs to the genus Methylobacterium. Nucleotide identity between Methylobacterium sp. 2A sequenced genome and the rest of the species that belong to the genus suggested that this species has not been described so far. In vitro, potato plants inoculated with Methylobacterium sp. 2A had a better performance when grown under 50 mM NaCl or when infected with Phytophthora infestans. We inoculated Methylobacterium sp. 2A in Arabidopsis thaliana roots and exposed these plants to salt stress (75 mM NaCl). Methylobacterium sp. 2A-inoculated plants, grown in control or salt stress conditions, displayed a higher density of lateral roots (p < 0.05) compared to noninoculated plants. Moreover, under salt stress, they presented a higher number of leaves and larger rosette diameter. In dual confrontation assays, Methylobacterium sp. 2A displayed biocontrol activity against P. infestans, Botrytis cinerea, and Fusarium graminearum, but not against Rhizoctonia solani, and Pythium dissotocum. In addition, we observed that Methylobacterium sp. 2A diminished the size of necrotic lesions and reduced chlorosis when greenhouse potato plants were infected with P. infestans. Methylobacterium sp. 2A produces indole acetic acid, solubilizes mineral phosphate and is able to grow in a N2 free medium. Whole-genome sequencing revealed metabolic pathways associated with its plant growth promoter capacity. Our results suggest that Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria (PGPR) that can alleviate salt stress, and restricts P. infestans infection in potato plants, emerging as a potential strategy to improve crop management.
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Affiliation(s)
- Cecilia Eugenia María Grossi
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Elisa Fantino
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico Serral
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Myriam Sara Zawoznik
- Cátedra de Química Biológica Vegetal, Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Darío Augusto Fernandez Do Porto
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Rita María Ulloa
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Química Biológica, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
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15
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Physiological response of tomato plant to chitosan-immobilized aggregated Methylobacterium oryzae CBMB20 inoculation under salinity stress. 3 Biotech 2019; 9:397. [PMID: 31656735 DOI: 10.1007/s13205-019-1923-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/25/2019] [Indexed: 10/25/2022] Open
Abstract
The use of plant growth promoting bacteria as bioinoculant to alleviate salt stress is a sustainable and eco-friendly approach in agriculture. However, the maintenance of the bacterial population in the soil for longer period is a major concern. In the present study, chitosan-immobilized aggregated Methylobacterium oryzae CBMB20 was used as a bioinoculant to improve tomato plant (Solanum lycopersicum Mill.) growth under salt stress. The chitosan-immobilized aggregated M. oryzae CBMB20 was able to enhance plant dry weight, nutrient uptake (N, P, K and Mg2+), photosynthetic efficiency and decrease electrolyte leakage under salt stress conditions. The oxidative stress exerted by elevated levels of salt stress was also alleviated by the formulated bioinoculant, as it up-regulated the antioxidant enzyme activities and enhanced the accumulation of proline which acts as an osmolyte. The chitosan-immobilized aggregated M. oryzae CBMB20 was able to decrease the excess Na+ influx into the plant cells and subsequently decreasing the Na+/K+ ratio to improve tomato plant growth under salt stress conditions. Therefore, it is proposed that the chitosan-immobilized aggregated M. oryzae CBMB20 could be used as a bioinoculant to promote the plant growth under salt stress conditions.
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16
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Calatrava V, Hom EFY, Llamas Á, Fernández E, Galván A. OK, thanks! A new mutualism between Chlamydomonas and methylobacteria facilitates growth on amino acids and peptides. FEMS Microbiol Lett 2019; 365:4828328. [PMID: 29385570 DOI: 10.1093/femsle/fny021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 01/24/2018] [Indexed: 12/15/2022] Open
Abstract
Nitrogen is a key nutrient for land plants and phytoplankton in terrestrial and aquatic ecosystems. The model alga Chlamydomonas reinhardtii can grow efficiently on several inorganic nitrogen sources (e.g. ammonium, nitrate, nitrite) as well as many amino acids. In this study, we show that Chlamydomonas is unable to use proline, hydroxyproline and peptides that contain these amino acids. However, we discovered that algal growth on these substrates is supported in association with Methylobacterium spp., and that a mutualistic carbon-nitrogen metabolic exchange between Chlamydomonas and Methylobacterium spp. is established. Specifically, the mineralization of these amino acids and peptides by Methylobacterium spp. produces ammonium that can be assimilated by Chlamydomonas, and CO2 photosynthetically fixed by Chlamydomonas yields glycerol that can be assimilated by Methylobacterium. As Chlamydomonas is an algal ancestor to land plants and Methylobacterium is a plant growth-promoting bacterium, this new model of mutualism may facilitate insights into the ecology and evolution of plant-bacterial interactions and design principles of synthetic ecology.
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Affiliation(s)
- Victoria Calatrava
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, 14071-Córdoba, Spain
| | - Erik F Y Hom
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Ángel Llamas
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, 14071-Córdoba, Spain
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, 14071-Córdoba, Spain
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, 14071-Córdoba, Spain
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17
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Chatterjee P, Kanagendran A, Samaddar S, Pazouki L, Sa TM, Niinemets Ü. Methylobacterium oryzae CBMB20 influences photosynthetic traits, volatile emission and ethylene metabolism in Oryza sativa genotypes grown in salt stress conditions. PLANTA 2019; 249:1903-1919. [PMID: 30877435 PMCID: PMC6875431 DOI: 10.1007/s00425-019-03139-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 05/05/2023]
Abstract
MAIN CONCLUSION Inoculation of endophytic Methylobacterium oryzae CBMB20 in salt-stressed rice plants improves photosynthesis and reduces stress volatile emissions due to mellowing of ethylene-dependent responses and activating vacuolar H+-ATPase. The objective of this study was to analyze the impact of ACC (1-aminocyclopropane-1-carboxylate) deaminase-producing Methylobacterium oryzae CBMB20 in acclimation of plant to salt stress by controlling photosynthetic characteristics and volatile emission in salt-sensitive (IR29) and moderately salt-resistant (FL478) rice (Oryza sativa L.) cultivars. Saline levels of 50 mM and 100 mM NaCl with and without bacteria inoculation were applied, and the temporal changes in stress response and salinity resistance were assessed by monitoring photosynthetic characteristics, ACC accumulation, ACC oxidase activity (ACO), vacuolar H+ ATPase activity, and volatile organic compound (VOC) emissions. Salt stress considerably reduced photosynthetic rate, stomatal conductance, PSII efficiency and vacuolar H+ ATPase activity, but it increased ACC accumulation, ACO activity, green leaf volatiles, mono- and sesquiterpenes, and other stress volatiles. These responses were enhanced with increasing salt stress and time. However, rice cultivars treated with CBMB20 showed improved plant vacuolar H+ ATPase activity, photosynthetic characteristics and decreased ACC accumulation, ACO activity and VOC emission. The bacteria-dependent changes were greater in the IR29 cultivar. These results indicate that decreasing photosynthesis and vacuolar H+ ATPase activity rates and increasing VOC emission rates in response to high-salinity stress were effectively mitigated by M. oryzae CBMB20 inoculation.
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Affiliation(s)
- Poulami Chatterjee
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Arooran Kanagendran
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
| | - Sandipan Samaddar
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Leila Pazouki
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
| | - Tong-Min Sa
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia.
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia.
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18
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Aburto-Medina A, Shahsavari E, Salzman SA, Kramer A, Ball AS, Allinson G. Elucidation of the microbial diversity in rivers in south-west Victoria, Australia impacted by rural agricultural contamination (dairy farming). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 172:356-363. [PMID: 30731266 DOI: 10.1016/j.ecoenv.2019.01.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
We assessed the water quality of south-west Victorian rivers impacted by the dairy industry using traditional water quality assessment together with culture-dependent (colilert/enterolert) and also culture-independent (next generation sequencing) microbial methods. The aim of the study was to identify relationships/associations between dairy farming intensity and water contamination. Water samples with high total and faecal coliforms (>1000 MPN cfu/100 ml), and with high nitrogen levels (TN) were observed in zones with a high proportion of dairy farming. Members of the genus Nitrospira, Rhodobacter and Rhodoplanes were predominant in such high cattle density zones. Samples from sites in zones with lower dairy farming activities registered faecal coliform numbers within the permissible limits (<1000 MPN cfu/100 ml) and showed the presence of a wide variety of microorganisms. However, no bacterial pathogens were found in the river waters regardless of the proportion of cattle. The data suggests that using the spatially weighted proportion of land used for dairy farming is a useful way to target at-risk sub-catchments across south west Victoria; further work is required to confirm that this approach is applicable in other regions.
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Affiliation(s)
- Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia.
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Scott A Salzman
- Department of Information Systems and Business Analytics, Deakin University, Warrnambool, Victoria 3280 Australia
| | - Andrew Kramer
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, Victoria 3085 Australia; Waikato Regional Council, Private Bag 3038, Waikato Mail Centre, Hamilton 3240, New Zealand
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Graeme Allinson
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
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19
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Shao Y, Li J, Wang Y, Yi F, Zhang Y, Cui P, Zhong W. Comparative genomics and transcriptomics insights into the C1 metabolic model of a formaldehyde-degrading strain Methylobacterium sp. XJLW. Mol Omics 2019; 15:138-149. [PMID: 30785446 DOI: 10.1039/c8mo00198g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively. XJLW has a chromosome DNA and a mega-plasmid DNA. Ten percent of genes on chromosome DNA are strain-specific in genus Methylobacterium. Transcriptome analysis results showed that 623 genes were significantly up-regulated and that 207 genes were significantly down-regulated for growth in methanol. Among the up-regulated genes, 90 genes belong to strain-specific regions and are densely distributed in three areas. A specific gene (A3862_27225) annotated as methyltransferase was found ranking in the top 4 of up-regulated genes. This methyltransferase may play a role in the specific C1 metabolism of XJLW. Methylobacterium sp. XJLW should contain a potential methyl transport pathway via the novel methyltransferase, which is different from known pathways. These findings provide the basis for additional possibilities, which improve the formaldehyde-degrading ability of Methylobacterium sp. XJLW.
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Affiliation(s)
- Yunhai Shao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Yanxin Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Fengmei Yi
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Yanan Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Peiwu Cui
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
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20
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Biodiversity of methylotrophic microbial communities and their potential role in mitigation of abiotic stresses in plants. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00190-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Yoshida Y, Iguchi H, Sakai Y, Yurimoto H. Pantothenate auxotrophy of Methylobacterium spp. isolated from living plants. Biosci Biotechnol Biochem 2018; 83:569-577. [PMID: 30475153 DOI: 10.1080/09168451.2018.1549935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A number of pink-pigmented facultative methylotrophs (PPFMs) belonging to Methylobacterium spp. isolated from living plant samples were found to require B vitamins for their growth in minimal medium, and most B vitamin-auxotrophic PPFMs required pantothenate (vitamin B5). Further investigation of pantothenate auxotrophy using the representative strain Methylobacterium sp. OR01 demonstrated that this strain cannot synthesize β-alanine, one of the precursors of pantothenate. β-alanine and several precursors of pantothenate restored the growth of Methylobacterium sp. OR01 in minimal medium. Furthermore, this strain could colonize leaves of Arabidopsis thaliana cultivated in medium without pantothenate or its precursors. Pantothenate, β-alanine and several precursors were detected in the suspension of A. thaliana leaves. These results suggest that pantothenate-auxotrophic PPFMs can symbiotically colonize the surface of plant leaves by acquiring β-alanine and other precursors, in addition to pantothenate. Finally, the fitness advantage of B vitamin auxotrophy of PPFMs in the phyllosphere environment is discussed.
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Affiliation(s)
- Yusuke Yoshida
- a Division of Applied Life Sciences, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | - Hiroyuki Iguchi
- a Division of Applied Life Sciences, Graduate School of Agriculture , Kyoto University , Kyoto , Japan.,b Department of Agriculture and Food Technology, Faculty of Bioenvironmental Science , Kyoto Gakuen University , Kameoka , Japan
| | - Yasuyoshi Sakai
- a Division of Applied Life Sciences, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | - Hiroya Yurimoto
- a Division of Applied Life Sciences, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
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22
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Green PN, Ardley JK. Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. Int J Syst Evol Microbiol 2018; 68:2727-2748. [PMID: 30024371 DOI: 10.1099/ijsem.0.002856] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Methylobacterium, when first proposed by Patt et al. in 1976, was a monospecific genus created to accommodate a single pink pigmented facultatively methylotrophic bacterium. The genus now has over 50 validly published species, however, the percentage 16S rRNA sequence divergence within Methylobacterium questions whether or not they can still be accommodated within one genus. Additionally, several strains are described as belonging to Methylobacterium, but nodulate legumes and in some cases are unable to utilize methanol as a sole carbon source. This study reviews and discusses the current taxonomic status of Methylobacterium. Based on 16S rRNA gene, multi-locus sequence analysis, genomic and phenotypic data, the 52 Methylobacterium species can no longer be retained in one genus. Consequently, a new genus, Methylorubrum gen. nov., is proposed to accommodate 11 species previously held in Methylobacterium. The reclassified species names are proposed as: Methylorubrum aminovorans comb. nov. (type strain TH-15T=NCIMB 13343T=DSM 8832T), Methylorubrum extorquens comb. nov. (type strain NCIMB 9399T=DSM 1337T), Methylorubrum podarium comb. nov. (type strain FM4T=NCIMB 14856T=DSM 15083T), Methylorubrum populi comb. nov. (type strain BJ001T=NCIMB 13946T=ATCC BAA-705T), Methylorubrum pseudosasae comb. nov. (type strain BL44T=ICMP 17622T=NBRC 105205T), Methylorubrum rhodesianum comb. nov. (type strain NCIMB 12249T=DSM 5687T), Methylorubrum rhodinum comb. nov. (type strain NCIMB 9421T=DSM 2163T), Methylorubrum salsuginis comb. nov. (type strain MRT=NCIMB 14847T=NCCB 100140T), Methylorubrum suomiense comb. nov. (type strain F20T=NCIMB 13778T=DSM 14458T), Methylorubrum thiocyanatum comb. nov. (type strain ALL/SCN-PT=NCIMB 13651T=DSM 11490T) and Methylorubrum zatmanii comb. nov. (type strain NCIMB 12243T=DSM 5688T). The taxonomic position of several remaining species is also discussed.
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Affiliation(s)
- Peter N Green
- 1NCIMB, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen AB21 9YA, UK
| | - Julie K Ardley
- 2School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia
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Ekimova GA, Fedorov DN, Tani A, Doronina NV, Trotsenko YA. Distribution of 1-aminocyclopropane-1-carboxylate deaminase and d-cysteine desulfhydrase genes among type species of the genus Methylobacterium. Antonie van Leeuwenhoek 2018. [DOI: 10.1007/s10482-018-1061-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Lee W, Kim S, Song I, Kwon Y, Park S, Oh BK, Oh HB, Lee J. Microbial production of uracil by an isolated Methylobacterium sp. WJ4 using methanol. Enzyme Microb Technol 2018; 111:63-66. [PMID: 29421038 DOI: 10.1016/j.enzmictec.2017.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/27/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
In this study, we report the production of uracil from methanol by an isolated methylotrophic bacterium, Methylobacterium sp. WJ4. The use of methanol as alternative carbon feedstock is attractive option in biotechnology. As a feedstock of biotechnological processes, methanol has distinct advantages over methane. This is not only due to physical and chemical considerations, but also to the properties of the pertinent organisms. Besides, with a wide array of biological activities and synthetic accessibility, uracil is considered as privileged structures in drug discovery. Uracil analogues have been applied to treatments of patients with cancer or viral infections. In this respect, it is meaningful to produce uracil using methanol. The effect of process parameters and methanol concentration for uracil production were investigated and optimized. Uracil production was remarkably increased to 5.76mgg cell dry weight-1 in optimized condition. The results were significant for further understanding of methylotrophic bacteria on uracil production.
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Affiliation(s)
- Wangjun Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Sangwoo Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Insu Song
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Yuhyun Kwon
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Soohyun Park
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Byung-Keun Oh
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea.
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Aswathy SK, Sridar R, Sivakumar U. Mitigation of drought in rice by a phyllosphere bacterium Bacillus altitudinis FD48. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajmr2017.8610] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Li O, Xiao R, Sun L, Guan C, Kong D, Hu X. Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing. PLoS One 2017; 12:e0184717. [PMID: 28931073 PMCID: PMC5607135 DOI: 10.1371/journal.pone.0184717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 08/29/2017] [Indexed: 01/22/2023] Open
Abstract
As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ) to 96.08% (YN), and Delftia (10.39-38.42%), Burkholderia (2.71-15.98%), Escherichia/Shigella (4.90-25.12%), Pseudomonas (2.68-30.72%) and Sphingomonas (1.83-2.05%) dominated in four planting bases. Pseudomonas (17.94-22.06%), Escherichia/Shigella (6.59-11.59%), Delftia (9.65-22.14%) and Burkholderia (3.12-11.05%) dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples.
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Affiliation(s)
- Ou Li
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
| | - Rong Xiao
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
| | - Lihua Sun
- Zhejiang Academy of Medical Sciences, Hangzhou, PR China
| | - Chenglin Guan
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
| | - Dedong Kong
- Agricultural Experiment Station, Zhejiang Univesity, Hangzhou, PR China
| | - Xiufang Hu
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
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Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA, Kwon SW, Whitman WB. Paenibacillus polysaccharolyticus sp. nov., a xylanolytic and cellulolytic bacteria isolated from leaves of Bamboo Phyllostachys aureosulcata. Int J Syst Evol Microbiol 2017; 67:2127-2133. [DOI: 10.1099/ijsem.0.001901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Munusamy Madhaiyan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Venkatakrishnan Sivaraj Saravanan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
- Department of Microbiology, Indira Gandhi College of Arts and Science, Kathirkamam 605009, Pondicherry, India
| | - Veeramuthu Duraipandiyan
- Addiriyah Research Chair for Environmental Studies, Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
- Entomology Research Institute, Loyola College, Chennai 600034, India
| | - Naif Abdullah Al-Dhabi
- Addiriyah Research Chair for Environmental Studies, Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA 30602-2605, USA
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Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico). Extremophiles 2017; 21:499-511. [DOI: 10.1007/s00792-017-0920-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
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Madhaiyan M, Poonguzhali S, Saravanan VS, Pragatheswari D, Duraipandiyan V, Al-Dhabi NA, Santhanakrishnan P. Paenibacillus methanolicus sp. nov., a xylanolytic, methanol-utilizing bacterium isolated from the phyllosphere of bamboo (Pseudosasa japonica). Int J Syst Evol Microbiol 2016; 66:4362-4366. [DOI: 10.1099/ijsem.0.001356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Munusamy Madhaiyan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641003, Tamilnadu, India
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641003, Tamilnadu, India
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | | | - Dhandapani Pragatheswari
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Veeramuthu Duraipandiyan
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, Riyadh-11451, Kingdom of Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, Riyadh-11451, Kingdom of Saudi Arabia
| | - Palani Santhanakrishnan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641003, Tamilnadu, India
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Minami T, Anda M, Mitsui H, Sugawara M, Kaneko T, Sato S, Ikeda S, Okubo T, Tsurumaru H, Minamisawa K. Metagenomic Analysis Revealed Methylamine and Ureide Utilization of Soybean-Associated Methylobacterium. Microbes Environ 2016; 31:268-78. [PMID: 27431374 PMCID: PMC5017803 DOI: 10.1264/jsme2.me16035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/16/2016] [Indexed: 01/29/2023] Open
Abstract
Methylobacterium inhabits the phyllosphere of a large number of plants. We herein report the results of comparative metagenome analyses on methylobacterial communities of soybean plants grown in an experimental field in Tohoku University (Kashimadai, Miyagi, Japan). Methylobacterium was identified as the most dominant genus (33%) among bacteria inhabiting soybean stems. We classified plant-derived Methylobacterium species into Groups I, II, and III based on 16S rRNA gene sequences, and found that Group I members (phylogenetically close to M. extorquens) were dominant in soybean-associated Methylobacterium. By comparing 29 genomes, we found that all Group I members possessed a complete set of genes for the N-methylglutamate pathway for methylamine utilization, and genes for urea degradation (urea carboxylase, urea amidolyase, and conventional urease). Only Group I members and soybean methylobacterial isolates grew in a culture supplemented with methylamine as the sole carbon source. They utilized urea or allantoin (a urea-related compound in legumes) as the sole nitrogen source; however, group III also utilized these compounds. The utilization of allantoin may be crucial in soybean-bacterial interactions because allantoin is a transported form of fixed nitrogen in legume plants. Soybean-derived Group I strain AMS5 colonized the model legume Lotus japonicus well. A comparison among the 29 genomes of plant-derived and other strains suggested that several candidate genes are involved in plant colonization such as csgG (curli fimbriae). Genes for the N-methylglutamate pathway and curli fimbriae were more abundant in soybean microbiomes than in rice microbiomes in the field. Based on these results, we discuss the lifestyle of Methylobacterium in the legume phyllosphere.
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Affiliation(s)
- Tomoyuki Minami
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Misue Anda
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Masayuki Sugawara
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Takakazu Kaneko
- Kazusa DNA Research Institute2–6–7 Kazusa-kamatari, Kisarazu, Chiba 292–0818Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
- Kazusa DNA Research Institute2–6–7 Kazusa-kamatari, Kisarazu, Chiba 292–0818Japan
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Takashi Okubo
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Hirohito Tsurumaru
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
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Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA, Pragatheswari D, Santhanakrishnan P, Kim SJ, Weon HY, Kwon SW. Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves. Int J Syst Evol Microbiol 2016; 66:4204-4210. [PMID: 27469580 DOI: 10.1099/ijsem.0.001336] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6-11 and 0-8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces, including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces. The determination of G+C ratio (69.5 mol%) and DNA-DNA hybridization values (13.4-31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA-DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).
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Affiliation(s)
- Munusamy Madhaiyan
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Republic of Singapore.,Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India.,Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Republic of Singapore
| | | | - Veeramuthu Duraipandiyan
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box. 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box. 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Dhandapani Pragatheswari
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Palani Santhanakrishnan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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Complete Genome Sequence of Methylobacterium sp. Strain AMS5, an Isolate from a Soybean Stem. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00144-16. [PMID: 26988053 PMCID: PMC4796132 DOI: 10.1128/genomea.00144-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nonrhizobial Methylobacterium spp. inhabit the phyllosphere of a wide variety of plants. We report here the complete genome sequence of Methylobacterium sp. AMS5, which was isolated from a soybean stem. The information is useful for understanding the molecular mechanisms of the interaction between nonrhizobial Methylobacterium spp. and plants.
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Zamani I, Bouzari M, Emtiazi G, Fanaei M. Rapid quantitative estimation of chlorinated methane utilizing bacteria in drinking water and the effect of nanosilver on biodegradation of the trichloromethane in the environment. Jundishapur J Microbiol 2015; 8:e14965. [PMID: 25834716 PMCID: PMC4377176 DOI: 10.5812/jjm.14965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 01/05/2014] [Accepted: 01/21/2014] [Indexed: 11/24/2022] Open
Abstract
Background: Halomethanes are toxic and carcinogenic chemicals, which are widely used in industry. Also they can be formed during water disinfection by chlorine. Biodegradation by methylotrophs is the most important way to remove these pollutants from the environment. Objectives: This study aimed to represent a simple and rapid method for quantitative study of halomethanes utilizing bacteria in drinking water and also a method to facilitate the biodegradation of these compounds in the environment compared to cometabolism. Materials and Methods: Enumeration of chlorinated methane utilizing bacteria in drinking water was carried out by most probable number (MPN) method in two steps. First, the presence and the number of methylotroph bacteria were confirmed on methanol-containing medium. Then, utilization of dichloromethane was determined by measuring the released chloride after the addition of 0.04 mol/L of it to the growth medium. Also, the effect of nanosilver particles on biodegradation of multiple chlorinated methanes was studied by bacterial growth on Bushnell-Haas Broth containing chloroform (trichloromethane) that was treated with 0.2 ppm nanosilver. Results: Most probable number of methylotrophs and chlorinated methane utilizing bacteria in tested drinking water were 10 and 4 MPN Index/L, respectively. Chloroform treatment by nanosilver leads to dechlorination and the production of formaldehyde. The highest growth of bacteria and formic acid production were observed in the tubes containing 1% chloroform treated with nanosilver. Conclusions: By combining the two tests, a rapid approach to estimation of most probable number of chlorinated methane utilizing bacteria is introduced. Treatment by nanosilver particles was resulted in the easier and faster biodegradation of chloroform by bacteria. Thus, degradation of these chlorinated compounds is more efficient compared to cometabolism.
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Affiliation(s)
- Isaac Zamani
- Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR Iran
| | - Majid Bouzari
- Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR Iran
- Corresponding author: Majid Bouzari, Department of Biology, Faculty of Science, University of Isfahan, P. O . BOX: 81746-73441, Isfahan, IR Iran. Tel: +98-3137932456, Fax: +98-3167932456, E-mail:
| | - Giti Emtiazi
- Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR Iran
| | - Maryam Fanaei
- Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR Iran
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Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee JS, Lee KC. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 2014; 65:578-586. [PMID: 25404481 DOI: 10.1099/ijs.0.069377-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel bacterial strains, designated Vu-144(T), Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144(T) was affiliated with an uncultivated lineage of the phylum Bacteroidetes. Its closest phylogenetic neighbour was the recently described species Niastella populi, a member of the family Chitinophagaceae, with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1-APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1-UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45-60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144(T) represents a novel genus and species in the family Chitinophagaceae, for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144(T) ( = KCTC 22378(T) = NCIMB 14473(T)).
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Affiliation(s)
- Munusamy Madhaiyan
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604.,Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Murugaiyan Senthilkumar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Dhandapani Pragatheswari
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yusong-gu, Daejeon 305-806, Republic of Korea
| | - Keun-Chul Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yusong-gu, Daejeon 305-806, Republic of Korea
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35
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Kwak MJ, Jeong H, Madhaiyan M, Lee Y, Sa TM, Oh TK, Kim JF. Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS One 2014; 9:e106704. [PMID: 25211235 PMCID: PMC4161386 DOI: 10.1371/journal.pone.0106704] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/31/2014] [Indexed: 11/19/2022] Open
Abstract
Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.
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Affiliation(s)
- Min-Jung Kwak
- Department of Systems Biology, and Division of Life Sciences, Yonsei University, Seodaemun-gu, Seoul, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Haeyoung Jeong
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Munusamy Madhaiyan
- Department of Agricultural Chemistry, Chungbuk National University, Heungdeok-gu, Cheongju, Republic of Korea
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Heungdeok-gu, Cheongju, Republic of Korea
| | - Tong-Min Sa
- Department of Agricultural Chemistry, Chungbuk National University, Heungdeok-gu, Cheongju, Republic of Korea
| | - Tae Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- 21C Frontier Microbial Genomics and Applications Center, Yuseong-gu, Daejeon, Republic of Korea
| | - Jihyun F. Kim
- Department of Systems Biology, and Division of Life Sciences, Yonsei University, Seodaemun-gu, Seoul, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
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36
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Madhaiyan M, Poonguzhali S. Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. Int J Syst Evol Microbiol 2014; 64:2376-2384. [DOI: 10.1099/ijs.0.057232-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Two strains of Gram-negative, methylotrophic bacteria, isolated because of their abilities to promote plant growth, were subjected to a polyphasic taxonomic study. The isolates were strictly aerobic, motile, pink-pigmented, facultatively methylotrophic, non-spore-forming rods. The chemotaxonomic characteristics of the isolates included the presence of C18 : 1ω7c as the major cellular fatty acid. The DNA G+C contents of strains BL36T and BL47T were 69.4 and 69.8 mol%, respectively. 16S rRNA gene sequence analysis of strains BL36T and BL47T placed them under the genus
Methylobacterium,
with the pairwise sequence similarity between them and the type strains of closely related species ranging from 97.2 to 99.0 %. On the basis of their phenotypic and phylogenetic distinctiveness and the results of DNA–DNA hybridization analysis, the isolates represent two novel species within the genus
Methylobacterium
, for which the names Methylobacterium pseudosasicola sp. nov. (type strain BL36T = NBRC 105203T = ICMP 17621T) and Methylobacterium phyllostachyos sp. nov. (type strain BL47T = NBRC 105206T = ICMP 17619T) are proposed.
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Affiliation(s)
- Munusamy Madhaiyan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
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37
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Madhaiyan M, Poonguzhali S, Saravanan VS, Kwon SW. Rhodanobacter glycinis sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizoplane of field-grown soybean. Int J Syst Evol Microbiol 2014; 64:2023-2028. [PMID: 24651305 DOI: 10.1099/ijs.0.055525-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
A novel, yellow-pigmented bacterium, designated strain MO64(T), was isolated from the rhizoplane of field-grown soybean, collected from an experimental plot at Coimbatore, India. Cells were Gram-reaction-negative, motile, non-spore-forming rods that produced yellow-pigmented colonies on R2A agar. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MO64(T) belonged to the genus Rhodanobacter. Strain MO64(T) was related most closely to Rhodanobacter ginsengisoli GR17-7(T) (98.0% 16S rRNA gene sequence similarity), Rhodanobacter spathiphylli B39(T) (97.9%), Rhodanobacter panaciterrae LnR5-47(T) (97.7%), Rhodanobacter terrae GP18-1(T) (97.6%), Rhodanobacter soli DCY45(T) (97.3%) and Rhodanobacter caeni MJ01(T) (97.2%); levels of similarity to the type strains of all other recognized species of the genus Rhodanobacter were less than 97.0%. Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C(16 : 0), iso-C(15 : 0), C(17 : 0) cyclo, iso-C(17 : 1)ω9c, iso-C(17 : 0) and iso-C(11 : 0) as the major fatty acids) also supported the affiliation of strain MO64(T) with the genus Rhodanobacter. The G+C content of the genomic DNA was 64 mol%. The results of DNA-DNA hybridization and phenotypic analysis showed that strain MO64(T) can be distinguished from all known species of the genus Rhodanobacter and therefore represents a novel species of the genus, for which the name Rhodanobacter glycinis sp. nov. is proposed. The type strain is MO64(T) ( = ICMP 17626(T) = NBRC 105007(T)).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Venkatakrishnan Sivaraj Saravanan
- Department of Microbiology, Indira Gandhi College of Arts and Science, Pondicherry University, Kathirkamam 605009, Pondicherry, India
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
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38
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Curran SA, Hollan I, Erridge C, Lappin DF, Murray CA, Sturfelt G, Mikkelsen K, Førre OT, Almdahl SM, Fagerhol MK, Goodyear CS, Riggio MP. Bacteria in the adventitia of cardiovascular disease patients with and without rheumatoid arthritis. PLoS One 2014; 9:e98627. [PMID: 24874661 PMCID: PMC4038603 DOI: 10.1371/journal.pone.0098627] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 02/17/2014] [Indexed: 12/31/2022] Open
Abstract
The incidence of atherosclerosis is significantly increased in rheumatoid arthritis (RA). Infection is one factor that may be involved in the pathogenesis of both diseases. The cause of RA and atherosclerosis is unknown, and infection is one of the factors that may be involved in the pathogenesis of both diseases. The aims of this study were to identify bacteria in the aortic adventitia of patients with cardiovascular disease (CVD) in the presence and absence of RA, and to determine the effect of identified candidate pathogens on Toll-like receptor (TLR)-dependent signalling and the proinflammatory response. The aortic adventitia of 11 CVD patients with RA (RA+CVD) and 11 CVD patients without RA (CVD) were collected during coronary artery bypass graft surgery. Bacteria were detected in four samples from CVD patients and three samples from RA+CVD patients and identified by 16S rRNA gene sequencing. Methylobacterium oryzae was identified in all three RA+CVD samples, representing 44.1% of the bacterial flora. The effect of M. oryzae on TLR-dependent signalling was determined by transfection of HEK-293 cells. Although mild TLR2 signalling was observed, TLR4 was insensitive to M. oryzae. Human primary macrophages were infected with M. oryzae, and a TLDA qPCR array targeting 90 genes involved in inflammation and immune regulation was used to profile the transcriptional response. A significant proinflammatory response was observed, with many of the up-regulated genes encoding proinflammatory cytokines (IL-1α, IL-1β, IL-6, TNF-α) and chemokines (CCR7, IL-8). The aortic adventitia of CVD patients contains a wide range of bacterial species, and the bacterial flora is significantly less diverse in RA+CVD than CVD patients. M. oryzae may stimulate an proinflammatory response that may aggravate and perpetuate the pathological processes underlying atherosclerosis in RA patients.
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Affiliation(s)
- Samuel A Curran
- Dental School, University of Glasgow, Glasgow, United Kingdom
| | - Ivana Hollan
- Hospital for Rheumatic Diseases, Lillehammer, Norway, and Feiring Heart Clinic, Feiring, Norway
| | - Clett Erridge
- Department of Cardiovascular Sciences, University of Leicester, Glenfield General Hospital, Leicester, United Kingdom
| | - David F Lappin
- Dental School, University of Glasgow, Glasgow, United Kingdom
| | - Colin A Murray
- Dental School, University of Glasgow, Glasgow, United Kingdom
| | - Gunnar Sturfelt
- Department of Rheumatology, Lund University Hospital, Lund, Sweden
| | | | - Oystein T Førre
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Sven M Almdahl
- Department of Surgery, University Hospital of North Norway, Tromsø, Norway
| | - Magne K Fagerhol
- Department of Immunology and Transfusion Medicine, Ullevaal University Hospital, Oslo, Norway
| | - Carl S Goodyear
- Institute of Infection Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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39
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Kim K, Kwak C, Lee Y, Sa T. Effect of co-inoculation of Brevibacterium iodinum RS16 and Methylobacterium oryzae CBMB20 on the early growth of crop plants in Saemangeum reclaimed soil. ACTA ACUST UNITED AC 2014. [DOI: 10.7745/kjssf.2014.47.1.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere. Antonie van Leeuwenhoek 2013; 105:367-76. [PMID: 24297603 DOI: 10.1007/s10482-013-0085-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 11/22/2013] [Indexed: 10/26/2022]
Abstract
A pink-pigmented, Gram negative, aerobic, facultatively methylotrophic bacterium, strain BL44(T), was isolated from bamboo leaves and identified as a member of the genus Methylobacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed similarity values of 98.7-97.0 % with closely related type strains and showed highest similarity to Methylobacterium zatmanii DSM 5688(T) (98.7 %) and Methylobacterium thiocyanatum DSM 11490(T) (98.7 %). Methylotrophic metabolism in this strain was confirmed by PCR amplification and sequencing of the mxaF gene coding for the α-subunit of methanol dehydrogenase. Strain BL44(T) produced three known quorum sensing signal molecules with similar retention time to C8, C10 and C12-HSLs when characterized by GC-MS. The fatty acid profiles contained major amounts of C18:1 ω7c, iso-3OH C17:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), which supported the grouping of the isolate in the genus Methylobacterium. The DNA G+C content was 66.9 mol%. DNA relatedness of the strain BL44(T) to its most closely related strains ranged from 12-43.3 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain BL44(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium pseudosasae sp. nov. is proposed (type strain BL44(T) = NBRC 105205(T) = ICMP 17622(T)).
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41
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Duganella
sacchari sp. nov. and
Duganella
radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane. Int J Syst Evol Microbiol 2013; 63:1126-1131. [DOI: 10.1099/ijs.0.040584-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains, designated Sac-22T and Sac-41T, were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class
Betaproteobacteria
, their closest relatives being
Pseudoduganella violaceinigra
and
Duganella zoogloeoides
with 16S rRNA gene sequence pairwise similarities of 96.4–97.2 % to the two novel strains. Strains Sac-22T and Sac-41T shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22T and 54.9 mol% for strain Sac-41T. Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22T and Sac-41T from all recognized species of the genus
Duganella
, it was concluded that strains represent two novel species in the genus
Duganella
for which the names
Duganella
sacchari sp. nov. (type strain Sac-22T = KCTC 22381T = NCIMB 14475T) and
Duganella
radicis sp. nov. (type strain Sac-41T = KCTC 22382T = NCIMB 14476T) are proposed.
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42
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Wellner S, Lodders N, Glaeser SP, Kämpfer P. Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces. Int J Syst Evol Microbiol 2013; 63:2690-2699. [PMID: 23291886 DOI: 10.1099/ijs.0.047787-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium. The closest relatives of strains C34(T) and T5 were Methylobacterium gnaphalii 23e(T) (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833(T) (97.0 and 97.2 %, respectively). Strain TA73(T) showed the highest sequence similarities to Methylobacterium marchantiae JT1(T) and Methylobacterium bullatum F3.2(T) (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27(T) and Methylobacterium brachiatum DSM 19569(T) (both 97.8 %), Methylobacterium cerastii C15(T) and Methylobacterium radiotolerans JCM 2831(T) (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73(T) and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34(T) and T5. Physiological and biochemical analysis, including DNA-DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA-DNA hybridization studies also showed high similarities between strains C34(T) and T5 (59.6-100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium trifolii sp. nov. (type strain TA73(T) = LMG 25778(T) = CCM 7786(T)) and Methylobacterium thuringiense sp. nov. (type strain C34(T) = LMG 25777(T) = CCM 7787(T)) are proposed.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - N Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Yano T, Kubota H, Hanai J, Hitomi J, Tokuda H. Stress tolerance of Methylobacterium biofilms in bathrooms. Microbes Environ 2012. [PMID: 23207727 PMCID: PMC4070686 DOI: 10.1264/jsme2.me12146] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A comprehensive survey of microbial flora within pink biofilms in bathrooms was performed. Pink biofilms develop relatively rapidly in bathrooms, can be difficult to remove, and are quick to recur. Bacterium-sized cells were found to be predominant in 42 pink biofilms in Japan using a scanning electron microscope. Methylobacterium strains were detected from all samples in bathrooms by an isolation method. To explain this predominance, 14 biofilm samples were analyzed by fluorescence in situ hybridization. Methylobacterium was indicated to be the major genus in all biofilms. The isolated Methylobacterium survived after contact with 1.0% cleaning agents, including benzalkonium chloride for 24 h. Their tolerance did not differ under biofilm-like conditions on fiber reinforced plastics (FRP), a general material of bath tubs, floors, and walls. Also, the strains exhibited higher tolerance to desiccation than other isolated species on FRP. Some Methylobacterium survived and exhibited potential to grow after four weeks of desiccation without any nutrients. These specific characteristics could be a cause of their predominance in bathrooms, an environment with rapid flowing water, drying, low nutrients, and occasional exposure to cleaning agents.
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Affiliation(s)
- Takehisa Yano
- R&D-Safety Science Research, Kao Corporation, Tochigi, Japan
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44
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Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee KC, Lee JS. Methylobacillus rhizosphaerae sp. nov., a novel plant-associated methylotrophic bacterium isolated from rhizosphere of red pepper. Antonie van Leeuwenhoek 2012; 103:475-84. [DOI: 10.1007/s10482-012-9828-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 10/06/2012] [Indexed: 11/25/2022]
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45
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Kim KY, Hwang SW, Saravanan VS, Sa TM. Effect of Brevibacterium iodinum RS16 and Methylobacterium oryzae CBMB20 Inoculation on Seed Germination and Early Growth of Maize and Sorghum-sudangrass hybrid Seedling under Different Salinity Levels. ACTA ACUST UNITED AC 2012. [DOI: 10.7745/kjssf.2012.45.1.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Dourado MN, Andreote FD, Dini-Andreote F, Conti R, Araújo JM, Araújo WL. Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association. Genet Mol Biol 2012; 35:142-8. [PMID: 22481887 PMCID: PMC3313503 DOI: 10.1590/s1415-47572012005000017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 12/09/2011] [Indexed: 11/21/2022] Open
Abstract
The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.
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Affiliation(s)
- Manuella Nóbrega Dourado
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
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47
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Wellner S, Lodders N, Kämpfer P. Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. Syst Appl Microbiol 2011; 34:621-30. [PMID: 22000032 DOI: 10.1016/j.syapm.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/17/2011] [Accepted: 08/23/2011] [Indexed: 11/26/2022]
Abstract
On the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (DGGE analysis) methods, we investigated the influence of the host plant species Trifolium repens and Cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on Methylobacterium species. Methylobacterium abundance was significantly higher on leaves of T. repens (mean value 2.0×10(7) CFU PPFM per g leaf) than on leaves of C. holosteoides (mean value 2.0×10(6) CFU per g leaf). Leaves from the sampling site Schorfheide-Chorin showed slightly lower Methylobacterium numbers than leaves of the other sampling sites. Land-use and sampling period had no consistent influence on Methylobacterium community size. Methylobacterium community composition was very similar over both sampling periods, all three sampling sites, all land-use types and both plant species. Moreover, no relationship between geographic and genetic distance was observed. Community composition of selected Proteobacteria was influenced by plant species, geographic location and land-use. Often, differences in community composition could be observed between meadows, mown pastures and pastures but not between different kinds of meadows (cutted once versus three times) and mown pastures (fertilized versus non-fertilized). The results also indicate, that whether there are differences between land-use types or not strongly depends on the investigated host plant species and ecosystem. Besides Methylobacterium, representatives of Methylophilus were detected. The results indicate that Methylobacterium species are generally abundant and stable members of the phyllosphere community whereas other genera occur more occasionally, and that Methylobacterium clearly dominates the methylotrophic phyllosphere community.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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48
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Knief C, Dengler V, Bodelier PLE, Vorholt JA. Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp. nov. Antonie van Leeuwenhoek 2011; 101:169-83. [DOI: 10.1007/s10482-011-9650-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 09/24/2011] [Indexed: 11/27/2022]
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49
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Fedorov DN, Doronina NV, Trotsenko YA. Phytosymbiosis of aerobic methylobacteria: New facts and views. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711040047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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50
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Lee MK, Chauhan PS, Yim WJ, Lee GJ, Kim YS, Park KW, Sa TM. Foliar Colonization and Growth Promotion of Red Pepper (Capsicum annuum L.) by Methylobacterium oryzae CBMB20. ACTA ACUST UNITED AC 2011. [DOI: 10.3839/jabc.2011.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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