1
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Jahan R, McDonald IR. Diversity of Methylobacterium species associated with New Zealand native plants. FEMS Microbiol Lett 2023; 370:fnad124. [PMID: 37985695 PMCID: PMC10699869 DOI: 10.1093/femsle/fnad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
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Affiliation(s)
- Rowshan Jahan
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
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2
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Vega-Celedón P, Bravo G, Velásquez A, Cid FP, Valenzuela M, Ramírez I, Vasconez IN, Álvarez I, Jorquera MA, Seeger M. Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants. Microorganisms 2021; 9:microorganisms9030538. [PMID: 33807836 PMCID: PMC7998784 DOI: 10.3390/microorganisms9030538] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a & Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.
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Affiliation(s)
- Paulina Vega-Celedón
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
- Correspondence: (P.V.-C.); (M.S.); Tel.: +56-322654685 (P.V.-C.)
| | - Guillermo Bravo
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Alexis Velásquez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Fernanda P. Cid
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile; (F.P.C.); (M.A.J.)
- Center of Plant-Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile
| | - Miryam Valenzuela
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Ingrid Ramírez
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Ingrid-Nicole Vasconez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Inaudis Álvarez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
| | - Milko A. Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile; (F.P.C.); (M.A.J.)
- Center of Plant-Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 1145, Temuco 4811230, Chile
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.B.); (A.V.); (M.V.); (I.-N.V.); (I.Á.)
- Center of Biotechnology “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, General Bari 699, Valparaíso 2390136, Chile;
- Correspondence: (P.V.-C.); (M.S.); Tel.: +56-322654685 (P.V.-C.)
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3
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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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4
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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: 97] [Impact Index Per Article: 16.2] [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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5
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Lee Y, Jeon CO. Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system. Int J Syst Evol Microbiol 2017; 68:299-304. [PMID: 29160200 DOI: 10.1099/ijsem.0.002500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A reddish pink-pigmented, Gram-stain-negative, aerobic and methylotrophic bacterial strain, designated strain IER25-16T, was isolated from a laboratory air conditioning system in the Republic of Korea. Cells were motile rods showing catalase- and oxidase-positive reactions. Strain IER25-16T grew at 10-40 °C (optimum, 30 °C), at pH 4.0-7.0 (optimum, pH 5.0-7.0) and in the presence of 0-1.0 % (w/v) NaCl (optimum, 0 %). The major respiratory quinone was ubiquinone-10 and ubiquinone-9 was also detected as the minor respiratory quinone. Summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) was detected as the predominant fatty acids. The genomic DNA G+C content of strain IER25-16T was 70.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain IER25-16T belonged to the genus Methylobacterium of the class Alphaproteobacteria. Strain IER25-16T was most closely related to Methylobacterium platani PMB02T (97.9 %), Methylobacterium aquaticum GR16T (97.9 %) and Methylobacterium tarhaniae N4211T (97.5 %). The average nucleotide identity and in silico DNA-DNA hybridization values between strain IER25-16T and M. platani, M. aquaticum and M. tarhaniae were 88.3, 88.8 and 89.6 % and 36.2, 37.3 and 39.3 %, respectively. The phenotypic and chemotaxonomic features and the phylogenetic inference clearly suggested that strain IER25-16T represents a novel species of the genus Methylobacterium, for which the name Methylobacteriumfrigidaeris sp. nov. is proposed. The type strain is strain IER25-16T (=KACC 19280T=JCM 32048T).
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Affiliation(s)
- Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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6
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Pérez-López E, Olivier CY, Luna-Rodríguez M, Dumonceaux TJ. Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences. Int J Syst Evol Microbiol 2016; 66:5600-5613. [PMID: 27667728 PMCID: PMC5244502 DOI: 10.1099/ijsem.0.001501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas are unculturable, phytopathogenic bacteria that cause economic losses worldwide. As unculturable micro-organisms, phytoplasma taxonomy has been based on the use of the 16S rRNA-encoding gene to establish 16Sr groups and subgroups based on the restriction fragment length polymorphism (RFLP) pattern resulting from the digestion of amplicon (in vitro) or sequence (in silico) with seventeen restriction enzymes. Problems such as heterogeneity of the ribosomal operon and the inability to differentiate closely related phytoplasma strains has motivated the search for additional markers capable of providing finer differentiation of phytoplasma strains. In this study we developed and validated a scheme to classify phytoplasmas based on the use of cpn60 universal target (cpn60 UT) sequences. Ninety-six cpn60 UT sequences from strains belonging to 19 16Sr subgroups were subjected to in silico RFLP using pDRAW32 software, resulting in 25 distinctive RFLP profiles. Based on these results we delineated cpn60 UT groups and subgroups, and established a threshold similarity coefficient for groups and subgroups classifying all the strains analysed in this study. The nucleotide identity among the reference strains, the correspondence between in vitro and in silico RFLP, and the phylogenetic relationships of phytoplasma strains based on cpn60 UT sequences are also discussed.
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Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas Xalapa, Veracruz, México
| | - Chrystel Y. Olivier
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Mauricio Luna-Rodríguez
- Laboratorio de Alta Tecnología de Xalapa - DGI, Universidad Veracruzana, Médicos 5, Unidad del Bosque Xalapa, Veracruz, México
| | - Tim J. Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Correspondence Tim J. Dumonceaux
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7
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Tani A, Sahin N, Fujitani Y, Kato A, Sato K, Kimbara K. Methylobacterium Species Promoting Rice and Barley Growth and Interaction Specificity Revealed with Whole-Cell Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF/MS) Analysis. PLoS One 2015; 10:e0129509. [PMID: 26053875 PMCID: PMC4460032 DOI: 10.1371/journal.pone.0129509] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/08/2015] [Indexed: 11/18/2022] Open
Abstract
Methylobacterium species frequently inhabit plant surfaces and are able to utilize the methanol emitted from plants as carbon and energy sources. As some of the Methylobacterium species are known to promote plant growth, significant attention has been paid to the mechanism of growth promotion and the specificity of plant-microbe interactions. By screening our Methylobacterium isolate collection for the high growth promotion effect in vitro, we selected some candidates for field and pot growth tests for rice and barley, respectively. We found that inoculation resulted in better ripening of rice seeds, and increased the size of barley grains but not the total yield. In addition, using whole-cell matrix-assister laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, we identified and classified Methylobacterium isolates from Methylobacterium-inoculated rice plants. The inoculated species could not be recovered from the rice plants, and in some cases, the Methylobacterium community structure was affected by the inoculation, but not with predomination of the inoculated species. The isolates from non-inoculated barley of various cultivars grown in the same field fell into just two species. These results suggest that there is a strong selection pressure at the species level of Methylobacterium residing on a given plant species, and that selection of appropriate species that can persist on the plant is important to achieve growth promotion.
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Affiliation(s)
- Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- * E-mail:
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Mugla, Turkey
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Akiko Kato
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Kazuhide Kimbara
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
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Kämpfer P, Glaeser SP, Gräber M, Rabenstein A, Kuever J, Busse HJ. Pseudochelatococcus lubricantis gen. nov., sp. nov. and Pseudochelatococcus contaminans sp. nov. from coolant lubricants. Int J Syst Evol Microbiol 2015; 65:147-153. [DOI: 10.1099/ijs.0.067652-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, rod-shaped, non-spore-forming bacteria, isolated from metal working fluids were investigated to determine their taxonomic positions. On the basis of 16S rRNA gene sequence phylogeny, both strains (MPA 1113T and MPA 1105T) formed a distinct cluster with 97.7 % sequence similarity between them, which was in the vicinity of members of the genera
Methylobacterium
,
Camelimonas
,
Chelatococcus
,
Bosea
,
Salinarimonas
and
Microvirga
to which they showed low sequence similarities (below 94 %). The predominant compounds in the polyamine pattern and in the quinone system of the two strains were spermidine and ubiquinone Q-10, respectively. The polar lipid profiles were composed of the major compounds: phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, major or moderate amounts of diphosphatidylglycerol, two unidentified glycolipids and three unidentified aminolipids. Several minor lipids were also detected. The major fatty acids were either C19 : 0 cyclo ω8c or C18 : 1ω7c. The results of fatty acid analysis and physiological and biochemical tests allowed both, the genotypic and phenotypic differentiation of the isolates from each other, while the chemotaxonomic traits allowed them to be differentiated from the most closely related genera. In summary, low 16S rRNA gene sequence similarities and marked differences in polar lipid profiles, as well as in polyamine patterns, is suggestive of a novel genus for which the name Pseudochelatococcus gen. nov. is proposed. MPA 1113T ( = CCM 8528T = LMG 28286T = CIP 110802T) and MPA 1105T ( = CCM 8527T = LMG 28285T) are proposed to be the type strains representing two novel species within the novel genus, Pseudochelatococcus gen. nov., for which the names Pseudochelatococcus lubricantis sp. nov. and Pseudochelatococcus contaminans sp. nov. are suggested, respectively.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Marco Gräber
- Bremen Institute for Materials Testing, Department of Microbiology, Bremen, Germany
| | - Andreas Rabenstein
- Bremen Institute for Materials Testing, Department of Microbiology, Bremen, Germany
| | - Jan Kuever
- Bremen Institute for Materials Testing, Department of Microbiology, Bremen, Germany
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
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9
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Qu Z, Jiang F, Chang X, Qiu X, Ren L, Fang C, Peng F. Psychroglaciecola arctica gen. nov., sp. nov., isolated from Arctic glacial foreland soil. Int J Syst Evol Microbiol 2014; 64:1817-1824. [DOI: 10.1099/ijs.0.060913-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel pink-pigmented, facultatively methylotrophic strain, designated M6-76T, was isolated from glacial foreland soil near Ny-Ålesund, Svalbard Archipelago, Norway. Cells of strain M6-76T were rod-shaped (0.4–0.7×0.8–2.0 µm), Gram-stain-negative, aerobic and motile by a single polar flagellum. Growth occurred at 4–28 °C (optimum 18 °C) and at pH 5–8 (optimum pH 7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M6-76T belonged to the family
Methylobacteriaceae
. The 16S rRNA gene sequence of the novel strain showed 94.6 %, 94.0 % and 93.9 % sequence similarity to those of
Methylobacterium salsuginis
MRT,
Methylobacterium organophilum
ATCC 27886T and
Microvirga subterranea
FaiI4T, respectively. Cells could utilize methanol as the sole source of carbon and energy but not formate. The major respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown polar lipids. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0. The DNA G+C content was 67 mol%. The polyphasic data presented in this study indicated that the isolate should be classified as representing a novel species of a new genus within the family
Methylobacteriaceae
. The name Psychroglaciecola
arctica gen. nov., sp. nov. is therefore proposed for the isolate. The type strain of the type species is M6-76T ( = CCTCC AB 2013033T = KACC 17684T).
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Affiliation(s)
- Zhihao Qu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fan Jiang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xia Qiu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Lvzhi Ren
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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Kolb S, Stacheter A. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front Microbiol 2013; 4:268. [PMID: 24046766 PMCID: PMC3763247 DOI: 10.3389/fmicb.2013.00268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/19/2013] [Indexed: 01/06/2023] Open
Abstract
The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.
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Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
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11
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Tani A, Sahin N. Methylobacterium
haplocladii sp. nov. and
Methylobacterium
brachythecii sp. nov., isolated from bryophytes. Int J Syst Evol Microbiol 2013; 63:3287-3292. [DOI: 10.1099/ijs.0.048215-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pink-pigmented, facultatively methylotrophic bacteria, strains 87eT and 99bT, were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eT and 99bT were found to be related to
Methylobacterium organophilum
ATCC 27886T (97.1 % and 97.7 %, respectively). Strains 87eT and 99bT showed highest 16S rRNA gene similarity to
Methylobacterium gnaphalii
23eT (98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genus
Methylobacterium
with validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7c and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eT and 99bT from their phylogenetically closest relatives. We propose that strains 87eT and 99bT represent novel species within the genus
Methylobacterium
, for which the names
Methylobacterium
haplocladii sp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) and
Methylobacterium
brachythecii sp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.
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Affiliation(s)
- Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, 48170 Kotekli, Mugla, Turkey
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12
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Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin N. Methylobacterium tarhaniae sp. nov., isolated from arid soil. Int J Syst Evol Microbiol 2013; 63:2823-2828. [PMID: 23315404 DOI: 10.1099/ijs.0.049551-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211(T), isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211(T) belonged to the genus Methylobacterium. Strain N4211(T) was most closely related to Methylobacterium aquaticum GR16(T) (98.56 %), Methylobacterium platani PMB02(T) (97.95 %) and Methylobacterium variabile GR3(T) (97.2 %), and the phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C18 : 1 cis11/t9/t6). The DNA G+C content was 67.3 mol%. DNA-DNA relatedness of strain N4211(T) and the most closely related strains M. aquaticum DSM 16371(T) and M. platani KCTC 12901(T) were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA-DNA hybridization data, strain N4211(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium tarhaniae sp. nov. is proposed. The type strain is N4211(T)( = KCTC 23615(T) = DSM 25844(T)).
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Affiliation(s)
- Aysel Veyisoglu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Mustafa Camas
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Demet Tatar
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Kiymet Guven
- Department of Biology, Faculty of Science, Anadolu University, Eskisehir-Turkey
| | - Anil Sazak
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
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13
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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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14
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High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis. PLoS One 2012; 7:e40784. [PMID: 22808262 PMCID: PMC3395638 DOI: 10.1371/journal.pone.0040784] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/13/2012] [Indexed: 11/28/2022] Open
Abstract
Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.
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