Abstract
Strain SB0023/3 T, isolated from spores of the arbuscular mycorrhizal fungus Glomus iranicum var. tenuihypharum, was analysed to determine whether it represents a new species. It was studied for its applicability in the field of agriculture to reduce the input of nitrogen fertilizers. Comparative analysis of the 16S rRNA gene sequence shows the strain to be affiliated to the genus Methylobacterium, the closest similarities (98.7%) being shared with Methylobacterium dankookense. Further phylogenomic analysis through Up-to-date Bacterial Core Gene (UBCG) confirmed Methylobacterium dankookense as its closest relative. Average Nucleotide Identity (ANI) and in silico DNA–DNA hybridization (DDH) were lower than 92% and 44%, respectively, of the values shown by its phylogenetic relatives. Its genome had an approximate length of 6.05 Mb and the G + C content of the genome was 70.1 mol%. The main cellular fatty acid was Summed Feature 8 (C18:1ω7c and/or C18:1ω6c). It is a Gram-staining-negative, pink-pigmented, strictly aerobic and facultative methylotroph; it grows at 28 ºC and can grow at up to 3% salinity in the presence of sodium chloride. All the data collected support the naming of a novel species to accommodate the strain SB0023/3 T, for which the name Methylobacterium symbioticum sp. nov. is proposed. The type strain is SB0023/3 T (=CECT 9862 T =PYCC 8351 T).
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Abbreviations
- AMF:
-
Arbuscular mycorrhizal fungi
- ANI:
-
Average Nucleotide Identity
- BLAST:
-
Basic Local Alignment Search Tool
- UBCG:
-
Up-to-date Bacterial Core Gene
- CECT:
-
Colección Española de Cultivos Tipo
- DDH:
-
DNA–DNA hybridization
- SCSIE:
-
Servicio Central de Soporte a la Investigación Experimental
- GGDC:
-
Genome-to-Genome Distance Calculator
- GSI:
-
Gene Support Index
- NCBI:
-
National Center for Biotechnology Information
- PYCC:
-
Portuguese Yeast Culture Collection
- RAST:
-
Rapid Annotation using Subsystem Technology
- SPAD:
-
Soil–Plant Analyses Development
References
Smith SE, Read DJ (2008) Mycorrhizal symbiosis. Academic Press, Cambdrige
Fernández F, Juarez J, Nicolás E et al (2017) Application of Arbuscular Mycorrhizae Glomus iranicum var. tenuihypharum var. nova in Intensive Agriculture: a study case. J Agric Sci Technol B 7(221):247. https://doi.org/10.17265/2161-6264/2017.04.001
Kapoor R, Sharma D, Bhatnagar AK (2008) Arbuscular mycorrhizae in micropropagation systems and their potential applications. Sci Hortic (Amsterdam) 116:227–239
Bonfante P, Anca I-A (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 63:363–383. https://doi.org/10.1146/annurev.micro.091208.073504
Barea JM, Tobar RM, Azcón-Aguilar C (1996) Effect of a genetically modified Rhizobium meliloti inoculant on the development of arbuscular mycorrhizas, root morphology, nutrient uptake and biomass accumulation in Medicago sativa. New Phytol 134:361–369. https://doi.org/10.1111/j.1469-8137.1996.tb04641.x
Wamberg C, Christensen S, Jakobsen I et al (2003) The mycorrhizal fungus (Glomus intraradices) affects microbial activity in the rhizosphere of pea plants (Pisum sativum). Soil Biol Biochem 35:1349–1357. https://doi.org/10.1016/S0038-0717(03)00214-1
Mayo K, Davis RE, Motta J (2007) Stimulation of germination of spores of Glomus versiforme by spore-associated bacteria. Mycologia 78:426. https://doi.org/10.2307/3793046
Johansson JF, Paul LR, Finlay RD (2004) Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiol Ecol 48:1–13
Madhaiyan M, Poonguzhali S, Sa T (2007) Characterization of 1-aminocyclopropane-1-carboxylate (ACC) deaminase containing Methylobacterium oryzae and interactions with auxins and ACC regulation of ethylene in canola (Brassica campestris). Planta 226:867–876. https://doi.org/10.1007/s00425-007-0532-0
Green PN, Ardley JK (2018) 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 68:2727–2748. https://doi.org/10.1099/ijsem.0.002856
Patt TE, Cole GC, Hanson RS (1976) Methylobacterium, a New genus of facultatively Methylotrophic Bacteria. Int J Syst Bacteriol 26:226–229. https://doi.org/10.1099/00207713-26-2-226
Van Dien SJ, Okubo Y, Hough MT et al (2003) Reconstruction of C3 and C4 metabolism in Methylobacterium extorquens AM1 using transposon mutagenesis. Microbiology 149:601–609. https://doi.org/10.1099/mic.0.25955-0
Toyama H, Anthony C, Lidstrom ME (1998) Construction of insertion and deletion mxa mutants of Methylobacterium extorquens AM1 by electroporation. FEMS Microbiol Lett 166:1–7. https://doi.org/10.1016/S0378-1097(98)00282-1
Wellner S, Lodders N, Kampfer P (2012) Methylobacterium cerastii sp. nov., isolated from the leaf surface of Cerastium holosteoides. Int J Syst Evol Microbiol 62:917–924. https://doi.org/10.1099/ijs.0.030767-0
Omer ZS, Tombolini R, Gerhardson B (2004) Plant colonization by pink-pigmented facultative methylotrophic bacteria (PPFMs). FEMS Microbiol Ecol 47:319–326. https://doi.org/10.1016/S0168-6496(04)00003-0
Abanda-Nkpwatt D, Musch M, Tschiersch J et al (2006) Molecular interaction between Methylobacterium extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site. J Exp Bot 57:4025–4032. https://doi.org/10.1093/jxb/erl173
Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA (2014) Phosphate-solubilizing activity of aerobic methylobacteria. Microbiology 82:864–867. https://doi.org/10.1134/s0026261714010020
Ryan RP, Germaine K, Franks A et al (2008) Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 278:1–9
Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84:11–18
Rodríguez H, Fraga R, Gonzalez T, Bashan Y (2006) Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil 287:15–21
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Parks DH, Imelfort M, Skennerton CT et al (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(1043):1055
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75
Yoon S-H, Ha S-M, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Altschul SF, Madden TL, Schäffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Jukes TH, Cantor C (2013) Evolution of protein molecules. Mammalian protein metabolism. Elsevier, Amsterdam, pp 21–132
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Na S-I, Kim YO, Yoon S-H et al (2018) UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285. https://doi.org/10.1007/s12275-018-8014-6
Rodriguez LM, Konstantinidis KT (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peerj Preprints. https://doi.org/10.7287/peerj.preprints.1900v1
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086
Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316–324
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681
Daniel RM, Curran MP (1981) A method for the determination of nitrate reductase. J Biochem Biophys Methods 4:131–132. https://doi.org/10.1016/0165-022X(81)90026-9
García-Delgado M, Rodríguez-Cruz MS, Lorenzo LF et al (2007) Seasonal and time variability of heavy metal content and of its chemical forms in sewage sludges from different wastewater treatment plants. Sci Total Environ 382:82–92. https://doi.org/10.1016/j.scitotenv.2007.04.009
Lee SW, Oh HW, Lee KH, Ahn TY (2010) Methylobacterium dankookense sp. nov., isolated from drinking water. J Microbiol 47:716–720. https://doi.org/10.1007/s12275-009-0126-6
Chun J, Oren A, Ventosa A et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Ciufo S, Kannan S, Sharma S et al (2018) Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 68:2386–2392. https://doi.org/10.1099/ijsem.0.002809
Goris J, Konstantinidis KT, Klappenbach JA et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Dourado MN, Bogas AC, Pomini AM et al (2013) Methylobacterium-plant interaction genes regulated by plant exudate and quorum sensing molecules. Braz J Microbiol 44:1331–1339
Schauer S, Kampfer P, Wellner S et al (2011) Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort. Int J Syst Evol Microbiol 61:870–876. https://doi.org/10.1099/ijs.0.021915-0
Schrader LE, Hageman RH (2008) Regulation of nitrate reductase activity in corn (Zea mays L.) seedlings by endogenous metabolites. PLANT Physiol 42:1750–1756. https://doi.org/10.1104/pp.42.12.1750
Hoffman BM, Lukoyanov D, Yang Z-Y et al (2014) Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 114:4041–4062. https://doi.org/10.1021/cr400641x
Kwak MJ, Jeong H, Madhaiyan M et al (2014) Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS ONE 9:e106704. https://doi.org/10.1371/journal.pone.0106704
Camilli A, Bassler BL (2006) Bacterial small-molecule signaling pathways. Science 311:1113–1116
Acknowledgments
The authors from CEBAS-CSIC would like to thank the Fundación Seneca of the Region of Murcia for its financial support within the Research Groups of 468 Excellence Programme of the Region of Murcia (Grant No. 19896/GERM/15). This research was partially funded by the Spanish funded body CDTI (Grant No. IDI 20170147). We are grateful to Dr Aharon Oren (The Hebrew University of Jerusalem, Israel) for his help with the specific nomenclature and etymology. We also thank Philip and Alvaro Thomas for checking the English.
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Conceived and designed the experiments: JM, FF and JAP. Isolation and morphological and phenotypical characterization: FC, AB, RT and FF. Molecular characterization and genomic comparisons: JAP, MR, JM, TL, RA and DRA. In Vitro and field trials: AB, FF and RL. JAP wrote the draft of the manuscript; and JM, TL, DRA and FF revised and implemented the manuscript. All authors read and approved the final manuscript.
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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and whole genome sequences of the type strain of Methylobacterium symbioticum are MN154398 and GCA_902141845, respectively.
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Pascual, J.A., Ros, M., Martínez, J. et al. Methylobacterium symbioticum sp. nov., a new species isolated from spores of Glomus iranicum var. tenuihypharum. Curr Microbiol 77, 2031–2041 (2020). https://doi.org/10.1007/s00284-020-02101-4
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DOI: https://doi.org/10.1007/s00284-020-02101-4