Skip to main content
Log in

Methylobacterium symbioticum sp. nov., a new species isolated from spores of Glomus iranicum var. tenuihypharum

  • Published:
Current Microbiology Aims and scope Submit manuscript

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).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

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

  1. Smith SE, Read DJ (2008) Mycorrhizal symbiosis. Academic Press, Cambdrige

    Google Scholar 

  2. 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

    Article  CAS  Google Scholar 

  3. Kapoor R, Sharma D, Bhatnagar AK (2008) Arbuscular mycorrhizae in micropropagation systems and their potential applications. Sci Hortic (Amsterdam) 116:227–239

    Article  Google Scholar 

  4. 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

    Article  PubMed  CAS  Google Scholar 

  5. 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

    Article  Google Scholar 

  6. 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

    Article  CAS  Google Scholar 

  7. 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

    Article  Google Scholar 

  8. Johansson JF, Paul LR, Finlay RD (2004) Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiol Ecol 48:1–13

    Article  CAS  PubMed  Google Scholar 

  9. 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

    Article  PubMed  CAS  Google Scholar 

  10. 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

    Article  PubMed  CAS  Google Scholar 

  11. 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

    Article  CAS  Google Scholar 

  12. 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

    Article  PubMed  CAS  Google Scholar 

  13. 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

    Article  PubMed  CAS  Google Scholar 

  14. 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

    Article  PubMed  CAS  Google Scholar 

  15. 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

    Article  PubMed  CAS  Google Scholar 

  16. 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

    Article  PubMed  CAS  Google Scholar 

  17. 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

    Article  Google Scholar 

  18. Ryan RP, Germaine K, Franks A et al (2008) Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 278:1–9

    Article  CAS  PubMed  Google Scholar 

  19. 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

    Article  CAS  PubMed  Google Scholar 

  20. 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

    Article  CAS  Google Scholar 

  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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. 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

    Google Scholar 

  23. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153

    Article  PubMed  CAS  Google Scholar 

  24. 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

    Article  CAS  Google Scholar 

  25. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Jukes TH, Cantor C (2013) Evolution of protein molecules. Mammalian protein metabolism. Elsevier, Amsterdam, pp 21–132

    Google Scholar 

  28. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. 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

    Article  PubMed  CAS  Google Scholar 

  30. 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

    Article  Google Scholar 

  31. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. 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

    Article  PubMed  Google Scholar 

  33. 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

    Article  PubMed  PubMed Central  Google Scholar 

  34. 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

    Article  PubMed  CAS  Google Scholar 

  35. 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

    Article  PubMed  CAS  Google Scholar 

  36. 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

    Article  PubMed  CAS  Google Scholar 

  37. 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

    Article  PubMed  CAS  Google Scholar 

  38. 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

    Article  CAS  Google Scholar 

  39. 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

    Article  PubMed  CAS  Google Scholar 

  40. 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

    Article  PubMed  PubMed Central  Google Scholar 

  41. 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

    Article  PubMed  CAS  Google Scholar 

  42. 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

    Article  PubMed  Google Scholar 

  43. 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

    Article  PubMed  CAS  Google Scholar 

  44. 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

    Article  Google Scholar 

  45. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Camilli A, Bassler BL (2006) Bacterial small-molecule signaling pathways. Science 311:1113–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Contributions

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.

Corresponding author

Correspondence to Jose Antonio Pascual.

Ethics declarations

Conflict of interest

The authors declare that they do not have conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-020-02101-4

Navigation