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

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

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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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Correspondence to Jose Antonio Pascual.

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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 (2020). https://doi.org/10.1007/s00284-020-02101-4

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