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Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants

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Abstract

In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T =  KACC 17594T).

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Acknowledgements

This work was supported by the Temasek Foundation and the Singapore Economy Development Board (EDB). The genome sequencing was conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. We also acknowledge assistance of Nikos C. Kyrpides, Tanja Woyke, Nicole Shapiro, and the other members of the JGI microbial genome sequencing team.

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Authors and Affiliations

  1. Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore

    Munusamy Madhaiyan, Tan Hian Hwee Alex & Lianghui Ji

  2. Department of Microbiology, Indira Gandhi College of Arts and Science, Kathirkamam, Pondicherry, 605009, India

    Venkatakrishnan Sivaraj Saravanan

  3. Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA

    Joseph S. Wirth

  4. Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea

    Soo-Jin Kim, Hang-Yeon Weon & Soon-Wo Kwon

  5. Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA, 30602-2605, USA

    William B. Whitman

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  1. Munusamy Madhaiyan
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Contributions

MM and THHA isolated the strains, cultivated, performed electron microscopic analysis and deposited the strains, MM, JSW and VSS, constructed the 16S phylogeny and wrote the manuscript, analysed the data and prepared tables and figures, JSW MM and WBW constructed the genome based phylogeny and genome sequencing, MM, SJK, HYW and SWK have conducted the biochemical analysis, polar lipids and polyamine determination, LJ supervised the study. All authors read and approved the final version of the manuscript.

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Correspondence to Munusamy Madhaiyan or Lianghui Ji.

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The 16S rRNA gene sequences of the strains JS21-1T and S6-262T were deposited in GenBank/EMBL/DDBJ under the accession numbers are KX893410 and JQ660211, respectively. The draft genome sequences of the strains JS21-1T and S6-262T are available at the following accessions FNZZ00000000.1 and FOCF00000000.1, respectively.

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Madhaiyan, M., Saravanan, V.S., Wirth, J.S. et al. Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie van Leeuwenhoek 113, 1617–1632 (2020). https://doi.org/10.1007/s10482-020-01468-5

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