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Saccharopolyspora oryzae sp. nov., isolated from rhizosphere soil of the wild rice species Oryza rufipogon

The Journal of Antibiotics volume 76, pages 658–664 (2023)Cite this article

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Abstract

A novel actinobacterium, designated as strain WRP15-2T, was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98.7%). However, the digital DNA-DNA hybridization and average nucleotide identity values among these strains confirmed that the microorganism represented a novel member of the genus Saccharopolyspora. Chemotaxonomic data revealed that strain WRP15-2T possessed MK-9(H4) as the predominant menaquinone. It contained meso-diaminopimelic acid as the diagnostic diaminopimelic acid and arabinose, galactose, and ribose as predominant whole-cell sugars. The detected phospholipids were dominated by phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxy-phosphatidylmethylethanolamine, and phosphatidylcholine. The predominant cellular fatty acids were iso-C16:0, C16:0, and iso-C15:0. The G + C content of the genomic DNA was 69.5%. Based on these genotypic and phenotypic data, it is supported that strain WRP15-2T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora oryzae sp. nov. is proposed. The type strain is WRP15-2T ( = TBRC 15728T = NBRC 115560T).

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Acknowledgements

This research is funded by Kasetsart University through the Graduate School Fellowship Program to Sirikarn Kammanee. We are grateful to Ms Duangkamon Boonchuay for sample collection. We would also like to thank UGSAS-GU via the “Microbiology Laboratory Station for IC-GU12” at Kasetsart University.

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Authors and Affiliations

  1. Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand

    Sirikarn Kammanee, Supattra Muangham, Waranya Butdee, Chollachai Klaysubun & Kannika Duangmal

  2. National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathumthani, 12120, Thailand

    Supattra Muangham

  3. Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan

    Yasuhiro Igarashi

  4. Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand

    Kannika Duangmal

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Correspondence to Kannika Duangmal.

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Kammanee, S., Muangham, S., Butdee, W. et al. Saccharopolyspora oryzae sp. nov., isolated from rhizosphere soil of the wild rice species Oryza rufipogon. J Antibiot 76, 658–664 (2023). https://doi.org/10.1038/s41429-023-00647-6

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