Comparative genomics and proposal of Streptomyces radicis sp. nov., an endophytic actinomycete from roots of plants in Thailand

Nattakorn Kuncharoen; Masahiro Yuki; Takuji Kudo; Moriya Okuma; Auttaporn Booncharoen; Wuttichai Mhuantong; Somboon Tanasupawat

doi:10.1016/j.micres.2021.126889

Comparative genomics and proposal of Streptomyces radicis sp. nov., an endophytic actinomycete from roots of plants in Thailand

Microbiol Res. 2022 Jan:254:126889. doi: 10.1016/j.micres.2021.126889. Epub 2021 Oct 13.

Authors

Nattakorn Kuncharoen¹, Masahiro Yuki², Takuji Kudo², Moriya Okuma², Auttaporn Booncharoen³, Wuttichai Mhuantong⁴, Somboon Tanasupawat⁵

Affiliations

¹ Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand.
² Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
³ Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand.
⁴ Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand.
⁵ Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand. Electronic address: somboon.T@chula.ac.th.

PMID: 34689101
DOI: 10.1016/j.micres.2021.126889

Abstract

Strains DS1-2^T and AZ1-7, which were isolated from roots of plants, were taxonomically characterized based on polyphasic taxonomic and taxogenomic approaches. Both strains were Gram-stain-positive and filamentous bacteria which contained LL-diaminopimelic acid in cell-wall peptidoglycan and glucose and ribose in whole-cell hydrolysates. MK-9(H₆), MK-10(H₆), MK-9(H₈), MK-10(H₈) and MK-10(H₄) were major menaquinones; iso-C_16:0 and iso-C_16:1G were predominant cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannoside presented as major phospholipids; and the DNA G+C contents of 73.2 mol%. Strains DS1-2^T and AZ1-7 showed 97.6-98.0 % 16S rRNA gene sequence similarity, 81.0-82.0 % ANIb, 84.8-85.3 % ANIm and 22.0-23.1 % digital DDH to their related type strains: S. specialis GW41-1564^T and S. hoynatensis S1412^T. Comparative genomics results of these strains and their related type strains also revealed the differences and distributions of key genes associated with stress responses, environmental variables, plant interactions and bioactive metabolites. Based on the phenotypic, chemotaxonomic and genomic data, strains DS1-2^T and AZ1-7 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces radicis sp. nov. is proposed. The type strain is DS1-2^T (=JCM 32152^T =KCTC 39738^T =TISTR 2403^T).

Keywords: Comparative genomics; Draft genomes; Endophytic actinomycetes; Plants roots; Streptomyces.

Publication types

Review

MeSH terms

Endophytes* / classification
Endophytes* / genetics
Genome, Bacterial* / genetics
Genomics
Plant Roots* / microbiology
Plants* / microbiology
RNA, Ribosomal, 16S / genetics
Streptomyces* / classification
Streptomyces* / genetics
Thailand

Substances

RNA, Ribosomal, 16S