Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide

Hairong He; Jiarui Huang; Zhenzhu Zhao; Pengqiang Du; Jiansong Li; Jile Xin; Huifang Xu; Weisheng Feng; Xiaoke Zheng

doi:10.1016/j.heliyon.2023.e19543

Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide

Heliyon. 2023 Aug 28;9(9):e19543. doi: 10.1016/j.heliyon.2023.e19543. eCollection 2023 Sep.

Authors

Hairong He¹, Jiarui Huang¹, Zhenzhu Zhao¹, Pengqiang Du², Jiansong Li³, Jile Xin¹, Huifang Xu¹, Weisheng Feng¹, Xiaoke Zheng¹

Affiliations

¹ College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China.
² College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, China.
³ Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou, 318000, China.

Abstract

Rehmannia glutinosa, a valuable medicinal plant, is threatened by ring rot, a condition that greatly affects its yield and quality. Interactions between plant and the rhizosphere soil microbiome in the context of pathogen invasion are generally more specific, with recruitment of specialized microbes potentially antagonistic to a certain pathogen. Isolation of microorganisms from rhizosphere soil of healthy and ring rot-infected R. glutinosa was carried out to screen antifungal microbes. A strain designated RerS4 isolated from ring rot-infected R. glutinosa rhizosphere soil with strong antifungal activities was selected for further study. RerS4 was taxonomically characterized as the genus Streptomyces according to its morphology and 16S rRNA sequences that were most closely related to Streptomyces racemochromogenes NRRL B-5430^T (99.72%) and Streptomyces polychromogenes NBRC 13072^T (99.72%). A new lipopeptide isolated from RerS4 showed restrained proliferation, but was devoid of significant antibacterial and antioxidant activity with minimum inhibitory concentration (MIC) values of 20.3 ± 2.5 and 70.8 ± 3.7 μg/mL and half-maximal inhibitory concentration (IC₅₀) values of 23.3 ± 0.8 and 58.8 ± 2.9 μg/mL, respectively. In addition, we report the complete genome sequence of Streptomyces sp. RerS4, which consists of a 7,301,482 bp linear chromosome and a 242,139 bp plasmid. Genome analysis revealed that Streptomyces sp. RerS4 contained 25 biosynthetic gene clusters (BGCs) for secondary metabolites, among which 68% had low similarities with known BGCs, leading us to believe that Streptomyces sp. RerS4 could produce valuable bioactive compounds.

Keywords: Genome sequence analysis; Lipopeptide; Secondary metabolites; Streptomyces.