Isolated from Populus euphratica rhizosphere soil, and mining their metabolites

Jia-Xin Zhang; Yi-Huang Chen; Xinrong Luo; Li-Li Zhang; Xiao-Xia Luo

doi:10.3389/fmicb.2025.1530786

Isolated from Populus euphratica rhizosphere soil, and mining their metabolites

Front Microbiol. 2025 Feb 19:16:1530786. doi: 10.3389/fmicb.2025.1530786. eCollection 2025.

Authors

Jia-Xin Zhang^#^{1

2}, Yi-Huang Chen^{1

2}, Xinrong Luo^{1

2}, Li-Li Zhang^{1

2}, Xiao-Xia Luo^{1

2}

Affiliations

¹ Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Xinjiang, China.
² College of Life Sciences and Technology, Tarim University, Xinjiang, China.

^# Contributed equally.

Abstract

Introduction: The microbial community in desert ecosystems is a vital and highly active component. Streptomyces, one of the dominant genera within this community, exhibits significant capabilities in metabolic degradation and the synthesis of secondary metabolites.

Methods: To investigate the metabolic potential of Streptomyces desertis, two strains of Streptomyces were isolated from rhizosphere soil samples of Populus euphratica in the Taklimakan Desert during the initial phase of this study, TRM 70351^T and TRM 70361^T.

Results: The identification of these strains as belonging to the genus Streptomyces was confirmed through 16S rRNA sequencing. All calculated Average Nucleotide Identity (ANI) values were below the 95% cut-off recommended for distinguishing distinct species, and the estimated digital DNA-DNA hybridization (dDDH) values were all below the suggested threshold of 70% for species delineation. Results from phylogenetic, genomic, phenotypic, and chemotaxonomic analyses confirmed that TRM 70351^T and TRM 70361^T represent two new species within the genus Streptomyces, designated as Streptomyces solitudinis sp. nov. and Streptomyces rubellus sp. nov. The type strain for Streptomyces solitudinis sp. nov. is TRM 70351^T ( = CCTCC AA 2020049^T = LMG 32404^T), while the type strain for Streptomyces rubellus sp. nov. is TRM 70361^T ( = CCTCC AA 2020043^T = JCM 35793^T). Notably, Among the identified gene clusters of TRM 70351^T, cluster 12.1 was predicted to be the biosynthetic gene cluster responsible for producing the aminoglycoside compound streptomycin, exhibiting a similarity of 55%. In this study, HSQC-TOCSY was employed to detect the presence of aminoglycosides in fermentation medium No. 1, while LC-MS/MS was utilized to analyze the molecular fragments of neomycin and streptomycin in the alkaline aqueous phase sample of the fermentation product. The mixture was eluted using methanol and ammonia water in a 3:1 ratio, leading to the further separation of the compounds daidzein and Tridec-1-ene.

Discussion: This study has enhanced the species resources of Streptomyces deserticum and the diversity of aminoglycoside compound-producing bacteria. TRM 70351^T exhibited unique metabolic potential, indicating that further studies could be conducted in the future.

Keywords: Streptomyces rubellus sp. nov; Streptomyces solitudinis sp. nov; Taklimakan Desert; aminoglycosides; genome analysis.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was supported by the Tarim University President gene project “Preparation and application of phosphonic acid producing biocontrol agents” (TDZKZD202202), supported by Study on the biosynthesis mechanism and combination biosynthesis of indole oxazole antibiotics in actinomycetes (32360009), and Diversity of typical soil actinomycetes in different habitats of the Tarim River and screening of phosphonic acid producing strains (2022-XBQNXZ-019), and Tarim University Innovation Program (BTYJXM-2024-K30).