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Multilocus sequence analysis of Streptomyces griseus isolates delineating intraspecific diversity in terms of both taxonomy and biosynthetic potential

Antonie van Leeuwenhoek volume 98, pages 237–248 (2010)Cite this article

Abstract

Systematics can provide a fundamental framework for understanding the relationships and diversification of organisms. Multilocus sequence analysis (MLSA) has shown great promise for an elaborate taxonomic grouping of streptomycete diversity. To evaluate the practical significance of MLSA as a valuable systematic tool for streptomycetes, we examined six endophytic Streptomyces griseus isolates and two S. griseus reference strains possessing obvious antagonistic activities and identical 16S rRNA gene sequences, using both housekeeping genes and secondary metabolic genes. All the eight strains contained PKS-I and NRPS genes, but not PKS-II genes, and showed similar diversity in both the MLSA phylogeny based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) and fingerprinting of KS-AT genes. We also inferred a phylogeny based on concatenated amino acid sequences of representative KS-AT genes from the strains, which displayed a topology correlated well with those of housekeeping-gene MLSA and KS-AT fingerprinting. The good congruence observed between phylogenies based on the different datasets verified that the MLSA scheme provided robust resolution at intraspecific level and could predict the overall diversity of secondary metabolic potential within a Streptomyces species, despite somewhat of a discrepancy with antimicrobial data. It is therefore feasible to apply MLSA to dissecting natural diversity of streptomycetes for a better understanding of their evolution and ecology, as well as for facilitating their bioprospecting.

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Acknowledgments

We are grateful to professors Cheng-Lin Jiang and Li-Hua Xu (Yunnan University, China) for their help in plant sample collection, and to Ms. Jing Gong (Institute of Microbiology, CAS) for her assistance in phenotypic analysis. This work was supported by the Natural Science Foundation of China (NSFC, No. 30670002) and by the Specialized Research Fund for State Key Laboratories of China.

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  1. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China

    Xiaoying Rong, Ning Liu, Jisheng Ruan & Ying Huang

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  1. Xiaoying Rong
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  2. Ning Liu
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  4. Ying Huang
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Correspondence to Ying Huang.

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Supplementary Fig. S1

Phylogenetic neighbour-joining tree based on five-gene concatenated sequences, showing relationships of the eight S. griseus strains and related type strains. The scale bar indicates 1% difference in nucleotide sequences. (PPT 99 kb)

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Rong, X., Liu, N., Ruan, J. et al. Multilocus sequence analysis of Streptomyces griseus isolates delineating intraspecific diversity in terms of both taxonomy and biosynthetic potential. Antonie van Leeuwenhoek 98, 237–248 (2010). https://doi.org/10.1007/s10482-010-9447-z

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Keywords

  • Streptomyces griseus
  • Multilocus sequence analysis
  • KS-AT
  • Intraspecific diversity
  • Secondary metabolic potential