Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study
ABSTRACT Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to prelimi...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2025-05-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01692-24 |
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| author | Ziguang Deng Wei Yang Tongtong Lin Yaohai Wang Xiaojing Hua Xiaoyu Jiang Junhao Chen Dan Liu Zhiqiang Ye Yu Zhang Michael Lynch Hongan Long Jiao Pan |
| author_facet | Ziguang Deng Wei Yang Tongtong Lin Yaohai Wang Xiaojing Hua Xiaoyu Jiang Junhao Chen Dan Liu Zhiqiang Ye Yu Zhang Michael Lynch Hongan Long Jiao Pan |
| author_sort | Ziguang Deng |
| collection | DOAJ |
| description | ABSTRACT Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to preliminarily investigate the biodiversity and genetic structure of Streptomyces in soils of China from different dimensions, using recently developed cost-efficient amplicon and whole-genome library preparation methods. Amplicon analysis showed that Actinobacteria were among the most abundant bacteria, with 0.3% of amplicon sequence variants (ASVs) belonging to Streptomyces. Meanwhile, we successfully isolated 136 Streptomyces natural strains and assembled their genomes, including 26 previously unreported species, underscoring the need for further exploration of soil Streptomyces in China. Population genetics analysis revealed that homologous recombination may primarily drive the extensive genetic diversity observed in Streptomyces, as well as a complex population structure. Complementing this, pan-genome analysis shed light on gene diversity within Streptomyces and led to the discovery of rare genes, further emphasizing the vast genetic diversity of this genus. Additionally, multiple metabolic gene clusters were found in these Streptomyces strains, as well as some potentially unique or uncommon ones were found. These findings not only highlight the biological and metabolic diversity of Streptomyces but also provide a technical framework for future studies on the global biodiversity and evolution of this genus.IMPORTANCEStreptomyces, a prominent group of Actinobacteria, holds significant importance in ecosystems and biotechnology due to their diverse array of metabolic products. However, research on the biodiversity of soil Streptomyces across extensive geographical scales in China has been limited, and their genetic diversity has rarely been evaluated using modern population genetics principles. This pilot study successfully addresses these gaps by conducting a preliminary exploration on the biodiversity of Streptomyces in Chinese soils from multiple perspectives, providing valuable insights for a deeper understanding of their biodiversity and a novel technical framework for future large-scale explorations of its diversity. |
| format | Article |
| id | doaj-art-e4eb56c594cc41d3b63f641d794f48da |
| institution | DOAJ |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-e4eb56c594cc41d3b63f641d794f48da2025-08-20T03:11:29ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-05-0113510.1128/spectrum.01692-24Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot studyZiguang Deng0Wei Yang1Tongtong Lin2Yaohai Wang3Xiaojing Hua4Xiaoyu Jiang5Junhao Chen6Dan Liu7Zhiqiang Ye8Yu Zhang9Michael Lynch10Hongan Long11Jiao Pan12Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaSchool of Life Sciences, Central China Normal University, Wuhan, Hubei Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaBiodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USAKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaKey Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, ChinaABSTRACT Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to preliminarily investigate the biodiversity and genetic structure of Streptomyces in soils of China from different dimensions, using recently developed cost-efficient amplicon and whole-genome library preparation methods. Amplicon analysis showed that Actinobacteria were among the most abundant bacteria, with 0.3% of amplicon sequence variants (ASVs) belonging to Streptomyces. Meanwhile, we successfully isolated 136 Streptomyces natural strains and assembled their genomes, including 26 previously unreported species, underscoring the need for further exploration of soil Streptomyces in China. Population genetics analysis revealed that homologous recombination may primarily drive the extensive genetic diversity observed in Streptomyces, as well as a complex population structure. Complementing this, pan-genome analysis shed light on gene diversity within Streptomyces and led to the discovery of rare genes, further emphasizing the vast genetic diversity of this genus. Additionally, multiple metabolic gene clusters were found in these Streptomyces strains, as well as some potentially unique or uncommon ones were found. These findings not only highlight the biological and metabolic diversity of Streptomyces but also provide a technical framework for future studies on the global biodiversity and evolution of this genus.IMPORTANCEStreptomyces, a prominent group of Actinobacteria, holds significant importance in ecosystems and biotechnology due to their diverse array of metabolic products. However, research on the biodiversity of soil Streptomyces across extensive geographical scales in China has been limited, and their genetic diversity has rarely been evaluated using modern population genetics principles. This pilot study successfully addresses these gaps by conducting a preliminary exploration on the biodiversity of Streptomyces in Chinese soils from multiple perspectives, providing valuable insights for a deeper understanding of their biodiversity and a novel technical framework for future large-scale explorations of its diversity.https://journals.asm.org/doi/10.1128/spectrum.01692-24Streptomycesbiodiversitygenetic diversitymetabolic gene clustersevolution |
| spellingShingle | Ziguang Deng Wei Yang Tongtong Lin Yaohai Wang Xiaojing Hua Xiaoyu Jiang Junhao Chen Dan Liu Zhiqiang Ye Yu Zhang Michael Lynch Hongan Long Jiao Pan Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study Microbiology Spectrum Streptomyces biodiversity genetic diversity metabolic gene clusters evolution |
| title | Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study |
| title_full | Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study |
| title_fullStr | Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study |
| title_full_unstemmed | Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study |
| title_short | Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study |
| title_sort | multidimensional insights into the biodiversity of streptomyces in soils of china a pilot study |
| topic | Streptomyces biodiversity genetic diversity metabolic gene clusters evolution |
| url | https://journals.asm.org/doi/10.1128/spectrum.01692-24 |
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