Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis
Abstract Background The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, bu...
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BMC
2025-06-01
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| Series: | Microbiome |
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| Online Access: | https://doi.org/10.1186/s40168-025-02136-4 |
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| author | Xianhe Cao Qingjun Yuan Chengcheng Hu Hanxing Zhang Xianyun Sun Binbin Yan Xiaojing Ma Long Zhang Luqi Huang Shaojie Li Zhenying Zhang |
| author_facet | Xianhe Cao Qingjun Yuan Chengcheng Hu Hanxing Zhang Xianyun Sun Binbin Yan Xiaojing Ma Long Zhang Luqi Huang Shaojie Li Zhenying Zhang |
| author_sort | Xianhe Cao |
| collection | DOAJ |
| description | Abstract Background The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, but ancestral microbiota suitable for C. chinensis remain largely uncharted. Results The amplicon data analyses revealed that habitat transition strongly influenced the rhizosphere microbial communities. The rhizomicrobiomes of wild C. chinensis encompassed a more diverse array of ecological groups and exhibited a greater functional diversity compared to their cultivated counterparts. A higher proportion of beneficial fungi was observed in the rhizosphere of wild C. chinensis, while the cultivated plants had a higher population of pathogenic fungi. Furthermore, a well-documented plant-growth-promoting rhizobacterium genus, Paraburkholderia, was found to play an essential role in the resistance of the wild C. chinensis to potential disease caused by Ilyonectria. Two strains of Paraburkholderia (Paraburkholderia nemoris and Paraburkholderia phytofirmans) were isolated, and in vitro experiments confirmed that these isolates possess various growth-promoting properties and antagonistic activities against known pathogens for C. chinensis root rot. Both of the Paraburkholderia isolates could markedly promote the plant immune response and enhance the overall health of the cultivated C. chinensis. Conclusions By a comprehensive comparison of the rhizosphere microbiome between wild and cultivated C. chinensis, the promising bacterial genus Paraburkholderia was identified as a beneficial microbe significantly promoting the growth of C. chinensis, providing pivotal insights for future endeavors aimed at engineering the rhizosphere microbiome of C. chinensis, as well as other medicinal herbs. Video Abstract |
| format | Article |
| id | doaj-art-deaab5c842f0449481ad7ffb52fecf2f |
| institution | Kabale University |
| issn | 2049-2618 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj-art-deaab5c842f0449481ad7ffb52fecf2f2025-08-20T04:01:36ZengBMCMicrobiome2049-26182025-06-0113112110.1186/s40168-025-02136-4Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensisXianhe Cao0Qingjun Yuan1Chengcheng Hu2Hanxing Zhang3Xianyun Sun4Binbin Yan5Xiaojing Ma6Long Zhang7Luqi Huang8Shaojie Li9Zhenying Zhang10State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesJiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesState Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesShandong Jinniu Group Co., LtdState Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesAbstract Background The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, but ancestral microbiota suitable for C. chinensis remain largely uncharted. Results The amplicon data analyses revealed that habitat transition strongly influenced the rhizosphere microbial communities. The rhizomicrobiomes of wild C. chinensis encompassed a more diverse array of ecological groups and exhibited a greater functional diversity compared to their cultivated counterparts. A higher proportion of beneficial fungi was observed in the rhizosphere of wild C. chinensis, while the cultivated plants had a higher population of pathogenic fungi. Furthermore, a well-documented plant-growth-promoting rhizobacterium genus, Paraburkholderia, was found to play an essential role in the resistance of the wild C. chinensis to potential disease caused by Ilyonectria. Two strains of Paraburkholderia (Paraburkholderia nemoris and Paraburkholderia phytofirmans) were isolated, and in vitro experiments confirmed that these isolates possess various growth-promoting properties and antagonistic activities against known pathogens for C. chinensis root rot. Both of the Paraburkholderia isolates could markedly promote the plant immune response and enhance the overall health of the cultivated C. chinensis. Conclusions By a comprehensive comparison of the rhizosphere microbiome between wild and cultivated C. chinensis, the promising bacterial genus Paraburkholderia was identified as a beneficial microbe significantly promoting the growth of C. chinensis, providing pivotal insights for future endeavors aimed at engineering the rhizosphere microbiome of C. chinensis, as well as other medicinal herbs. Video Abstracthttps://doi.org/10.1186/s40168-025-02136-4Coptis chinensisWildCultivatedHabitat transitionRhizosphere microbiomePlant-growth-promoting rhizobacteria |
| spellingShingle | Xianhe Cao Qingjun Yuan Chengcheng Hu Hanxing Zhang Xianyun Sun Binbin Yan Xiaojing Ma Long Zhang Luqi Huang Shaojie Li Zhenying Zhang Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis Microbiome Coptis chinensis Wild Cultivated Habitat transition Rhizosphere microbiome Plant-growth-promoting rhizobacteria |
| title | Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis |
| title_full | Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis |
| title_fullStr | Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis |
| title_full_unstemmed | Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis |
| title_short | Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis |
| title_sort | wild wisdom meets cultivation comparative rhizomicrobiome analysis unveils the key role of paraburkholderia in growth promotion and disease suppression in coptis chinensis |
| topic | Coptis chinensis Wild Cultivated Habitat transition Rhizosphere microbiome Plant-growth-promoting rhizobacteria |
| url | https://doi.org/10.1186/s40168-025-02136-4 |
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