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Objective To study the endophytic microbiota in different ecological niches of pepper (Capsicum annuum L.) seedlings at various stages following Ralstonia solanacearum infection, aiming to explore the endophyte migration dynamics triggered by R. solanacearum infection. Methods The copy number of R. solanacearum was quantified by quantitative real-time PCR (qPCR). Samples from roots, stems, and leaves of both infected and healthy pepper plants were collected at 1, 4, and 7 days post-inoculation (dpi). High-throughput amplicon sequencing was employed to analyze the endophytic bacterial and fungal communities. Dual-dimensional analyses integrating microbial copy number and community structures were conducted to elucidate the spatiotemporal dynamics of endophytic microbiota and pathogen proliferation characteristics under R. solanacearum invasion. Results The copy number of R. solanacearum continuously increased in roots and stems post-inoculation, peaking in leaves at 4 dpi and then significantly declining. The infection induced pronounced alterations in endophytic bacterial communities across all tissues, with temporal effects outweighing tissue-specific variations. Roots exhibited heightened sensitivity to pathogen invasion. At 7 dpi, the relative abundance of Bacillota in endophytic bacteria in the plants increased significantly. At the genus level, the relative abundance of Rhizobium, Pseudomonas, and endogenous fungi Fusarium and Aspergillus increased significantly compared with that in the control group. The beta diversity indices and structures of endophytic microbiota in all tissues underwent marked changes during infection. Pseudomonas emerged as a signature bacterial genus in roots, while Aspergillus dominated stems and leaves as a fungal indicator. The co-occurrence network analysis revealed greater complexity of the endophytic microbiota in infected plants, with an elevated proportion of negative correlation edges. Ascomycota served as pivotal network hubs, reflecting enhanced antagonistic interactions and inter-microbial associations under pathogen stress. Ten potential antagonistic microbial taxa were identified, including six bacterial taxa of Clostridia (Bacillota). Conclusion This study delineates the proliferation pattern of R. solanacearum in pepper seedlings and characterizes the structural and migration dynamics of endophytic microbiota following pathogen invasion.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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