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Vanilla, a vital spice crop, faces significant challenges from soil-borne diseases caused by Fusarium oxysporum, affecting its sustainable cultivation. This study utilized quantitative polymerase chain reaction (qPCR) and high-throughput sequencing to assess the impact of rotating black pepper, pandan, and sweet rice tea on pathogen levels and the rhizosphere soil microbial communities of vanilla plants cultivated in a pot environment. Incorporating pandan and sweet rice tea into the crop rotation significantly reduced the prevalence of F. oxysporum and enhanced both the abundance and diversity of the rhizosphere soil bacteria. Three distinct microbial community structures associated with fallow, monoculture, and crop rotation conditions were identified. Notably, the rotations involving pandan and sweet rice tea showed no significant differences in the bacterial and fungal community compositions. Crop rotation notably increased the relative abundance of key phyla such as Acidobacteria, Chloroflexi, Rokubacteria and Ascomycota. Moreover, the relative abundance of the dominant bacterial genus Nocardioides increased at the genus level, with a relative abundance of 64.26% after pepper rotation, 98.54% after pandan rotation, and 63.07% after sweet rice tea rotation. The core microbiome, featuring species such as Terriglobus, Kribbella, Myxococcus, Acremonium and Sarocladium, showed a particularly strong response to the presence of pandan, suggesting a closer network interaction among fungal species post-rotation. Additionally, crop rotation was found to significantly raise the soil pH, which, along with the altered bacterial and fungal community structures, emerged as critical factors in disease suppression. Collectively, our results suggest that integrating the economically valuable spice crop pandan into the rotation schedule in vanilla monoculture systems can significantly reduce the incidence of soil-borne diseases, offering a sustainable cultivation strategy for vanilla.
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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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