BACKGROUND Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators-protists-are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. RESULTS We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. CONCLUSIONS We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. Video Abstract.

中文翻译：

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根际原生生物是植物健康的关键决定因素。


背景技术植物健康受到根际微生物组的密切影响，根际微生物组是在植物生长过程中发生显着变化的复杂生物体组合。然而，大多数根际微生物组研究都集中在该微生物组的一部分，特别是细菌和真菌。目前尚不清楚其他微生物成分，尤其是关键的微生物组捕食者（原生生物）如何与植物健康相关。在这里，我们研究了整体根际微生物组，包括细菌、微生物真核生物（真菌和原生生物）以及功能性微生物代谢基因。我们在番茄植株整个生长过程中研究了这些群落和功能基因，这些植株要么出现疾病症状，要么在田间条件下保持健康。结果我们发现原生生物可以最好地预测植物生长过程中的病原体动态。更具体地说，在植物建立时，后来的健康植物和患病植物之间的以微生物为食的吞噬原生生物群落是不同的。这些吞噬细胞的相对丰度与植物生长过程中的病原体丰度呈负相关，这表明捕食者与被捕食者的相互作用会影响病原体的表现。此外，吞噬性原生生物可能通过增强参与减轻病原体成功的病原体抑制次级代谢基因来改变细菌功能。结论我们说明了原生生物作为与植物健康相关的微生物组功能的自上而下控制器的重要性。我们提出，包括细菌和原生生物在内的整体微生物组视角，为预测植物性能提供了最佳的下一步。视频摘要。