Data from: Assembly and ecological function of the root microbiome across angiosperm plant species

Across plants and animals, host-associated microbial communities play fundamental roles in host nutrition, development, and immunity. The factors that shape host–microbiome interactions are poorly understood, yet essential for understanding the evolution and ecology of these symbioses. Plant roots assemble two distinct microbial compartments from surrounding soil: the rhizosphere (microbes surrounding roots) and the endosphere (microbes within roots). Root-associated microbes were key for the evolution of land plants and underlie fundamental ecosystem processes. However, it is largely unknown how plant evolution has shaped root microbial communities, and in turn, how these microbes affect plant ecology, such as the ability to mitigate biotic and abiotic stressors. Here we show that variation among 30 angiosperm species, which have diverged for up to 140 million years, affects root bacterial diversity and composition. Greater similarity in root microbiomes between hosts leads to negative effects on plant performance through soil feedback, with specific microbial taxa in the endosphere and rhizosphere potentially affecting competitive interactions among plant species. Drought also shifts the composition of root microbiomes, most notably by increasing the relative abundance of the Actinobacteria. However, this drought response varies across host plant species, and host-specific changes in the relative abundance of endosphere Streptomyces are associated with host drought tolerance. Our results emphasize the causes of variation in root microbiomes and their ecological importance for plant performance in response to biotic and abiotic stressors.

在动植物体系中，与宿主共生的微生物群落于宿主营养获取、生长发育及免疫调控过程中发挥核心功能。尽管调控宿主-微生物组互作的机制对解析这类共生关系的演化与生态意义至关重要，但目前对其认知仍较为匮乏。植物根系可从周遭土壤中募集形成两类截然不同的微生物生态位：根际（rhizosphere，即根系周边的微生物群落）与根内空间（endosphere，即根系内部的微生物群落）。根系相关微生物是陆生植物演化的关键支撑因素，同时也是核心生态系统过程的基础。然而，目前学界仍未明确植物演化如何塑造根系微生物群落，亦不清楚这些微生物如何影响植物生态，例如其缓解生物与非生物胁迫的能力。本研究发现，30个分化时长可达1.4亿年的被子植物（angiosperm）物种间的演化差异，会显著影响根系细菌的多样性与群落组成。宿主间根系微生物组的相似性越高，越会通过土壤反馈效应对植物生长表现产生负面影响；根内空间与根际中的特定微生物类群，或可调控植物物种间的竞争互作关系。干旱胁迫同样会改变根系微生物组的群落组成，最显著的特征为放线菌门（Actinobacteria）的相对丰度显著提升。不过，这种干旱响应模式因宿主植物物种而异；根内空间链霉菌属（Streptomyces）相对丰度的宿主特异性变化，与宿主的干旱耐受性呈显著相关。本研究结果明确了根系微生物组群落差异的成因，及其在植物应对生物与非生物胁迫时对植株生长表现的生态重要性。