Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.

干旱是限制农业生产力的主要非生物胁迫。先前的田间实验表明，干旱会降低根部和根际微生物组的多样性。这些变化最终如何影响植物健康仍然难以捉摸。为此，我们结合了还原论、过渡论和生态学方法，应用于主要谷类作物高粱，以确定强烈影响干旱胁迫植物表型的关键根部相关微生物。将五十三种拟南芥相关细菌应用于高粱种子，并监测它们对根生长的影响。两种节杆菌菌株引起拟南芥和高粱的根部生长抑制（RGI）。在合成群落的背景下，Variovorax菌株能够保护植物免受节杆菌引起的 RGI 侵害。作为一个过渡系统，高通量表型被用来测试合成群落。在干旱胁迫期间，节杆菌定殖的植物生长速度和叶片含水量降低。被节杆菌和Variovorax定殖的植物表现得与对照植物一样好或更好。与此同时，我们进行了一项田间试验，其中对高粱在干旱条件下进行了评估。通过将土壤特性数据纳入微生物组分析，我们用一种新方法解释了实验噪音，并能够观察节杆菌丰度之间的负相关性和植物生长。验证了这种方法后，我们交叉引用了高通量表型和田间实验的数据集，并以高置信度报告了与干旱胁迫下植物生长呈正相关的细菌列表。总之，三层实验系统成功地跨越了实验室与田间的差距，并鉴定了干旱条件下对高粱有益和有害的菌株。