Table_2_The Influence of Contrasting Microbial Lifestyles on the Pre-symbiotic Metabolite Responses of Eucalyptus grandis Roots.XLSX

Plant roots co-inhabit the soil with a diverse consortium of microbes of which a number attempt to enter symbiosis with the plant. These microbes may be pathogenic, mutualistic, or commensal. Hence, the health and survival of plants is heavily reliant on their ability to perceive different microbial lifestyles and respond appropriately. Emerging research suggests that there is a pivotal role for plant root secondary metabolites in responding to microbial colonization. However, it is largely unknown if plants are able to differentiate between microbes of different lifestyles and respond differently during the earliest stages of pre-symbiosis (i.e., prior to physical contact). In studying plant responses to a range of microbial isolates, we questioned: (1) if individual microbes of different lifestyles and species caused alterations to the plant root metabolome during pre-symbiosis, and (2) if these early metabolite responses correlate with the outcome of the symbiotic interaction in later phases of colonization.
We compared the changes of the root tip metabolite profile of the model tree Eucalyptus grandis during pre-symbiosis with two isolates of a pathogenic fungus (Armillaria luteobubalina), one isolate of a pathogenic oomycete (Phytophthora cinnamomi), two isolates of an incompatible mutualistic fungus (Suillus granulatus), and six isolates of a compatible mutualistic fungus (Pisolithus microcarpus). Untargeted metabolite profiling revealed predominantly positive root metabolite responses at the pre-symbiosis stage, prior to any observable phenotypical changes of the root tips. Metabolite responses in the host tissue that were specific to each microbial species were identified. A deeper analysis of the root metabolomic profiles during pre-symbiotic contact with six strains of P. microcarpus showed a connection between these early metabolite responses in the root with later colonization success. Further investigation using isotopic tracing revealed a portion of metabolites found in root tips originated from the fungus. RNA-sequencing also showed that the plant roots undergo complementary transcriptomic reprogramming in response to the fungal stimuli. Taken together, our results demonstrate that the early metabolite responses of plant roots are partially selective toward the lifestyle of the interacting microbe, and that these responses can be crucial in determining the outcome of the interaction.

植物根系与多样的微生物群落共同栖息于土壤中，其中诸多微生物试图与植物建立共生关系。这些微生物可分为致病型、互利共生型与共栖型。因此，植物的健康与生存高度依赖其感知不同微生物生活方式并做出恰当响应的能力。新兴研究表明，植物根系次生代谢物（secondary metabolites）在响应微生物定殖过程中发挥关键作用。然而，在预共生（pre-symbiosis，即物理接触前）的最早阶段，植物是否能够区分不同生活方式的微生物并做出差异化响应，目前尚不清楚。在针对一系列微生物分离株的植物响应研究中，我们提出了两个科学问题：（1）不同生活方式与物种的单个微生物是否会在预共生阶段改变植物根系的代谢组；（2）这些早期代谢响应是否与定殖后期共生相互作用的结局相关。
我们比较了模式树种巨桉（Eucalyptus grandis）的根尖代谢谱在预共生阶段的变化，其分别与两株致病真菌黄盖蜜环菌（Armillaria luteobubalina）、一株致病卵菌肉桂疫霉菌（Phytophthora cinnamomi）、两株不相容互利共生真菌点柄乳牛肝菌（Suillus granulatus）以及六株相容互利共生真菌小果硬马勃（Pisolithus microcarpus）进行共培养。非靶向代谢组学分析（untargeted metabolite profiling）显示，在预共生阶段，即根尖尚未出现任何可观测表型变化时，根系代谢产物整体呈现正向响应。我们还在宿主组织中鉴定出针对每种微生物物种的特异性代谢响应。针对与六株小果硬马勃（Pisolithus microcarpus）菌株预共生接触时的根系代谢组进行深入分析，结果表明根系的这些早期代谢响应与后期定殖成功率存在关联。
进一步的同位素示踪实验证实，部分在根尖中检测到的代谢产物来源于真菌。RNA测序（RNA-sequencing）结果同样显示，植物根系会响应真菌刺激发生相应的转录组重编程（transcriptomic reprogramming）。综上，我们的研究结果表明，植物根系的早期代谢响应会部分针对互作微生物的生活方式表现出选择性，且这些响应对于决定互作结局至关重要。