Table_5_Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora.XLSX

Understanding plant-microbe interactions with the possibility to modulate the plant’s microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.

探究可调控植物微生物组的植物-微生物互作机制，对于构建更高产、可持续的现代农业策略以及维护自然生态系统至关重要。因此，核心科学问题在于如何设计可诱导宿主产生预期表型的细菌联合体。本研究旨在鉴定小单孢菌属（Micromonospora）与已知宿主植物互作过程中潜在的基因组特征。本研究选取覆盖多样生境的74个小单孢菌属基因组，通过整合微生物-植物相关特征筛选与现有植物宿主蛋白质组比对的新型生物信息学流程，构建了全潜在植物相关基因数据库。所获菌株可划分为三个聚类簇，且与三类生境高度相关：植物关联生境、土壤/根际生境以及海洋/红树林生境。无论分离来源如何，多数菌株均携带经常规筛选的植物促生长特征编码基因，但在植物定殖相关性状上存在显著差异。当使用从三类生境中筛选出的代表性小单孢菌属菌株接种拟南芥（Arabidopsis thaliana）后，对应植株的表型出现显著差异。本研究结果表明，所鉴定的基因组特征可辅助筛选出最有可能成功定殖植物并促进植株健康的菌株。此外，本研究结果还提示，仅依靠植物促生长标记物，不足以作为筛选可提升作物产量、修复生态系统的有益细菌的可靠指标。