Riesco Raúl, Ortúzar Maite, Fernández-Ábalos José Manuel, Trujillo Martha E
Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain.
Front Plant Sci. 2022 Mar 25;13:872356. doi: 10.3389/fpls.2022.872356. eCollection 2022.
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 and known host plants. Seventy-four 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 plants were inoculated with representative 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.
了解植物与微生物的相互作用以及调控植物微生物组的可能性，对于设计提高农业生产力和可持续性的新策略以及维持自然生态系统至关重要。因此，一个关键问题是如何设计能产生所需宿主表型的细菌群落。这项工作旨在确定参与[具体细菌名称]与已知宿主植物相互作用的潜在基因组特征。使用一种新颖的生物信息学管道，对代表不同环境的74个[具体细菌名称]基因组进行分析，以生成所有潜在植物相关基因的数据库，该管道结合了对微生物 - 植物相关特征筛选以及与现有植物宿主蛋白质组的比较。这些菌株分为三个簇，与几种环境高度相关：植物相关、土壤/根际和海洋/红树林。无论其分离来源如何，大多数菌株都共享编码常见筛选的植物生长促进特征的基因，同时观察到与植物定殖相关性状的差异。当用从这三种环境中选出的代表性[具体细菌名称]菌株接种植物时，相应植物表型存在显著差异。我们的结果表明，所确定的基因组特征有助于选择最有可能成功定殖植物并促进其健康的菌株。这些结果还表明，仅植物生长促进标记并不是选择有益细菌以提高作物产量和恢复生态系统的良好指标。
