Designing robust synthetic microbiota for increasing plant productivity

 描述（由申请人提供）：植物根在复杂的微生物群落中生长，与根以及彼此之间形成相互作用，范围从致病性到相互性[1]。这些社区发现无论是在（根面）或根的内生隔室（EC）内或在接近根表面（根际），拥有一个巨大的基因组功能性状库，可以利用提高作物性能。事实上，从植物根部分离的大量细菌菌株可以积极地影响植物表型，例如芽大小、发芽率或病原体抗性[2，3]。然而，由于天然微生物群落的复杂性，以及这些群落中代谢交换的普遍性，当作为益生菌应用于生长在异源、常设微生物群落中的植物时，这种单一菌株几乎总是无效的。用细菌聚生体接种植物，所述细菌聚生体捕获分类群内的功能范围，或提供来自不同分类群的重叠功能，具有在受控条件下并最终在田间环境中持续影响植物性能和持久性的更高潜力。由于设计和测试微生物聚生体比测试给定表型的单个分离株要复杂得多，因此需要制定和测试有助于构建此类群落的设计原则。该提案旨在设计和测试方法，通过优化互利的微生物-微生物相互作用来设计有益的微生物财团。这将通过整合基因组学和代谢组学信息来实现，以设计预计将最大化互利和最小化拮抗相互作用的聚生体。这些预测将在围隔生态系统植物定殖实验中得到检验。微生物聚生体的设计将平行地由两个主要原则指导：（a）植物和细菌性能与细菌多样性水平相关的假设，以及（B）代谢互补性水平 在植物微生物组内，微生物组内的相互作用是互利相互作用水平的预测，因此，微生物组生产力。有益植物微生物组的生产力反过来应该提高植物生产力。为了检验这些假设，将使用从拟南芥根中分离的200个基因组测序的细菌菌株的多样化文库。细菌聚生体将以如下定义的使基因组多样性和代谢互补性的范围最大化的方式构建。一系列的gnotobiotic A.将用这些聚生体接种拟南芥，并测量植物生长、发芽、开花时间、种子产量、对真菌感染的抗性和转录谱。将基因组衍生的群落功能预测与可测量的表型联系起来，将有助于我们推断出首先应用于受控环境并最终应用于田间环境的设计原则。

 DESCRIPTION (provided by applicant): Plant roots grow within complex microbial communities, forming interactions with the root and with each other, ranging from pathogenesis to mutuality [1]. These communities found either on (rhizoplane) or within the root's endophytic compartments (EC) or in close proximity to the root surface (rhizosphere), hold a vast genomic functional trait reservoir that may be harnessed for improving crop performance. Indeed, a large number of bacterial strains isolated from plant roots can positively affect plant phenotypes such as shoot size, germination rate or pathogen resistance [2, 3]. However, due to the complexity of natural microbial communities, and the prevalence of metabolic exchange in these communities, such single strains are nearly always ineffective when applied as probiotics to plants growing in heterologous, standing microbial communities. Inoculating plants with bacterial consortia that either capture the functional range within a taxon, or provide overlapping function from diverse taxa, has a higher potential of consistently affecting plant performance and persistence under controlled conditions and, ultimately, in field settings. As designing and testing microbial consortia is exponentially more complex than testing single isolates for a given phenotype, there is a need for formulating and testing design principles that will assist in constructing such communities. This proposal aims to devise and test methods to design beneficial microbial consortia by optimizing mutually beneficial microbe-microbe interactions. This will be achieved by integrating genomic and metabolomic information to design consortia that are predicted to maximize mutually beneficial and minimize antagonistic interactions. These predictions will be tested in mesocosm plant colonization experiments. The design of microbial consortia will be guided in parallel by two main principles: (a) the hypothesis that plant and bacterial performance correlate with the level of bacterial diversity and (b) that the level of metabolic complementarity within the plant microbiome is predictive of the level of mutually beneficial interactions, and thu, of microbiome productivity. The productivity of a beneficial plant microbiome, should, in turn, increase plant productivity. In order to test these hypotheses, a diverse library of 200 genome-sequenced bacterial strains isolated from Arabidopsis thaliana roots will be used. Bacterial consortia will be constructed in a way that maximizes the ranges of genomic diversity and metabolic complementarity, as defined below. An array of gnotobiotic A. thaliana will be inoculated with these consortia and plant growth, germination, flowering time, seed yield, resistance to fungal infection and transcriptional profiles will be measured. Linking genome-derived predictions of community function to measurable phenotypes will help us infer design principles that will be applied first in controlled settings and ultimately in field settings.