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Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants.
Scientific Reports ( IF 4.6 ) Pub Date : 2020-05-26 , DOI: 10.1038/s41598-020-65277-6
Wiebke Bünger 1 , Xun Jiang 1 , Jana Müller 1, 2 , Thomas Hurek 1 , Barbara Reinhold-Hurek 1
Affiliation  

Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision. The aerobic strains were isolated from roots or rhizomes of Oryza sativa and O. longistaminata. Two of them are the first cultivated endophytes of Verrucomicrobia, as validated by confocal laser scanning microscopy inside rice roots after re-infection under sterile conditions. This extended known verrucomicrobial niche spaces. Two strains were promoting root growth of rice. Discovery of root compartment-specific Verrucomicrobia permitted an across-phylum comparison of the genomic conformance to life in soil, rhizoplane or inside roots. Genome-wide protein domain comparison with niche-specific reference bacteria from distant phyla revealed signature protein domains which differentiated lifestyles in these microhabitats. Our study enabled us to shed light into the dark microbial matter of root Verrucomicrobia, to define genetic drivers for niche adaptation of bacteria to plant roots, and provides cultured strains for revealing causal relationships in plant-microbe interactions by reductionist approaches.



中文翻译:

新型栽培内生Verrucomicrobia揭示了细菌与植物结合的深层特征。

尽管复杂的根微生物群落与植物健康,生长和生产力相关,但对这些植物-微生物相互作用的分子基础还知之甚少。Verrucomicrobia是根际中的大都会主义者,但是由于培养成员的比例较低,它们的适应性和功能是难以置信的。在这里,我们报告从水稻中分离出的四个栽培的Verrucomicrobia,推测代表了四个新物种和一个新的细分。从水稻(Oryza sativa)O. longistaminata)的根或根茎中分离出有氧菌株。其中两个是Verrucomicrobia的第一个栽培内生,在无菌条件下再次感染后,通过共聚焦激光扫描显微镜在稻根内部进行了验证。这扩展了已知的疣疣利基空间。两种菌株正在促进水稻的根系生长。根室特异性Verrucomicrobia的发现允许对在土壤,根际平面或根内部生活的基因组一致性进行跨门比较。全基因组蛋白结构域与来自远处的利基特异性参考细菌的比较揭示了标志性蛋白结构域,这些蛋白结构域在这些微生境中使生活方式有所不同。我们的研究使我们能够深入了解根微生物的黑暗微生物定义了细菌对植物根系的生态位适应的遗传驱动力,并通过还原论方法提供了培养菌株以揭示植物-微生物相互作用中的因果关系。

更新日期:2020-05-26
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