Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development.
Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development.
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DOI：
10.1128/mbio.02723-20
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发表时间：
2021-01-19
期刊：
影响因子：
6.4
通讯作者：
Bergelson J
中科院分区：
文献类型：
--
作者：
Beilsmith K;Perisin M;Bergelson J
开发可以提高植物产量或阻止病原体的合成微生物群落需要在几个方面进行基础研究，包括微生物在植物组织中的定植效率，植物基因如何塑造微生物群落，以及微生物与微生物在群落组装中的相互作用。这些方面的发现取决于植物微生物组调查的空间和时间尺度。为了研究野外条件下细菌定植的时空动态，我们在密歇根州的两个地点种植和取样拟南芥2年，并通过测序16S rRNA基因扩增子来调查细菌定植的时空动态。马赛克和动态组合揭示了植物是一个随年龄分化的组织栖息地拼凑物。虽然组合主要在根和芽之间发生变化，但扩增子序列变异（asv）也能分化层球组织。组合多样性的增加表明，随着时间的推移，变异分布更广泛，相对于组织差异，在早期定植中随机变异的重要性降低。随着组织发育的转变，根和层球的组合变得更加明显。这种模式是由常见的变异驱动的，而不是那些局限于特定组织或在一个发育阶段短暂出现的变异。模式也严重依赖于精细的系统发育分辨率：当asv在粗略的分类水平上分组时，它们与宿主组织和年龄的关联减弱。因此，所观察到的定植的时空变化取决于细菌特征，而这些特征在家族水平上并不广泛共享。一些殖民者在进入特定组织方面一直更成功，这可以从它们在不同地点和年份的可重复的空间流行分布中得到证明。然而，这些变异并没有超过植物组合，而是随着时间的推移变得更加均匀。总之，这些结果表明，组织类型的增加效应与特定asv的定植瓶颈有关，而不是与它们在建立后支配其他殖民者的能力有关。
Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed. To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampled Arabidopsis thaliana during 2 years at two Michigan sites and surveyed colonists by sequencing 16S rRNA gene amplicons. Mosaic and dynamic assemblages revealed the plant as a patchwork of tissue habitats that differentiated with age. Although assemblages primarily varied between roots and shoots, amplicon sequence variants (ASVs) also differentiated phyllosphere tissues. Increasing assemblage diversity indicated that variants dispersed more widely over time, decreasing the importance of stochastic variation in early colonization relative to tissue differences. As tissues underwent developmental transitions, the root and phyllosphere assemblages became more distinct. This pattern was driven by common variants rather than those restricted to a particular tissue or transiently present at one developmental stage. Patterns also depended critically on fine phylogenetic resolution: when ASVs were grouped at coarse taxonomic levels, their associations with host tissue and age weakened. Thus, the observed spatial and temporal variation in colonization depended upon bacterial traits that were not broadly shared at the family level. Some colonists were consistently more successful at entering specific tissues, as evidenced by their repeatable spatial prevalence distributions across sites and years. However, these variants did not overtake plant assemblages, which instead became more even over time. Together, these results suggested that the increasing effect of tissue type was related to colonization bottlenecks for specific ASVs rather than to their ability to dominate other colonists once established.