Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection
Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection
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DOI：
10.1073/pnas.1908600116
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发表时间：
2020-01-14
影响因子：
11.1
通讯作者：
Koskella, Britt
中科院分区：
文献类型：
--
作者：
Morella, Norma M.;Weng, Francis Cheng-Hsuan;Koskella, Britt
人们对植物微生物组越来越感兴趣，因为它涉及植物健康和农业可持续性。一个关键的未回答的问题是，我们是否可以选择在目标宿主定殖后仍然强大的植物微生物组。我们使用连续传代实验通过选择番茄叶际微生物组来解决这个问题。从从田间生长的番茄植物产生的多样化微生物群落开始，我们在5种植物基因型中接种重复植物进行4次45-d传代，在每次传代时对微生物群落进行测序。我们观察到随着时间的推移，细菌（165扩增子测序）和真菌（内部转录间隔区扩增子测序）社区在重复线上的一致变化，以及在实验过程中普遍丧失多样性，这表明在叶际中自然观察到的微生物群落可能是短暂的或在实验环境中适应性差。我们发现，宿主基因型和环境塑造微生物组成，但基因型的相对重要性随着时间的推移而下降。此外，使用群落聚结实验，我们发现实验结束时的细菌群落对起始细菌群落的入侵具有鲁棒性。这些结果强调，选择一个稳定的微生物组，很好地适应特定的宿主环境确实是可能的，强调这种方法在农业和其他领域的巨大潜力。鉴于微生物组在没有本文所述的相互宿主进化（共同进化）的情况下对选择的一致反应，未来的研究应该解决这种适应如何影响宿主健康。
There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field -grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (165 amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.