Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed
Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed
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DOI：
10.1186/s40168-020-00805-0
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发表时间：
2020-02-14
期刊：
影响因子：
15.5
通讯作者：
Lee, Yong-Hwan
中科院分区：
文献类型：
--
作者：
Kim, Hyun;Lee, Kiseok Keith;Lee, Yong-Hwan
背景植物相关微生物组受宿主和环境因素的影响，通过提供营养物质和减轻非生物和生物胁迫来支持其宿主。虽然已知参与植物生长和免疫的宿主遗传因素塑造微生物群落的组成，但宿主进化对微生物群落的影响还不清楚。结果我们的证据表明，宿主物种形成和驯化形状种子细菌和真菌群落结构。水稻的基因组类型对两个群落的组成变化都有贡献，表现出与微生物组成显著的共生关系。驯化后，细菌和真菌群落的丰度不平等也普遍增加。然而，细菌群落的组成是相对保守的，而真菌的成员发生了显着变化。通过随机森林模型分析，进一步证实了这些驯化效应。随着这些变化，跨界网络的中心类群也通过驯化从真菌转移到细菌。此外，微生物群的母体遗传被揭示为微生物跨代传播的主要途径。结论我们的研究结果表明，进化过程随机影响的微生物群落的整体组成，而在驯化过程中的环境的巨大变化有助于组装的微生物在水稻种子中的确定性方式。这项研究进一步为宿主进化和微生物组提供了新的见解，微生物组是植物，微生物群落和周围环境的起点。
Background Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved in plant growth and immunity are known to shape compositions of microbial communities, the effects of host evolution on microbial communities are not well understood. Results We show evidence that both host speciation and domestication shape seed bacterial and fungal community structures. Genome types of rice contributed to compositional variations of both communities, showing a significant phylosymbiosis with microbial composition. Following the domestication, abundance inequality of bacterial and fungal communities also commonly increased. However, composition of bacterial community was relatively conserved, whereas fungal membership was dramatically changed. These domestication effects were further corroborated when analyzed by a random forest model. With these changes, hub taxa of inter-kingdom networks were also shifted from fungi to bacteria by domestication. Furthermore, maternal inheritance of microbiota was revealed as a major path of microbial transmission across generations. Conclusions Our findings show that evolutionary processes stochastically affect overall composition of microbial communities, whereas dramatic changes in environments during domestication contribute to assembly of microbiotas in deterministic ways in rice seed. This study further provides new insights on host evolution and microbiome, the starting point of the holobiome of plants, microbial communities, and surrounding environments.