Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes.
Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes.
复制标题
DOI：
10.1186/s40168-022-01422-9
复制
发表时间：
2022-12-09
期刊：
影响因子：
15.5
通讯作者：
中科院分区：
文献类型：
--
作者：
植物和与之相关的微生物群构成了一个被称为全生物的物种集合。植物种子微生物群落在养分吸收和逆境缓解中起着重要作用。然而，垂直传播的核心内生菌在很大程度上仍未被探索。为深入了解水稻种子核心内生菌的垂直传播规律，对4个地理位置的5个微生境（土壤、根际、根、茎和种子）的6个水稻品种的2个世代进行了大规模的微生物区系分析。结果表明，微生境是水稻微生物区系组成的主要驱动因素，而地理位置和水稻品种是水稻微生物区系组成的主要驱动因素。结果表明，水稻根际微生物区系的多样性和网络复杂性由远到近、由稻表到稻内、由地下到地上依次递减。结果表明，水稻根、茎和种子的微生物区系受外界环境的影响较小。水稻核心细菌内生菌主要由14个扩增子序列变异体（ampliconsequencevariant，ASVs）组成，其中10个ASVs，特别是ASV_2（泛菌属）和ASV_48（黄单胞菌属），因其存在于水稻外部微生境中的频率较低，且常从水稻种子中分离得到，故被鉴定为潜在的垂直传播类群。分离自亲本和子代种子的泛菌属（Pantoea）和黄单胞菌属（Xanthomonas）的基因组序列均显示出高度的核苷酸和核心蛋白同源性，表明种子内生菌在世代间存在垂直遗传。计算机模拟预测结果表明，种子内生菌泛菌属和黄单胞菌属的基因组长度较短、代谢复杂性低、具有多种植物促生特性。我们还发现所有的泛菌属和黄单胞菌属的菌株都具有纤维素酶活性，并产生吲哚-3-乙酸。但大多数菌株对稻瘟病菌、稻瘟病菌等水稻主要病原菌的拮抗作用不明显。oryzaepv.米。总体而言，我们的研究揭示了微生境，而不是特定地点的环境因素或宿主品种，塑造了水稻微生物组。我们发现了水稻微生物组的垂直传播模式和关键分类群，这导致了可培养种子内生菌的分离，并研究了它们在植物-微生物组相互作用中的潜在作用。我们的研究结果提供了垂直传播的微生物群落的见解，并提出了通过操纵种子相关微生物群落来提高植物适应性的新途径。视频摘要在线版本包含补充材料，请登录10. 1186/s40168-022-01422-9。
Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core vertically transmitted endophytes remain largely unexplored. To gain valuable insights into the vertical transmission of rice seed core endophytes, we conducted a large-scale analysis of the microbiomes of two generations of six different rice varieties from five microhabitats (bulk soil, rhizosphere, root, stem, and seed) from four geographic locations. We showed that the microhabitat rather than the geographic location and rice variety was the primary driver of the rice microbiome assemblage. The diversity and network complexity of the rice-associated microbiome decreased steadily from far to near the roots, rice exterior to interior, and from belowground to aboveground niches. Remarkably, the microbiomes of the roots, stems, and seeds of the rice interior compartments were not greatly influenced by the external environment. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs), 10 of which, especially ASV_2 (Pantoea) and ASV_48 (Xanthomonas), were identified as potentially vertically transmitted taxa because they existed across generations, were rarely present in exterior rice microhabitats, and were frequently isolated from rice seeds. The genome sequences of Pantoea and Xanthomonas isolated from the parental and offspring seeds showed a high degree of average nucleotide and core protein identity, indicating vertical transmission of seed endophytes across generations. In silico prediction indicated that the seed endophytes Pantoea and Xanthomonas possessed streamlined genomes with short lengths, low-complexity metabolism, and various plant growth-promoting traits. We also found that all strains of Pantoea and Xanthomonas exhibited cellulase activity and produced indole-3-acetic acid. However, most strains exhibited insignificant antagonism to the major pathogens of rice, such as Magnaporthe oryzae and X. oryzae pv. oryzae. Overall, our study revealed that microhabitats, rather than site-specific environmental factors or host varieties, shape the rice microbiome. We discovered the vertically transmitted profiles and keystone taxa of the rice microbiome, which led to the isolation of culturable seed endophytes and investigation of their potential roles in plant-microbiome interactions. Our results provide insights on vertically transmitted microbiota and suggest new avenues for improving plant fitness via the manipulation of seed-associated microbiomes. Video Abstract The online version contains supplementary material available at 10.1186/s40168-022-01422-9.
登录
查看更多内容
影响因子：
9.8
作者：
Bordenstein SR;Theis KR
通讯作者：
Theis KR
影响因子：
4.5
作者：
Frank AC;Saldierna Guzmán JP;Shay JE
通讯作者：
Shay JE
影响因子：
3.4
作者：
Brady, Carrie;Cleenwerck, Ilse;Coutinho, Teresa
通讯作者：
Coutinho, Teresa
影响因子：
3
作者：
Deng Y;Jiang YH;Yang Y;He Z;Luo F;Zhou J
通讯作者：
Zhou J
影响因子：
4.4
作者：
Eyre, Alexander W.;Wang, Mengying;Dean, Ralph A.
通讯作者：
Dean, Ralph A.