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Coupling the endophytic microbiome with the host transcriptome in olive roots
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2021-08-21 , DOI: 10.1016/j.csbj.2021.08.035 Antonio J Fernández-González 1 , Jorge A Ramírez-Tejero 2 , María Patricia Nevado-Berzosa 2 , Francisco Luque 2 , Manuel Fernández-López 1 , Jesús Mercado-Blanco 3
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2021-08-21 , DOI: 10.1016/j.csbj.2021.08.035 Antonio J Fernández-González 1 , Jorge A Ramírez-Tejero 2 , María Patricia Nevado-Berzosa 2 , Francisco Luque 2 , Manuel Fernández-López 1 , Jesús Mercado-Blanco 3
Affiliation
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The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson’s correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of . While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.
中文翻译：
将橄榄根中的内生微生物组与宿主转录组耦合
橄榄遗传对环境和农业气候条件的反应与宿主相关的地下微生物群的组成、结构和功能之间的联系从未在全生物概念框架下进行过研究。早期鉴定了两组在相同环境、土壤和农艺条件下生长的品种，并显示出最高（AH）和最低（AL）相对丰度。我们现在的目标是：i）比较上述细菌属中相对丰度显着不同的两组的根转录组谱； ii) 检查其根际和根内圈微生物群共现网络； iii) 通过相关性和共现网络分析将根宿主转录组模式与根微生物群落的组成联系起来。两组之间的橄榄基因表达存在显着差异。根内圈微生物群的共现网络也明显不同。皮尔逊的相关分析首次描绘了根宿主转录组和内生群落之间发生的相互作用。为了进一步确定关键操作分类单元 (OTU) 和基因，随后的共现网络分析显示 32 个差异表达基因 (DEG) 和 19 个 OTU 之间存在显着的相互作用。总体而言，AH 组中所有上调基因与除 之外的所有 OTU 之间均检测到负相关。虽然在相同条件下生长的两组橄榄品种表现出显着不同的微生物特征，但最引人注目的发现是揭示了这些特征与每组差异基因表达模式之间的强相关性。 总之，这项研究展示了植物-微生物组通讯的整体观点。
更新日期：2021-08-21
中文翻译：
将橄榄根中的内生微生物组与宿主转录组耦合
橄榄遗传对环境和农业气候条件的反应与宿主相关的地下微生物群的组成、结构和功能之间的联系从未在全生物概念框架下进行过研究。早期鉴定了两组在相同环境、土壤和农艺条件下生长的品种，并显示出最高（AH）和最低（AL）相对丰度。我们现在的目标是：i）比较上述细菌属中相对丰度显着不同的两组的根转录组谱； ii) 检查其根际和根内圈微生物群共现网络； iii) 通过相关性和共现网络分析将根宿主转录组模式与根微生物群落的组成联系起来。两组之间的橄榄基因表达存在显着差异。根内圈微生物群的共现网络也明显不同。皮尔逊的相关分析首次描绘了根宿主转录组和内生群落之间发生的相互作用。为了进一步确定关键操作分类单元 (OTU) 和基因，随后的共现网络分析显示 32 个差异表达基因 (DEG) 和 19 个 OTU 之间存在显着的相互作用。总体而言，AH 组中所有上调基因与除 之外的所有 OTU 之间均检测到负相关。虽然在相同条件下生长的两组橄榄品种表现出显着不同的微生物特征，但最引人注目的发现是揭示了这些特征与每组差异基因表达模式之间的强相关性。 总之，这项研究展示了植物-微生物组通讯的整体观点。
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