University of Florida, Institute of Food and Agricultural Sciences, Southwest Florida Research and Education Center, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
Sci Rep. 2021 May 12;11(1):10068. doi: 10.1038/s41598-021-89569-7.
While our understanding of plant-microbe interactions in the rhizosphere microbiome (rhizobiome) has increased, there is still limited information on which taxa and functions drive these rhizobiome interactions. Focusing on the core rhizobiome (members common to two or more microbial assemblages) of crops may reduce the number of targets for determining these interactions, as they are expected to have greater influence on soil nutrient cycling and plant growth than the rest of the rhizobiome. Here, we examined whether the characterization of a core rhizobiome on the basis of only taxonomic or functional traits rather than the combined analysis of taxonomic and functional traits provides a different assessment of the core rhizobiome of agricultural crops. Sequences of the bacterial 16S rRNA gene from six globally important crops were analyzed using two different approaches in order to identify and characterize the taxonomic and functional core rhizobiome. For all crops examined, we found significant differences in the taxonomic and functional composition between the core rhizobiomes, and different phyla, genera, and predicted microbial functions were dominant depending on the core rhizobiome type. Network analysis indicated potentially important taxa were present in both taxonomic and functional core rhizobiomes. A subset of genera and predicted functions were exclusively or predominately present in only one type of core rhizobiome while others were detected in both core rhizobiomes. These results highlight the necessity of including both taxonomy and function when assessing the core rhizobiome, as this will enhance our understanding of the relationships between microbial taxa and soil health, plant growth, and agricultural sustainability.
虽然我们对根际微生物组（根瘤菌组）中的植物-微生物相互作用的理解有所增加，但对于哪些分类群和功能驱动这些根瘤菌组相互作用的信息仍然有限。关注作物的核心根瘤菌（两个或更多微生物组合中共有的成员）可能会减少确定这些相互作用的目标数量，因为它们预计比根瘤菌组的其余部分对土壤养分循环和植物生长有更大的影响。在这里，我们研究了仅基于分类或功能特征而不是分类和功能特征的综合分析来描述核心根瘤菌是否会对农业作物的核心根瘤菌提供不同的评估。使用两种不同的方法分析了来自六种全球重要作物的细菌 16S rRNA 基因序列，以识别和描述分类和功能核心根瘤菌。对于所有检查的作物，我们发现核心根瘤菌之间在分类和功能组成上存在显著差异，并且不同的门、属和预测的微生物功能取决于核心根瘤菌的类型而占主导地位。网络分析表明，潜在的重要类群存在于分类和功能核心根瘤菌中。一组属和预测功能仅存在于一种核心根瘤菌中，而其他功能则存在于两种核心根瘤菌中。这些结果强调了在评估核心根瘤菌时必须同时考虑分类和功能，因为这将增强我们对微生物类群与土壤健康、植物生长和农业可持续性之间关系的理解。
