Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach

There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (Aspalathus linearis), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread Mesorhizobium ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities.   

Methods
BAM data was de-multiplexed by bioinformatician (Weihong Qi ), via the Functional Genomics Center (FGC) in Zurich, the service that produced the reads. This individual is acknowledged in the manuscript related to this dataset.

鉴于植物宿主、气候及土壤条件对细菌多样性的综合影响，研究根际细菌的生态地理学因素引起了广泛关注。尤其是对于仍保留野生种群的大豆类作物而言，这一问题显得尤为重要，因为作物种植对未受干扰的根际细菌群落的影响得以在此得到探讨。在本研究中，我们采用群落预测方法，描述了南非特有的大豆类作物南非红茶（Aspalathus linearis）根瘤细菌群落的多样性。研究旨在揭示培养与野生红茶种群中根瘤群落组成的模式是否与地理距离、植物性状以及植物种群类型（即栽培或野生）相关。我们识别出一系列占主导地位且分布广泛的根瘤菌属（Mesorhizobium）ZOTUs，每个ZOTU定义了一种根瘤群落类型。红茶的栽培对根瘤细菌多样性产生了区域性和局部性影响，而根瘤群落的地理起源是预测根瘤群落结构的最强指标。除栽培对根瘤细菌多样性的影响外，本研究还表明，在区域尺度上，混合了扩散限制和生态漂变的作用，而在局部尺度上，不同植物种群的选择作用共同塑造了红茶根瘤细菌群落的生态地理学特征。

方法
BAM数据由生物信息学家（魏宏庆）通过苏黎世的基因功能学中心（FGC）进行去重，该中心提供了测序服务。此个人在相关数据集的论文中得到了认可。