BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.

中文翻译：

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在哥伦比亚的原生和农业土壤中破译野生和现代普通豆（菜豆）的根际微生物组。

背景技术现代农作物品种通常在远离其野生近缘种起源中心的农业管理良好的土壤中种植。这种栖息地的扩展如何影响植物微生物组组装尚不清楚。结果在这里，我们调查了从原生土壤到农业土壤的转变是否影响野生和现代普通豆（菜豆）的根瘤菌群落组装，并且是否导致根瘤菌多样性的消耗。大豆基因型对根瘤菌组装的影响在农业土壤中比在自然土壤中更为突出。尽管在总共15,925个中，在原生土壤和农业土壤中生长的所有八个豆类共有113个操作分类单位，但该核心微生物组占所有序列读段的很大一部分（25.9％）。与天然土壤相比，仅在农业土壤的普通豆根际发现了更多的OTU，而与野生种相比，在现代豆种的根际中发现了更多的OTU。共现分析进一步表明，与天然土壤相比，农业土壤中豆根际微生物组相互作用的复杂性降低了。结论总的来说，这些结果表明普通豆的生境从其原生土壤环境扩展到农业环境对根际细菌多样性具有出乎意料的总体积极影响，并导致对根际微生物组装配的豆基因型依赖性更强。