ABSTRACT

Managed agricultural ecosystems are unique systems where crops and microbes are intrinsically linked. This study focuses on discerning microbiome successional patterns across all plant organs and tests for evidence of niche differentiation along temporal and spatial axes. Soybean plants were grown in an environmental chamber till seed maturation. Samples from various developmental stages (emergence, growth, flowering and maturation) and compartments (leaf, stem, root and rhizosphere) were collected. Community structure and composition were assessed with 16S rRNA gene and ITS region amplicon sequencing. Overall, the interaction between spatial and temporal dynamics modulated alpha and beta diversity patterns. Time lag analysis on measured diversity indices highlighted a strong temporal dependence of communities. Spatial and temporal interactions influenced the relative abundance of the most abundant genera, whilst random forest predictions reinforced the observed localisation patterns of abundant genera. Overall, our results show that spatial and temporal interactions tend to maintain high levels of biodiversity within the bacterial/archaeal community, whilst in fungal communities OTUs within the same genus tend to have overlapping niches.

中文翻译：

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时空相互作用调节大豆微生物组

摘要

受管理的农业生态系统是独特的系统，其中作物和微生物之间存在内在联系。这项研究侧重于识别所有植物器官上的微生物组演替模式，并测试沿时空轴的生态位分化证据。大豆植物在环境室中生长直至种子成熟。收集了不同发育阶段（出芽，生长，开花和成熟）和隔室（叶，茎，根和根际）的样品。用16S rRNA基因和ITS区扩增子测序评估了群落结构和组成。总的来说，时空动力学之间的相互作用调节了α和β的多样性模式。对测得的多样性指数的时滞分析强调了社区强烈的时间依赖性。时空相互作用影响了最丰富属的相对丰度，而随机森林预测则增强了所观察到的丰富属的定位模式。总体而言，我们的结果表明，时空相互作用倾向于在细菌/古细菌群落中维持较高水平的生物多样性，而在真菌群落中，同一属的OTU倾向于具有重叠的生态位。