Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V1B7, Canada.
Energy, Mining, and Environment, Natural Resource Council Canada, 6100 avenue Royalmount, Montréal, Québec, H4P 2R2, Canada.
FEMS Microbiol Ecol. 2021 Jan 8;97(1). doi: 10.1093/femsec/fiaa206.
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.
受人为管理的农业生态系统是一个独特的系统，其中作物和微生物内在地联系在一起。本研究专注于识别整个植物器官中的微生物群落演替模式，并测试沿时间和空间轴的生态位分化证据。大豆植株在环境室中生长直至种子成熟。从不同发育阶段（出苗、生长、开花和成熟）和隔室（叶、茎、根和根际）收集样本。使用 16S rRNA 基因和 ITS 区扩增子测序评估群落结构和组成。总体而言，空间和时间动态的相互作用调节了 alpha 和 beta 多样性模式。对测量多样性指数的时滞分析突出了群落的强烈时间依赖性。空间和时间的相互作用影响最丰富属的相对丰度，而随机森林预测则加强了丰富属的观察到的本地化模式。总体而言，我们的结果表明，空间和时间的相互作用倾向于在细菌/古菌群落内维持高水平的生物多样性，而在真菌群落中，同一属内的 OTUs 往往具有重叠的生态位。
