Copeland Julia K, Yuan Lijie, Layeghifard Mehdi, Wang Pauline W, Guttman David S
Mol Plant Microbe Interact. 2015 Mar;28(3):274-85. doi: 10.1094/MPMI-10-14-0331-FI.
The leaf microbiome is influenced by both biotic and abiotic factors. Currently, we know little about the relative importance of these factors in determining microbiota composition and dynamics. To explore this issue, we collected weekly leaf samples over a 98-day growing season from multiple cultivars of common bean, soybean, and canola planted at three locations in Ontario, Canada, and performed Illumina-based microbiome analysis. We find that the leaf microbiota at the beginning of the season is very strongly influenced by the soil microbiota but, as the season progresses, it differentiates, becomes significantly less diverse, and transitions to having a greater proportion of leaf-specific taxa that are shared among all samples. A phylogenetic investigation of communities by reconstruction of unobserved states imputation of microbiome function inferred from the taxonomic data found significant differences between the soil and leaf microbiome, with a significant enrichment of motility gene categories in the former and metabolic gene categories in the latter. A network co-occurrence analysis identified two highly connected clusters as well as subclusters of putative pathogens and growth-promoting bacteria. These data reveal some of the complex ecological dynamics that occur in microbial communities over the course of a growing season and highlight the importance of community succession.
叶片微生物组受生物和非生物因素的影响。目前，我们对这些因素在决定微生物群组成和动态方面的相对重要性了解甚少。为了探究这个问题，我们在加拿大安大略省三个地点种植的多个菜豆、大豆和油菜品种的98天生长季节中每周采集叶片样本，并进行基于Illumina的微生物组分析。我们发现，季节开始时的叶片微生物群受到土壤微生物群的强烈影响，但随着季节的推进，它会分化，多样性显著降低，并转变为具有更高比例的在所有样本中共享的叶片特异性分类群。通过对从分类数据推断的微生物组功能进行未观察状态重建的群落系统发育调查发现，土壤和叶片微生物组之间存在显著差异，前者的运动基因类别显著富集，后者的代谢基因类别显著富集。网络共现分析确定了两个高度连接的簇以及假定病原体和促生长细菌的子簇。这些数据揭示了生长季节中微生物群落发生的一些复杂生态动态，并突出了群落演替的重要性。
