Boutin Sophie, Laforest-Lapointe Isabelle
Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
Sci Rep. 2025 Jul 15;15(1):25620. doi: 10.1038/s41598-025-10729-0.
Manipulating plant microbiomes is foreseen as a key biocontrol avenue to tackle the accelerating challenges of global change in agriculture. Several recent studies have identified the spatiotemporal dynamics of phyllosphere microbial communities, stressing the need to understand plant microbiome drivers to design efficient biocontrol interventions. Yet, these works are often performed on small sample counts, rarely provide sufficient information on the relative impact of time or local environment, and are seldom repeated to assess reproducibility. To address these limits, we performed a longitudinal sampling across multiple orchards of contrasting agricultural practices to study the ecological drivers of phyllosphere bacterial communities of apple tree (Malus domestica, Borkh.). We sampled up to eight apple cultivars at six orchards (three conventional, three organic) in the Eastern Townships (Canada) in 2022 and 2023. In contrast with common cross-sectional microbiome studies, our work builds on a two-year sampling design, thus allowing for the evaluation of the reproducibility of previous plant microbiome research. Our results support previous findings indicating that site and time are major drivers of apple tree bacterial community structure, yet their relative influence vary across the two sampling years. In addition, our data showed that leaf and flower bacterial alpha diversity is lower at organic sites compared to conventional sites. Overall, this study provides a comprehensive longitudinal multi-site study design highlighting the value of assessing reproducibility in plant microbiome studies and paving the way for future research in this field.
操纵植物微生物群被视为应对农业全球变化加速挑战的关键生物防治途径。最近的几项研究已经确定了叶际微生物群落的时空动态，强调需要了解植物微生物群驱动因素，以设计有效的生物防治干预措施。然而，这些研究通常样本数量较少，很少提供关于时间或当地环境相对影响的足够信息，并且很少重复进行以评估可重复性。为了解决这些局限性，我们在多个农业实践不同的果园进行了纵向采样，以研究苹果树（苹果属，Borkh.）叶际细菌群落的生态驱动因素。2022年和2023年，我们在加拿大东部乡镇的六个果园（三个传统果园、三个有机果园）对多达八个苹果品种进行了采样。与常见的横断面微生物组研究不同，我们的工作基于两年的采样设计，从而能够评估先前植物微生物组研究的可重复性。我们的结果支持了先前的研究结果，即地点和时间是苹果树细菌群落结构的主要驱动因素，但其相对影响在两个采样年份有所不同。此外，我们的数据表明，与传统果园相比，有机果园的叶片和花朵细菌α多样性较低。总体而言，这项研究提供了一个全面的纵向多地点研究设计，突出了评估植物微生物组研究中可重复性的价值，并为该领域的未来研究铺平了道路。
