Song Yang, Atza Elisa, Sánchez-Gil Juan J, Akkermans Doretta, de Jonge Ronnie, de Rooij Peter G H, Kakembo David, Bakker Peter A H M, Pieterse Corné M J, Budko Neil V, Berendsen Roeland L
Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands.
Numerical Analysis, Delft Institute of Applied Mathematics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands.
Nat Microbiol. 2025 Jan;10(1):28-40. doi: 10.1038/s41564-024-01872-x. Epub 2024 Dec 27.
Potato vigour, the growth potential of seed potatoes, is a key agronomic trait that varies significantly across production fields due to factors such as genetic background and environmental conditions. Seed tuber microbiomes are thought to influence plant health and crop performance, yet the precise relationships between microbiome composition and potato vigour remain unclear. Here we conducted microbiome sequencing on seed tuber eyes and heel ends from 6 potato varieties grown in 240 fields. By using time-resolved drone imaging of three trial fields in the next season to track crop development, we were able to link microbiome composition with potato vigour. We used microbiome data at varying taxonomic resolutions to build random forest predictive models and found that amplicon sequence variants provided the highest predictive accuracy for potato vigour. The model revealed variety-specific relationships between the seed tuber microbiome and next season's crop vigour in independent trial fields. With a coefficient of determination value of 0.69 for the best-performing variety, the model accurately predicted vigour in seed tubers from fields not previously included in the analysis. Moreover, the model identified key microbial indicators of vigour from which a Streptomyces, an Acinetobacter and a Cellvibrio amplicon sequence variant stood out as the most important contributors to the model's accuracy. This study shows that seed potato vigour can be reliably predicted based on the microbiota associated with seed tuber eyes, potentially guiding future microbiome-informed breeding strategies.
种薯活力，即种薯的生长潜力，是一个关键的农艺性状，由于遗传背景和环境条件等因素，在不同的生产田块中差异显著。种薯微生物群被认为会影响植物健康和作物表现，然而微生物群组成与种薯活力之间的确切关系仍不清楚。在此，我们对在240块田块种植的6个马铃薯品种的种薯芽眼和薯尾进行了微生物群测序。通过对下一季三个试验田进行时间分辨无人机成像来跟踪作物生长发育，我们得以将微生物群组成与种薯活力联系起来。我们使用不同分类分辨率的微生物群数据构建随机森林预测模型，发现扩增子序列变体对种薯活力的预测准确性最高。该模型揭示了独立试验田中种薯微生物群与下一季作物活力之间的品种特异性关系。对于表现最佳的品种，决定系数值为0.69，该模型准确预测了先前未纳入分析的田块中种薯的活力。此外，该模型确定了活力的关键微生物指标，其中链霉菌、不动杆菌和纤维弧菌的扩增子序列变体是模型准确性的最重要贡献者。这项研究表明，基于与种薯芽眼相关的微生物群可以可靠地预测种薯活力，这可能为未来基于微生物群的育种策略提供指导。
