González Máximo, Araya-Angel Juan Pablo, Muñoz Ashlie, Alfaro-Flores Adalid, Cardinale Massimiliano, Stoll Alexandra
Laboratorio Fisiología y Hologenómica Vegetal, Centro de Estudios Avanzados en Zonas Áridas, CEAZA, La Serena 1720256, Chile.
Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, La Serena 1720256, Chile.
Microorganisms. 2025 Jul 1;13(7):1550. doi: 10.3390/microorganisms13071550.
The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, (wild species), var. (Cherry tomato), and the landrace 'Poncho Negro' and the modern cultivar 'Cal Ace', grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant-microbe interactions.
驯化过程不仅降低了番茄基因型的等位基因多样性，还影响了与微生物招募、其组成及其在植物宿主不同区室中的多样性相关的遗传性状。此外，这一过程包括从自然土壤到农业土壤的转变，这两种土壤在养分有效性、理化性质和农业实践方面存在差异。因此，现代栽培品种可能无法招募对其野生近缘种有益的微生物类群，从而可能失去重要的生态功能。在本研究中，我们分析了四种番茄基因型（野生种）、var.（樱桃番茄）以及地方品种“Poncho Negro”和现代栽培品种“Cal Ace”在自然土壤和农业土壤中生长时的系统发育关系和根际微生物群。使用16S rRNA（细菌）和ITS2（真菌）扩增子测序鉴定微生物群落，从而实现跨域分类特征分析。虽然土壤类型是总体微生物多样性的主要驱动因素，但宿主基因型影响特定微生物类群的招募，这些类群根据基因型和土壤类型的遗传多样性表现出不同的招募模式。此外，共现网络分析确定了两个主要聚类：第一，类群与特定基因型或土壤类型没有任何优先关联，而第二个聚类揭示了与自然土壤中的真菌类群和农业土壤中的细菌类群相关的特定微生物模式。最后，功能分析表明，番茄驯化导致特定功能丧失，且与土壤类型无关。这些发现突出了植物基因型作为微生物群落组装中的微调因子的作用，对旨在恢复有益植物-微生物相互作用的育种策略具有启示意义。
