Roots can recruit beneficial microorganisms to suppress plant pathogens. However, conventional and organic practices differently shape the soil microbiome and consequently the root protection. Here, we investigated the suppressive activity of soil microbiome against the root-knot nematode (RKN) Meloidogyne incognita in horticultural areas under organic or conventional practices and the microbiome profiles in non-inoculated (RKN-absent) and inoculated (RKN-present) rhizospheres. Soils were collected from neighboring areas under long-term conventional or organic practices, but physicochemically similar. After a set of bio-tests in autoclaved and non-autoclaved soils, we concluded that the soil suppressiveness was of biological origin. However, plant growth, RKN suppression and defense induction were higher in organic soils. Also, RKN was highly suppressed when the organic soil microbiome was transferred to infested substrates. We used Illumina MiSeq platform to determine bacterial and fungal profiles in organic and conventional tomato rhizospheres, inoculated or not with M. incognita. Our data suggest that despite the higher bacterial abundance in the conventional RKN-absent rhizosphere, the organic RKN-present rhizosphere recruited more efficiently antagonistic bacteria and fungi. Microbiome α-diversity increased in the organic RKN-present rhizosphere. Antagonistic bacterial genera Pseudomonas, Serratia, Bradyrhizobium, Burkholderia and Azospirillum and fungal genera Beauveria, Clonostachys, Metarhizium, Purpureocillium and Arthrobotrys were highly abundant only in the organic RKN-present rhizosphere. This work suggests the organic and conventional practices interfere in the rhizosphere microbiome composition and consequently in the suppression of RKN, where organic practices intensified the assembly of bacterial and fungal antagonists in the presence of M. incognita.

根部可以招募有益微生物来抑制植物病原体。然而，传统和有机实践对土壤微生物群的影响不同，从而对根系保护产生了不同的影响。在这里，我们研究了土壤微生物组对根结线虫 (RKN)南方根结线虫的抑制活性在有机或传统做法下的园艺领域以及未接种（RKN 缺失）和接种（RKN 存在）根际中的微生物组谱。土壤是在长期的常规或有机实践下从邻近地区收集的，但物理化学性质相似。在高压灭菌和非高压灭菌土壤中进行了一组生物测试后，我们得出结论，土壤抑制作用是生物起源的。然而，有机土壤中的植物生长、RKN 抑制和防御诱导较高。此外，当有机土壤微生物组转移到受感染的基质时，RKN 受到高度抑制。我们使用 Illumina MiSeq 平台来确定有机和传统番茄根际中的细菌和真菌特征，接种或未接种M. incognita. 我们的数据表明，尽管在传统的 RKN 缺失根际中细菌丰度更高，但有机 RKN 存在的根际更有效地招募了拮抗细菌和真菌。存在有机 RKN 的根际微生物组 α 多样性增加。拮抗细菌属假单胞菌属，沙雷菌属，根瘤菌，鼻疽和固氮螺菌和真菌属白僵菌，Clonostachys，绿僵菌，Purpureocillium和孢节仅在有机 RKN 存在的根际中高度丰富。这项工作表明，有机和常规做法会干扰根际微生物组的组成，从而抑制 RKN，其中有机做法在南方根结线虫存在的情况下加强了细菌和真菌拮抗剂的组装。