Diversidad y prevalencia de nematodos fitoparásitos en patrones de Prunus en España, con énfasis en la microbiota del suelo y agentes de control biológico

The genus Prunus includes more than 400 species of trees and shrubs distributed worldwide. Several of these species provide nuts and fruits that are highly appreciated by consumers and are of great economic value, including almond, apricot, cherry, nectarine, peach, and plum. Almond (Prunus dulcis) is one of the oldest domesticated trees in the world and plays a crucial cultural and economic role in Mediterranean societies. Specifically, Spain is one of the world’s leading almond producers has the largest area devoted to its cultivation. In recent decades, almond production has undergone a major revolution driven by the widespread adoption of new rootstocks and management practices. These innovations have enabled the transition from traditional rainfed groves in marginal areas to intensive irrigated systems with higher productivity. However, such intensification may increase the incidence and severity of plant pests and diseases. Plant-parasitic nematodes (PPNs) are among the most damaging soil-borne pathogens affecting Prunus trees, limiting their growth, productivity, and even survival. Nematodes are microscopic animals that inhabit nearly every ecosystem and occupy all trophic levels in the soil food web. While many are free-living and play key ecological roles, several genera of PPNs pose a significant threat to Prunus crops. Specifically, the most damaging PPN genera include root-knot nematodes (RKNs; Meloidogyne spp.), root-lesion nematodes (RLNs; Pratylenchus spp.), dagger nematodes (Xiphinema spp.), and ring nematodes (Criconemoides spp.). Their capacity to survive under unfavourable conditions, wide host range, microscopic size, and ease of spread make their eradication challenging. Currently, the most sustainable and environmentally friendly strategies to manage PPNs in perennial crops are the use of RKN-resistant rootstocks and biological control agents (BCAs). Therefore, deciphering the diversity of nematodes, the factors affecting their distribution, and the soil microbiota associated with Prunus crops is essential for developing effective management practices. This Doctoral Thesis aimed to unravel the diversity of PPNs, study the influence of environmental factors on the variation of nematode community composition, and determine the presence of potential indigenous BCAs. To investigate the current problems associated with PPNs in Prunus crops, a comprehensive survey was conducted across 218 sampling points in 186 commercial groves covering the principal Prunus-producing areas in Spain. A total of 84 PPN species, belonging to 32 genera, were identified through an integrative taxonomic approach combining morphological, morphometric, and molecular data. This research provides a complete characterization of 24 Paratylenchus species, including five newly described species, and two newly described species of the genus Criconema isolated from the Prunus rhizosphere, as well as from adjacent natural habitats and neighbouring crops. Morphological, morphometric, and molecular data generated in this research confirm the substantial cryptic diversity within both genera and underscore the need to apply integrative taxonomy for accurate species identification. This survey also revealed the presence of PPN species considered among the most damaging for Prunus spp., including Meloidogyne arenaria, M. incognita, M. javanica, Pratylenchus penetrans, and Pra. vulnus. To study main drivers shaping nematode assemblage composition, 19 climatic variables, 12 soil physicochemical parameters, and 5 categorical variables related to agronomic management practices were considered. Our results indicate that soil physicochemical properties and climate conditions were the most influential factors determining the distribution and abundance of PPNs. This research revealed the presence of several antagonist organisms with known activity against RKNs, including Metacordyceps chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperellum. However, the levels of Meloidogyne egg parasitism observed were insufficient to exert significant biological control under field conditions. Our findings highlight the need to preserve biodiversity and improve agricultural soil quality to enhance the activity and effectiveness of native BCAs and promote soil suppressiveness.