Editorial: Soil Microbial Communities to Promote Suppressiveness against Soil-Borne Pathogens and Diseases

Jose Ignacio Marín-Guirao¹Dongdong Yan²Francesco Di Gioia³Massimo Pugliese⁴Jesus Dionisio Fernandez-Bayo^5*

• ¹Andalusian Institute of Agricultural and Fisheries Research Training (IFAPA), La Mojonera, Spain
• ²Chinese Academy of Agricultural Sciences, Beijing, China
• ³The Pennsylvania State University - University Park Campus, University Park, United States
• ⁴University of Turin - Agroinnova, Grugliasco, Italy
• ⁵Department of Soil Science and Agricultural Chemistry. University of Granada., Granada, Spain

The phaseout of methyl bromide, stringent regulations on fumigant application, and the consumer demand for safer food, are leading farmers towards the adoption of more sustainable soil management practices for the control of soil-borne pathogens (Rosskopf et al., 2024). In this context, organic amendment-based approaches like soil biofumigation, biosolarization, and anaerobic soil disinfestation have emerged as promising alternatives to the use of synthetic soil fumigants. Especially, for their ability to suppress soilborne pathogens while preserving soil health and the environment. However, their widespread adoption is still limited mainly by technical and sustainability constraints, such as the variability in efficacy across soils and climates, the relatively high cost, the type of amendment, and the use of impermeable plastic barriers. Given these limitations, new approaches aimed at enhancing natural soil suppressiveness and on shifting soil microbial communities against soil-borne pathogens have gained increasing attention. Soil microorganisms, whether native or introduced ex-novo, play a pivotal role in providing ecosystem services that can contribute to this goal, enhancing both soil and plant health. Thus, harnessing this biological potential offers a promising pathway to reduce agrochemical dependency and increase the resilience of cropping systems.The main aim of this research topic was to expand knowledge on how soil management practices influence microbial communities and their ability to suppress soil-borne pathogens. The focus spans both fundamental understanding and practical implications, addressing the effects of soil amendments, microbial community shifts associated with disease suppression, interactions with plant defense mechanisms, and the overall effects on soil health and crop yield. Collectively, the 12 articles included in this research topic reflect a growing body of evidence on how soil microbial communities can contribute to the sustainable management of soil-borne pathogens and enhance soil health and productivity (Table 1). Crop genotype and previous cultivation practices have also been identified as major factors influencing the composition and assembly of soil and rhizosphere microbial communities. Shi et al. demonstrated that the deterministic assembly of biocontrolassociated microbial communities in the rhizosphere of Panax notoginseng was particularly evident during the third year of root development and was influenced by plant genetic pathways. Transcriptomic analyses revealed that genes involved in protein export, alkaloid and amino acid biosynthesis, along with associated transcription factors, contributed to the recruitment of beneficial microbial taxa. Tian et al. showed that allylisothiocyanate fumigation significantly alters soil microbial diversity and composition, notably promoting Actinomycetota and suppressing Pseudomonadota. However, its effects on endophytic bacterial communities differed among pepper genotypes, highlighting the complex interactions among fumigation, soil microbiota, and plant internal microbiomes.Finally, crop rotation and intercropping have proven to be effective strategies for disease management linked to soil microbiome modulation. Hong et al. showed that rotating vanilla with pandan or sweet rice tea significantly reduced Fusarium wilt by decreasing F. oxysporum abundance, enhancing fungal diversity, and enriching beneficial microbial taxa. In addition, soil pH raised along with the altered microbial communities, was directly associated with pathogen suppression and enhanced vanilla disease resistance. Wang et al. demonstrated that inter-cropping Torreya grandis with Polygonatum sibiricum enhanced soil microbial diversity, reduced the relative abundance of fungal genera, including potential soil-borne pathogens (e.g., Cladosporium, Fusarium, Neocosmospora), and enriched microbial groups involved in carbon and nitrogen cycling.These findings further support the role of diversified plant systems in fostering microbial diversity and pathogen suppression. The studies in this article collection offer valuable frameworks for transitioning toward more sustainable alternatives in the management of soil-borne pathogens. Together, this topic, underscore the importance of managing soil microbial communities as a cornerstone of any sustainable strategy aimed at improving soil and plant health. They provide compelling evidence that biotic and abiotic interventions, including microbial inoculants, organic amendments, genotype selection, and cropping system diversification, can enhance pathogen suppression by promoting beneficial taxa and restructuring microbial networks. Nevertheless, the complexity of microbial interactions, underlying mechanisms and key microbial traits in disease-suppressive soils, remain largely elusive. Therefore, recognizing that each agroecosystem presents unique conditions and challenges, tailored approaches are required for the successful generation of diseasesuppressive soils.