The intensification of agriculture exacerbates continuous cropping obstacles, threatening global food security. Chemical fumigation effectively suppresses soil-borne diseases, however, it also reduces microbial diversity, disrupts ecological networks, and impairs essential ecosystem functions. Although organic amendments exhibit great potential in restoring soil health, a comprehensive understanding of post-fumigation microbial recovery and functional reconstruction strategies still remains elusive. This review introduces the “ecological vacuum” concept and proposes a “targeted reconstruction” framework based on fumigation-amendment synergy. We systematically summarize the antimicrobial mechanisms of chemical fumigants and their adverse effects on microbial diversity, network interactions, resistance and resilience and key ecosystem services. Building on this, we further elucidate how organic amendments promote beneficial microbes colonization, guide functional recovery and stabilize soil micro-ecosystem following fumigation. It was demonstrated that compost, straw and wormcast could provide resources and habitats for beneficial microbes colonization and community assembly. Seaweed extracts and bio-organic fertilizers promote nutrient cycling, pathogen suppression, and plant growth through enzymes, antibiotics, and signaling molecules. Humic acid and biochar improve soil structure, alleviate acidification and strengthen ecosystem stability. These insights advance sustainable soil management strategies that combine fumigation with precision amendments to enhance soil health and agricultural productivity.
Zhang et al. (2026) studied this question.