suppressing pathogens, and underpinning plant health. Yet, the very practices that have boosted crop yields-intensive tillage, monoculture, and heavy usage of chemical fertilizer-often disturbs the ecological balance of these communities, creating a paradox where high productivity comes at the cost of long-term soil health and resilience. This Research Topic was conceived to explore the dynamic interaction between agricultural management strategies and soil microbial communities, with the goal of harnessing their potential for disease suppression and ecosystem sustainability.The collection of articles presented here tackles this challenge from multiple aspects, collectively illustrating that the path to sustainable agriculture lies not in managing soil as a passive substrate, but in cultivating it as a living ecosystem. By integrating highthroughput sequencing, functional gene analysis, and field experimentation, these studies move beyond descriptive accounts of microbial composition to reveal the mechanisms by which management practices can steer the microbiome toward beneficial outcomes.A central theme emerging from this Research Topic is the power of crop diversification.In a comprehensive review, Zhang et al. elucidated the potential of biological nitrogen fixation (BNF) in rice paddies-a system traditionally reliant on synthetic nitrogen. The authors dissect the paradox that while mineral nitrogen suppresses diazotroph activity, strategic management-such as straw incorporation and the selection of ammoniumtolerant bacterial strains-can sustain BNF within realistic fertilization regimes. This work highlights that enhancing a key ecosystem service is not about replacing synthetic inputs but about optimizing them in concert with biological processes. Complementing this, Liu et al.provided compelling field evidence from a citrus orchard, showing that long-term grass mulching significantly enhances soil nutrients, enzyme activities, and the abundance of beneficial Proteobacteria while reducing fungal pathogens. Crucially, the study links these microbial shifts to improved fruit quality, demonstrating that diversification can create a positive feedback loop where soil health and crop productivity are mutually reinforced.The principle of diversification is further explored across cropping systems. Liu et al.demonstrated that rotating processing tomatoes with maize or seed pumpkin profoundly alters soil microecology. Their work reveals that rotation not only reshapes bacterial and fungal community composition but also enhances network complexity-a topological feature associated with greater functional stability and resiliencecontrasting sharply with the simplified, less connected networks found under continuous monoculture, which are more vulnerable to disturbance. Similarly, Gu et al.showd that intercropping tobacco with soybean or maize improves soil fertility and microbial network modularity, fostering a more robust ecosystem. Notably, the study identifies distinct effects: tobacco-soybean intercropping enhanced nitrogen availability via legume symbiosis, while tobacco-maize intercropping enriched functional taxa like Actinobacteria, underscoring that the choice of companion crop can be tailored to specific soil health objectives. In a contrasting case, Wooliver et al.offered a nuanced view from a four-year field experiment in the United States, finding that while cover cropping and crop rotation did not increase overall microbial diversity, they strongly influenced community composition-reducing fungal plant pathogens and transiently increasing arbuscular mycorrhizal fungi (AMF). This work is a crucial reminder that diversity metrics alone are insufficient; the functional composition of the community is a more sensitive indicator of management impacts. Zhang et al. further examined continuous cropping obstacles in Ganoderma leucocontextum cultivation, revealing a shift from bacterial-to fungal-dominated communities over the growth cycle, with Ganoderma itself becoming the dominant genus at maturity alongside decreasing polysaccharides and increasing triterpenoid acids-findings that link microbial succession to both fungal productivity and bioactive compound accumulation.Beyond diversification, the direct application of soil amendments represents another powerful lever for microbiome management. Zheng et al. investigated the coapplication of biochar and Bacillus subtilis in dryland soils, finding a synergistic effect that increased microbial biomass, altered bacterial and fungal community structure, and enhanced enzyme activity. This work exemplifies a "dual-mechanism" approach, where a structural amendment (biochar) and a biological inoculant work in concert to reshape the soil environment and its biota. The theme of synergy is powerfully extended by Chen et al., who explored the combined use of Bacillus spp. with graphene oxide (GO) in the rhizosphere of peach trees suffering from anthracnose. Their results show that the combined treatments were more effective than either agent alone in restoring soil physicochemical properties and microbial community function toward a healthy state.This study opens a new frontier in "nanobio" interventions, suggesting that the unique properties of nanomaterials can be harnessed to potentiate the effects of beneficial microbes.In the context of disease, Sun et al. identified Ralstonia as the key pathogen in ginger wilt, demonstrating that disease dramatically reshapes the rhizosphere microbiotareducing beneficial phyla like Acidobacteria and enriching a pathogenic consortium with enhanced stress-tolerance potential. This study underscores the importance of diagnosing the specific microbial dysbiosis associated with a disease to target interventions effectively. The use of microbial inoculants alone is also explored, with Fernández-Pastrana et al. demonstrating that a humic-rich biofertilizer fortified with Bacillus or Pseudomonas strains not only increased alfalfa yield and quality but also maintained microbial diversity and, intriguingly, lowered soil resistance to β-lactam antibiotics-a novel finding with significant implications for the One Health approach.While management aims to enhance beneficial microbes, it must also mitigate the negative impacts of agriculture on the climate. Sun et al. addressed this critical intersection by investigating how partial substitution of chemical nitrogen with organic amendments reduces nitrous oxide (N₂O) emissions in tea plantations. Their structural equation modeling reveals that the substitution alters soil pH and microbial biomass, which in turn modulates the abundance of key denitrification genes (nirS, nirK, nosZ), ultimately curbing N₂O release. This work elegantly demonstrates that managing for soil health can simultaneously deliver climate mitigation benefits. Collectively, these articles advance a transformative vision for agroecosystem management: one where soils are managed not as inert growing media but as dynamic, living systems whose microbial constituents can be deliberately cultivated to support productivity, resilience, and environmental health. The emerging paradigm emphasizes functional outcomes over taxonomic metrics, synergistic interventions over singleagent solutions, and ecological selectivity over broad-spectrum disruption. Future research should prioritize the translation of these mechanistic insights from controlled experiments into practical, scalable management strategies that reconcile the demands of food production with the imperatives of environmental stewardship.We extend our gratitude to all the authors, reviewers, and editorial staff who contributed to this Research Topic. Their collective efforts provide a rich and compelling foundation for future research aimed at unlocking the full potential of the soil microbiome for a sustainable and food-secure future.
Shen et al. (Thu,) studied this question.