Maintaining soil health is fundamental to sustaining agricultural productivity, however, the intricate role of soil microbial diversity in this process is not fully understood. Current research acknowledges that soil microorganisms including bacteria, fungi, and archaea are pivotal in driving essential soil functions such as nutrient cycling, organic matter decomposition, and disease suppression. However, the impacts of global environmental changes and intensive agricultural practices on the diversity of these microorganisms remain a critical gap in the literature. This gap is significant because a decline in microbial diversity could severely compromise soil health, and consequently crop productivity. Here, we provide a comprehensive review of the factors influencing soil microbial diversity and examine their implications for crop performance. We assess both natural factors such as soil pH, moisture, temperature, and vegetation type as well as human-induced factors including tillage systems and fertilizer application. The review synthesizes recent findings on how these factors shape microbial communities and their functional roles in nutrient cycling, soil structure formation, and disease suppression. Our analysis highlights the mechanisms by which microbial diversity enhances plant growth and yield, addressing the gap in understanding the direct links between microbial diversity and agricultural outcomes. Our findings underscore the urgent need for sustainable agricultural practices that protect and enhance microbial diversity to safeguard long-term soil fertility and crop productivity. By addressing the challenges in manipulating soil microbial communities and integrating microbial ecology with crop management practices, this research advances our ability to sustain agricultural systems in the face of global environmental changes.

Current agricultural practices face numerous challenges, including declining soil fertility and heavy reliance on chemical inputs. Rhizosphere microbial metabolites have emerged as promising agents for enhancing crop health and yield in a sustainable manner. These metabolites, including phytohormones, antibiotics, and volatile organic compounds, play critical roles in promoting plant growth, boosting resistance to pathogens, and improving resilience to environmental stresses. This review comprehensively outlines the mechanisms through which rhizosphere microbial metabolites influence crop health, traits, functional components, and yield. It also discusses the potential applications of microbial secondary metabolites in biofertilizers and highlights the challenges associated with their production and practical use. Measures to overcome these challenges are proposed, alongside an exploration of the future development of the functional fertilizer industry. The findings presented here provide a scientific basis for utilizing rhizosphere microbial metabolites to enhance agricultural sustainability, offering new strategies for future crop management. Integrating these microbial strategies could lead to increased crop productivity, improved quality, and reduced dependence on synthetic chemical inputs, thereby supporting a more environmentally friendly and resilient agricultural system.

Background: Ecologically derived synthetic communities can provide robust plant benefits, yet generalizable rules for assembling multifunctional consortia remain limited. We hypothesized that a “top-down” community assembled from an ecological core would yield complementary functions and resilience superior to reductionist mixes. Results: We distilled an eight-member, Bacillus-dominated synthetic community (hereafter referred to as SynCom) from a rice–duckweed agroecosystem by targeting taxa consistently shared across soil, root and shoot niches. Under greenhouse conditions, the SynCom concurrently promoted rice growth and suppressed sheath blight caused by Rhizoctonia solani , reducing the final disease index by 70% without detectable phytotoxicity. Leave-one-member perturbations (−Dx), combined with untargeted LC–MS profiling and qRT-PCR of biosynthetic genes, revealed a division-of-labor architecture: individual strains specialized in auxin production, siderophore-linked iron mobilization, or lipopeptide/polyketide-based antagonism. These complementary yet partially redundant contributions mapped members, metabolite pools, plant outcomes and rendered community performance resilient to single-member loss. Across −Dx contrasts, the complete SynCom uniquely recovered the full suite of plant-growth metabolites (e.g., indole-3-acetic acid, acetoin/2,3-butanediol) together with antimicrobial chemistries (e.g., surfactin, bacillomycin, fengycin, difficidin). We formalize an assembly heuristic, ecological core, complementary functions, redundancy check, that links ecological origin to predictable, multi-trait performance. Conclusions: A top-down, ecology-guided route can generate a multifunction SynCom with demonstrated greenhouse efficacy and mechanistic transparency. By coupling-member perturbations with multi-omics readouts, our study provides a transferable rule for building resilient plant-associated consortia and a tractable framework for future genetic and in-plant chemical confirmations.

Solenopsis invicta, often known as the red imported fire ants (RIFAs), is a well-known global invasive ant species that can be found in agricultural, urban, and natural environments worldwide. Simultaneously, it also inhabits the soil. Biochar is generated by the pyrolysis of organic matter under high-temperature anoxic environments and widely used in agricultural ecosystems and soil amendment. However, to date, it remains unknown as to whether soil application of biochar has a negative effect on RIFAs. In our study, we investigated the toxicity and irritability effects of different amounts of biochar (0%, 1%, 2%, 5%, 10%, and 20%) introduced into the soil on red fire ants; upon comparison with the control soil (0% biochar), the application of 1%, 2%, and 5% biochar did not result in significantly different results. But the utilization of biochar at a concentration over 10% effectively repelled the RIFAs, resulting in their departure from the treated soils. High doses of biochar were able to cause death of red fire ants; the mortality rate of red fire ants reached 55.56% after 11 days of 20% biochar treatment. We also evaluated the effects of biochar on four behaviors of red fire ants, namely aggregation, walking, grasping, and attacking; 20% of the biochar treatment group reduced aggregation by 64.22% and this value was 55.22%, 68.44%, and 62.36% for walking, grasping, and attacking. Finally, we measured the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) enzyme activity and malondialdehyde (MDA) content in red fire ants; the results showed that the activities of the three enzymes increased with the increase in biochar addition, which indicated that a high dose of biochar induced oxidative stress in red fire ants. Our results indicate that biochar has the potential to cause toxicity and repel red imported fire ants (RIFAs) in a manner that is dependent on the concentration. We propose that biochar could be utilized in the control and manufacturing of baits for red fire ant management. This work establishes a foundation for the prevention and management of red fire ants and the logical utilization of biochar.