Continuous cropping problems constitute threats to perennial plant health and survival. Soil conditioners have the potential to enhance plant disease resistance in continuous cropping systems. However, how microbes and metabolites of the rhizosphere respond to soil conditioner addition remains largely unknown, but this knowledge is paramount to providing innovative strategies to enhance plant adaptation in continuous cropping systems. Here, we found that a biochar conditioner significantly improved plant survival rates in a continuous cropping system. The biochar-induced rhizosphere significantly alters the fungal community, causing a decline in fungal diversity and the downregulation of soil microbial community functionality. Specifically, the biochar-induced rhizosphere causes a reduction in the relative abundance of pathogenic Fusarium sp. and phenolic acid concentration, whose variations are the primary causes of continuous cropping problems. Conversely, we observed an unexpected bacterial diversity increase in rhizospheric and non-rhizospheric soils. Our research further identified key microbial taxa in the biochar-induced rhizosphere, namely, Monographella, Acremonium, Geosmithia, and Funneliformis, which enhance soil nutrient availability, suppress Fusarium sp., mitigate soil acidification, and reduce phenolic acid concentrations. Collectively, we highlight the critical role of regular microbial communities and metabolites in determining plant health during continuous cropping and propose a synthetic microbial community framework for further optimizing the ecological functions of the rhizosphere.

Continuous monoculture of Panax notoginseng leads to severe replant disease, yet the mechanisms by which root exudates mediate rhizosphere microbiome assembly and pathogen enrichment remain poorly understood. Here, we demonstrate that long-term root exudate accumulation acts as an ecological filter, driving the fungal community toward a phylogenetically impoverished, pathogen-dominated state. Specifically, exudates enriched the soil-borne pathogen Fusarium while reducing the abundance of potentially antagonistic fungi. In contrast, bacterial communities exhibited higher resilience, with exudates selectively enriching oligotrophic taxa such as Terrimonas and MND1, but suppressing nitrifying bacteria (e.g., Nitrospira) and plant-growth-promoting rhizobacteria (PGPR). Microbial functional profiling revealed a shift in nitrogen cycling, characterized by suppressed nitrification and enhanced nitrate reduction. Crucially, co-occurrence network analysis identified bacterial taxa strongly negatively correlated with Fusarium, providing a synthetic community blueprint for biocontrol strategies. Our study establishes a mechanistic link between root exudate accumulation and negative plant–soil feedback in monoculture systems, highlighting microbiome reprogramming as a key driver of replant disease. These insights offer novel avenues for manipulating rhizosphere microbiomes to sustain crop productivity in intensive agricultural systems.

The rhizosphere serves as the primary defense against pathogens, but rhizosphere metabolites can also act as carbon sources and signaling molecules that attract soil borne pathogenic fungi to the destruction of rhizosphere defenses. We propose that whether reducing rhizosphere metabolites improves complex microbial networks defense. Here, we found that reducing rhizosphere metabolites altered fungal community structure more than bacteria, resulting in a downward trend in fungal diversity, soil-borne pathogenic fungal Fusarium abundance, and soil microbial community functions, e.g., metabolic functions, enzyme activities, and protein expression. However, the trend is more favorable to plant growth, which might be explained by the combined effect of the upward trend in bacterial diversity in the rhizosphere and bulk soil. Furthermore, we identified biomarkers Monographella , Acremonium , Geosmithia , and Funneliformis , which negatively correlated with other differential microbiology, play a competitive role in community member interactions. they optimized the microbial ecology with functions that mobilize soil nutrients, reduce pathogens and soil acidification, and lower phenolic acids. Integrating our findings proposes new avenues for understanding the complex soil rhizosphere mysteries of the critical role of metabolites in “soil environment - microorganisms - metabolites” ecology interactions and provides a design to build synthetic microbial community to enhance defense. IMPORTANCE: While rhizosphere metabolites are known to regulate microorganisms’ composition to enhance plant immunity cooperatively. However, they also have a harmful side, which attracts soil-borne pathogenic fungi to form synergistic damage that inhibits beneficial bacteria, produces autotoxicity, destroys the rhizosphere microbial ecology, and negatively affects soil productivity and plant health. Currently, our planet is experiencing unprecedented anthropogenic-induced changes. Moreover, the complex and dynamic ecological network in the rhizosphere-an important microbial hotspot-is among the most fascinating yet elusive topics in microbial ecology. Whether reduced rhizosphere metabolites improves the microbial ecological networks remains unknown. Our findings revealed that reduced rhizosphere metabolites decrease fungal diversity, microbial community function, and pathogen abundance, while increase bacterial diversity, soil nutrients, pH, and similar factors. It is clear that reduced rhizosphere metabolites is undoubtedly beneficial for plant health and the rhizosphere ecology. Ultimately, This study provided a new comprehensive understanding of how fungi and bacteria assemble and alter in the rhizosphere and bulk soil when reduced rhizosphere metabolites. Understanding the critical role of rhizosphere metabolites in restoring micro-ecological balance will allow us to focus on regulating microbial community metabolism and root exudates, facilitate the discovery of new metabolites and interactions with microorganisms, and harness their the beneficial properties that contribute to rhizosphere microbial community assembly.

Seed germination of Paris polyphylla var. yunnanensis is intrinsically low, severely restricting its artificial propagation. Despite the known roles of ABA and GAs, the regulatory functions of other phytohormones in this process remain largely unexplored. In this study, we integrated transcriptomic and targeted metabolomic profiling to systematically investigate the dynamics of 34 phytohormones and global gene expression patterns across five germination stages of P. polyphylla seeds. Seven hormones showed significant changes during germination, including auxins, melatonin, cytokinins, and jasmonate, which exhibited distinct accumulation patterns. Integrative correlation analysis further uncovered candidate genes potentially involved in hormone biosynthesis and signaling. Collectively, our findings provide new insights into the hormonal regulation of seed germination in P. polyphylla, establish a foundational framework for understanding its germination mechanisms, and offer candidate molecular targets for improving seed propagation efficiency.