It is well established that root exudates play a crucial role in shaping the assembly of plant rhizosphere microbial communities. Nonetheless, our understanding of how different types of exudates influence the abundance of potential pathogens in soil remains insufficient. Investigating the effects of root exudates on soil-dwelling pathogenic fungi is imperative for a comprehensive understanding of plant–fungal interactions within soil ecosystems and for maintaining soil health. This study aimed to elucidate the effects of the principal components of root exudates—flavonoids (FLA), phenolic acids (PA), and organic acids (OA)—on soil microbial communities and soil properties, as well as to investigate their mechanisms of action on soil potential pathogenic fungi. The results demonstrated that the addition of these components significantly modified the composition and diversity of soil microbial communities, with OA treatment notably altering the composition of dominant microbial taxa. Furthermore, the introduction of these substances facilitated the proliferation of saprophytic fungi. Additionally, the incorporation of flavonoids, phenolic acids, and organic acids led to an increased abundance of potential pathogenic fungi in the soil, particularly in the FLA and PA treatments. It was observed that the addition of these substances enhanced soil fertility, pH, and antioxidant enzyme activity. Specifically, FLA and PA treatments reduced the abundance of dominant microbial taxa, whereas OA treatment altered the composition of these taxa. These findings suggest that the inclusion of flavonoids, phenolic acids, and organic acids could potentially augment the enrichment of soil potential pathogenic fungi by modulating soil properties and enzymatic activities. These results offer valuable insights into the interactions between plants and fungal communities in soil ecosystems and provide a scientific foundation for the management and maintenance of soil health.

Heterologous double-root grafting represents an effective strategy to mitigate challenges associated with continuous coffee cropping and reduce soil-borne diseases. However, its specific regulatory mechanism remains unclear. Therefore, a field experiment was conducted including six different grafting combinations for C. canephora cv. Robusta (Robusta) and Coffea Liberica (Liberica): Robusta scion with a homologous double root (R/RR), Liberica scion with a homologous double root (L/LL), Robusta scion with a heterologous double root (R/RL and L/RL), and Liberica scion with a heterologous double root (L/LR and R/LR); these combinations were conducted to clarify the effects of heterologous double-root grafting combinations on the root exudates and soil microbial diversity, structure, and function of Robusta and Liberica. The results demonstrated notable differences in root exudates, rhizosphere microbial structure, and function between Robusta and Liberica. Despite Liberica having lower diversity in its rhizosphere microbial communities and relatively higher levels of potential pathogenic bacteria, it showed stronger resistance to diseases. Roots of Robusta in heterologous double-root coffee seedlings significantly enhanced the secretion of resistance compounds, increased the relative abundance of potentially beneficial bacteria, and reduced the relative abundance of potential pathogenic fungi. This enhances the rhizosphere immunity of Robusta against soil-borne diseases. The results indicated that grafting onto Liberica roots can strengthen resistance mechanisms and enhance the rhizosphere immunity of Robusta, thereby mitigating challenges associated with continuous cropping.

Mulching cultivation with agricultural wastes is the main production pattern of coffee at present, but the effect of mulching cultivation on photosynthetic physiological processes of coffee plants is still not clear. Therefore, a randomized block design was adopted to establish a field experiment by one-year-old Coffee Canephora seedlings in this study. There were four types of mulch treatments, including non-mulch coffee waste (C), mulching coffee litter (L), mulching coffee cascara (cherry pericarp, P), and mulching coffee litter and cascara (LP) in this field experiment. Soil properties and microenvironment (e.g., moisture, temperature, pH, bulk density, organic matter content, alkali-hydrolyzed nitrogen content, available potassium content, and available potassium content), agronomic traits (e.g., specific leaf area, leaf area index, plant height, and relative chlorophyll content), and photosynthetic indices (e.g., photosynthesis, transpiration, respiration, stomatal conductance, intercellular CO₂ concentration, water use efficiency, and carbon use efficiency) were investigated to determine the effects of different coffee waste mulches on the photosynthetic physiology of coffee seedlings. The results show that coffee litter and cascara mulch significantly reduced soil temperature by 0.42 or 0.33 °C, respectively, and coffee litter rather than cascara mulch significantly increased the soil’s available potassium content by 46.28%, although coffee waste mulch did not affect other soil properties or microenvironment indices; coffee cascara mulching significantly increased the specific leaf area and net and gross photosynthesis of coffee by 45.46%, 78.33%, and 91.72%, respectively, but the mulching treatments did not affect stomatal conductance, transpiration, or carbon use efficiency in this study. Additionally, coffee cascara mulching increased leaf respiration and net and gross water use efficiency by 109.34%, 80.54%, and 104.95%, respectively. The coffee cascara mulching alone had the most significant positive impact on the photosynthetic index, followed by a combination of litter and cascara, litter alone, and the control treatment. The observed variations in the coffee photosynthetic index may be attributed to the reduction of soil temperature caused by mulching treatments rather than the increase in soil nutrients content. These results indicate that coffee cascara mulching could effectively promote photosynthesis and the growth of coffee seedlings by improving the soil microenvironment.

Improper disposal of coffee-processing by-products can cause environmental pollution, greenhouse gas emissions, and resource loss, whereas their reuse in coffee plantations may support sustainable production. This review systematically examines the material properties, stabilization methods, field application pathways, agronomic effects, quality responses, and environmental risks of coffee-pulp-type by-products in cultivation. Relevant studies published up to June 2026 were retrieved from Web of Science, Scopus, ScienceDirect, SpringerLink, Google Scholar, and CNKI and qualitatively synthesized along the soil–plant–quality continuum. Current evidence suggests that properly stabilized materials, applied at appropriate rates, can improve soil organic matter, structure, water and nutrient retention, microbial activity, plant growth, photosynthesis, and crop yield in plantations. They may also indirectly influence green bean quality by regulating sugars, amino acids, chlorogenic acids, and caffeine. However, these effects depend strongly on material properties, maturity, application rate, coffee genotype, soil and climatic conditions, and management practices. Excessive or insufficiently decomposed materials may cause soil acidification, phytotoxicity, oxygen depletion, nutrient imbalance, and yield–quality trade-offs. Overall, recycling within plantations can turn processing waste into farm inputs, reinforce on-farm carbon and nutrient cycles, ease disposal burdens, and advance BCG and wider circular-economy principles in practice.