Multi-omics integration reveals the microecological collapse driving primordia degeneration of Dictyophora rubrovolvata in novel organomineral substrate cultivation

The novel organomineral substrate (NOS) cultivation of Dictyophora rubrovolvata promotes rapid mycelial growth but suffers from mass primordia degeneration and necrosis with poorly understood microecological mechanisms. In this study, we employed metagenomics, untargeted metabolomics, and physicochemical profiling to elucidate the spatial-temporal dynamics of the substrate microenvironment across three developmental stages. Results demonstrated that the excessive initial primordia formation triggered rapid nutrient exhaustion, notably alkali-hydrolyzable nitrogen, accompanied by pH stress. This physicochemical deterioration coincided with a profound functional breakdown of the substrate microbiome, characterized by the sharp downregulation of core carbohydrate-active enzymes (CAZymes) and nitrogen-cycling genes (e.g., narG, nirK). Topological analysis revealed substantial topological differences and structural fragmentation in the cross-kingdom co-occurrence network observed between T2 and T3 stages, marked by a surge in competitive interactions. This structural collapse facilitated the explosive invasion of keystone pathogens, primarily Clathrus, Amaricoccus , and Chryseobacterium. Furthermore, metabolomic integration indicated that the proliferation of these late-stage opportunistic taxa was highly coupled with the marked accumulation of suspect allelopathic metabolites (e.g., 2,4-dichloro-6-nitrophenol) while simultaneously suppressing bacterial multidrug efflux pumps, thereby paralyzing the microecosystem’s detoxification capacity. Our tripartite network integration suggested that this coordinated biochemical stress and nutritional depletion exhibited strong covariation with the irreversible abortion of fruiting bodies. Conclusively, primordia degeneration of D. rubrovolvata in the organomineral substrate is tightly associated with a coordinated microecological shift characterized by rapid nutrient depletion, network destabilization, and biochemical stress. Importantly, these findings and the proposed mechanistic framework are specific to the high-load NOS cultivation matrix and cannot be directly extrapolated to traditional soil-based systems without longitudinal comparative multi-omics validation. Diagnosing these substrate-specific bottlenecks provides actionable engineering targets for formula optimization.