Microbial Co-inoculation for Biological Control of Seedling Diseases in Conifers: A Systematic Review of Defence Mechanisms and Host Transcriptomic Responses

ABSTRACT Root rot and damping-off pathogens, principally Heterobasidion annosum sensu lato and soilborne Rhizoctonia and Fusarium species, inflict severe economic and ecological losses in conifer forests globally. Biological control using beneficial microorganisms represents a sustainable alternative to chemical fungicides; however, the conditions under which microbial co-inoculation outperforms single-agent treatments, and the molecular defence mechanisms involved, remain poorly resolved. This systematic review synthesised experimental evidence published between 2005 and 2026 to evaluate microbial co-inoculation strategies against conifer root rot and damping-off, characterise host transcriptomic defence responses, and identify knowledge gaps limiting translational application. Structured searches of Web of Science Core Collection, PubMed, Scopus, and CABI Abstracts retrieved 920 records (430 unique after deduplication), of which 20 were included. Co-inoculation with functionally complementary agents, including ectomycorrhizal fungi, dark septate endophytes, antagonistic fungi, rhizobacteria, actinomycetes, and fungal-bacterial consortia, consistently outperformed single-agent treatments when applied prophylactically, achieving up to 74% and 92% reductions in disease severity and pathogen transcript abundance in the Pinus massoniana – Fusarium oxysporum and Picea abies – Heterobasidion parviporum systems, respectively. Defence priming emerged as the common mechanistic basis, operating through either transcriptional amplification or transcriptional restraint in ectomycorrhizal buffering contexts. The phenylpropanoid pathway, pathogenesis-related proteins, jasmonate/ethylene signalling genes, and peroxidases were the most consistently induced defence components. Co-inoculation efficacy depended on prophylactic timing, mechanistic complementarity among agents, and host–pathosystem receptivity. Major knowledge gaps include the absence of field-based trials, unidentified systemic priming signals, uncharacterised effector secretomes, and the absence of pathogen evolutionary and economic analyses.