Phytomycobiomes and Ecosystem Services: Mechanisms, Evidence and Routes to Application

Phytomycobiomes refer to the fungal consortia that inhabit plant tissues and the rhizosphere. Their documented functions include nutrient mobilization, carbon retention, stress mitigation and pathogen suppression, although measurable effects often depend on plant and soil conditions. In this review, we examine the current evidence for their ecological relevance and assess the molecular approaches most commonly used to characterize them. Arbuscular Mycorrhizal (AM) fungi, endophytes and saprotrophic taxa indicate measurable gains in nutrient acquisition, disease resistance and soil aggregation, although long-term consistency is rarely evaluated. Each function appears to have an explicit mechanistic attribution, with direct links between fungal groups, enzymatic pathways and measurable ecosystem outcomes. Several sequencing-based techniques are available, yet none offer complete accuracy. Internal Transcribed Spacer (ITS) amplicon surveys provide rapid taxonomic coverage but suffer from primer bias; shotgun metagenomics offers functional insight but at significant financial cost; and quantitative polymerase chain reaction (qPCR) assays remain useful for targeted quantification, whereas long-read technologies show promise but still lack widespread adoption. The field faces a number of unresolved constraints, including limited knowledge of host range, inconsistent performance under fluctuating environmental conditions and the absence of a standardized bioinformatic pipeline. Despite these limitations, we regard phytomycobiomes as viable candidates for replacing or reducing synthetic inputs, provided their application is guided by context-specific evidence rather than broad generalization.