The Pathomycosphere: A Spatially Defined Framework in Pathogen Ecology

Fungal pathogens have historically been studied as autonomous agents, as self-contained units independent of their associated microbiota, with disease outcomes attributed to fungal virulence factors acting on susceptible hosts. However, many pathogenic fungi harbor bacterial associates that influence their ecology, persistence and virulence. The pathobiome concept addressed this limitation by framing disease as an outcome of multi-kingdom interactions. Yet most pathobiome studies rely on correlative analyses of microbial abundances with pathogens, lacking spatial resolution to identify which microorganisms physically interact with pathogenic structures. Conversely, the hyphosphere provides micrometer-scale spatial resolution but has been investigated predominantly in non-pathogenic fungi. Here, we propose the pathomycosphere as a spatially defined and experimentally tractable subset of the pathobiome: a hypha-associated microbial assemblage in which physical association with the pathogenic member, prolonged or transient has a consequence for the pathogen's biology, with pathogenicity residing in the fungus, an associated microorganism or their interaction. This framework bridges the pathobiome and hyphosphere concepts by anchoring disease-associated microbial interactions to hyphal interface, where mechanistic investigation becomes feasible. Pathomycosphere provides operational tractability to explore microbial partnerships contributing to pathogenesis, and positions fungal-associated bacterial consortia as important components of pathogen biology with relevance to disease ecology beyond agricultural systems.