Hidden allies: Decoding the core endohyphal bacteriome of Aspergillus fumigatus

Abstract

Background Bacterial-fungal interactions that influence the behavior of one or both organisms are common in nature. Well-studied systems include endosymbiotic relationships that range from transient (facultative) to long-term (obligate) associations. Diverse endohyphal bacteria associate with fungal hosts, emphasizing the need to better comprehend the fungal bacteriome. We evaluated the hypothesis that the human fungal pathogen Aspergillus fumigatus harbors an endohyphal community of bacteria that influence the host phenotype. We analyzed whether 39 A. fumigatus strains, mainly clinical isolates, show stable association with diverse endohyphal bacteria. All fungal strains analyzed were derived from single-conidium cultures that were subjected to antibiotic and heat treatments. Results The fungal bacteriome, inferred through analysis of bacterial diversity within the fungal strains (short- and long- read sequencing methods), revealed the presence of core endohyphal bacterial genera (≤ 19). Microscopic analysis further confirmed the presence of endobacteria within the hyphae of distinct fungal strains. The fungal strains exhibited high genetic diversity and phenotypic heterogeneity in terms of drug susceptibility and virulence (using Galleria mellonella as an infection model). No correlations were observed between genomic or functional traits and bacteriome diversity. However, the abundance of the Bryobacter genus exhibited a positive correlation with fungal virulence; and the presence of other bacteria genera was correlated with posaconazole susceptibility. Based on the genetic pool of the endobacteriome of A. fumigatus both the functional annotation of prokaryotic taxa and the metabolic space could be predicted showing functional roles in major categories, for example, nitrogen fixation and chemoheterotrophy. Conclusions These observations suggest intricated metabolic dependencies between fungal strains and their endohyphal bacteria partners. Our study emphasizes the existence of complex interactions between fungi and bacteria and the need to better understand the relationship between endohyphal bacteria and fungal virulence.