Abstract
Background: Over the past several years, the scientific community has described the diversity of microbial communities in a variety of soils associated with plants, but at present, little is known about the specific diversity of the soil fungal microbiome involving bacteria colonizing the surface of fungi (i.e., exo-bacteria) or existing within fungal hypha (i.e., endobacteria). This study aimed to collect, identify, and characterize several fungi and their associated (endo- and exo-) microbiome obtained from the rhizosphere of six different plants. Microcosm devices called fungal highway columns, containing one of four plant-based media as attractants, were placed in the rhizosphere of six different plants. The isolated fungi and their associated endo- and exo- bacteria were identified by sequencing of the ITS (fungi) or 16S (bacteria) rRNA regions, followed by Scanning Electron Microscope (SEM), and fluorescence in situ hybridization (FISH) imaging.Results: Most of the fungi recovered are known plant pathogens, such as Fusarium, Pleosporales, and Cladosporium together with species associated with the soil, e.g. Kalmusia. The exo-bacteria recovered were previously described as plant promoters, such as Bacillus, Rhizobium, Acinetobacter or Ensifer. The interactions between fungi and exo-bacteria recovered from fungal highway columns were further investigated via confrontation assays. From the reconstruction of the potential co-occurring bacterial-fungal associations in the rhizosphere, we discovered that the most promiscuous exo-bacterium group (associated with diverse fungi) was Bacillus. From the study of the endobacterial community, emerged a core of shared endosymbionts with a potential implication in the nitrogen cycle.Conclusions: The present study demonstrated the importance of selecting and studying cultivable fungi and bacteria from the rhizosphere. Our findings demonstrated that at the rhizosphere level, the range of interactions between fungi and bacteria, both internal and external to the fungal hypha, could vary even among closely related species.