Diversity of fungal microbiome obtained from plant rhizoplanes

Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.

Effect of Endosymbiotic Bacteria on Fungal Resistance Toward Heavy Metals

Most studies on metal removal or tolerance by fungi or bacteria focus on single isolates, without taking into consideration that some fungi in nature may be colonized by endobacteria. To address this knowledge gap, we investigated the tolerance and removal of diverse metals with two fungal species: Linnemannia elongata containing Burkholderia-related endobacteria and Benniella erionia containing Mollicute-related endobacteria. Isogenic lines of both species were generated with antibiotic treatments to remove their respective endobacteria. Experiments involved comparing the isogenic lines and wild type fungi in relation to the minimum inhibitory concentration for the metals, the fungal ability to remove these different metals via atomic adsorption spectroscopy, and the interaction of the metals with specific functional groups of the fungi and fungi-bacteria to determine the role of the bacteria via attenuated total reflection fourier transformed infrared (ATR-FTIR). Finally, we determined the influence of different metal concentrations, associated with moderate and high fungal growth inhibition, on the presence of the endobacteria inside the fungal mycelium via quantitative real-time PCR. Results showed that the presence of the endosymbiont increased B. erionia resistance to Mn2+ and increased the removal of Fe2+ compared to isogenic lines. The absence of the endosymbiont in L. elongata increased the fungal resistance toward Fe2+ and improved the removal of Fe2+. Furthermore, when the bacterial endosymbiont was present in L. elongata, a decrease in the fungal resistance to Ca2+, Fe2+, and Cr6+was noticeable. In the ATR-FTIR analysis, we determined that C-H and C = O were the major functional groups affected by the presence of Cu2+, Mn2+, and Fe2+ for L. elongata and in the presence of Cu2+ and Ca2+ for B. eronia. It is noteworthy that the highest concentration of Pb2+ led to the loss of endobacteria in both L. elongata and B. eronia, while the other metals generally increased the concentration of endosymbionts inside the fungal mycelium. From these results, we concluded that bacterial endosymbionts of fungi can play a fundamental role in fungal resistance to metals. This study provides the first step toward a greater understanding of symbiotic interactions between bacteria and fungi in relation to metal tolerance and remediation.

Widespread bacterial diversity within the bacteriome of fungi

Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.

Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi

Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.