Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness

Abstract

Microbial interactions are major determinants in shaping microbiome structure and function. Although fungi are found across diverse microbiomes, the mechanisms through which fungi interact with other species remain largely uncharacterized. In this work, we explore the diversity of ways in which fungi can impact bacteria by characterizing interaction mechanisms across 16 different bacterial-fungal pairs, involving 8 different fungi and 2 bacteria (Escherichia coli and Pseudomonas psychrophila). Using random barcode transposon-site sequencing (RB-TnSeq), we identified a large number of bacterial genes and pathways important in fungal interaction contexts. Within each interaction, fungal partners elicit both antagonistic and beneficial effects. Using a panel of phylogenetically diverse fungi allowed us to identify interactions that were conserved across all species. Our data show that all fungi modulate the availability of iron and biotin, suggesting that these may represent conserved bacterial-fungal interactions. Several fungi also appear to produce previously uncharacterized antibiotic compounds. Generating a mutant in a master regulator of fungal secondary metabolite production showed that fungal metabolites are key shapers of bacterial fitness profiles during interactions. This work demonstrates a diversity of mechanisms through which fungi are able to interact with bacterial species. In addition to many species-specific effects, there appear to be conserved interaction mechanisms which may be important across microbiomes. INTRODUCTION .

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

“…Screening of various mutant collections helped to map these functional relationships in S. cerevisiae and annotate genomic data ( Hillenmeyer et al, 2008 ), although hundreds of genes remain with an unknown function ( Cherry, 2015 ). In Escherichia coli , a high proportion of unannotated genes were found to be involved in microbial interactions, thus investigating biotic interactions may offer new biological insight into genotype to phenotype mapping ( Pierce et al, 2021 ). In microbial ecology, identifying which genes are of importance for conserved or even specific microbial interactions is of interest as it contributes to understand their mechanism and their impact on species evolution.…”

“…In microbial ecology, identifying which genes are of importance for conserved or even specific microbial interactions is of interest as it contributes to understand their mechanism and their impact on species evolution. In that perspective, the recently introduced approach of performing co-cultures with collections of functional mutants ( N’guyen et al, 2020 ; Pierce et al, 2021 ), which are available in an increasing number of species owing to technology such as transposon-insertion sequencing ( Cain et al, 2020 ), is an interesting avenue to characterize microbial interactions.…”

“Microbial Wars” in a Stirred Tank Bioreactor: Investigating the Co-Cultures of Streptomyces rimosus and Aspergillus terreus, Filamentous Microorganisms Equipped With a Rich Arsenal of Secondary Metabolites

“…Eliciting their production under laboratory conditions is typically far from trivial, as it requires a specific set of environmental cues leading to the awakening of the underlying biosynthetic routes. Some of these stimuli are associated with the presence and biochemical activity of other species ( Netzker et al, 2015 ; Molloy and Hertweck, 2017 ; Deveau et al, 2018 ; Pierce et al, 2021 ). In natural environments, microbes interact with other organisms by means of physical contact, as well as through producing, recognizing and responding to chemical molecules.…”

A Small Molecule Coordinates Symbiotic Behaviors in a Host Organ

“…Conversely, the fungal species Fusarium fujikuroi and Botrytis cinerea produce bikaverin to inhibit invasion of ralsolamycin-producing strains of R. solanacearum (4,5). In cheese rind-derived microbial interactions, small molecules like zinc-coproporphyrin III and other siderophores mediate trace metal acquisition between bacteria and fungi (6,7). In both of these cases, specialized metabolites were central to understanding the observed phenotypes between the domains of life.…”