Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Abstract

Fungal-bacterial symbioses range from antagonisms to mutualisms and remain one of the least understood interdomain interactions despite their ubiquity as well as ecological and medical importance. To build a predictive conceptual framework for understanding interactions between fungi and bacteria in different types of symbioses, we surveyed fungal and bacterial transcriptional responses in the mutualism between Rhizopus microsporus (Rm) (ATCC 52813, host) and its Mycetohabitans (formerly Burkholderia) endobacteria versus the antagonism between a nonhost Rm (ATCC 11559) and Mycetohabitans isolated from the host, at two time points, before and after partner physical contact. We found that bacteria and fungi sensed each other before contact and altered gene expression patterns accordingly. Mycetohabitans did not discriminate between the host and nonhost and engaged a common set of genes encoding known as well as novel symbiosis factors. In contrast, responses of the host versus nonhost to endobacteria were dramatically different, converging on the altered expression of genes involved in cell wall biosynthesis and reactive oxygen species (ROS) metabolism. On the basis of the observed patterns, we formulated a set of hypotheses describing fungal-bacterial interactions and tested some of them. By conducting ROS measurements, we confirmed that nonhost fungi increased production of ROS in response to endobacteria, whereas host fungi quenched their ROS output, suggesting that ROS metabolism contributes to the nonhost resistance to bacterial infection and the host ability to form a mutualism. Overall, our study offers a testable framework of predictions describing interactions of early divergent Mucoromycotina fungi with bacteria. IMPORTANCE Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives

“…and one-third of them were isolated from the plant material, we hypothesize that the relationship between fungus and bacteria could be beneficial for plants, especially since it is postulated that the fungal role in relationships with endohyphal bacteria is providing a safe environment for them. However, data are still scarce, and physiological experiments using cleared and infected isogenic isolates, similar to those performed by Uehling et al ( 9 ), as well as comparative transcriptomics experiments of such strains ( 32 ) and sampling more strains from different locations around the world, are needed to assess the actual impact of Umbelopsis on plants as well as to examine how this impact changes with the presence of endobacteria.…”

Transcriptional profiles of a foliar fungal endophyte (Pestalotiopsis, Ascomycota) and its endohyphal bacterium (Luteibacter, Gammaproteobacteria) in co-culture support sulfur exchange and growth regulation

“…Metabolic studies also could illuminate the role secondary metabolites play in facilitating the establishment of fungal-bacterial partnerships, including both recruitment and invasion. In the R. microsporus and Mycetohabitans interaction, secondary metabolites are not thought to play a large role, as only one NRPS is upregulated and one PKS downregulated in R. microsporus (i.e., the natural host strain) when in contact with the bacterium (Lastovetsky et al ., 2020). In contrast the Ralstonia solanacearum lipopeptide, ralsolamycin, induced substantial developmental shifts in host fungi, enhancing bacterial entry into fungal chlamydospores (Spraker et al, 2016).…”

“…These results align with the changes in gene expression seen in other bacterial-fungal symbioses; a compatible Rhizopus microsporus isolate upregulates genes involved in cytoskeletal rearrangement and the cell wall when in contact with Mycetohabitans spp. (Lastovetsky et al, 2020). Notably, many of the genes related to cell structure that were not considered differentially expressed for our set FDR<0.01 are just beyond that probability threshold and typically have low L2FCs.…”

“…(formerly Burkholderia , Betaproteobacteria) and their host, Rhizopus microsporus (Mucoromycotina), represent one emerging model system for EHB based on the ability to independently culture and reintroduce the partners in vitro . Metabolic and transcriptomic studies have revealed changes in fungal lipid metabolism underlying their partnership formation, and a lack of reactive oxygen species burst in compatible partners (Lastovetsky et al ., 2016; Lastovetsky et al ., 2020). The unique requirement of Mycetohabitans spp.…”

In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi

“…CE4 chitin de-N-acetylases (CDAs) hydrolyse chitin, chitosan, and chitooligosaccharides and are responsible for fungal cell wall remodelling, which is especially important for pathogens during interactions with the host [43][44][45]. Interestingly, CE4 enzymes also play a role in symbiotic interaction between terrestrial fungi and their bacterial symbionts [46]. One might speculate that the abundant fungus-bacteria interactions in the aquatic environment of the gut may also be facilitated by the activity of CE4 proteins.…”