Research

Research in the lab covers all aspects of mycology. These three projects are the primary focus of our research:

Genetics of mushroom sex
Many of the most intriguing phenomena that have been recorded in fungi are found in the mushroom-forming fungi (Agaricomycetes). Among the most curious of these is the prolonged heterokaryotic phase of the life cycle in which cells consist of multiple genetically different nuclei. This cell type is an alternative to the typical diploid cells observed in plants and animals, and its occurrence suggests a dynamic union in which nuclei could be the direct targets of selection. Heterokaryons in mushroom fungi arise from the fusion of two homokaryons of different mating type; in many species the cells contain exactly two nuclei and are termed dikaryotic (Figure 1). A primary goal of our research in this area is to understand whether the nuclei of different mating type within a fungal mycelium can display individualism. In order to do this we are investigating nuclear ratios in fungi with multinucleate mycelia such as the root rot pathogen Heterobasidion parviporum (Figure 2) to determine whether nuclear ratios vary over time, space, and environment. DNA markers can be used to track individual nuclei and to measure the degree to which these nuclei cooperate or compete as their environments are shifted between extremes such as pH and nutrient source.

Another fascinating phenomenon of mushroom sex is the myriad mating types that are observed in a single species. This multitude of mating types confers a high level of promiscuity (or outbreeding efficiency) in which each homokaryotic individual is capable of mating with nearly every other homokaryotic individual it encounters. These data suggest that encounters between homokaryons are very rare events dictated by the dispersal biology of these fungi in which spores travel a long distance but after germination grow as a sedentary mycelium. We are also investigating how specific genetic changes (such as mutations or genome rearrangements) to the mating-type genes cause changes in mating system.

The majority of mushrooms have two mating-type loci (MAT-A and MAT-B). MAT-A genes encode transcription factors with a homeodomain motif, and the MAT-B genes encode pheromones and their receptors. We have developed molecular methods to clone mating-type genes from non-model species and explored the genetic changes responsible for the shift in mating system from one controlled by two loci (tetrapolar) to one controlled by a single mating-type locus (bipolar) in the fairies’ bonnets mushroom Coprinellus disseminatus and the white-rot fungus Phanerochaete chrysosporium. Results from both of these species suggest a convergent evolutionary mechanism involved in this mating system switch, specifically involving mutations to genes encoding pheromone receptors. These experiments have suggested that the homeodomain transcription factors are required to maintain the heterokaryotic condition, and the MAT-A mating type region displays a high level of gene order conservation relative to MAT-B and even other regions of the genome (Figure 3). Our future studies will investigate the function of pheromones and their receptors in controlling nuclear communication and organization in bipolar mushroom species.



Phylogeny of ancient fungal lineages
The “Tree of Life” is a major organizing principle for all of biological research and teaching. A major gap in our understanding of the Tree of Life is the order of the earliest branching lineages in the Kingdom Fungi. These groups include relatively morphologically simple, protist-like forms, including the Chytridiomycetes and microsporidia. We are researching the phylogeny of these basal lineages using molecular sequence data. Through an NSF sponsored research project involving many mycology groups throughout North America (AFTOL) we reconstructed the history of the earliest fungi as a grade of zoosporic (motile spore) species, implying an aquatic habitat for early fungi (Figure 4). The loss of spore motility appears to have happened several times, each loss coincident with an innovation in spore dispersal and a major radiation of terrestrial fungi. As with the systematic treatments of other groups, the phylogeny of basal fungal lineages is a continual work in progress. Our future research will focus on placement of novel lineages using multiple gene sequences, the majority of which are obligately parasitic, such as the intracellular parasitic chytrids Rozella and Olpidium.



Evolution of chytridiomycosis
Chytridiomycosis is a disease of amphibians implicated in amphibian population declines in several regions throughout the world. Its agent, Batrachochytrium dendrobatidis, is a fungus that invades the epidermis of the animal and death is presumably caused by asphyxiation, osmotic imbalance, or toxin production. Chytridiomycosis is an emerging infectious disease because it is newly described and has created a documented wave of decline among sensitive populations. We are trying to answer two unresolved questions regarding the population genetics of the species: 1) what is the geographic origin and population structure of the disease? 2) why has the disease spread so quickly despite some species being highly resistant? Two approaches are being used to answer these questions. Firstly, in collaboration with Christina Cuomo at the Broad Institute and Joyce Longcore at the University of Maine, we are investigating the pattern of polymorphism across the genome in multiple strains. These data provide insight into the number of historical recombination events in the species and suggest that the fungus is asexual but can undergo mitotic recombination. Secondly, in collaboration with an international group of amphibian disease researchers we are investigating a global population of isolates using multilocus sequence typing. The data suggest that the pathogen is a recently emerged diploid clone. We are currently testing the hypothesis that bullfrogs (which are relatively resistant to the infection) are the source population of the disease.