The Kingdom Fungi comprises one of the largest and most ecologically important groups of organisms on Earth. Fungi provide numerous essential functions including serving as beneficial partners and antagonistic pathogens with plants and animals, and central players in nutrient cycling through decomposition of most organic substrates. They are also an old kingdom, dating back to approximately 1 billion years. During their evolution they have undergone numerous biological transformations, which included morphological and biochemical innovations, that allowed them to move from aquatic environments and colonize early land ecosystems. These innovations include the loss of flagellum, the origin of the filamentous growth form that comprises the “body” of most fungi, and the ability to execute an extraordinary diversity of biochemical processes. Central to the evolution of these innovations, and the initial colonization of land, are a group of fungi known as the zygomycetes. Zygomycetes are common, but because they are microscopic and do not produce large fruiting bodies like mushrooms, they are significantly understudied. To advance our understanding of this critical group of organisms, we initiated the ZyGoLife project, which consisted of a large and diverse group of collaborative researchers.  Our goal was to collect large amounts of different types of data and integrate these data in testing hypotheses focused on the evolution and diversity of zygomycetes.  A summary of the major findings from this work include: 1) We clarified the relationships of the major lineages of Kingdom Fungi, and demonstrated that zygomycete fungi comprise two separate lineages, representing the first groups of fungi to lose the flagellum and colonize land. 2) Zygomycete fungi colonized land prior to plants and include some of the first fungi that plants formed symbiotic associations with when they evolved into terrestrial ecosystems. 3) We adopted and modified analytical techniques for sequencing the genomes of fungi that are currently not possible to maintain in pure culture. This will significantly promote the sequencing of fungi that cannot be cultured and participate in complex relationships with other organisms. 4) We sequenced the genomes of over 100 species of zygomycetes, across a phylogenetic diversity spanning over 100s of millions of years.  This depth and breadth of sampling allowed us to uncover previously undescribed metabolic diversity of fungi, and link it in a predictive manner with fungal ecology. 5) We demonstrated that Basidiobolus, a gastrointestinal symbiont of amphibians, represents a system for understanding Horizontal Gene Transfer between fungi and bacteria, and that this process is likely facilitated by the unique environmental conditions of the amphibian gastrointestinal system.  Fungal-bacterial interactions are common in nature but their dynamics are poorly understood. The Basidiobolus-amphibian symbiosis provides a tractable, experimental system for the study of the acquisition of novel metabolism by fungi and fungal-bacterial microbiome interactions. Notably, this research significantly increased the genomic resources available to the global research community.  Prior to ZyGoLife, there existed scant genomic resources for zygomycete fungi; after ZyGoLife there now exists hundreds of zygomycete genomes. This exponential increase in resources strengthens and advances basic and foundational research in genetics, genomics and computational biology of fungi, allowing the transfer of knowledge from model systems to a greater diversity of organisms.  As such, it stands to have broad impact in research related to biodiversity, ecology and conservation, complex interactions between fungi and other organisms, plant and human pathology, and bioprospecting for biologically active compounds with potential industrial and pharmaceutical applications. Importantly, research supported by this grant involved the cross-training of the next generation of young scientists in fungal biology, genomics and computational biology, who must be able to work in large, collaborative groups and approach scientific inquiry through the analysis of complex, heterogeneous data sets.

Last Modified: 12/31/2020
Modified by: Joseph W Spatafora