Carleton, J. P. | Search bioRxiv

bioRxiv2025

Unraveling the Genomic and Phylogenetic Complexity of the understudied microfungus Basidiobolus: Insights from 19 Newly Sequenced Genomes

Basidiobolus is a globally distributed genus of early-diverging fungi within Zoopagomycota, known for its presence in diverse ecological niches ranging from soil and decaying organic matter to vertebrate gastrointestinal tracts. Despite its ecological and medical relevance, the taxonomy and evolutionary relationships within the genus remain poorly resolved due to limited genomic resources. In this study, we present nineteen newly sequenced Basidiobolus genomes, expanding the available genomic data. Using short-read Illumina sequencing, assembly, and annotation pipelines, we characterize genic content, assess completeness, and explore biosynthetic gene content across isolates. Phylogenomic analysis reveals two major clades corresponding to B. meristosporus and B. ranarum, while B. heterosporus forms a distinct lineage. Several isolate clusters exhibit deep divergence suggestive of cryptic species, underscoring the need for expanded sampling and taxonomic revision. Functional annotations reveal a rich repertoire of biosynthetic gene clusters, including non-ribosomal peptide synthetases, polyketide synthases, and hybrid clusters, pointing to an underexplored reservoir of secondary metabolite diversity. These findings position Basidiobolus as a compelling model for investigating fungal evolution, ecological adaptation, and natural product biosynthesis.

genomics↗

bioRxiv2025

Impacts on the microbial fungal communities across water, sediment, and amphibian hosts across an urbanization gradient waterway in Worcester, Massachusetts

In a world of increasingly urbanized environments, it is critical to understand the impact of urbanization on microbial communities, including fungal communities, as a measure of ecosystem health, and to document how these environments are changing. Aquatic environments, in particular, can be highly sensitive to urbanization with removal of local habitat and inputs of wastewater and contaminants, leading to displacement or extinction of natural flora, fauna, and funga. Aquatic microbial communities, especially fungal communities, are extremely complex and far less characterized compared to their macro counterparts. Here, we characterized the fungal microbiome, i.e. "mycobiome", across multiple habitats-- water, sediment, and frog fecal matter from three species (American bullfrog (Lithobates catesbeianus), Green frog (Lithobates clamitans), and Pickerel frog (Lithobates palustris)) -- within the Tatnuck Brook waterway in Worcester, MA. The Tatnuck Brook waterway is a connected group of streams, ponds, and lakes that transition from protected areas at its headwaters, below the citys drinking water reservoir, to highly urbanized regions within Worcester. Using metabarcode sequencing, we found that water, sediment, and frog gut habitats harbor distinct fungal communities, but all exhibit parallel shifts in diversity along an urbanization gradient. In particular, we identified fungal taxa from the amphibian mycobiome and environmental samples that exhibited a range of sensitivities to urbanization. These taxa, including Basidiobolus, Cladosporium, and Lemonniera in fecal and sediment samples, as well as Candida, which was found in all habitats, are potential indicators of shifts in aquatic ecosystems due to urbanization. Their responses to urban stressors may serve as a baseline for further studies of aquatic fungal communities. IMPORTANCEAs cities grow, they can change nearby rivers, streams, and ponds in ways that affect plants, animals, and even tiny microbes. Fungi are an important part of these ecosystems because they help break down materials and can affect the health of animals like frogs. However, we still know very little about how fungi respond to urban environments. In this study, we looked at fungi living in water, sediment, and frog guts along a range of places from natural to highly developed areas in Worcester, Massachusetts. We found that some fungi were more common in cleaner, less developed sites, while others were more common in urban ones. These patterns suggest that fungi could be useful indicators of environmental health. Our work helps scientists better understand how urbanization affects nature and offers a new way to monitor and protect freshwater ecosystems.

ecology↗