Caledoniamyces theodoroui, gen. nov., sp. nov., a bulbous anaerobic gut fungus from the bovine rumen

Abstract

Anaerobic gut fungi (AGF) are members of the microbiome of herbivore digestive tracts, where they are important degraders of plant material. Culture-independent diversity studies have indicated that a broad diversity of these fungi still remain uncultured so far. This limits understanding of their ecology, physiology and potential for biotechnological exploitation. Here we describe the isolation and characterisation of the first cultured representatives of the Neocallimastigomycota clade NY9 / YL1, previously proposed as genus based on culture-independent sequence diversity studies. Two fungal strains, RF6 and RF9, were isolated from Jersey cow rumen fluid, alongside representatives of other genera including Orpinomyces and Neocallimastix. Phylogenetic analysis of the RF6 and RF9 rDNA ITS1 region and D1/D2 domain of 28S LSU rDNA gene revealed formation of a well-supported genus-level cluster. This cluster also contained sequences deposited for NY9 and YL1 and was distinct from other described genera. Isolates RF6 and RF9 displayed small 1-2 mm colonies with a compact structure on solid medium. Microscopy showed bulbous rhizoidal cells encased in amorphous material, possibly extracellular polymeric substances, indicating that the genus represents the third known genus of AGF with bulbous morphology. Both endogenous and exogenous sporangia were observed, which produced mono-flagellated zoospores. Isolate RF6 was able to grow robustly using cellulose and wheat straw as sole carbon sources. For this new genus, for which the type strain is RF6, we propose the name Caledoniamyces, referring to the origin in Scotland, and the species name C. theodoroui.