A closer look at Sporidiobolales: Ubiquitous microbial community members of plant and food biospheres

Abstract

Carotenoid-containing yeasts in Sporidiobolales (Microbotryomycetes, Pucciniomycotina, Basidiomycota) have been reported from contrasting ecosystems, including marine, soil, phylloplane, polar ice, and many others. Here, we present several analyses drawing on 583 new isolates collected from various substrates around the globe and publicly available sequences from numerous published environmental studies. We provide a multilocus phylogenetic reconstruction of the order, estimates for total species richness, a snapshot of global distribution patterns, and analysis of niche preferences in Sporidiobolales, emphasizing their occurrence in commercial crops and food products. We evaluated loci commonly used in fungal phylogenetics, finding that RNA polymerase II subunits 1 and 2 (RPB1, RPB2) are of little utility in this group. We have reconfirmed the monophyly of Sporidiobolales with three well-supported genera, which are, in descending order of number of species, Rhodotorula, Sporobolomyces, and Rhodosporidiobolus. From our data, we estimate ca. 260 species in Sporidiobolales, of which 42 are described, and ca. 52,000 species in Pucciniomycotina. The majority of data regarding Sporidiobolales are from North America and Europe, highlighting severe knowledge gaps for most of South and Central America and Africa.