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Five yeast isolates belonging to a candidate for novel species were obtained from rotting wood and the gut of a passalid beetle larva in a site of Amazonian rainforest biome in Brazil. Sequence analysis of the Internal Transcribed Spacer (ITS)-5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genusVanderwaltozyma. The closest relative of the novel species isVanderwaltozyma huisunica. These species differs due to 44 nt substitutions and 21 indels in the sequences of the ITS region, as well as by 15 substitutions and four indels in the sequences of the D1/D2 domains. A phylogenomic analysis of theVanderwaltozymaspecies with genomes sequenced showed that this novel species is an outgroup to the other species of this genus. We propose the nameVanderwaltozyma urihicolasp. nov. (CBS 18107^T, MycoBank MB 856975) to accommodate these isolates. The species is homothallic, producing one to two ascospores per ascus. The habitat ofV. urihicolais rotting wood in the Brazilian Amazonian rainforest biome. 

Abstract BackgroundCost-effective production of biofuels from lignocellulose requires the fermentation ofd-xylose. Many yeast species within and closely related to the generaSpathasporaandScheffersomyces(both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD⁺to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. ResultsWe screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressedXYLgenes from multipleScheffersomycesspecies in a strain ofSaccharomyces cerevisiae. RecombinantS. cerevisiaeexpressingXYL1fromScheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared toS. cerevisiaestrain expressingXYLgenes fromScheffersomyces stipitis. ConclusionCollectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeastSc. xylosifermentansas a potential source for genes that can be engineered intoS. cerevisiaeto improve xylose fermentation and biofuel production. 

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genusSaccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containingSaccharomycopsis lassenensis,Saccharomycopsis fermentans,Saccharomycopsis javanensis,Saccharomycopsis babjevae,Saccharomycopsis schoeniiandSaccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains withSaccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set ofSaccharomycopsisspecies whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer toSaccharomycopsis fodiensandSaccharomycopsissp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The nameSaccharomycopsis praedatoriasp. nov. is proposed to accommodate the novel species. The holotype ofSaccharomycopsis praedatoriais CBS 16589^T. The MycoBank number is MB849369.S. praedatoriawas able to kill cells ofSaccharomyces cerevisiaeby means of penetration with infection pegs, a trait common to most species ofSaccharomycopsis. 

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: trade-offs between performance efficiency and breadth; and the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1,154 yeast strains from 1,051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.