Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

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: (i) trade-offs between performance efficiency and breadth and (ii) 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 (1154 yeast strains from 1051 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 we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

Spathaspora quercus f.a., sp. nov., a novel yeast isolated from rotting wood and a lichen sample in Kyushu region, Japan

Four novel d-xylose assimilation yeast strains were isolated from rotting wood and a lichen sample collected in the Kyushu region of Japan. Species identifications were performed by analysing the internal transcribed spacer 5.8S region sequences and the D1/D2 variable domain of the large subunit rRNA gene. Phylogenetic analysis suggested that these isolates are closely related to Spathaspora species isolated in China, such as S. jiuxiensis and S. parajiuxiensis. These isolates also showed sequence similarity to deposited sequences labelled as Schwanniomyces. They did not produce asci and ascospores under any of the test conditions. Based on phylogenetic analysis and phenotypic differences, Spathaspora quercus f.a., sp. nov. is proposed to accommodate these isolates. The holotype of Spathaspora quercus f.a., sp. nov. is NBRC 116146T (CBS18366). This species is able to ferment d-xylose, and a d-xylose fermentation test revealed that this species produces a considerable amount of xylitol.

Yeasts from tropical forests: Biodiversity, ecological interactions, and as sources of bioinnovation

Tropical rainforests and related biomes are found in Asia, Australia, Africa, Central and South America, Mexico, and many Pacific Islands. These biomes encompass less than 20% of Earth's terrestrial area, may contain about 50% of the planet's biodiversity, and are endangered regions vulnerable to deforestation. Tropical rainforests have a great diversity of substrates that can be colonized by yeasts. These unicellular fungi contribute to the recycling of organic matter, may serve as a food source for other organisms, or have ecological interactions that benefit or harm plants, animals, and other fungi. In this review, we summarize the most important studies of yeast biodiversity carried out in these biomes, as well as new data, and discuss the ecology of yeast genera frequently isolated from tropical forests and the potential of these microorganisms as a source of bioinnovation. We show that tropical forest biomes represent a tremendous source of new yeast species. Although many studies, most using culture-dependent methods, have already been carried out in Central America, South America, and Asia, the tropical forest biomes of Africa and Australasia remain an underexplored source of novel yeasts. We hope that this review will encourage new researchers to study yeasts in unexplored tropical forest habitats.

The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species

This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. A total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.

Larval gut microbiome of Pelidnota luridipes (Coleoptera: Scarabaeidae): high bacterial diversity, different metabolic profiles on gut chambers and species with probiotic potential

Pelidnota luridipes Blanchard (1850) is a tropical beetle of the family Scarabaeidae, whose larvae live on wood without parental care. Microbiota of mid- and hindgut of larvae was evaluated by culture-dependent and independent methods, and the results show a diverse microbiota, with most species of bacteria and fungi shared between midgut and hindgut. We isolated 272 bacterial and 29 yeast isolates, identified in 57 and 7 species, respectively, while using metabarcoding, we accessed 1,481 and 267 OTUs of bacteria and fungi, respectively. The composition and abundance of bacteria and fungi differed between mid- and hindgut, with a tendency for higher richness and diversity of yeasts in the midgut, and bacteria on the hindgut. Some taxa are abundant in the intestine of P. luridipes larvae, such as Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria; as well as Saccharomycetales and Trichosporonales yeasts. Mid- and hindgut metabolic profiles differ (e.g. biosynthesis of amino acids, cofactors, and lipopolysaccharides) with higher functional diversity in the hindgut. Isolates have different functional traits such as secretion of hydrolytic enzymes and antibiosis against pathogens. Apiotrichum siamense L29A and Bacillus sp. BL17B protected larvae of the moth Galleria mellonella, against infection by the pathogens Listeria monocytogenes ATCC19111 and Pseudomonas aeruginosa ATCC 9027. This is the first work with the larval microbiome of a Rutelini beetle, demonstrating its diversity and potential in prospecting microbial products as probiotics. The functional role of microbiota for the nutrition and adaptability of P. luridipes larvae needs to be evaluated in the future.

Five new additions to the genus Spathaspora (Saccharomycetales, Debaryomycetaceae) from southwest China

Spathaspora is an important genus of d-xylose-fermenting yeasts that are poorly studied in China. During recent yeast collections in Yunnan Province in China, 13 isolates of Spathaspora were obtained from rotting wood and all represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and nuc 28S), five new species are proposed: Spathaspora elongata, Sp. mengyangensis, Sp. jiuxiensis, Sp. parajiuxiensis and Sp. rosae. Our results indicate a high species diversity of Spathaspora waiting to be discovered in rotting wood from tropical and subtropical southwest China. In addition, the two Candida species, C. jeffriesii and C. materiae, which are members of the Spathaspora clade based on phylogeny, are transferred to Spathaspora as new combinations.

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.

Starmera foglemanii sp. nov. and Starmera ilhagrandensis sp. nov., two novel yeast species isolated from ephemeral plant substrates

Four isolates of two novel ascosporogenous species belonging to the clade Starmera were obtained from cactus tissues and rotting wood in Brazil. Results of analyses of the sequences of the ITS and D1/D2 domains of the large subunit rRNA gene indicated that the two isolates of the cactophilic species are related to Starmera caribaea and Starmera pilosocereana, yeasts that are associated with cacti and require an organic source of sulfur for growth. We propose the novel species Starmera foglemanii sp. nov. (CBS 16113T; MycoBank number: MB 834400) to accommodate these isolates. The other two isolates are phylogenetically related to Candida dendrica, Candida laemsonensis and Candida berthetii, also in the Starmera clade. The novel species name Starmera ilhagrandensis sp. nov. (CBS 16316T; MycoBank number: MB 834402) is proposed for this species.

Production of ethanol and xylanolytic enzymes by yeasts inhabiting rotting wood isolated in sugarcane bagasse hydrolysate

Yeasts associated with rotting wood from four Atlantic Rain forest sites in Brazil were investigated using a culture medium based on sugarcane bagasse hydrolysate. A total of 330 yeast strains were isolated. Pichia manshurica, Candida pseudolambica, and Wickerhamomyces sp. 3 were the most frequently isolated species. Fourteen novel species were obtained in this study. All isolates were tested for their ability to ferment d-xylose and to produce xylanases. In the fermentation assays using d-xylose (30 g L^-1), the main ethanol producers were Scheffersomyces stipitis (14.08 g L^-1), Scheffersomyces sp. (7.94 g L^-1) and Spathaspora boniae (7.16 g L^-1). Sc. stipitis showed the highest ethanol yield (0.42 g g^-1) and the highest productivity (0.39 g L^-1h^-1). The fermentation results using hemicellulosic hydrolysate showed that Sc. stipitis was the best ethanol producer, achieving a yield of 0.32 g g^-1, while Sp. boniae and Scheffersomyces sp. were excellent xylitol producers. The best xylanase-producing yeasts at 50 °C belonged to the species Su. xylanicola (0.487 U mg^-1) and Saitozyma podzolica (0.384 U mg^-1). The results showed that rotting wood collected from the Atlantic Rainforest is a valuable source of yeasts able to grow in sugarcane bagasse hydrolysate, including species with promising biotechnological properties.

Catching speciation in the act-act 2: Metschnikowia lacustris sp. nov., a sister species to Metschnikowia dekortorum

The isolation of a single yeast strain in the clade containing Metschnikowia dekortorum, in the Amazon biome of Brazil, incited us to re-examine the species boundaries within the clade. The strain (UFMG-CM-Y6306) was difficult to position relative to neighbouring species using standard barcode sequences (ITS-D1/D2 rRNA gene region). Mating took place freely with α strains of M. bowlesiae, M. dekortorum, and M. similis, but two-spored asci, indicative of a fertile meiotic progeny, were formed abundantly only with certain strains of M. dekortorum. Accordingly, we examined mating success among every phylotype in the clade and constructed a phylogeny based on a concatenation of 100 of the largest orthologous genes annotated in draft genomes. The analyses confirmed membership of the Amazonian isolate in M. dekortorum, but also indicated that the species should be subdivided into two. As a result, we retain three original members of M. dekortorum in the species, together with the new isolate, and reassign six isolates recovered from Mesoamerican lacustrine habitats to Metschnikowia lacustris sp. nov. The type is UWOPS 12-619.2^T (isotype CBS 16250^T). MycoBank: MB 833751.

Integration of comprehensive data and biotechnological tools for industrial applications of Kluyveromyces marxianus

Among the so-called non-conventional yeasts, Kluyveromyces marxianus has extremely potent traits that are suitable for industrial applications. Indeed, it has been used for the production of various enzymes, chemicals, and macromolecules in addition to utilization of cell biomass as nutritional materials, feed and probiotics. The yeast is expected to be an efficient ethanol producer with advantages over Saccharomyces cerevisiae in terms of high growth rate, thermotolerance and a wide sugar assimilation spectrum. Results of comprehensive analyses of its genome and transcriptome may accelerate studies for applications of the yeast and may further increase its potential by combination with recent biotechnological tools including the CRISPR/Cas9 system. We thus review published studies by merging with information obtained from comprehensive data including genomic and transcriptomic data, which would be useful for future applications of K. marxianus.

Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade

Diutina catenulata (Candida catenulata) is an ascomycetous yeast that has been isolated from humans, animals and environmental sources. The species is a contaminant of dairy products, and has been linked to superficial and invasive infections in both humans and animals. Previous phylogenetic analyses have assigned the species to the Saccharomycetales, but failed to identify its specific clade. Here, we report the genome sequence of an environmental isolate of D. catenulata. Examination of the tRNA repertoire and coding potential of this species shows that it translates the CUG codon as serine and not leucine. In addition, two phylogenetic analyses using 204 ubiquitous gene family alignments and 3,826 single-copy genes both confirm the placement of the species in the Debaryomycetaceae/Metschnikowiaceae, or CTG-Ser clade. The sequenced isolate contains an MTLα idiomorph. However, unlike most MTL loci in related species, poly (A) polymerase (PAP) is not adjacent to MTLα1.

Scheffersomyces stambukii f.a., sp. nov., a d-xylose-fermenting species isolated from rotting wood

Two isolates representing a new species of Scheffersomyces were isolated from rotting wood samples collected in an Amazonian forest ecosystem in Brazil. Analysis of the sequences of the D1/D2 domains showed that this new species is phylogenetically related to Scheffersomyces NYMU 15730, a species without a formal description, and the two are in an early emerging position with respect to the xylose-fermenting subclade containing Scheffersomyces titanus and Scheffersomyces stipitis. Phylogenomic analyses using 474 orthologous genes placed the new species in an intermediary position between Scheffersomyces species and the larger genus Spathaspora and the Candida albicans/Lodderomyces clade. The novel species, Scheffersomyces stambukii f.a., sp. nov., is proposed to accommodate these isolates. The type strain of Scheffersomyces stambukii sp. nov. is UFMG-CM-Y427^T (=CBS 14217^T). The MycoBank number is MB 824093. In addition, we studied the xylose metabolism of this new species.