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.

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.

BACKGROUND: The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed. RESULTS: Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cystofilobasidiales have the highest number of intron-containing genes and highest number of introns per gene. The Patagonian strain showed 4.4 % of nucleotide sequence divergence compared to the European strains which differed from each other by only 0.073 %. All known genes related to the synthesis of astaxanthin were annotated. A hitherto unknown gene cluster potentially responsible for photoprotection (mycosporines) was found in the newly sequenced P. rhodozyma strains but was absent in the non-mycosporinogenic strain CBS 6938. A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, genes involved in sexual reproduction were found and annotated. CONCLUSIONS: A draft genome sequence of the type strain of P. rhodozyma is now available, and comparison with that of the Patagonian population suggests the latter deserves to be assigned to a distinct variety. An unexpected genetic trait regarding high occurrence of introns in P. rhodozyma and other Cystofilobasidiales was revealed. New genomic insights into fungal homothallism were also provided. The genetic basis of several additional photoprotective and antioxidant strategies were described, indicating that P. rhodozyma is one of the fungi most well-equipped to cope with environmental oxidative stress, a factor that has probably contributed to shaping its genome.

Yeasts vectored by migratory birds collected in the Mediterranean island of Ustica and description of Phaffomyces usticensis f.a. sp. nov., a new species related to the cactus ecoclade.

Nine yeast species belonging to genera Candida, Cryptococcus, Phaffomyces, Rhodotorula and Wickerhamomyces, and one species of Aureobasidium genus were isolated from the cloaca of migratory birds. Candida glabrata and C. inconspicua were the species most frequently isolated and Wickerhamomyces sylviae, which has recently been described as a new species isolated from bird cloaca, was again found. The majority of isolates showed the ability to grow up to 40 °C and/or at pH 3.0, two environmental conditions typical of the digestive tract of birds. The phylogenetic analysis of the D1/D2 domain of 26S rRNA gene placed the cultures of Phaffomyces in a new lineage that differed from the closest species, P. opuntiae, by 13 nucleotide substitutions. The new species was able to grow at 40 °C and at pH 2.5, which suggests a possible adaptation to the bird cloaca. Moreover, the ability to grow in the presence of digitonin at pH 3.7 and the assimilation of ethyl acetate indicates a potential cactophilic origin. For the first time, the presence of yeasts belonging to the Phaffomyces clade in Europe and also in non-cactus environments is reported. The new species is formally described as P. usticensis sp. nov. (PYCC 6346(T) = CBS 12958(T)).

Evidence for maintenance of sex determinants but not of sexual stages in red yeasts, a group of early diverged basidiomycetes.

BACKGROUND: The red yeasts are an early diverged group of basidiomycetes comprising sexual and asexual species. Sexuality is based on two compatible mating types and sexual identity is determined by MAT loci that encode homeodomain transcription factors, peptide pheromones and their receptors. The objective of the present study was to investigate the presence and integrity of MAT genes throughout the phylogenetic diversity of red yeasts belonging to the order Sporidiobolales. RESULTS: We surveyed 18 sexual heterothallic and self-fertile species and 16 asexual species. Functional pheromone receptor homologues (STE3.A1 and STE3.A2) were found in multiple isolates of most of the sexual and asexual species. For each of the two mating types, sequence comparisons with whole-genome data indicated that synteny tended to be conserved along the pheromone receptor region. For the homeodomain transcription factor, likelihood methods suggested that diversifying selection acting on the self/non-self recognition region promotes diversity in sexual species, while rapid evolution seems to be due to relaxed selection in asexual strains. CONCLUSIONS: The majority of both sexual and asexual species of red yeasts have functional pheromone receptors and homeodomain homologues. This and the frequent existence of asexual strains within sexual species, makes the separation between sexual and asexual species imprecise. Events of loss of sexuality seem to be recent and frequent, but not uniformly distributed within the Sporidiobolales. Loss of sex could promote speciation by fostering the emergence of asexual lineages from an ancestral sexual stock, but does not seem to contribute to the generation of exclusively asexual lineages that persist for a long time.

Yeast diversity in the acidic Rio Agrio-Lake Caviahue volcanic environment (Patagonia, Argentina).

The Rio Agrio and Lake Caviahue system (RAC), in Northwestern Patagonia, is a natural acidic environment. The aims of this study were to characterize the yeast community and to provide the first ecological assessment of yeast diversity of this extreme aquatic environment. Yeast occurrence and diversity were studied at seven sites where the water pH varied between 1.8 and 6.7. Yeast CFU counts in the river ranged from 30 to 1200 CFU L(-1), but in the Lake the values were lower (30-60 CFU L(-1)). A total of 25 different yeast species were found, 11 of which belonged to undescribed taxa. Among these was an unusual strongly acidophilic Cryptococcus species. The RAC yeast community resembles that of acidic aquatic environments resulting from anthropic activities such as the São Domingos mines in Portugal and the Rio Tinto in Spain, respectively. The isolated yeast species were organized into different grades of adaptation to the RAC aquatic system. Based on the proposed grades, Rhodotorula mucilaginosa, Rhodosporidium toruloides and two novel Cryptococcus species were the most adapted species. These Cryptococcus species are apparently specialists of acidic aquatic environments, and might bear physiological features that possibly account for their ability to thrive in such extreme environments.

Cryptococcus paraflavus sp. nov. (Tremellales), isolated from steppe plants in Russia.

Three strains related to Cryptococcus flavus were isolated from plants collected in the Prioksko-terrasny biosphere reserve (Russia). Physiological characterization, mycocinotyping, sequencing of the D1/D2 domain of the 26S rDNA and the ITS region revealed their separate taxonomic position. The name Cryptococcus paraflavus is proposed to accommodate these isolates (type strain VKM Y-2923).

Cryptococcus agrionensis sp. nov., a basidiomycetous yeast of the acidic rock drainage ecoclade, isolated from an acidic aquatic environment of volcanic origin.

Seventy-one strains were isolated from the River Agrio-Lake Caviahue acidic aquatic environment in Argentina. Strains were isolated mainly from the most acidic section of the river (pH 1.8-2.7). According to the mini/microsatellite-primed PCR technique and physiological data, these strains are representatives of a single novel species of the genus Cryptococcus. Analysis of the D1/D2 region of the large-subunit rRNA gene showed that the strains belong to the order Filobasidiales of the subphylum Agaricomycotina. The novel isolates formed a phylogenetic group with Cryptococcus ibericus, Cryptococcus aciditolerans and Cryptococcus metallitolerans, the most closely related species. This group, which is phylogenetically related to the Gastricus clade, is considered to be an ecoclade due to its peculiar ecology and physiology. The name Cryptococcus agrionensis sp. nov. is proposed to accommodate these isolates, with strain CRUB 1317(T) (=CBS 10799(T)=JCM 15321(T)) as the type strain.

Cryptococcus stepposus, a new filobasidiaceous yeast species found in the Prioksko-terrasny biosphere reserve in Russia.

Mycocinotyping of cryptococci from the Prioksko-terrasny reserve (Russia) has revealed three strains that have a unique mycocin-sensitivity profile. Sequencing results of the D1/D2 domain of the 26S rDNA and of the complete ITS region placed them in the Floriforme clade of the Filobasidiales lineage (Hymenomycetes). The three strains had identical sequences, which differed from those of known Filobasidium and Cryptococcus species. A novel species named Cryptococcus stepposus (type strain VKM Y-2918) is proposed to accommodate these isolates. Physiological characteristics distinguishing the novel species from other Cryptococcus species in the Floriforme clade are presented.

Cryptococcus silvicola nov. sp. from nature reserves of Russia and Portugal.

Nitrate-positive strains of a filobasidiaceous anamorphic yeast related to Cryptococcus cylindricus were isolated from forest litter in a Russian nature reserve and from a lichen in Portuguese one. Mycocinotyping and rDNA sequence analysis revealed that the strains represent a novel species, for which the name Cryptococcus silvicola (type strain VKM Y-2939=CBS 10099) is proposed.

Cryptococcus festucosus sp. nov. a new hymenomycetous yeast in the Holtermannia clade.

Five yeast strains belonging to the genus Cryptococcus Vuillemin were isolated from steppe plants and turf collected in the Prioksko-terrasny biosphere reserve (Moscow region, Russia). Sequence analyses of the D1/D2 domains of the 26S rDNA and of the internal transcribed spacer region revealed that these yeast strains and strain CBS 8016 have almost identical sequences and belong to the Holtermannia clade of the Tremellomycetidae (Basidiomycota, Hymenomycetes). A novel species named Cryptococcus festucosus (type strain VKM Y-2930) is proposed to accommodate these strains. Physiological characteristics and mycocin sensitivity patterns distinguishing Cryptococcus festucosus from the other species of this clade are presented.

Cryptococcus nemorosus sp. nov. and Cryptococcus perniciosus sp. nov., related to Papiliotrema Sampaio et al. (Tremellales).

Three mycocinogenic strains representing the genus Cryptococcus were isolated on glucuronate agar from plants and turf collected in the Prioksko-terrasny biosphere reserve (Russia). These isolates fit the standard description of Cryptococcus laurentii, but differ from its type strain in both their mycocin-sensitivity profiles and the killing patterns of their mycocins. Sequence analyses of the D1/D2 domain of the 26S rDNA and of the internal transcribed spacer region confirmed that these isolates represent two novel species, for which the names Cryptococcus nemorosus sp. nov. (type strain VKM Y-2906(T)) and Cryptococcus perniciosus sp. nov. (type strain VKM Y-2905(T)) are proposed. Morphological, physiological and biochemical characteristics, as well as mycocinotyping and molecular analysis, show a close affinity between these two novel anamorphic species and the teleomorphic species Papiliotrema bandonii (Tremellales).