Resolving the phylogenetic relationship between Chlamydomonas sp. UWO 241 and Chlamydomonas raudensis sag 49.72 (Chlorophyceae) with nuclear and plastid DNA sequences

The Antarctic psychrophilic green alga Chlamy-domonas sp. UWO 241 is an emerging model for studying microbial adaptation to polar environments. However, little is known about its evolutionary history and its phylogenetic relationship with other chlamydomonadalean algae is equivocal. Here, we attempt to clarify the phylogenetic position of UWO 241, specifically with respect to Chlamydomonas rau-densis SAG 49.72. Contrary to a previous report, we show that UWO 241 is a distinct species from SAG 49.72. Our phylogenetic analyses of nuclear and plastid DNA sequences reveal that UWO 241 represents a unique lineage within the Moewusinia clade (sensu Nakada) of the Chlamydomonadales (Chlorophyceae, Chlorophyta), closely affiliated to the marine species Chlamydomonas parkeae SAG 24.89.

Starmera pilosocereana sp. nov., a yeast isolated from necrotic tissue of cacti in a sandy coastal dune ecosystem

Two strains of a novel cactophilic yeast species were isolated from the columnar cactus Pilosocereus arrabidae in a sand dune ecosystem in Rio de Janeiro, Brazil. Phylogenetic analysis of sequences of the large subunit rRNA gene D1/D2 domains showed that the strains represent a sister species to Starmera caribaea, from which it differs by 21 nt substitutions and two indels. The novel species is heterothallic and the asci are deliquescent with the formation of two to four hat-shaped ascospores. The name Starmera pilosocereana sp. nov. is proposed for the species. The type strain is UFMG-CM-Y316T ( = CBS 13266T) and the allotype is UFMG-CM-Y346a ( = CBS 13265). The Mycobank number is MB 810683. In addition, Candida stellimalicola belonging to the Starmera clade, is reassigned to Starmera as a new combination.

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar

Identifying the ecological processes that underlie the distribution and abundance of species in microbial communities is a central issue in microbial ecology and evolution. Classical trade-off based niche theories of resource competition predict that co-occurrence in microbial communities is more likely when the residing species show trait divergence and complementary resource use. We tested the prediction that niche differentiation explained the co-occurrence of two yeast species (Metschnikowia reukaufii and M. gruessii) in floral nectar. Assessment of the phenotypic landscape showed that both species displayed a significantly different physiological profile. Comparison of utilization profiles in single versus mixed cultures indicated that these two species did not compete for most carbon and nitrogen sources. In mixed cultures, M. reukaufii grew better in sucrose solutions and in the presence of the antimicrobial compound digitonin than when grown as pure culture. M. gruessii, on the other hand, grew better in mixed cultures in glucose and fructose solutions. Overall, these results provide clear evidence that M. reukaufii and M. gruessii frequently co-occur in nectar and that they differ in their phenotypic response to variation in environmental conditions, suggesting that niche differentiation and resource partitioning are important mechanisms contributing to species co-occurrence in nectar yeast communities.

Description of Diutina gen. nov., Diutina siamensis, f.a. sp. nov., and reassignment of Candida catenulata, Candida mesorugosa, Candida neorugosa, Candida pseudorugosa, Candida ranongensis, Candida rugosa and Candida scorzettiae to the genus Diutina

Three strains (DMKU-RE28, DMKU-RE43T and DMKU-RE123) of a novel anamorphic yeast species were isolated from rice leaf tissue collected in Thailand. DNA sequence analysis demonstrated that the species forms a sister pair with Candida ranongensis CBS 10861T but differs by 24-30 substitutions in the LSU rRNA gene D1/D2 domains and 30-35 substitutions in the ITS region. A phylogenetic analysis based on both the small and the large rRNA gene subunits confirmed this connection and demonstrated the presence of a clade that also includes Candida catenulata, Candida mesorugosa, Candida neorugosa, Candida pseudorugosa, Candida rugosa and Candida scorzettiae. The clade is not closely affiliated to any known teleomorphic genus, and forms a well-separated lineage from currently recognized genera of the Saccharomycetales. Hence, the genus Diutina gen. nov. is proposed to accommodate members of the clade, including Diutina siamensis f.a. sp. nov. and the preceding seven Candida species. The type strain is DMKU-RE43T ( = CBS 13388T = BCC 61183T = NBRC 109695T).

Yamadazyma riverae sp. nov., a yeast species isolated from plant materials

Nine strains of a novel yeast species were isolated from rotting wood, tree bark, ant nests or living as endophytes in leaves of Vellozia gigantea. Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species was related to Candida insectorum in the Yamadazyma clade. The novel species differed from closely related species by 10 and 11 substitutions in the ITS region and the D1/D2 domains of the large subunit of the rRNA gene, respectively. The species is heterothallic and forms asci with one to two hat-shaped ascospores. The name Yamadazyma riverae sp. nov. is proposed for the novel species. The type strain is UFMG-CM-Y444T ( = CBS 14121T) and the allotype strain is TT12 ( = CBS 14098 = UFMG-CM-Y577). The Mycobank number is MB 813221.

Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials

Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related to C. japonica, C. maesa and C. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the name C. xylosilytica sp. nov. is proposed. The type strain of C. xylosilytica sp. nov. is NRRL YB-2097(T) ( = CBS 13984(T) = UFMG-CM-Y347(T)) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428.

Ogataea mangiferae sp. nov., a methylotrophic yeast isolated from mango leaves

Five strains of a novel methanol-assimilating yeast species were isolated from mango (Mangifera indica) leaves collected at the campus of the Federal University of Minas Gerais in Brazil. The sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit of the rRNA gene showed that this species belongs to the Ogataea clade and is related to O. allantospora, O. chonburiensis, O. dorogensis, O. kodamae, O. paradorogensis and Candida xyloterini (Ogataea clade). The novel species differs in the D1/D2 domains of the large subunit of the rRNA gene by 12 to 40 substitutions from these Ogataea species. The name Ogataea mangiferae sp. nov. is proposed for this novel species. The type strain of Ogataea mangiferae sp. nov. is UFMG-CM-Y253T ( = CBS 13492T). The Mycobank number is MB 811646.

The diversity and extracellular enzymatic activities of yeasts isolated from water tanks of Vriesea minarum, an endangered bromeliad species in Brazil, and the description of Occultifur brasiliensis f.a., sp. nov

The diversity of yeast species collected from the bromeliad tanks of Vriesea minarum, an endangered bromeliad species, and their ability to produce extracellular enzymes were studied. Water samples were collected from 30 tanks of bromeliads living in a rupestrian field site located at Serrada Piedade, Minas Gerais state, Brazil, during both the dry and rainy seasons. Thirty-six species were isolated, representing 22 basidiomycetous and 14 ascomycetous species. Occultifur sp., Cryptococcus podzolicus and Cryptococcus sp. 1 were the prevalent basidiomycetous species. The yeast-like fungus from the order Myriangiales, Candida silvae and Aureobasidium pullulans were the most frequent ascomycetous species. The diversity of the yeast communities obtained between seasons was not significantly different, but the yeast composition per bromeliad was different between seasons. These results suggest that there is significant spatial heterogeneity in the composition of populations of the yeast communities within bromeliad tanks, independent of the season. Among the 352 yeast isolates tested, 282 showed at least one enzymatic activity. Protease activity was the most widely expressed extracellular enzymatic activity, followed by xylanase, amylase, pectinase and cellulase activities. These enzymes may increase the carbon and nitrogen availability for the microbial food web in the bromeliad tank of V. minarum. Sequence analyses revealed the existence of 10 new species, indicating that bromeliad tanks are important sources of new yeasts. The novel species Occultifur brasiliensis, f.a., sp. nov., is proposed to accommodate the most frequently isolated yeast associated with V. minarum. The type strain of O. brasiliensis, f.a., sp. nov. is UFMG-CM-Y375(T) (= CBS 12687(T)). The Mycobank number is MB 809816.

Metschnikowia drakensbergensis sp. nov. and Metschnikowia caudata sp. nov., endemic yeasts associated with Protea flowers in South Africa

In a taxonomic study of yeasts recovered from nectar of flowers and associated insects in South Africa, 11 strains were found to represent two novel species. Morphological and physiological characteristics and sequence analyses of the large-subunit rRNA gene D1/D2 region, as well as the actin, RNA polymerase II and elongation factor 2 genes, showed that the two novel species belonged to the genus Metschnikowia. Metschnikowia drakensbergensis sp. nov. (type strain EBD-CdVSA09-2T = CBS 13649T = NRRL Y-63721T; MycoBank no. MB809688; allotype EBD-CdVSA10-2A = CBS13650A = NRRL Y-63720A) was recovered from nectar of Protea roupelliae and the beetle Heterochelus sp. This species belongs to the large-spored Metschnikowia clade and is closely related to Metschnikowia proteae, with which mating reactions and single-spored asci were observed. Metschnikowia caudata sp. nov. (type strain EBD-CdVSA08-1T = CBS 13651T = NRRL Y-63722T; MycoBank no. MB809689; allotype EBD-CdVSA57-2A = CBS 13729A = NRRL Y-63723A) was isolated from nectar of Protea dracomontana, P. roupelliae and P. subvestita and a honeybee, and is a sister species to Candida hainanensis and Metschnikowia lopburiensis. Analyses of the four sequences demonstrated the existence of three separate phylotypes. Intraspecies matings led to the production of mature asci of unprecedented morphology, with a long, flexuous tail. A single ascospore was produced in all compatible crosses, regardless of sequence phylotype. The two species appear to be endemic to South Africa. The ecology and habitat specificity of these novel species are discussed in terms of host plant and insect host species.

Hagleromyces gen. nov., a yeast genus in the Saccharomycetaceae, and description of Hagleromyces aurorensis sp. nov., isolated from water tanks of bromeliads

Three strains of a novel yeast species were isolated from water tanks (phytotelmata) of a bromeliad species collected in the state of Tocantins, Brazil. Analysis of sequences for the region spanning the SSU rRNA gene, the internal transcribed spacer, the 5.8S rRNA gene and the D1/D2 domains of the LSU rRNA gene and RNA polymerase II gene showed that these novel yeasts belong to a species that is distinct from all recognized ascomycetous yeast species. Based on the results of gene sequence analyses, a novel species representing a new genus in the Saccharomycetaceae is proposed. The novel species is assigned to the genus Hagleromyces gen. nov. The three isolates of the novel yeast species failed to form sexual spores alone or in mixtures. The name Hagleromyces aurorensis sp. nov. is proposed to accommodate these isolates. The type strain of H. aurorensis sp. nov. is UFMG-CM-Y311T ( = CBS 13264T).

Kodamaea transpacifica f.a., sp. nov., a yeast species isolated from ephemeral flowers and insects in the Galápagos Islands and Malaysia: further evidence for ancient human transpacific contacts

Twenty-four yeast strains were isolated from ephemeral flowers of Ipomoea spp. and Datura sp. and their associated insects in the Galápagos Archipelago, Ecuador, and from Ipomoea spp. and associated insects in the Cameron Highlands, Malaysia. Sequences of the D1/D2 domains of the large subunit rRNA gene indicated that these strains belong to a novel yeast species of the Kodamaea clade, although the formation of ascospores was not observed. The closest relative is Candida restingae. The human-mediated dispersion of this species by transpacific contacts in ancient times is suggested. The name Kodamaea transpacifica f.a., sp. nov. is proposed to accommodate these isolates. The type strain is CLQCA-24i-070T ( = CBS 12823T = NCYC 3852T); MycoBank number MB 803609.

Starmerella neotropicalis f. a., sp. nov., a yeast species found in bees and pollen

A novel yeast species was found repeatedly and in high cell densities in underground-nesting stingless bees of the species Melipona quinquefasciata and their provisions in northern Minas Gerais (Brazil). One additional strain was isolated from bee-collected pollen in Cuba. Phylogenetic analyses based on rRNA gene sequences (D1/D2 large subunit gene and internal transcribed spacer) indicated that the novel species belongs to the Starmerella clade and is most closely related to Candida (iter. nom. Starmerella) apicola. Growth reactions on carbon and nitrogen sources were typical of those observed in related species of the Starmerella clade. PCR-fingerprinting with mini- and microsatellite specific primers allowed the distinction of the novel species from Candida apicola, Candida bombi and a yet undescribed species represented by strain CBS 4353. On the basis of phylogenetic relationships, the novel species is assigned to the genus Starmerella despite the failure to observe sexual reproduction after extensive mating tests. We propose the name Starmerella neotropicalis f. a., sp. nov. (Mycobank MB 804285) and designate UFMG PST 09(T) ( = MUCL 53320(T) = CBS 12811(T)) as the type strain.

Wickerhamiella slavikovae sp. nov. and Wickerhamiella goesii sp. nov., two yeast species isolated from natural substrates

Two novel yeast species were isolated during three independent studies of yeasts associated with natural substrates in Brazil and Taiwan. Analysis of the sequences of the D1/D2 domains of the large subunit rRNA gene showed that these novel species belong to the Wickerhamiella clade. The first was isolated from freshwater and a leaf of sugar cane (Saccharum officinarum) in Brazil and from leaves of Wedelia biflora in Taiwan. Described here as Wickerhamiella slavikovae sp. nov., it differs by 56 nucleotide substitutions and 19 gaps in the D1/D2 region of the large subunit rRNA gene from Candida sorbophila, the least divergent species. The second species, named Wickerhamiella goesii sp. nov., was isolated from leaves and the rhizosphere of sugar cane collected in Rio de Janeiro, Brazil. The species differs by 54 nucleotide substitutions and nine gaps in the D1/D2 domains from Candida drosophilae, its least divergent relative. The type strains are Wickerhamiella slavikovae sp. nov. IMUFRJ 52096T ( = CBS 12417T = DBVPG 8032T) and Wickerhamiella goesii sp. nov. IMUFRJ 52102T ( = CBS 12419T = DBVPG 8034T).

Sugiyamaella xylanicola sp. nov., a xylan-degrading yeast species isolated from rotting wood

Four strains of a novel yeast species were isolated from rotting-wood samples in an Atlantic rainforest site in the state of Minas Gerais, Brazil. These yeasts were obtained from enrichments using yeast nitrogen base (YNB)-d-xylose or YNB-xylan media. The novel yeast species produces bacilliform ascospores typical of the genus Sugiyamaella, and its closest described relative in terms of sequence similarity is Candida (iter. nom. Sugiyamaella) marionensis. The yeast is able to grow in medium with xylan as sole carbon source and produces extracellular enzymes with xylanolytic activities. The novel species Sugiyamaella xylanicola sp. nov. is proposed to accommodate these isolates. The type strain is UFMG-CA-32.1(T) (=CBS 12683(T) =CBMAI 1467(T)).

Moniliella carnis sp. nov. and Moniliella dehoogii sp. nov., two novel species of black yeasts isolated from meat processing environments

Thirteen strains of yeasts typical of the genus Moniliella were isolated from fermenting meat and meat processing tools in Vietnam. PCR fingerprints generated by primer (GAC)5 subdivided the strains into two distinctive genetic groups. In a phylogenetic tree based on D1/D2 large subunit rRNA gene sequences, the strains formed a well-supported clade with Moniliella spathulata and Moniliella suaveolens but represented two new lineages. The names Moniliella carnis sp. nov. and Moniliella dehoogii sp. nov. are proposed. The two novel species can be distinguished from each other and from known species of Moniliella based on phenotypic characteristics. It is assumed that the yeasts were associated with fatty substances that contaminated the meat processing tools. The type strain of Moniliella carnis is KFP 246T ( = CBS 126447T = NRRL Y-48681T) and the type strain of Moniliella dehoogii is KFP 211T ( = CBS 126564T = NRRL Y-48682T).

Wickerhamiella dulcicola sp. nov. and Wickerhamiella cachassae sp. nov., yeasts isolated from cachaça fermentation in Brazil

Six strains of two novel yeast species were isolated from sugar-cane juice and fermentation vats of cachaça production in Brazil. The sequences of the D1/D2 domains of the large-subunit rRNA gene showed that these species belong to the Wickerhamiella clade, and their closest described relative in terms of sequence similarity is Candida (iter. nom. Wickerhamiella) drosophilae. The type strain of Wickerhamiella cachassae sp. nov. is UFMG-D5L7(T) ( = CBS 12587(T)  = CBMAI 1469(T)) and the type strain of Wickerhamiella dulcicola sp. nov. is UFMG-TOL15(T) ( = CBS 12588(T)  = CBMAI 1468(T)).

Kazachstania rupicola sp. nov., a yeast species isolated from water tanks of a bromeliad in Brazil

Two isolates of a novel yeast species were obtained from water tanks (phytotelmata) of the bromeliad Vriesea minarum collected in a tableland ('campo rupestre') ecosystem in Brazil. The sequences of the D1/D2 domains of the large-subunit rRNA gene showed that this species is related to Kazachstania exigua and others, from which it differs by 8-10 nucleotide substitutions. The novel species Kazachstania rupicola sp. nov. is proposed to accommodate these isolates. The type strain is UFMG-BRO-80(T) ( = CBS 12684(T)  = CBMAI 1466(T)).

Saccharomycopsis fodiens sp. nov., a rare predacious yeast from three distant localities

Three strains representing a novel yeast species were recovered as part of independent collections from flower-associated nitidulid beetles in Australia, Costa Rica and the Galapagos Islands, Ecuador. Analysis of the D1/D2 domains of the large subunit rRNA gene indicated that the species belongs to the genus Saccharomycopsis, although the formation of ascospores was not observed. The yeast is capable of necrotrophic parasitism by means of infection pegs when mixed with other yeasts or filamentous fungi. Of particular interest is the fact that despite the large distances separating the isolation sites of the three strains, other strains of the species have not been recovered in other samples of flower-associated nitidulids even though these habitats have been sampled extensively. It is suggested that the dispersal of the yeast may be linked to human historical factors. The name Saccharomycopsis fodiens sp. nov. is proposed for the yeast. The type strain is UWOPS 95-697.4T ( = CBS 8332T = NRRL Y-48786T).

Diversity and physiological characterization of D-xylose-fermenting yeasts isolated from the Brazilian Amazonian Forest

Background

This study is the first to investigate the Brazilian Amazonian Forest to identify new D-xylose-fermenting yeasts that might potentially be used in the production of ethanol from sugarcane bagasse hemicellulosic hydrolysates.

Methodology/Principal Findings

A total of 224 yeast strains were isolated from rotting wood samples collected in two Amazonian forest reserve sites. These samples were cultured in yeast nitrogen base (YNB)-D-xylose or YNB-xylan media. Candida tropicalis, Asterotremella humicola, Candida boidinii and Debaryomyces hansenii were the most frequently isolated yeasts. Among D-xylose-fermenting yeasts, six strains of Spathaspora passalidarum, two of Scheffersomyces stipitis, and representatives of five new species were identified. The new species included Candida amazonensis of the Scheffersomyces clade and Spathaspora sp. 1, Spathaspora sp. 2, Spathaspora sp. 3, and Candida sp. 1 of the Spathaspora clade. In fermentation assays using D-xylose (50 g/L) culture medium, S. passalidarum strains showed the highest ethanol yields (0.31 g/g to 0.37 g/g) and productivities (0.62 g/L·h to 0.75 g/L·h). Candida amazonensis exhibited a virtually complete D-xylose consumption and the highest xylitol yields (0.55 g/g to 0.59 g/g), with concentrations up to 25.2 g/L. The new Spathaspora species produced ethanol and/or xylitol in different concentrations as the main fermentation products. In sugarcane bagasse hemicellulosic fermentation assays, S. stipitis UFMG-XMD-15.2 generated the highest ethanol yield (0.34 g/g) and productivity (0.2 g/L·h), while the new species Spathaspora sp. 1 UFMG-XMD-16.2 and Spathaspora sp. 2 UFMG-XMD-23.2 were very good xylitol producers.

Conclusions/Significance

This study demonstrates the promise of using new D-xylose-fermenting yeast strains from the Brazilian Amazonian Forest for ethanol or xylitol production from sugarcane bagasse hemicellulosic hydrolysates.

Nectar yeasts of two southern Spanish plants: the roles of immigration and physiological traits in community assembly

Recent studies have shown that dense yeast populations often occurring in floral nectar are numerically dominated by a few species from the flower–insect interface specialized genus Metschnikowia, while generalist yeast species commonly occurring on leaf surfaces, soil, freshwater, and air were rarely isolated from nectar samples. This study was designed to understand the main factors responsible for the assembly of nectar yeast communities, by combining field experiments with laboratory tests characterizing the physiological abilities of all yeast species forming the pool of potential colonizers for two Spanish flowering plants (Digitalis obscura and Atropa baetica). Yeast frequency and species richness were assessed in external sources (bee glossae, air, plant phylloplane) as well as in pollinator rewards (pollen, nectar). Yeasts were most frequent in external sources (air, flower-visiting insects), less so in the proximate floral environment (phylloplane), and least in pollen and nectar. Nectar communities appeared to be considerably impoverished versions of those in insect glossae and phylloplane. Nectar, pollen, and insect yeast assemblages differed in physiological characteristics from those in other substrates. Nectarivorous Metschnikowia were not more resistant than other yeast species to plant secondary compounds and high sugar concentrations typical of nectar, but their higher growth rates may be decisive for their dominance in ephemeral nectar communities.

Kazachstania bromeliacearum sp. nov., a yeast species from water tanks of bromeliads

Cultures of a novel nutritionally specialized, fermentative yeast species were isolated from 34 water tanks of five bromeliad species, two mangrove sediment samples and one swamp water sample in Rio de Janeiro, Brazil. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species belongs to the genus Kazachstania. The novel species differs from Kazachstania martiniae by 11 substitutions and 2 gaps in the sequence of the domains D1/D2 of the LSU rRNA gene. The name Kazachstania bromeliacearum sp. nov. is proposed for the novel species. The type strain is IMUFRJ 51496T ( = CBS 7996T  = DBVPG 6864T  = UFMG BR-174T).