Alvaro Fonseca | Universidade Nova de Lisboa (original) (raw)

Papers by Alvaro Fonseca

Research paper thumbnail of Partitioning yeast diversity on biome, biotope, plot and species scales

ABSTRACT Complete species recovery and robust species identification are both crucial for accurat... more ABSTRACT Complete species recovery and robust species identification are both crucial for accurate biodiversity assessment of yeasts in the environment. We set out to analyse the relationship between species richness values in soils and sampling at several hierarchical levels: (i) different plots within a forest sampled in the same season, (ii) forests of the same type studied in the same season, and (iii) forests of the same type studied in different seasons. By using species richness estimations, we determined the adequate sampling effort in a habitat. Our results revealed that yeast communities in soils are: (1) generally species-poor in a single plot; (2) highly dissimilar between plots or across spatial and environmental transects; (3) globally diverse with up to 25% more species discovered with every new forest or season sampled; (4) understudied and may contain up to 20% hitherto undescribed species. Furthermore, we assessed species boundaries in several clades of Tremellomycetes and tested for the presence of cryptic species from the same environments using multi-locus sequence analysis (MLSA) approaches. Our results showed that ITS-LSU rRNA sequences are often unable to distinguish cryptic species and demonstrated the usefulness of network-based methods over tradi4onal phylogenetic trees for adequate species delimitation. This work was partly supported by Fundação para a Ciência e a Tecnologia (Portugal), projects PTDC/BIA- MIC/113051/2009, PTDC/BIA-BIC/4585/2012, PEst-OE/BIA/UI0457/2011.

Research paper thumbnail of Professor Isabel Spencer-Martins 1951-2008 OBITUARY

Fems Yeast Research, 2008

Research paper thumbnail of Genetic variation and species boundaries in the basidiomycetous yeasts Cryptococcus victoriae and C. carnescens (Tremellales) - a multigene approach

Cryptococcus victoriae and C. carnescens are phenotypically indistinguishable sister species that... more Cryptococcus victoriae and C. carnescens are phenotypically indistinguishable sister species that may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. victoriae and C. carnescens was based on LSU and ITS sequence analyses, but very little is known on their intraspecific genetic variability or population structure. In the present study we examined 100 strains of the two species from different substrates and geographic locations, and used an MLST approach to assess genetic variation and re-examine species boundaries. The following six loci were chosen for sequencing: the LSU rRNA gene (D1/D2 domains), the ITS region, the IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1 alpha (TEF1). We performed separate phylogenetic analyses to determine the discriminatory power of each locus. Amplification of IGS1 was inconsistent ...

Research paper thumbnail of Yeast Biogeography and the Effects of Species Recognition Approaches: The Case Study of Widespread Basidiomycetous Species from Birch Forests in Russia

Current Microbiology, 2014

Research paper thumbnail of Molecular and Genetic Evidence for a Tetrapolar Mating System in the Basidiomycetous Yeast Kwoniella mangrovensis and Two Novel Sibling Species

Eukaryotic Cell, 2013

Kwoniella mangrovensis has been described as a sexual species with a bipolar mating system. Phylo... more Kwoniella mangrovensis has been described as a sexual species with a bipolar mating system. Phylogenetic analysis of multiple genes places this species together with Kwoniella heveanensis in the Kwoniella clade, a sister clade to that containing two pathogenic species of global importance, Cryptococcus neoformans and Cryptococcus gattii , within the Tremellales. Recent studies defining the mating type loci ( MAT ) of species in these clades showed that, with the exception of C. neoformans and C. gattii , which are bipolar with a single biallelic multigene MAT locus, several other species feature a tetrapolar mating system with two unlinked loci (homeodomain [HD] and pheromone/receptor [P/R] loci). We characterized several strains from the original study describing K. mangrovensis ; two MAT regions were amplified and sequenced: the STE20 gene (P/R locus) and the divergently transcribed SXI1 and SXI2 genes (HD locus). We identified five different mating types with different STE20 / SX...

Research paper thumbnail of Examination of genetic variation and species boundaries in the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales) using a multigene approach

Cryptococcus flavescens and C. terrestris are phenotypically undistinguishable sister species, wh... more Cryptococcus flavescens and C. terrestris are phenotypically undistinguishable sister species, which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on LSU and ITS sequence analyses, but very little is known on their intraspecific genetic variability or population structure. In the present study we studied 50 strains of the two species from different substrates and geographic locations, and used an MLST approach to assess genetic variation and reexamine species boundaries. The following five loci were chosen for sequencing: the LSU rRNA gene (D1/D2 domains), the ITS region, the IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1) and translation elongation factor 1 alpha (TEF1). We performed separate phylogenetic analyses to determine the discriminatory power of each locus. The TEF gene fragment showed the highest inter- and intraspecific variability (23 alleles...

Research paper thumbnail of Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

Research paper thumbnail of Cryptococcus haglerorum, sp. nov., an anamorphic basidiomycetous yeast isolated from nests of the leaf-cutting ant Atta sexdens

Anton Leeuwenhoek Int J Gen M, 2003

Research paper thumbnail of Multigene Assessment of the Species Boundaries and Sexual Status of the Basidiomycetous Yeasts Cryptococcus flavescens and C. terrestris (Tremellales)

PloS one, 2015

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species tha... more Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20)....

Research paper thumbnail of PYCC–a repository of Mediterranean yeast diversity

Research paper thumbnail of Cryptococcus Vuillemin (1901)

Research paper thumbnail of Cryptococcus haglerorum, sp nov., an anamorphic basidiomycetous yeast isolated from nests of the leaf-cutting ant Atta sexdens

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 2003

Research paper thumbnail of Yeast Biogeography and the Effects of Species Recognition Approaches: The Case Study of Widespread Basidiomycetous Species from Birch Forests in Russia

Current Microbiology, 2014

Understanding diversity and distribution patterns of fungi, including yeasts, ultimately depends ... more Understanding diversity and distribution patterns of fungi, including yeasts, ultimately depends on accuracy of species recognition. However, different approaches to yeast species recognition often result in different entities or operational taxonomic units. We studied the effects of using different yeast species recognition approaches, namely morphological species recognition (MSR) and phylogenetic species recognition (PSR), on the distribution patterns of widespread basidiomycetous yeasts. Hence, we have revised a collection of yeast fungi isolated from spatially remote birch forests in the Moscow Region and Western Siberia with molecular typing and identification tools. PCR fingerprinting and rDNA sequencing analyses of strains of nine species previously identified on the basis of morphological and physiological tests (MSR) yielded 21 phylogenetic species (PSR), including three currently undescribed taxa. The number of distinct phylogenetic species comprised within a single morphospecies ranged from one to seven. A total of ten species were found in both regions, whereas the distribution of 11 yeasts was restricted to a single region only. Both geographical region and type of substrate (plant or soil) influence yeast distribution. Cryptococcus wieringae, C. victoriae, C. magnus, and Leucosporidium scottii were frequently found on plant substrates, whereas C. terricola and C. podzolicus were associated to soil substrates. Occurrence of C. magnus, C. albidus and Sporobolomyces roseus was found to depend on the geographical region. Microsatellite-PCR fingerprinting, MSP-PCR, applied to studying yeast intraspecific variability revealed three different types of distribution: (a) variability that depends on geographical factors (Curvibasidium cygneicollum, C. podzolicus, C. victoriae), (b) genetic identity irrespectively of the region of isolation (Rhodotorula pinicola, C. terricola), and (c) high degree of genetic variability that did not correlate with region of sampling (C. albidus and C. magnus). Electronic supplementary material The online version of this article (Cryptococcus aff. victoriae CBS 8979 (AF406892) Cryptococcus heimaeyensis isolate AY-73 (FN357212) Cryptococcus aff. victoriae CBS 8999 (AF406893) Cryptococcus heimaeyensis CBS 8933 (DQ000317) Cryptococcus aff. victoriae CBS 9025 (AF406898) Cryptococcus peneaus CBS 2409 (AB035051) Cryptococcus taibaiensis CBS 9912 (AY557601) Cryptococcus sp. CBS 2993 (AB035052) Cryptococcus aff. victoriae CBS 9024 (AF406897) Cryptococcus foliicola isolate AY-78 (FN357211) Cryptococcus foliicola CBS 9920 (AY557599) Cryptococcus sp. CBS 6578 (AB035053) Cryptococcus carnescens isolate AY-87 (FN357213) Cryptococcus carnescens CBS 973 (AB035054) Cryptococcus victoriae CBS 8915 (AY040652) Cryptococcus victoriae isolate AY-92 (FN357206) Cryptococcus victoriae CBS 9006 (AF406900) Cryptococcus victoriae CBS 8937 Cryptococcus victoriae CBS 8685 (AF363647), Type strain Cryptococcus victoriae CBS 9268 Cryptococcus victoriae CBS 9264 Cryptococcus victoriae CBS 8920 (AY040650) Cryptococcus victoriae CBS 9009 (AF406901) Cryptococcus victoriae CBS 9000 (AF406899) Cryptococcus victoriae isolate AY-99 (FN357207) Cryptococcus victoriae CBS 9265 Cryptococcus victoriae CBS 6550 (AF444711) Cryptococcus victoriae CBS 9267 Cryptococcus victoriae isolate AY-68 (FN357201) Cryptococcus victoriae isolate AY-93 (FN357202) Cryptococcus aff. victoriae CBS 9013 (AF406895) Cryptococcus victoriae CBS 8908 (AY040653) Cryptococcus victoriae isolate AY-82 (FN357203) Cryptococcus victoriae isolate AY-84 (FN357205) Cryptococcus victoriae isolate AY-81 (FN357204) Cryptococcus victoriae CBS 8884 (AF444741) Cryptococcus victoriae CBS 9206 Cryptococcus victoriae isolate AY-97 (FN357214) Cryptococcus aff. victoriae CBS 8993 (AF408633) Cryptococcus tephrensis "var. soli" CBS 8968 Cryptococcus "victoriae" CBS 9799 Cryptococcus aff. victoriae CBS 9023 (AF406896) Cryptococcus sp isolate AY-77 (FN357208) Cryptococcus tephrensis "var. soli" CBS 8934 Cryptococcus aff. victoriae CBS 9012 (AF406894) Cryptococcus tephrensis "var. tephrensis" CBS 8935 (DQ000318), Type strain Cryptococcus tephrensis isolate AY-95 (FN357215) Cryptococcus tephrensis isolate AY-100 (FN357209) Cryptococcus tephrensis isolate AY-103 (FN357210) Cryptococcus tephrensis isolate AY-94 (FN357216) Cryptococcus dimennae CBS 5770 (AF075489) Bullera globispora CBS 6981 (AF075509)

Research paper thumbnail of Cryptococcus yarrowii sp. nov., a novel yeast species from Portugal

Antonie van Leeuwenhoek, 1991

A novel species of the basidiomycetous genus Cryptococcus is described as Cr. yarrowii based on t... more A novel species of the basidiomycetous genus Cryptococcus is described as Cr. yarrowii based on the study of an isolate from a decayed mushroom collected in Portugal. DNA-DNA homology with the type strain of the phenotypically similar species Cr. albidus was 10 +/- 2%.

Research paper thumbnail of Comparative genomics suggests primary homothallism of pneumocystis species

mBio, 2015

Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis ... more Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jiroveci...

Research paper thumbnail of Rhodosporidium lusitaniae sp. nov., a Novel Homothallic Basidiomycetous Yeast Species from Portugal that Degrades Phenolic Compounds

Systematic and Applied Microbiology, 1992

ABSTRACT

Research paper thumbnail of Validation of <I>Kwoniella heveanensis</I>, teleomorph of the basidiomycetous yeast <I>Cryptococcus heveanensis</I>

Mycotaxon, 2011

ABSTRACT Kwoniella heveanensis, recently published in an electronic journal and without a designa... more ABSTRACT Kwoniella heveanensis, recently published in an electronic journal and without a designated holotype, is validated as the name of the newly discovered teleomorph of Cryptococcus heveanensis.

Research paper thumbnail of Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

Research paper thumbnail of Farysizyma gen. nov., an anamorphic genus in the Ustilaginales to accommodate three novel epiphytic basidiomycetous yeast species from America, Europe and Asia

FEMS Yeast Research, 2008

Among many isolates that resulted from four independent surveys of yeasts associated with plants ... more Among many isolates that resulted from four independent surveys of yeasts associated with plants in Brazil, the USA, Portugal and Taiwan, we have characterized eighteen basidiomycetous strains, two of which were conspecific with the type strain of Rhodotorula acheniorum, whereas the remaining sixteen isolates appeared not to correspond to any previously described species. Microsatellite-PCR fingerprinting with primers M13 and (GTG) 5 confirmed that the latter strains formed three genetically distinct groups. Each group was considered to represent a distinct species based on nucleotide sequences of the D1/D2 domains of the 26S rRNA gene and the internal transcribed spacer (ITS) region. Phylogenetic analyses of sequence data placed the putative novel species in a clade with R. acheniorum and the dimorphic smut fungus Farysia chardoniana. A novel anamorphic genus, Farysizyma, is created to accommodate the three undescribed species, which were named Farysizyma itapuensis, Farysizyma setubalensis and Farysizyma taiwaniana. A new combination, Farysizyma acheniorum, is proposed for R. acheniorum, which may represent the yeast-phase anamorph of Farysia thuemenii.

Research paper thumbnail of Assessment of phylloplane yeasts on selected Mediterranean plants by FISH with group- and species-specific oligonucleotide probes

FEMS Microbiology Ecology, 2000

A previous culture-dependent survey of phylloplane yeasts from selected Mediterranean plants show... more A previous culture-dependent survey of phylloplane yeasts from selected Mediterranean plants showed that a few species were present in high densities in almost all leaf samples, regardless of the plant type, location or sampling season. However, a few species appeared to be restricted to Cistus albidus leaves, namely Cryptococcus cistialbidi. Here, we describe a culture-independent FISH assay to detect and quantify whole yeast cells in leaf washings. After optimization, the technique was used to check the apparent association between C. albidus leaves and C. cistialbidi and the abundance and ubiquity of other basidiomycetous yeast species such as Erythrobasidium hasegawianum and Sporobolomyces spp. in leaf samples from this and other neighboring plants (Acer monspessulanum and Quercus faginea). No yeast cells were detected in Pistacia lentiscus leaf samples. We were also able to demonstrate that three phylloplane yeasts (C. cistialbidi, E. hasegawianum and Sporobolomyces spp.) appeared to be log-normally distributed among individual C. albidus leaves. The log-normal distribution has important implications for the quantification of phylloplane yeasts based on the washing and plating of bulk leaf samples, which will tend to overestimate the size of the respective populations and become an error source in yeast surveys or related biocontrol studies. FEMS Microbiol Ecol 71 (2010) 61-72 c

Research paper thumbnail of Partitioning yeast diversity on biome, biotope, plot and species scales

ABSTRACT Complete species recovery and robust species identification are both crucial for accurat... more ABSTRACT Complete species recovery and robust species identification are both crucial for accurate biodiversity assessment of yeasts in the environment. We set out to analyse the relationship between species richness values in soils and sampling at several hierarchical levels: (i) different plots within a forest sampled in the same season, (ii) forests of the same type studied in the same season, and (iii) forests of the same type studied in different seasons. By using species richness estimations, we determined the adequate sampling effort in a habitat. Our results revealed that yeast communities in soils are: (1) generally species-poor in a single plot; (2) highly dissimilar between plots or across spatial and environmental transects; (3) globally diverse with up to 25% more species discovered with every new forest or season sampled; (4) understudied and may contain up to 20% hitherto undescribed species. Furthermore, we assessed species boundaries in several clades of Tremellomycetes and tested for the presence of cryptic species from the same environments using multi-locus sequence analysis (MLSA) approaches. Our results showed that ITS-LSU rRNA sequences are often unable to distinguish cryptic species and demonstrated the usefulness of network-based methods over tradi4onal phylogenetic trees for adequate species delimitation. This work was partly supported by Fundação para a Ciência e a Tecnologia (Portugal), projects PTDC/BIA- MIC/113051/2009, PTDC/BIA-BIC/4585/2012, PEst-OE/BIA/UI0457/2011.

Research paper thumbnail of Professor Isabel Spencer-Martins 1951-2008 OBITUARY

Fems Yeast Research, 2008

Research paper thumbnail of Genetic variation and species boundaries in the basidiomycetous yeasts Cryptococcus victoriae and C. carnescens (Tremellales) - a multigene approach

Cryptococcus victoriae and C. carnescens are phenotypically indistinguishable sister species that... more Cryptococcus victoriae and C. carnescens are phenotypically indistinguishable sister species that may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. victoriae and C. carnescens was based on LSU and ITS sequence analyses, but very little is known on their intraspecific genetic variability or population structure. In the present study we examined 100 strains of the two species from different substrates and geographic locations, and used an MLST approach to assess genetic variation and re-examine species boundaries. The following six loci were chosen for sequencing: the LSU rRNA gene (D1/D2 domains), the ITS region, the IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1 alpha (TEF1). We performed separate phylogenetic analyses to determine the discriminatory power of each locus. Amplification of IGS1 was inconsistent ...

Research paper thumbnail of Yeast Biogeography and the Effects of Species Recognition Approaches: The Case Study of Widespread Basidiomycetous Species from Birch Forests in Russia

Current Microbiology, 2014

Research paper thumbnail of Molecular and Genetic Evidence for a Tetrapolar Mating System in the Basidiomycetous Yeast Kwoniella mangrovensis and Two Novel Sibling Species

Eukaryotic Cell, 2013

Kwoniella mangrovensis has been described as a sexual species with a bipolar mating system. Phylo... more Kwoniella mangrovensis has been described as a sexual species with a bipolar mating system. Phylogenetic analysis of multiple genes places this species together with Kwoniella heveanensis in the Kwoniella clade, a sister clade to that containing two pathogenic species of global importance, Cryptococcus neoformans and Cryptococcus gattii , within the Tremellales. Recent studies defining the mating type loci ( MAT ) of species in these clades showed that, with the exception of C. neoformans and C. gattii , which are bipolar with a single biallelic multigene MAT locus, several other species feature a tetrapolar mating system with two unlinked loci (homeodomain [HD] and pheromone/receptor [P/R] loci). We characterized several strains from the original study describing K. mangrovensis ; two MAT regions were amplified and sequenced: the STE20 gene (P/R locus) and the divergently transcribed SXI1 and SXI2 genes (HD locus). We identified five different mating types with different STE20 / SX...

Research paper thumbnail of Examination of genetic variation and species boundaries in the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales) using a multigene approach

Cryptococcus flavescens and C. terrestris are phenotypically undistinguishable sister species, wh... more Cryptococcus flavescens and C. terrestris are phenotypically undistinguishable sister species, which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on LSU and ITS sequence analyses, but very little is known on their intraspecific genetic variability or population structure. In the present study we studied 50 strains of the two species from different substrates and geographic locations, and used an MLST approach to assess genetic variation and reexamine species boundaries. The following five loci were chosen for sequencing: the LSU rRNA gene (D1/D2 domains), the ITS region, the IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1) and translation elongation factor 1 alpha (TEF1). We performed separate phylogenetic analyses to determine the discriminatory power of each locus. The TEF gene fragment showed the highest inter- and intraspecific variability (23 alleles...

Research paper thumbnail of Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

Research paper thumbnail of Cryptococcus haglerorum, sp. nov., an anamorphic basidiomycetous yeast isolated from nests of the leaf-cutting ant Atta sexdens

Anton Leeuwenhoek Int J Gen M, 2003

Research paper thumbnail of Multigene Assessment of the Species Boundaries and Sexual Status of the Basidiomycetous Yeasts Cryptococcus flavescens and C. terrestris (Tremellales)

PloS one, 2015

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species tha... more Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20)....

Research paper thumbnail of PYCC–a repository of Mediterranean yeast diversity

Research paper thumbnail of Cryptococcus Vuillemin (1901)

Research paper thumbnail of Cryptococcus haglerorum, sp nov., an anamorphic basidiomycetous yeast isolated from nests of the leaf-cutting ant Atta sexdens

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 2003

Research paper thumbnail of Yeast Biogeography and the Effects of Species Recognition Approaches: The Case Study of Widespread Basidiomycetous Species from Birch Forests in Russia

Current Microbiology, 2014

Understanding diversity and distribution patterns of fungi, including yeasts, ultimately depends ... more Understanding diversity and distribution patterns of fungi, including yeasts, ultimately depends on accuracy of species recognition. However, different approaches to yeast species recognition often result in different entities or operational taxonomic units. We studied the effects of using different yeast species recognition approaches, namely morphological species recognition (MSR) and phylogenetic species recognition (PSR), on the distribution patterns of widespread basidiomycetous yeasts. Hence, we have revised a collection of yeast fungi isolated from spatially remote birch forests in the Moscow Region and Western Siberia with molecular typing and identification tools. PCR fingerprinting and rDNA sequencing analyses of strains of nine species previously identified on the basis of morphological and physiological tests (MSR) yielded 21 phylogenetic species (PSR), including three currently undescribed taxa. The number of distinct phylogenetic species comprised within a single morphospecies ranged from one to seven. A total of ten species were found in both regions, whereas the distribution of 11 yeasts was restricted to a single region only. Both geographical region and type of substrate (plant or soil) influence yeast distribution. Cryptococcus wieringae, C. victoriae, C. magnus, and Leucosporidium scottii were frequently found on plant substrates, whereas C. terricola and C. podzolicus were associated to soil substrates. Occurrence of C. magnus, C. albidus and Sporobolomyces roseus was found to depend on the geographical region. Microsatellite-PCR fingerprinting, MSP-PCR, applied to studying yeast intraspecific variability revealed three different types of distribution: (a) variability that depends on geographical factors (Curvibasidium cygneicollum, C. podzolicus, C. victoriae), (b) genetic identity irrespectively of the region of isolation (Rhodotorula pinicola, C. terricola), and (c) high degree of genetic variability that did not correlate with region of sampling (C. albidus and C. magnus). Electronic supplementary material The online version of this article (Cryptococcus aff. victoriae CBS 8979 (AF406892) Cryptococcus heimaeyensis isolate AY-73 (FN357212) Cryptococcus aff. victoriae CBS 8999 (AF406893) Cryptococcus heimaeyensis CBS 8933 (DQ000317) Cryptococcus aff. victoriae CBS 9025 (AF406898) Cryptococcus peneaus CBS 2409 (AB035051) Cryptococcus taibaiensis CBS 9912 (AY557601) Cryptococcus sp. CBS 2993 (AB035052) Cryptococcus aff. victoriae CBS 9024 (AF406897) Cryptococcus foliicola isolate AY-78 (FN357211) Cryptococcus foliicola CBS 9920 (AY557599) Cryptococcus sp. CBS 6578 (AB035053) Cryptococcus carnescens isolate AY-87 (FN357213) Cryptococcus carnescens CBS 973 (AB035054) Cryptococcus victoriae CBS 8915 (AY040652) Cryptococcus victoriae isolate AY-92 (FN357206) Cryptococcus victoriae CBS 9006 (AF406900) Cryptococcus victoriae CBS 8937 Cryptococcus victoriae CBS 8685 (AF363647), Type strain Cryptococcus victoriae CBS 9268 Cryptococcus victoriae CBS 9264 Cryptococcus victoriae CBS 8920 (AY040650) Cryptococcus victoriae CBS 9009 (AF406901) Cryptococcus victoriae CBS 9000 (AF406899) Cryptococcus victoriae isolate AY-99 (FN357207) Cryptococcus victoriae CBS 9265 Cryptococcus victoriae CBS 6550 (AF444711) Cryptococcus victoriae CBS 9267 Cryptococcus victoriae isolate AY-68 (FN357201) Cryptococcus victoriae isolate AY-93 (FN357202) Cryptococcus aff. victoriae CBS 9013 (AF406895) Cryptococcus victoriae CBS 8908 (AY040653) Cryptococcus victoriae isolate AY-82 (FN357203) Cryptococcus victoriae isolate AY-84 (FN357205) Cryptococcus victoriae isolate AY-81 (FN357204) Cryptococcus victoriae CBS 8884 (AF444741) Cryptococcus victoriae CBS 9206 Cryptococcus victoriae isolate AY-97 (FN357214) Cryptococcus aff. victoriae CBS 8993 (AF408633) Cryptococcus tephrensis "var. soli" CBS 8968 Cryptococcus "victoriae" CBS 9799 Cryptococcus aff. victoriae CBS 9023 (AF406896) Cryptococcus sp isolate AY-77 (FN357208) Cryptococcus tephrensis "var. soli" CBS 8934 Cryptococcus aff. victoriae CBS 9012 (AF406894) Cryptococcus tephrensis "var. tephrensis" CBS 8935 (DQ000318), Type strain Cryptococcus tephrensis isolate AY-95 (FN357215) Cryptococcus tephrensis isolate AY-100 (FN357209) Cryptococcus tephrensis isolate AY-103 (FN357210) Cryptococcus tephrensis isolate AY-94 (FN357216) Cryptococcus dimennae CBS 5770 (AF075489) Bullera globispora CBS 6981 (AF075509)

Research paper thumbnail of Cryptococcus yarrowii sp. nov., a novel yeast species from Portugal

Antonie van Leeuwenhoek, 1991

A novel species of the basidiomycetous genus Cryptococcus is described as Cr. yarrowii based on t... more A novel species of the basidiomycetous genus Cryptococcus is described as Cr. yarrowii based on the study of an isolate from a decayed mushroom collected in Portugal. DNA-DNA homology with the type strain of the phenotypically similar species Cr. albidus was 10 +/- 2%.

Research paper thumbnail of Comparative genomics suggests primary homothallism of pneumocystis species

mBio, 2015

Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis ... more Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jiroveci...

Research paper thumbnail of Rhodosporidium lusitaniae sp. nov., a Novel Homothallic Basidiomycetous Yeast Species from Portugal that Degrades Phenolic Compounds

Systematic and Applied Microbiology, 1992

ABSTRACT

Research paper thumbnail of Validation of <I>Kwoniella heveanensis</I>, teleomorph of the basidiomycetous yeast <I>Cryptococcus heveanensis</I>

Mycotaxon, 2011

ABSTRACT Kwoniella heveanensis, recently published in an electronic journal and without a designa... more ABSTRACT Kwoniella heveanensis, recently published in an electronic journal and without a designated holotype, is validated as the name of the newly discovered teleomorph of Cryptococcus heveanensis.

Research paper thumbnail of Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

Research paper thumbnail of Farysizyma gen. nov., an anamorphic genus in the Ustilaginales to accommodate three novel epiphytic basidiomycetous yeast species from America, Europe and Asia

FEMS Yeast Research, 2008

Among many isolates that resulted from four independent surveys of yeasts associated with plants ... more Among many isolates that resulted from four independent surveys of yeasts associated with plants in Brazil, the USA, Portugal and Taiwan, we have characterized eighteen basidiomycetous strains, two of which were conspecific with the type strain of Rhodotorula acheniorum, whereas the remaining sixteen isolates appeared not to correspond to any previously described species. Microsatellite-PCR fingerprinting with primers M13 and (GTG) 5 confirmed that the latter strains formed three genetically distinct groups. Each group was considered to represent a distinct species based on nucleotide sequences of the D1/D2 domains of the 26S rRNA gene and the internal transcribed spacer (ITS) region. Phylogenetic analyses of sequence data placed the putative novel species in a clade with R. acheniorum and the dimorphic smut fungus Farysia chardoniana. A novel anamorphic genus, Farysizyma, is created to accommodate the three undescribed species, which were named Farysizyma itapuensis, Farysizyma setubalensis and Farysizyma taiwaniana. A new combination, Farysizyma acheniorum, is proposed for R. acheniorum, which may represent the yeast-phase anamorph of Farysia thuemenii.

Research paper thumbnail of Assessment of phylloplane yeasts on selected Mediterranean plants by FISH with group- and species-specific oligonucleotide probes

FEMS Microbiology Ecology, 2000

A previous culture-dependent survey of phylloplane yeasts from selected Mediterranean plants show... more A previous culture-dependent survey of phylloplane yeasts from selected Mediterranean plants showed that a few species were present in high densities in almost all leaf samples, regardless of the plant type, location or sampling season. However, a few species appeared to be restricted to Cistus albidus leaves, namely Cryptococcus cistialbidi. Here, we describe a culture-independent FISH assay to detect and quantify whole yeast cells in leaf washings. After optimization, the technique was used to check the apparent association between C. albidus leaves and C. cistialbidi and the abundance and ubiquity of other basidiomycetous yeast species such as Erythrobasidium hasegawianum and Sporobolomyces spp. in leaf samples from this and other neighboring plants (Acer monspessulanum and Quercus faginea). No yeast cells were detected in Pistacia lentiscus leaf samples. We were also able to demonstrate that three phylloplane yeasts (C. cistialbidi, E. hasegawianum and Sporobolomyces spp.) appeared to be log-normally distributed among individual C. albidus leaves. The log-normal distribution has important implications for the quantification of phylloplane yeasts based on the washing and plating of bulk leaf samples, which will tend to overestimate the size of the respective populations and become an error source in yeast surveys or related biocontrol studies. FEMS Microbiol Ecol 71 (2010) 61-72 c