Species delimitation in the genus Lipomyces by nuclear genome comparison

North-to-South diversity of lipomycetaceous yeasts in soils evaluated with a cultivation-based approach from 11 locations in Japan

To understand the species distribution, diversity, and density of lipomycetaceous yeasts in soil based on their north-to-south location in Japan, 1146 strains were isolated from soil samples at 11 locations from Hokkaido to Okinawa Prefecture and taxonomically characterized. Lipomycetaceous yeast strains were isolated efficiently from soil by selecting watery mucoid-like colonies on agar plates with nitrogen-depleted medium. Twenty-four (80%) of the 30 known species of the genus Lipomyces were isolated from the soil samples collected in Japan, including species recently proposed. Among the species isolated, L. starkeyi was the most predominant in Japan, except on Iriomote Island, Okinawa, and accounted for 60-98% of the isolated strains. Lipomyces yarrowii was the dominant species on Iriomote Island (64%). The second most dominant species were L. chichibuensis in Saitama Prefecture and L. doorenjongii from Yamaguchi to Okinawa Prefecture. The species diversity of lipomycetaceous yeasts was in Japan and the significant correlation with the latitude of the sampling sites was revealed.

Lipomyces chichibuensis sp. nov., isolated in Japan, and reidentification of the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae

We isolated two strains of a novel Lipomyces species from soil collected in Chichibu forest, Saitama prefecture, Japan. Based on their morphological and biochemical characteristics, along with multilocus sequence typing using the D1/D2 domain of the large-subunit (LSU) rRNA gene, the internal transcribed spacer (ITS) region and the translation elongation factor 1 alpha gene (EF-1α), the two strains were shown to represent a novel species of the genus Lipomyces, described as Lipomyces chichibuensis sp. nov. (type strain CB08-2T = NBRC 109582T = CBS 12929T; Mycobank no. MB808164). In addition, we reidentified the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae maintained in culture collections based on phenotypic characters and/or DNA–DNA hybridization to ensure correct future identification of species of the genus Lipomyces. The correct type strains of L. kononenkoae and L. spencermartinsiae are NBRC 107661T ( = CBS 2514T) and NBRC 10376T ( = CBS 5608T), respectively.

Polyphasic re-examination of Debaryomyces hansenii strains and reinstatement of D. hansenii, D. fabryi and D. subglobosus

The type species of the genus Debaryomyces, Debaryomyces hansenii, is a highly heterogeneous species. It has been isolated from a large diversity of natural sources including fruit, air, water, soil, but most frequently from processed food products. The species delineation of this yeast species urgently needs clarification. The heterogeneity in taxonomic characteristics has resulted in the description of varieties linked to D. hansenii. The aim of this study was to re-examine and classify D. hansenii using a polyphasic approach. A total of 65 D.hansenii isolates were examined, 57 representing the variety hansenii and nine the variety fabryi. The selection of strains for DNA reassociation and phylogenetic analysis was based on polymerase chain reaction mediated fingerprints using four mini- and microsatellite-specific primers. The discriminating power of growth at 35 °C and 37 °C was re-examined and ascospore production was observed. DNA reassociations and phylogenetic analyses were performed on selected isolates from each of the clusters obtained from the DNA fingerprint analyses. The data indicated the presence of three distinct species within the D. hansenii group, which were represented by type strains of former species and that are proposed to be reinstated: D. hansenii (CBS 767^T = MUCL 49680^T), D. fabryi (CBS 789^T = MUCL 49731^T) and D. subglobosus (CBS 792^T = MUCL 49732^T).

Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to Dipodascopsis

Phylogenetic relationships among species assigned to genera of the family Lipomycetaceae were determined from analysis of the nearly entire large, subunit rRNA gene, the small subunit rRNA gene, mitochondrial small subunit rRNA gene and the translation elongation factor-1alpha gene. Monophyly of the Lipomycetaceae was strongly supported, and currently described species appear genetically unique. The multigene analysis provided no support for maintaining the genera Kawasakia, Smithiozyma, Waltomyces or Zygozyma, and it is proposed that species in these genera be assigned to the genus Lipomyces. The monotypic genus Babjevia is a member of the Dipodascopsis clade and it is proposed to reassign Babjevia anomala to Dipodascopsis. The proposed changes will result in the Lipomycetaceae having two ascosporic genera, Lipomyces and Dipodascopsis, and the anamorphic genus Myxozyma.

Total DNA preparation excluding extracellular acidic polysaccharide from Lipomyces yeasts and its application to taxonomic studies

A preparation method of total DNA from Lipomyces yeasts was improved in order to exclude extracellular acidic polysaccharide thoroughly. The method combined an ultracentrifuge and polyethylene glycol precipitation with the usual method. The total DNAs obtained were analyzed for G + C content and by DNA-DNA hybridization. The results all agreed almost completely with literature data. All the DNA samples prepared using this method were pure enough for these taxonomic analyses and could also be used as templates of PCR for amplification of small subunit ribosomal DNA and the internal transcribed spacer region.

Four new species in Lipomyces

For new species in Lipomyces are described. In terms of nuclear genome comparison the genus Lipomyces comprises three species-clusters. A key to the nine species now assigned to the genus, is given. The delimitation of species by (i) rRNA nucleotide sequence analyses of the 18S and 25S subunits and (II) nDNA homology determinations, do not invariably lead to the recognition of congruent taxa. The family of the Lipomycetaceae, nevertheless provides an illuminative model for phylogenetic studies in terms of more appropriate ribosomal nucleotide sequence analyses of both its teleomorphic and anamorphic members.