Abstract
BackgroundAn understanding of the role of yeasts in the environment has been uncertain because estimates of population size and diversity have often been based on species identifications that were determined from a limited number of phenotypic characteristics. DNA-based species identification has now become widely used, allowing an accurate assessment of species in different habitats. However, there are still problems in classification because some genera are polyphyletic. Consequently, the identification of yeasts and measurement of their diversity at the genus level remains difficult, as does assignment of genera to higher taxonomic ranks.Methodology/Principal FindingsA total of 1021 yeast strains was isolated from soil samples and plant materials collected from Japan’s subtropical Iriomote Island and the cool temperate Rishiri Island. Based on sequence analyses of the D1/D2 domain of the LSU rRNA gene, these 1021 strains were tentatively classified into 183 species, with apparent new species accounting for approximately half of the total species isolated (60 and 46, Iriomote and Rishiri, respectively). The yeast species composition was statistically different between the two sites with only 15 species in common. Rarefaction curves of respective sources/areas gave distinctive patterns when the threshold of sequence identity became broader, indicating that the yeast diversity was distinct at the different taxonomic levels compared.Conclusions/SignificanceOur isolation study of yeasts in Japan has enabled us to expand the inventory of species diversity because a large number of new species was observed in the sampling areas. Further, we propose use of a particular diversity threshold as an “indicator” to recognize species, genera and higher taxonomic ranks.
Highlights
Since the Convention on Biological Diversity went into effect in 1993, studies of species diversity have increased dramatically and are aimed at conserving biodiversity and ensuring sustainable use. This has resulted in around 500–600 prokaryote species being described each year. This statistic has not been published for yeasts; 56 new species were listed in 2010 in MycoBank, suggesting that many yet undescribed yeast species exist
Most ascomycetous yeasts are members of the Saccharomycotina [1], and they may not be as common as basidiomycetous yeasts in certain environments [2]
A neighbor-joining tree of isolates based on the unique sequences (D1/D2 region of the LSU rRNA gene) showed that the species were widely distributed on the phylogenetic tree, and we found no branch particular to the sampling area or source (Figure 1 and Figure S1 (a)–(d))
Summary
Since the Convention on Biological Diversity went into effect in 1993, studies of species diversity have increased dramatically and are aimed at conserving biodiversity and ensuring sustainable use. Conclusions/Significance: Our isolation study of yeasts in Japan has enabled us to expand the inventory of species diversity because a large number of new species was observed in the sampling areas. According to present isolation data, basidiomycetous yeast genera, such as the genera Cryptococcus and Sporobolomyces, are common in soils and on plant leaves.
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