ORIGINAL PAPER Assessment of endophytic yeast diversity in rice leaves by a culture-independent approach Manee Tantirungkij . Rujikan Nasanit . Savitree Limtong Received: 28 April 2015 / Accepted: 23 June 2015 / Published online: 30 June 2015 Ó Springer International Publishing Switzerland 2015 Abstract Endophytic microorganisms inhabit inter- nal plant tissues in the host plant without causing any symptoms or negative effects. Although the diversity of endophytes has been evaluated by both culture- dependent and culture-independent methods, less information is available on yeast communities. There- fore, in this study a culture-independent method was used to examine endophytic yeasts associated with rice leaves based on the large subunit of ribosomal DNA using a semi-nested PCR technique. Sequence analysis indicated that the colonization frequency and the relative species frequency (RF) of endophytic yeast phylotypes were 0.41 and 0.06, respectively, and the majority of the yeast phylotypes were basid- iomycetous yeasts. The phylotypes were designated as five known species (Cryptococcus victoriae, Debary- omyces hansenii, Debaryomyces vindobonensis, Meyerozyma guilliermondii and Pseudozyma antarc- tica), together with seventeen phylotypes closest to Candida metapsilosis, Cryp. foliicola, Cryp. laurentii, Pseudozyma abaconensis, Pseudozyma aphidis and Trichosporon asahii, among which some could be novel species. The most prevalent phylotypes were those closest to Cryp. foliicola (47.5 % RF) followed by D. hansenii (22.8 % RF) and P. antarctica (16.8 % RF). The presence of the phylotypes related to species known for their potential applications as biocontrol agents and plant growth promoting hormone produc- ers suggests that they may have valuable applications. In addition, our findings revealed the occurrence of novel phylotypes at high frequency, which should encourage extensive studies to discover novel yeast species and to understand their roles in the rice leaves. Keywords Endophyte  Yeast  Rice  Culture-independent diversity  PCR  Cryptococcus Introduction Endophytic microorganisms comprising bacteria, fil- amentous fungi and yeasts inhabit internal tissues of M. Tantirungkij Central Laboratory and Greenhouse Complex, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand R. Nasanit Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom 73000, Thailand S. Limtong (&) Department of Microbiology, Faculty of Sciences, Kasetsart University, Bangkok 10900, Thailand e-mail: fscistl@ku.ac.th S. Limtong Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok 10900, Thailand 123 Antonie van Leeuwenhoek (2015) 108:633–647 DOI 10.1007/s10482-015-0519-y