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Analysis of Fungal Flora in Indoor Dust by Ribosomal DNA Sequence Analysis, Quantitative PCR, and Culture ^,

M. Pitkäranta,^1* T. Meklin,^2, A. Hyvärinen,² L. Paulin,¹ P. Auvinen,¹ A. Nevalainen,² and H. Rintala²

Institute of Biotechnology, P.O. Box 56, FIN-00014 University of Helsinki, Finland,¹ Environmental Microbiology Laboratory, National Public Health Institute, P.O. Box 95, FI-70701 Kuopio, Finland²

Received 27 March 2007/ Accepted 20 October 2007

In recent years increasing attention has been given to the potential health effects of fungal exposure in indoor environments. We used large-scale sequencing of the fungal internal transcribed spacer region (ITS) of nuclear ribosomal DNA to describe the mycoflora of two office buildings over the four seasons. DNA sequencing was complemented by cultivation, ergosterol determination, and quantitative PCR analyses. Sequences of 1,339 clones were clustered into 394 nonredundant fungal operational taxonomical units containing sequences from 18 fungal subclasses. The observed flora differed markedly from that recovered by cultivation, the major differences being the near absence of several typical indoor mold genera such as Penicillium and Aspergillus spp. and a high prevalence of basidiomycetes in clone libraries. A total of 55% of the total diversity constituted of unidentifiable ITS sequences, some of which may represent novel fungal species. Dominant species were Cladosporium cladosporioides and C. herbarum, Cryptococcus victoriae, Leptosphaerulina americana and L. chartarum, Aureobasidium pullulans, Thekopsora areolata, Phaeococcomyces nigricans, Macrophoma sp., and several Malassezia species. Seasonal differences were observed for community composition, with ascomycetous molds and basidiomycetous yeasts predominating in the winter and spring and Agaricomycetidae basidiomycetes predominating in the fall. The comparison of methods suggested that the cloning, cultivation, and quantitative PCR methods complemented each other, generating a more comprehensive picture of fungal flora than any of the methods would give alone. The current restrictions of the methods are discussed.

Published ahead of print on 2 November 2007.

Supplemental material for this article may be found at http://aem.asm.org/.

Present address: Technology Centre Teknia, Ltd., P.O. Box 1188, FI-70211 Kuopio, Finland.