Surveying the biodiversity of the Cryptomycota using a targeted PCR approach

Cryptomycota is a newly discovered phylum of early-diverging fungi that is estimated to comprise a massive amount of unstudied biodiversity. Known primarily from environmental DNA sequences, the group contains few formally described and successfully cultured genera, all known as obligate endoparasites. Numerous studies have detected Cryptomycota as DNA sequences in aquatic, terrestrial, and animal associated habitats, though no study to date has specifically targeted the group by PCR. In this study, we developed Cryptomycota-specific and preferential primers for the 18S rRNA gene in order to facilitate studies on the biodiversity and ecology of the group. The diversity of sequences and habitat association of Cryptomycota was surveyed across three environments: freshwater sediment, marine sediment, and soil. The new primers were able to recover a large proportion of Cryptomycota sequences: of 56 sequences cloned or directly sequenced, 44 were unique OTUs and (39/44) 88.6 % were phylogenetically affiliated with Cryptomycota. This study expands the boundary of current Cryptomycota sequence diversity; unique Cryptomycota OTUs were spread across six of 12 supported Cryptomycota sub clades. Freshwater sediments and soil were consistently amplified with the Cryptomycotapreferential primers. Our results suggest that Cryptomycota are ubiquitous and phylogenetically diverse components of essentially all terrestrial and aquatic ecosystems, whose ecological functions should be better explored. a 2014 Elsevier Ltd and The British Mycological Society. All rights reserved. Introduction essential for understanding ecosystem functioning. Many Among the many groups containing overlooked biodiversity on Earth, fungi are projected to comprise a large proportion. Currently, the number of described fungal species is approximately 100 000 (Kirk et al., 2008), but recent biodiversity estimates based on DNA sequence analysis suggest as many as 5.1 million or more species of fungi may exist (Blackwell, 2011; Taylor et al., 2014). Fungi have a diversity of ecological roles and, therefore, cataloging their true biodiversity will be e University of Florida, G zarus). thology, University of Flo h Mycological Society. Al undescribed fungi are likely to be microscopic and among the early-diverging branches, because these are enriched for obligately biotrophic species, or species with complex growth requirements such as the anaerobic rumen chytrids and the pathogens of invertebrates (Gleason et al., 2010). The difficulty of culturing these obligate parasites greatly limits our ability to research and observe them relative to other fungi. Only with recent molecular advances have we been able to target the missing diversity with techniques such as DNA ainesville, FL 32611-0680, USA. Tel.: þ1 248 410 3916. rida, Gainesville, FL 32611-0680, USA.