Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high‐throughput sequencing sets

Abstract

Fungi are everywhere and interact with humans in countless ways, but a large group of fungi called 'Cryptomycota' has escaped detection until very recently. Still, the extent of diversity and ecological habits of this group remain largely unknown. We interrogated publically available 18S rRNA gene datasets, obtained via high-throughput sequencing from marine and freshwater samples, for Cryptomycota sequences. Contrary to previous work, we found evidence of substantial Cryptomycota diversity in the marine upper water column. Additionally, we produced a sequencing set from a groundwater aquifer, an environment unrepresented among 18S rRNA gene pyrosequencing sets. The Cryptomycota community in this aquifer sample appears distinct from the community in both freshwater and marine environments with evidence of a unique aquifer clade. This study significantly expands the boundary of known Cryptomycota sequence diversity and characterizes the phylogenetic distribution of this diversity in aquatic environments. Furthermore, the approach utilized is generalizable to discovery of novel micro-eukaryotic diversity from any lineage.

Local–global overlap in diversity informs mechanisms of bacterial biogeography

“…Previous investigation has shown that nucleotide distances between different variable regions of the rRNA gene are tightly correlated (Livermore and Mattes, 2013) which indicates that this is a reasonable approximation. The use of phylogenetic diversity and previously defined reference OTUs dramatically reduces the sensitivity of our results to this potential issue.…”

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

“…In particular, high-throughput sequencing (HTS) technologies enable documentation and characterization of hundreds to thousands of species simultaneously from biological samples. These methods have been used successfully to uncover diversity and community composition of fungi in various substrates and localities, including little-studied habitats such as mangroves, aquatic ecosystems, and arctic soils (Arfi et al 2012;Blaalid et al 2013;Livermore and Mattes 2013). Similarly to other amplicon-based methods, HTS techniques are sensitive to PCR and primer biases (Lindahl et al 2013).…”

Surveying the biodiversity of the Cryptomycota using a targeted PCR approach

“…Previous studies have found Cryptomycota are highly diverse in freshwater habitats, yet have identified clades that were dominated by marine or aquifer sequences (Livermore and Mattes, 2013). We found freshwater sediment and soil representatives both widely distributed across the Cryptomycota phylogeny.…”

“…These fungi are quite common in aquatic and marine environments where their abundance may range from 0.02 to 30 % of all eukaryotic sequences, with an average of 3.5 % across 13 studies (Livermore and Mattes, 2013). While direct ecosystem effects from parasites of producers are more readily observed, Rozella and similar hyperparasites may have a considerable regulatory role on population sizes of zoosporic fungi that are parasites of primary consumers in lakes (Gleason et al, 2012(Gleason et al, , 2014.…”

“…Cryptomycota diversity has been categorized on the basis of habitat origin (Jones et al, 2011b;Livermore and Mattes, 2013), but our ability to identify ecological patterns that could explain their function in the environment is impeded by either insufficient sampling of the tree or short next-generation DNA sequences. Better understanding of the ecology and morphology has been difficult for the group and, therefore, while it is clear Cryptomycota are pervasive, frequently encountered in a variety of habitats, and likely parasitic, it is mostly uncertain which hosts they may have or if they may actually contain saprotrophic or bacterivorous taxa.…”