Fungi associated with biological soil crusts in desert grasslands of Utah and Wyoming

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

Assessment of Fungal Diversity in Minqin County, a Typical Arid Region in Northwestern China

Minqin County is located in the Shiyang River Basin. As a typical arid area, it is eroded by the Badain Jaran and Tengger Desert all year round, and knowledge of the fungal diversity in this area is limited. Therefore, fungal community structure and distribution in the soil of the artificial forest, desert transition zone, farmland, and desert were investigated using amplicon sequencing of the fungal ITS gene. Ten fungal phyla and 23 classes were identified, including 1131 fungi OTUs, Sordariomycetes, Dothideomycetes, Pezizomycetes, and Agaricomycetes were the most abundant classes. Although most OTUs are shared among habitats, fungal community composition among samples was highly variable, which may influence the design of restoration practices in this area.

Keratinophilic fungi: Specialized fungal communities in a desert ecosystem identified using cultured-based and Illumina sequencing approaches

Soil fungi in desert ecosystems are adapted to harsh environmental conditions such as high soil surface temperatures and limited organic matter and water. Given limited carbon inputs from plant material, heterotrophic fungi likely use unconventional sources of carbon in these systems. A baiting method was used to culture keratinophilic fungi from biocrust and rhizosphere soils in an arid grassland in Utah, USA. Fungi were baited using llama and sheep wool, horsehair, and snakeskin on two media, and pure cultures were identified using ITS and LSU rRNA sequences. One hundred-eighteen fungal colonies were grown, representing a total of 32 Operational Taxonomic Units (OTUs) at 97 % similarity. Cultures were dominated by the phylum Ascomycota (88 %) followed by Mucoromycota (8.6 %) and Basidiomycota (3.4 %). The orders Pleosporales, Eurotiales, Hypocreales, and Sordariales were commonly isolated, with the dominant taxa Alternaria (27 %), Aspergillus (22 %), Fusarium (11 %), and Chaetomium (8%). Thirty percent of the fungi isolated have the capacity to degrade keratin in vitro using a keratin azure assay, with Penicillium showing the highest degradation followed by Geomyces, Alternaria, and Fusarium. Although keratin degraders can be infectious, dermatophytes associated with skin infections were not isolated in culture or detected in Illumina sequencing. Illumina sequencing was used to determine general patterns in seasonal variation and habitat preference of keratinophiles. Alternaria was the most abundant genus with >70 % of the sequences. The combination of Illumina data with culture-dependent approaches facilitated the characterization of a specialized community and confirmed the low abundance of dermatophytes in this arid site.

Cultured Microfungal Communities in Biological Soil Crusts and Bare Soils at the Tabernas Desert, Spain

We examined the variations in microfungal communities from different surface types (cyanobacterial crusts, lichen-dominated crusts, and noncrusted bare surface) at two different positions—north-oriented slope and sun-exposed plain in the Tabernas Desert, Spain. A total of 77 species from 46 genera was isolated using the soil dilution plate method. The studied mycobiota, similar to the majority of desert mycobiotas, was dominated by melanin-containing species. However, in the Tabernas crusts, unlike the studied crusts of the Negev Desert (Israel) and the Tengger Desert (China), melanized fungi with large multicellular spores were much less abundantly represented, while the thermotolerant group, Aspergillus spp., remarkably contributed to the communities’ structure. Density of microfungal isolates positively correlated with chlorophyll content indicating possible significant influence of organic matter content on fungal biomass. The variations in crust composition, biomass, and the position of habitats were accompanied by the variations in microfungal community structure, diversity level, and isolate densities, with the communities at the plain sun-exposed position being much less variable than the communities at the north-oriented position. The study shows that microclimatic and edaphic factors play an essential role in the development of crust and noncrust microfungal communities, and their structure can be a sensitive indicator of changing environmental conditions at a microscale.

Exophiala crusticola anam. nov. (affinity Herpotrichiellaceae), a novel black yeast from biological soil crusts in the Western United States

A novel black yeast-like fungus,Exophiala crusticola, is described based on two closely related isolates from biological soil crust (BSC) samples collected on the Colorado Plateau (Utah) and in the Great Basin desert (Oregon), USA. Their morphology places them in the anamorphic genusExophiala, having affinities to the familyHerpotrichiellaceae(Ascomycota). Phylogenetic analysis of their D1/D2 large subunit nuclear ribosomal RNA (LSU nrRNA) gene sequences suggests that they represent a distinct species. The closest known putative relative toExophiala crusticolaisCapronia coronataSamuels, isolated from decorticated wood in Westland County, New Zealand. The holotype forExophiala crusticolaanam. nov. is UAMH 10686 and the type strain is CP141bT(=ATCC MYA-3639T=CBS 119970T=DSM 16793T). Dark-pigmented fungi appear to constitute an important heterotrophic component of soil crusts andExophiala crusticolarepresents the first description of a dematiaceous fungus isolated from BSCs.