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Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.

Journal impact factors were devised to qualify and compare university library holdings but are frequently repurposed for use in ranking applications, research papers, and even individual applicants in mycology and beyond. The widely held assumption that mycological studies published in journals with high impact factors add more to systematic mycology than studies published in journals without high impact factors nevertheless lacks evidential underpinning. The present study uses the species hypothesis system of the UNITE database for molecular identification of fungi and other eukaryotes to trace the publication history and impact factor of sequences uncovering new fungal species hypotheses. The data show that journal impact factors are poor predictors of discovery potential in systematic mycology. There is no clear relationship between journal impact factor and the discovery of new species hypotheses for the years 2000–2021. On the contrary, we found journals with low, and even no, impact factor to account for substantial parts of the species hypothesis landscape, often discovering new fungal taxa that are only later picked up by journals with high impact factors. Funding agencies and hiring committees that insist on upholding journal impact factors as a central funding and recruitment criterion in systematic mycology should consider using indicators such as research quality, productivity, outreach activities, review services for scientific journals, and teaching ability directly rather than using publication in high impact factor journals as a proxy for these indicators. [ABSTRACT FROM AUTHOR]

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.