ITS rDNA Barcodes Clarify Molecular Diversity of Aquatic Hyphomycetes

Abstract

Aquatic hyphomycetes are key microbial decomposers of allochthonous organic matter in freshwater ecosystems. Although their importance in carbon flow and food webs in streams is widely recognized, there are still gaps in our understanding of their molecular diversity and distribution patterns. Our study utilized the growing database of ITS rDNA barcodes of aquatic hyphomycetes (1252 sequences) and aimed to (i) produce new barcodes for some lesser-known taxa; (ii) clarify the taxonomic placement of some taxa at the class or order level, based on molecular data; and (iii) provide insights into the biogeographical origins of some taxa. This study increased the number of aquatic hyphomycete species with available ITS barcodes from 119 (out of ~300 species described) to 136. Phylogenetically, the 136 species were distributed between 2 phyla, 6 classes, and 10 orders of fungi. Future studies should strive to increase the database of ITS sequences, especially focusing on species with unclear phylogenetic relationships (incertae sedis) and with few sequences available. The geographical distribution of species with available ITS sequences included 50 countries from five continents, but 6 countries had more than 20 species associated, showing a bias toward the northern hemisphere, likely due to sampling bias.

Exploring environmental microfungal diversity through serial single cell screening

“…In our study, a proportion of more than one-third of the cells showed sigmoid morphologies. Hence, using a molecular barcode for the identification of less represented taxa among sigmoid cells, as performed in our workflow, has the potential to significantly improve our understanding of aquatic fungal diversity [Bärlocher 2010;Nilsson et al 2019], taking into account that aquatic hyphomycetes and other aquatic fungi are taxonomically highly divergent [Franco-Duarte et al 2022][Grossart et al 2019. As the ITS region as single marker may not be robust enough to cover this diversity [Kauserud 2023], an extension to the neighboring SSU and LSU regions holds to benefit of a more robust phylogenetic placement, and its reusability in future environmental amplicon studies, which usually depend on either one of these three ribosomal regions.…”

“…Tetracladium is represented by a well-defined clade (SI-Supplementary data: Figure S1), however no clear separation among the species of both genera is apparent [Baschien et al 2013;Franco-Duarte et al 2022]. Although having less data for the FRO, this pattern seems to persists when considering the ITS, SSU and LSU region, seperately (SI-Supplementary data: Figure S2-S4), or all three regions together (Figure 2).…”

“…The vast majority of the existing molecular data is constricted to the ITS region, the formal barcode for molecular identification of fungal DNA [Schoch et al 2012]. Yet, for aquatic hyphomycetes, only for about 42% of described species (136 out of approximately 323 described species) have an ITS barcode sequence listed in GenBank [Franco-Duarte et al 2022] . Although ITS sequence data has been key to the large advancement of mycological discoveries, there are significant drawbacks when selecting this region as a sole genetic barcode, making it often not adequate to study the broth of fungal lineages.…”

Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome

“…After exploring fungal rRNA genes, Schoch et al in 2012 identified the ITS as the possible universal DNA barcode identifier for fungi [ 24 , 62 ] , although currently, it is still not clear which of the two ITS components has the better resolution in strain prediction. Recent findings has shown that both regions suffer from amplification biases, resulting in an uneven representation of synthetic fungal communities [ 63 - 65 ] : ITS1-based PCR appears to favor Basidiomycota, whereas Ascomycota seems to be favored by ITS2-based PCR [ 66 - 68 ] , although this consideration should not be generalized. In fact, there are known ascomycetes species (such as the ones belonging to the genera Saccharomyces and Komagataella ) that are discriminated with greater resolution by employing the ITS1 marker [ 69 ] .…”

Recent studies on aero-aquatic fungi, with special reference to diversity of conidial morphology and convergent evolution

“…Only a few aero-aquatic fungi belong to Basidiomycota and Orbiliomycetes. On the other hand, the aquatic mitosporic fungi (Ingoldian fungi) were also found polyphyletic among Ascomycota and Basidiomycota, while their major lineages belong to Helotiales, Leotiomycetes, followed by Dothideomycetes, Sordariomycetes, Basidiomycota and Orbiliomycetes (Duarte et al, 2013;Franco-Duarte et al, 2022). Thus, it is presumed that the almost the same groups of Ascomycota and only the small number of species of Basidiomycota have evolved to adapt to freshwater habi-tats as aero-aquatic fungi or aquatic fungi by applying their own strategy for conidial dispersal and colonization on substrates.…”