Fungal and fungal-like diversity in marine sediments from the maritime Antarctic assessed using DNA metabarcoding

Abstract

We assessed the fungal and fungal-like sequence diversity present in marine sediments obtained in the vicinity of the South Shetland Islands (Southern Ocean) using DNA metabarcoding through high-throughput sequencing (HTS). A total of 193,436 DNA reads were detected in sediment obtained from three locations: Walker Bay (Livingston Island) at 52 m depth (48,112 reads), Whalers Bay (Deception Island) at 151 m (104,704) and English Strait at 404 m (40,620). The DNA sequence reads were assigned to 133 distinct fungal amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Glomeromycota, Monoblepharomycota, Mucoromycota and Rozellomycota and the fungal-like Straminopila. Thelebolus balaustiformis, Pseudogymnoascus sp., Fungi sp. 1, Ciliophora sp., Agaricomycetes sp. and Chaetoceros sp. were the dominant assigned taxa. Thirty-eight fungal ASVs could only be assigned to higher taxonomic levels, and may represent taxa not currently included in the available databases or represent new taxa and/or new records for Antarctica. The total fungal community displayed high indices of diversity, richness and moderate to low dominance. However, diversity and taxa distribution varied across the three sampling sites. In Walker Bay, unidentified fungi were dominant in the sequence assemblage. Whalers Bay sediment was dominated by Antarctic endemic and cold-adapted taxa. Sediment from English Strait was dominated by Ciliophora sp. and Chaetoceros sp. These fungal assemblages were dominated by saprotrophic, plant and animal pathogenic and symbiotic taxa. The detection of an apparently rich and diverse fungal community in these marine sediments reinforces the need for further studies to characterize their richness, functional ecology and potential biotechnological applications.

Endolithic Fungal Diversity in Antarctic Oligocene Rock Samples Explored Using DNA Metabarcoding

“…The ecological functional group assignments in the current study are similar to our recent metabarcoding studies of fungal communities in various Antarctic habitats [26,28,29,72,74,86,87]. Our ASV assignments suggest the presence of a diverse fungal community associated with the Oligocene rock samples analysed.…”

Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base “St. Kliment Ohridski” on Livingston Island, Antarctica

“…Still, the unusually high share of unidentified ASVs around the Bulgarian Antarctic base "St. Kliment Ohridski" pointed to a hotspot of novel fungal species that requires further investigation. High amounts of unclassified fungal tags were reported also in another study on Livingston Island in particular [27], as well as in other studies in Maritime Antarctica in general, in some of which they have been reported to be predominant [28,29]. Investigating such locations can contribute significantly to understanding the fungal diversity in polar regions, offering potential biotechnological applications, including drug discovery.…”

Salinity and resource availability as drivers of Baltic benthic fungal diversity

“…It can also include extracellular DNA from dead or inactive fungi (relic DNA; Carini et al, 2016Carini et al, , 2020Miettinen et al, 2019), despite some literature stating that relic DNA did not affect the biodiversity assessment of bacterial communities (Gustave et al, 2019;Lennon et al, 2018). The use of a single primer pair targeting only one section of the ITS region could also create a PCR amplification bias (Amend et al, 2019); however, this is a common practice in fungal diversity studies using metabarcoding (da Silva et al, 2022;Gonçalves et al, 2020;Polinski et al, 2019). The taxonomical classification is still limited by the existing reference databases and fungi diversity studies, as observed by the percentages of unclassified fungi at the phylum and class levels observed in this study (32.65% and 40.77%, respectively).…”

“…The application of environmental DNA (eDNA) metabarcoding has already promoted the development of the existent knowledge on phylogeny, taxonomy, and ecology of terrestrial and aquatic fungi (Cuadros‐Orellana, 2013; da Silva et al., 2022; Marčiulynienė et al., 2021). This was possible by targeting the internal transcribed spacer (ITS) region, which has been suggested as the fungal universal barcode, particularly useful in deeper taxonomic analysis of fungi from well‐described taxonomic groups (Schoch et al., 2012).…”

“…The use of recent high‐throughput next‐generation sequencing techniques in metabarcoding, which enables an efficient large‐scale analysis of DNA samples (Taberlet et al., 2012), has led to a better understanding of fungal diversity (Picard, 2017; Polinski et al., 2019; Rämä et al., 2016). Environmental metabarcoding thus offers a powerful technique to analyze still unexplored benthic habitats (da Silva et al., 2022; Gonçalves et al., 2022; Li et al., 2016; Polinski et al., 2019; Wu et al., 2023). These techniques have rarely been employed in the study of coastal benthic fungal diversity, particularly in the brackish Baltic Sea and at large spatial scales (i.e.…”