DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica
Authors: Carlos Augusto Rosa
Thamar Holanda da Silva
Ot√°vio Henrique Bezerra Pinto
Peter Convey
Luiz Henrique Rosa
Michael Stech
Mayara Baptistucci Ogaki
Micheline Carvalho-Silva
Paulo E A S C√¢mara
Journal: Scientific Reports (2020)
Discipline: Multidisciplinary
Keywords: soil fungal diversity; DNA metabarcoding analysis; Deception Island; Antarctica; phyla
Affiliations: Laborat√≥rio de Microbiologia Polar & Conex√µes Tropicais, Departamento de Microbiologia, Instituto de Ci√™ncias Biol√≥gicas, Universidade Federal de Minas Gerais, P. O. Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil. ., Laborat√≥rio de Microbiologia Polar & Conex√µes Tropicais, Departamento de Microbiologia, Instituto de Ci√™ncias Biol√≥gicas, Universidade Federal de Minas Gerais, P. O. Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil., Departamento de Biologia Celular, Universidade de Bras√≠lia, Bras√≠lia, Brazil., Naturalis Biodiversity Center, Leiden, The Netherlands., British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK., Departamento de Bot√¢nica, Universidade de Bras√≠lia, Bras√≠lia, Brazil.

Abstract:  We assessed soil fungal diversity at two sites on Deception Island, South Shetland Islands, Antarctica using DNA metabarcoding analysis. The first site was a relatively undisturbed area, and the second was much more heavily impacted by research and tourism. We detected 346 fungal amplicon sequence variants dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Chytridiomycota. We also detected taxa belonging to the rare phyla Mucoromycota and Rozellomycota, which have been difficult to detect in Antarctica by traditional isolation methods. Cladosporium sp., Pseudogymnoascus roseus, Leotiomycetes sp. 2, Penicillium sp., Mortierella sp. 1, Mortierella sp. 2, Pseudogymnoascus appendiculatus and Pseudogymnoascus sp. were the most dominant fungi. In addition, 440,153 of the total of 1,214,875 reads detected could be classified only at the level of Fungi. In both sampling areas the DNA of opportunistic, phytopathogenic and symbiotic fungi were detected, which might have been introduced by human activities, transported by birds or wind, and/or represent resident fungi not previously reported from Antarctica. Further long-term studies are required to elucidate how biological colonization in the island may be affected by climatic changes and/or other anthropogenic influences. 

Retracted: No

PubPeer comments:
 An interesting study, undoubtedly. But all the more the pity that authors as well as prior-to-publication reviewers in such high-profile journal were rather heedless in some aspects. Look at Figure 2, for instance. There the Fungi on Y-axis should be unclassified Fungi. As the authors well know, Fungi is the name of the kingdom. The next taxonomic level is a phylum. The phyla found in the study are also indicated in the graphs in this Figure 2. As the values represent percentages, it makes a reader wonder why the sum of phyla does not produce 100%? At this point a reader, who should have a firsthand experience with the methods and data processing, understand that by u201cFungiu201d the authors meant only unclassified ones. But then another question emerges, namely why the percentage of this unclassified Fungi is so high? Naturally, in any study there is a number of OTUs that cannot be assigned a taxonomy, mainly due to the two reasons: the fungi their DNA had not been found before and or the relevant ITS sequence info had not been added into the database. However, most of the time the relative abundance of unclassified Fungi ranges 2-15% of the total number of fungal sequence reads, not more. Therefore the next question is about why in this study the percentage is so high (over 40%?). Moreover, the reader (mind it, the reader who is more or less into the filed!) started to suspect that the authors calculated percentage on the basis of the total number of sequence reads, fished with the primers used. As the ITS primers are not strictly specific for Fungi, the obtained set of sequence reads include other eucaryotes. The authors should have clearly indicated in the M M section that they removed all non-fungal sequences and proceed with fungal diversity analysis from this point. And the last comment concerning Figure 2. Why indicate percentage with 2 decimals? Why not 3 or 5, for that matter? It is a calculated number, so even the 2 decimals are an overkill. Overall, this Figure produces an impression that the bioinformatic data were analyzed and prepared for visualization by a person who seems to be a bit not too much into the microbiology per se, I am afraid. And it also raises the issue of adequate reviewing prior to publication. ,