Assessment of fungal diversity present in lakes of Maritime Antarctica using DNA metabarcoding: a temporal microcosm experiment

Enzymes and biosurfactants of industrial interest produced by culturable fungi present in sediments of Boeckella Lake, Hope Bay, north-east Antarctic Peninsula

This study characterized cultivable fungi present in sediments obtained from Boeckella Lake, Hope Bay, in the north-east of the Antarctic Peninsula, and evaluated their production of enzymes and biosurfactants of potential industrial interest. A total of 116 fungal isolates were obtained, which were classified into 16 genera within the phyla Ascomycota, Basidiomycota and Mortierellomycota, in rank. The most abundant genera of filamentous fungi included Pseudogymnoascus, Pseudeurotium and Antarctomyces; for yeasts, Thelebolales and Naganishia taxa were dominant. Overall, the lake sediments exhibited high fungal diversity and moderate richness and dominance. The enzymes esterase, cellulase and protease were the most abundantly produced by these fungi. Ramgea cf. ozimecii, Holtermanniella wattica, Leucosporidium creatinivorum, Leucosporidium sp., Mrakia blollopis, Naganishia sp. and Phenoliferia sp. displayed enzymatic index > 2. Fourteen isolates of filamentous fungi demonstrated an Emulsification Index 24% (EI24%) ≥ 50%; among them, three isolates of A. psychrotrophicus showed an EI24% > 80%. Boeckella Lake itself is in the process of drying out due to the impact of regional climate change, and may be lost completely in approaching decades, therefore hosts a threatened community of cultivable fungi that produce important biomolecules with potential application in biotechnological processes.

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

In this study, we evaluated the fungal diversity present associated with cores of Oligocene rocks using a DNA metabarcoding approach. We detected 940,969 DNA reads grouped into 198 amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Mucoromycota, Rozellomycota, Blastocladiomycota, Monoblepharomycota, Zoopagomycota, Aphelidiomycota (Fungi) and the fungal-like Oomycota (Stramenopila), in rank abundance order. Pseudogymnoascus pannorum, Penicillium sp., Aspergillus sp., Cladosporium sp., Aspergillaceae sp. and Diaporthaceae sp. were assessed to be dominant taxa, with 22 fungal ASVs displaying intermediate abundance and 170 being minor components of the assigned fungal diversity. The data obtained displayed high diversity indices, while rarefaction indicated that the majority of the diversity was detected. However, the diversity indices varied between the cores analysed. The endolithic fungal community detected using a metabarcoding approach in the Oligocene rock samples examined contains a rich and complex mycobiome comprising taxa with different lifestyles, comparable with the diversity reported in recent studies of a range of Antarctic habitats. Due to the high fungal diversity detected, our results suggest the necessity of further research to develop strategies to isolate these fungi in culture for evolutionary, physiological, and biogeochemical studies, and to assess their potential role in biotechnological applications.

Fungal diversity present in snow sampled in summer in the north-west Antarctic Peninsula and the South Shetland Islands, Maritime Antarctica, assessed using metabarcoding

We assessed the fungal diversity present in snow sampled during summer in the north-west Antarctic Peninsula and the South Shetland Islands, maritime Antarctica using a metabarcoding approach. A total of 586,693 fungal DNA reads were obtained and assigned to 203 amplicon sequence variants (ASVs). The dominant phylum was Ascomycota, followed by Basidiomycota, Mortierellomycota, Chytridiomycota and Mucoromycota. Penicillium sp., Pseudogymnoascus pannorum, Coniochaeta sp., Aspergillus sp., Antarctomyces sp., Phenoliferia sp., Cryolevonia sp., Camptobasidiaceae sp., Rhodotorula mucilaginosa and Bannozyma yamatoana were assessed as abundant taxa. The snow fungal diversity indices were high but varied across the different locations sampled. Of the fungal ASVs detected, only 28 were present all sampling locations. The 116 fungal genera detected in the snow were dominated by saprotrophic taxa, followed by symbiotrophic and pathotrophic. Our data indicate that, despite the low temperature and oligotrophic conditions, snow can host a richer mycobiome than previously reported through traditional culturing studies. The snow mycobiome includes a complex diversity dominated by cosmopolitan, cold-adapted, psychrophilic and endemic taxa. While saprophytes dominate this community, a range of other functional groups are present.

A Deep Insight into the Diversity of Microfungal Communities in Arctic and Antarctic Lakes

We assessed fungal diversity in water and sediment samples obtained from five Arctic lakes in Ny-Ålesund (Svalbard Islands, High Arctic) and five Antarctic lakes on Livingston and Deception Islands (South Shetland Islands), using DNA metabarcoding. A total of 1,639,074 fungal DNA reads were detected and assigned to 5980 ASVs amplicon sequence variants (ASVs), with only 102 (1.7%) that were shared between the two Polar regions. For Arctic lakes, unknown fungal taxa dominated the sequence assemblages, suggesting the dominance of possibly undescribed fungi. The phylum Chytridiomycota was the most represented in the majority of Arctic and Antarctic samples, followed by Rozellomycota, Ascomycota, Basidiomycota, and the less frequent Monoblepharomycota, Aphelidiomycota, Mortierellomycota, Mucoromycota, and Neocallimastigomycota. At the genus level, the most abundant genera included psychrotolerant and cosmopolitan cold-adapted fungi including Alternaria, Cladosporium, Cadophora, Ulvella (Ascomycota), Leucosporidium, Vishniacozyma (Basidiomycota), and Betamyces (Chytridiomycota). The assemblages displayed high diversity and richness. The assigned diversity was composed mainly of taxa recognized as saprophytic fungi, followed by pathogenic and symbiotic fungi.

Communities of culturable freshwater fungi present in Antarctic lakes and detection of their low-temperature-active enzymes

We evaluated the diversity and enzymatic activities of culturable fungi recovered from cotton baits submerged for 2 years in Hennequin Lake, King George Island, and from benthic biofilms in Kroner Lake, Deception Island, South Shetland Islands, maritime Antarctica. A total of 154 fungal isolates were obtained, representing in rank abundance the phyla Ascomycota, Basidiomycota and Mortierellomycota. Thelebolus globosus, Goffeauzyma sp., Pseudogymnoascus verrucosus and Metschnikowia australis were the most abundant taxa. The fungal community obtained from the biofilm was more diverse and richer than that recovered from the cotton baits. However, diversity indices suggested that the lakes may harbour further fungal diversity. The capabilities of all cultured fungi to produce the extracellular enzymes cellulase, protease, lipase, agarase, carrageenase, invertase, amylase, esterase, pectinase, inulinase and gelatinase at low temperature were evaluated. All enzymes were detected, but the most widely produced were protease and pectinase. The best enzymatic indices were obtained from Holtermanniella wattica (for invertase, esterase), Goffeauzyma sp. (amylase), Metschnikowia australis (protease), Mrakia blollopis (cellulase, pectinase), Pseudogymnoascus verrucosus (agarase, carrageenase) and Leucosporidium fragarium (inulinase). The detection of multiple enzymes reinforces the ecological role of fungi in nutrient cycling in Antarctic lakes, making nutrients available to the complex aquatic food web. Furthermore, such low-temperature-active enzymes may find application in different biotechnological processes, such as in the textile, pharmaceutical, food, detergent and paper industries, as well as environmental application in pollutant bioremediation processes.

Taxonomy and Phylogeny of Hyphomycetous Muriform Conidial Taxa from the Tibetan Plateau, China

During the investigation of lignicolous freshwater fungi in the Tibetan Plateau habitat, fifteen collections were isolated from submerged decaying wood. Fungal characteristics are commonly found as punctiform or powdery colonies with dark pigmented and muriform conidia. Multigene phylogenetic analyses of combined ITS, LSU, SSU and TEF DNA sequences showed that they belong to three families in Pleosporales. Among them, Paramonodictys dispersa, Pleopunctum megalosporum, Pl. multicellularum and Pl. rotundatum are established as new species. Paradictyoarthrinium hydei, Pleopunctum ellipsoideum and Pl. pseudoellipsoideum are reported as new records on the freshwater habitats in Tibetan Plateau, China. The morphological descriptions and illustrations of the new collections are provided.

Cryptic fungal diversity revealed by DNA metabarcoding in historic wooden structures at Whalers Bay, Deception Island, maritime Antarctic

We provide the first assessment of fungal diversity associated with historic wooden structures at Whalers Bay (Heritage Monument 71), Deception Island, maritime Antarctic, using DNA metabarcoding. We detected a total of 177 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Monoblepharomycota, Rozellomycota, and Zoopagomycota. The assemblages were dominated by Helotiales sp. 1 and Herpotrichiellaceae sp. 1. Functional assignments indicated that the taxa detected were dominated by saprotrophic, plant and animal pathogenic, and symbiotic taxa. Metabarcoding revealed the presence of a rich and complex fungal community, which may be due to the wooden structures acting as baits attracting taxa to niches sheltered against extreme conditions, generating a hotspot for fungi in Antarctica. The sequences assigned included both cosmopolitan and endemic taxa, as well as potentially unreported diversity. The detection of DNA assigned to taxa of human and animal opportunistic pathogens raises a potential concern as Whalers Bay is one of the most popular visitor sites in Antarctica. The use of metabarcoding to detect DNA present in environmental samples does not confirm the presence of viable or metabolically active fungi and further studies using different culturing conditions and media, different growth temperatures and incubation periods, in combination with further molecular approaches such as shotgun sequencing are now required to clarify the functional ecology of these fungi.

Soil Fungal Diversity and Ecology Assessed Using DNA Metabarcoding along a Deglaciated Chronosequence at Clearwater Mesa, James Ross Island, Antarctic Peninsula

We studied the fungal diversity present in soils sampled along a deglaciated chronosequence from para- to periglacial conditions on James Ross Island, north-east Antarctic Peninsula, using DNA metabarcoding. A total of 88 amplicon sequence variants (ASVs) were detected, dominated by the phyla Ascomycota, Basidiomycota and Mortierellomycota. The uncommon phyla Chytridiomycota, Rozellomycota, Monoblepharomycota, Zoopagomycota and Basidiobolomycota were detected. Unknown fungi identified at higher hierarchical taxonomic levels (Fungal sp. 1, Fungal sp. 2, Spizellomycetales sp. and Rozellomycotina sp.) and taxa identified at generic and specific levels (Mortierella sp., Pseudogymnoascus sp., Mortierella alpina, M. turficola, Neoascochyta paspali, Penicillium sp. and Betamyces sp.) dominated the assemblages. In general, the assemblages displayed high diversity and richness, and moderate dominance. Only 12 of the fungal ASVs were detected in all chronosequence soils sampled. Sequences representing saprophytic, pathogenic and symbiotic fungi were detected. Based on the sequence diversity obtained, Clearwater Mesa soils contain a complex fungal community, including the presence of fungal groups generally considered rare in Antarctica, with dominant taxa recognized as cold-adapted cosmopolitan, endemic, saprotrophic and phytopathogenic fungi. Clearwater Mesa ecosystems are impacted by the effects of regional climatic changes, and may provide a natural observatory to understand climate change effects over time.

A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait

BACKGROUND

In the ice-free area of maritime Antarctica, fungi are the essential functioning group in terrestrial and marine ecosystems. Until now, no study has been conducted to comprehensively assess fungal communities in various habitats in Antarctica. We aimed to characterize fungal communities in the eleven habitats (i.e., soil, seawater, vascular plant, dung, moss, marine alga, lichen, green alga, freshwater, feather) in the Fildes Region (maritime Antarctica) using next-generation sequencing.

RESULTS

A total of 12 known phyla, 37 known classes, 85 known orders, 164 known families, 313 known genera, and 320 known species were detected. Habitat specificity rather than habitat overlap determined the composition of fungal communities, suggesting that, although fungal communities were connected by dispersal at the local scale, the environmental filter is a key factor driving fungal assemblages in the ice-free Antarctica. Furthermore, 20 fungal guilds and 6 growth forms were detected. Many significant differences in the functional guild (e.g., lichenized, algal parasite, litter saprotroph) and growth form (e.g., yeast, filamentous mycelium, thallus photosynthetic) existed among different habitat types.

CONCLUSION

The present study reveals the high diversity of fungal communities in the eleven ice-free Antarctic habitats and elucidates the ecological traits of fungal communities in this unique ice-free area of maritime Antarctica. The findings will help advance our understanding of fungal diversity and their ecological roles with respect to habitats on a neighbourhood scale in the ice-free area of maritime Antarctica.

Diversity, distribution and ecology of fungal communities present in Antarctic lake sediments uncovered by DNA metabarcoding

We assessed fungal diversity in sediments obtained from four lakes in the South Shetland Islands and James Ross Island, Antarctica, using DNA metabarcoding. We detected 218 amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Chytridiomycota. In addition, the rare phyla Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Monoblepharomycota, Rozellomycota and Zoopagomycota as well as fungal-like Straminopila belonging to the phyla Bacillariophyta and Oomycota were detected. The fungal assemblages were dominated by unknown fungal taxa (Fungal sp. 1 and Fungal sp. 2), followed by Talaromyces rubicundus and Dactylonectria anthuriicola. In general, they displayed high diversity, richness and moderate dominance. Sequences representing saprophytic, pathogenic and symbiotic fungi were detected, including the phytopathogenic fungus D. anthuriicola that was abundant, in the relatively young Soto Lake on Deception Island. The lake sediments studied contained the DNA of rich, diverse and complex fungal communities, including both fungi commonly reported in Antarctica and other taxa considered to be rare. However, as the study was based on the use of environmental DNA, which does not unequivocally confirm the presence of active or viable organisms, further studies using other approaches such as shotgun sequencing are required to elucidate the ecology of fungi in these Antarctic lake sediments.

Fungal diversity in a sediment core from climate change impacted Boeckella Lake, Hope Bay, north-eastern Antarctic Peninsula assessed using metabarcoding

We studied the fungal DNA present in a lake sediment core obtained from Trinity Peninsula, Hope Bay, north-eastern Antarctic Peninsula, using metabarcoding through high-throughput sequencing (HTS). Sequences obtained were assigned to 146 amplicon sequence variants (ASVs) primarily representing unknown fungi, followed by the phyla Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota and Mortierellomycota. The most abundant taxa were assigned to Fungal sp., Pseudeurotium hygrophilum, Rozellomycota sp. 1, Pseudeurotiaceae sp. 1 and Chytridiomycota sp. 1. The majority of the DNA reads, representing 40 ASVs, could only be assigned at higher taxonomic levels and may represent taxa not currently included in the sequence databases consulted and/or be previously undescribed fungi. Different sections of the core were characterized by high sequence diversity, richness and moderate ecological dominance indices. The assigned diversity was dominated by cosmopolitan cold-adapted fungi, including known saprotrophic, plant and animal pathogenic and symbiotic taxa. Despite the overall dominance of Ascomycota and Basidiomycota and psychrophilic Mortierellomycota, members of the cryptic phyla Rozellomycota and Chytridiomycota were also detected in abundance. As Boeckella Lake may cease to exist in approaching decades due the effects of local climatic changes, it also an important location for the study of the impacts of these changes on Antarctic microbial diversity.

Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK

Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10453-022-09760-9.

Ecological succession of fungal and bacterial communities in Antarctic mosses affected by a fairy ring disease

We evaluated fungal and bacterial diversity in an established moss carpet on King George Island, Antarctica, affected by 'fairy ring' disease using metabarcoding. A total of 127 fungal and 706 bacterial taxa were assigned. Ascomycota dominated the fungal assemblages, followed by Basidiomycota, Rozellomycota, Chytridiomycota, Mortierellomycota and Monoblepharomycota. The fungal community displayed high indices of diversity, richness and dominance, which increased from healthy through infected to dead moss samples. A range of fungal taxa were more abundant in dead rather than healthy or fairy ring moss samples. Bacterial diversity and richness were greatest in healthy moss and least within the infected fairy ring. The dominant prokaryotic phyla were Actinobacteriota, Proteobacteria, Bacteroidota and Cyanobacteria. Cyanophyceae sp., whilst consistently dominant, were less abundant in fairy ring samples. Our data confirmed the presence and abundance of a range of plant pathogenic fungi, supporting the hypothesis that the disease is linked with multiple fungal taxa. Further studies are required to characterise the interactions between plant pathogenic fungi and their host Antarctic mosses. Monitoring the dynamics of mutualist, phytopathogenic and decomposer microorganisms associated with moss carpets may provide bioindicators of moss health.

Application of Polyaluminium Chloride Coagulant in Urban River Water Treatment Influenced the Microbial Community in River Sediment

Polyaluminium chloride (PAC) has been widely used as a chemical coagulant in water treatment. However, little is known about the impact of PAC performance on the microbial community in sediments. In this study, the archaeal, bacterial, and fungal communities in urban river sediments with and without PAC treatment were investigated. Prokaryotic diversity decreased at the PAC addition site (A2) and increased along with the river flow (from A3 to A4), while eukaryotic diversity was the opposite. The abundance of core microbiota showed a similar trend. For example, the dominant Proteobacteria presented the highest relative abundance in A1 (26.8%) and the lowest in A2 (15.3%), followed by A3 (17.5%) and A4 (23.0%). In contrast, Rozellomycota was more dominant in A2 (56.6%) and A3 (58.1%) than in A1 (6.2%) and A4 (16.3%). Salinity, total dissolved solids, and metal contents were identified as the key physicochemical factors affecting the assembly of core microorganisms. The predicted functions of archaea and fungi were mainly divided into methane cycling and saprotrophic nutrition, respectively, while bacterial function was more diversified. The above findings are helpful to enhance our understanding of microorganism response to PAC and have significance for water treatment within the framework of microecology.

Diversity of fungal DNA in lake sediments on Vega Island, north-east Antarctic Peninsula assessed using DNA metabarcoding

We assessed the diversity of fungal DNA present in sediments of three lakes on Vega Island, north-east Antarctic Peninsula using metabarcoding through high-throughput sequencing (HTS). A total of 640,902 fungal DNA reads were detected, which were assigned to 224 taxa of the phyla Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota and Mortierellomycota, in rank order of abundance. The most abundant genera were Pseudogymnoascus, Penicillium and Mortierella. However, a majority (423,508, 66%) of the reads, representing by 43 ASVs, could only be assigned at higher taxonomic levels and may represent taxa not currently included in the sequence databases used or be new or previously unreported taxa present in Antarctic lakes. The three lakes were characterized by high sequence diversity, richness, and moderate dominance indices. The ASVs were dominated by psychrotolerant and cosmopolitan cold-adapted Ascomycota, Basidiomycota and Mortierellomycota commonly reported in Antarctic environments. However, other taxa detected included unidentified members of Rozellomycota and Chytridiomycota species not previously reported in Antarctic lakes. The assigned diversity was composed mainly of taxa recognized as decomposers and pathogens of plants and invertebrates.