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

Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats

The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.

Lichens and Health-Trends and Perspectives for the Study of Biodiversity in the Antarctic Ecosystem

Lichens are an important vegetative component of the Antarctic terrestrial ecosystem and present a wide diversity. Recent advances in omics technologies have allowed for the identification of lichen microbiomes and the complex symbiotic relationships that contribute to their survival mechanisms under extreme conditions. The preservation of biodiversity and genetic resources is fundamental for the balance of ecosystems and for human and animal health. In order to assess the current knowledge on Antarctic lichens, we carried out a systematic review of the international applied research published between January 2019 and February 2024, using the PRISMA model (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). Articles that included the descriptors "lichen" and "Antarctic" were gathered from the web, and a total of 110 and 614 publications were retrieved from PubMed and ScienceDirect, respectively. From those, 109 publications were selected and grouped according to their main research characteristics, namely, (i) biodiversity, ecology and conservation; (ii) biomonitoring and environmental health; (iii) biotechnology and metabolism; (iv) climate change; (v) evolution and taxonomy; (vi) reviews; and (vii) symbiosis. Several topics were related to the discovery of secondary metabolites with potential for treating neurodegenerative, cancer and metabolic diseases, besides compounds with antimicrobial activity. Survival mechanisms under extreme environmental conditions were also addressed in many studies, as well as research that explored the lichen-associated microbiome, its biodiversity, and its use in biomonitoring and climate change, and reviews. The main findings of these studies are discussed, as well as common themes and perspectives.

Psychrophilic fungi from the world's roof, II: Species delimitation within an integrative taxonomic framework

Southeast Qinghai-Tibet Plateau, which harbors large numbers of marine glaciers and spans across two worldwide "biodiversity hotspots," is facing massive habitat loss in the context of global warming, and the biodiversity of coldadapted fungi in this unique area is also suffering drastic reduction. In this study, we selected 23 fungal isolates that represented the most commonly encountered psychrophilic taxa isolated from soil or water samples of marine glaciers in the southeast Qinghai-Tibet Plateau for detailed taxonomic studies. Incorporating morphological characteristics, multilocus phylogenetic analyses, and the results of four widely used molecular species delimitation methods, including two distance-based: Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), and two tree-based: Bayesian Poisson Tree Processes (bPTP) and generalized mixed Yule coalescent model (GMYC), seven Gelida (formerly Psychrophila) species, including six new species, and two Tetracladium species, including one new species, were described. As the genus name Psychrophila is an illegitimate later homonym of a plant genus, we proposed the new name Gelida as a replacement for Psychrophila and transferred four illegitimate Psychrophila species to Gelida as new combinations. Our study provides a valuable perspective on how to delimit robust and accurate species boundaries within an integrative taxonomic framework, which is especially important for efficient biodiversity assessment and conservation of the fungal groups that are facing serious habitat loss.

High diversity of fungal ecological groups from ice-free pristine and disturbed areas in the Fildes Peninsula, King George Island, Antarctica

Ice-free areas are habitats for most of Antarctica's terrestrial biodiversity. Although fungal communities are an important element of these habitats, knowledge of their assemblages and ecological functions is still limited. Herein, we investigated the diversity, composition, and ecological functionality of fungal communities inhabiting sediments from ice-free areas across pristine and anthropogenically impacted sites in the Fildes Peninsula on King George Island, Antarctica. Samples were collected from both pristine and disturbed areas. We used the internal transcribed spacer (ITS1) region via Illumina sequencing of 34 sediment samples for fungal identification. The Ascomycota (14.6%) and Chytridiomycota (11.8%) were the most dominant phyla, followed by Basidiomycota (8.1%), Rozellomycota (7.0%), Mucoromycota (4.0%), while 34.9% of the fungal diversity remained unidentified. From a total of 1073 OTUs, 532 OTUs corresponded to 114 fungal taxa at the genus level, and 541 OTUs remained unassigned taxonomically. The highest diversity, with 18 genera, was detected at site A-3. At the genus level, there was no preference for either pristine or disturbed sites. The most widely distributed genera were Betamyces (Chytridiomycota), occurring in 29 of the 34 sites, and Thelebolus (Ascomycota), detected in 8 pristine sites and 7 disturbed sites. The Glomeraceae gen. incertae sedis was more common in disturbed sites. A total of 23 different ecological guilds were recorded, with the most abundant guilds being undefined saprotrophs, plant pathogens, plant saprotrophs, pollen saprotrophs, and endophytes. The fungal communities did not show significant differences between pristine and disturbed sites, suggesting that the anthropogenic impact is either not too intense or prolonged, that the spatial distance between the sampled sites is small, and/or that the environmental factors are similar. Although our study revealed a high fungal diversity with various ecological specializations within these communities, nearly one-third of the diversity could not be assigned to any specific taxonomic category. These findings highlight the need for further taxonomic research on fungal species inhabiting ice-free areas. Without identifying the species present, it is difficult to assess potential biodiversity loss due to environmental changes and/or human activities.

OmicShare tools: A zero-code interactive online platform for biological data analysis and visualization

The OmicShare tools platform is a user-friendly online resource for data analysis and visualization, encompassing 161 bioinformatic tools. Users can easily track the progress of projects in real-time through an overview interface. The platform has a powerful interactive graphics engine that allows for the custom-tailored modification of charts generated from analyses. The visually appealing charts produced by OmicShare improve data interpretability and meet the requirements for publication. It has been acknowledged in over 4000 publications and is available in https://www.omicshare.com/tools/.

Trends in Antarctic soil fungal research in the context of environmental changes

Antarctic soils represent one of the most pristine environments on Earth, where highly adapted and often endemic microbial species withstand multiple extremes. Specifically, fungal diversity is extremely low in Antarctic soils and species distribution and diversity are still not fully characterized in the continent. Despite the unique features of this environment and the international interest in its preservation, several factors pose severe threats to the conservation of inhabiting ecosystems. In this light, we aimed to provide an overview of the effects on fungal communities of the main changes endangering the soils of the continent. Among these, the increasing human presence, both for touristic and scientific purposes, has led to increased use of fuels for transport and energy supply, which has been linked to an increase in unintentional environmental contamination. It has been reported that several fungal species have evolved cellular processes in response to these soil contamination episodes, which may be exploited for restoring contaminated areas at low temperatures. Additionally, the effects of climate change are another significant threat to Antarctic ecosystems, with the expected merging of previously isolated ecosystems and their homogenization. A possible reduction of biodiversity due to the disappearance of well-adapted, often endemic species, as well as an increase of biodiversity, due to the spreading of non-native, more competitive species have been suggested. Despite some studies describing the specialization of fungal communities and their correlation with environmental parameters, our comprehension of how soil communities may respond to these changes remains limited. The majority of studies attempting to precisely define the effects of climate change, including in situ and laboratory simulations, have mainly focused on the bacterial components of these soils, and further studies are necessary, including the other biotic components.

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

As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.

Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities

Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling.