Taxonomic and phenotypic characterization of yeasts isolated from worldwide cold rock-associated habitats

Seasonality Is the Main Determinant of Microbial Diversity Associated to Snow/Ice around Concordia Station on the Antarctic Polar Plateau

The French-Italian Concordia Research Station, situated on the Antarctic Polar Plateau at an elevation of 3233 m above sea level, offers a unique opportunity to study the presence and variation of microbes introduced by abiotic or biotic vectors and, consequently, appraise the amplitude of human impact in such a pristine environment. This research built upon a previous work, which explored microbial diversity in the surface snow surrounding the Concordia Research Station. While that study successfully characterized the bacterial assemblage, detecting fungal diversity was hampered by the low DNA content. To address this knowledge gap, in the present study, we optimized the sampling by increasing ice/snow collected to leverage the final DNA yield. The V4 variable region of the 16S rDNA and Internal Transcribed Spacer (ITS1) rDNA was used to evaluate bacterial and fungal diversity. From the sequencing, we obtained 3,352,661 and 4,433,595 reads clustered in 930 and 3182 amplicon sequence variants (ASVs) for fungi and bacteria, respectively. Amplicon sequencing revealed a predominance of Basidiomycota (49%) and Ascomycota (42%) in the fungal component; Bacteroidota (65.8%) is the main representative among the bacterial phyla. Basidiomycetes are almost exclusively represented by yeast-like fungi. Our findings provide the first comprehensive overview of both fungal and bacterial diversity in the Antarctic Polar Plateau's surface snow/ice near Concordia Station and to identify seasonality as the main driver of microbial diversity; we also detected the most sensitive microorganisms to these factors, which could serve as indicators of human impact in this pristine environment and aid in planetary protection for future exploration missions.

A New Expression System Based on Psychrotolerant Debaryomyces macquariensis Yeast and Its Application to the Production of Cold-Active β-d-Galactosidase from Paracoccus sp. 32d

Yeasts provide attractive host/vector systems for heterologous gene expression. The currently used yeast-based expression platforms include mesophilic and thermotolerant species. A eukaryotic expression system working at low temperatures could be particularly useful for the production of thermolabile proteins and proteins that tend to form insoluble aggregates. For this purpose, an expression system based on an Antarctic psychrotolerant yeast Debaryomyces macquariensis strain D50 that is capable of growing at temperatures ranging from 0 to 30 °C has been developed. The optimal physical culture conditions for D. macquariensis D50 in a fermenter are as follows: temperature 20 °C, pH 5.5, aeration rate of 1.5 vvm, and a stirring speed of 300 rpm. Four integrative plasmid vectors equipped with an expression cassette containing the constitutive GAP promoter and CYC1 transcriptional terminator from D. macquariensis D50 were constructed and used to clone and express a gene-encoding cold-active β-d-galactosidase of Paracoccus sp. 32d. The yield was 1150 U/L of recombinant yeast culture. Recombinant D. macquariensis D50 strains were mitotically stable under both selective and non-selective conditions. The D. macquariensis D50 host/vector system has been successfully utilized for the synthesis of heterologous thermolabile protein, and it can be an alternative to other microbial expression systems.

Yeast Diversity in the Qaidam Basin Desert in China with the Description of Five New Yeast Species

The Qaidam Basin is the highest and one of the largest and driest deserts on Earth. It is considered a mars analog area in China. In contrast to numerous studies concerning its geology, geophysical, and chemistry, relatively few studies have reported microbial diversity and distribution in this area. Here, we investigated culturable yeast diversity in the northeast Qaidam Basin. A total of 194 yeast strains were isolated, and 12 genera and 21 species were identified, among which 19 were basidiomycetous yeasts. Naganishia albida, N. adeliensis, and Filobasidium magnum were the three most dominant species and were distributed in thirteen samples from eight locations. Five new species (Filobasidium chaidanensis, Kondoa globosum, Symmetrospora salmoneus, Teunia nitrariae, and Vishniacozyma pseudodimennae) were found and described based on ITS and D1D2 gene loci together with phenotypic characteristics and physiochemical analysis. Representative strains from each species were chosen for the salt-tolerant test, in which species showed different responses to different levels of NaCl concentrations. Further, the strain from soil can adapt well to the higher salt stress compared to those from plants or lichens. Our study represents the first report of the yeast diversity in the Qaidam Basin, including five new species, and also provides further information on the halotolerance of yeasts from the saline environment in mars analog.

Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities

In the harshest environmental conditions of the Antarctic desert, normally incompatible with active life, microbes are adapted to exploit the cryptoendolithic habitat (i.e., pore spaces of rocks) and represent the predominant life-forms. In the rocky niche, microbes take advantage of the thermal buffering, physical stability, protection against UV radiation, excessive solar radiation, and water retention-of paramount importance in one of the driest environments on Earth. In this work, high-throughput sequencing and culture-dependent approaches have been combined, for the first time, to untangle the diversity and distribution of black fungi in the Antarctic cryptoendolithic microbial communities, hosting some of the most extreme-tolerant microorganisms. Rock samples were collected in a vast area, along an altitudinal gradient and opposite sun exposure-known to influence microbial diversity-with the aim to compare and integrate results gained with the two approaches. Among black fungi, Friedmanniomyces endolithicus was confirmed as the most abundant taxon. Despite the much stronger power of the high-throughput sequencing, several species were not retrieved with DNA sequencing and were detectable by cultivation only. We conclude that both culture-dependent and -independent analyses are needed for a complete overview of black fungi diversity. The reason why some species remain undetectable with molecular methods are speculated upon. The effect of environmental parameters such as sun exposure on relative abundance was clearer if based on the wider biodiversity detected with the molecular approach.

Endolithic microbial composition in Helliwell Hills, a newly investigated Mars-like area in Antarctica

The diversity and composition of Antarctic cryptoendolithic microbial communities in the Mars-analogue site of Helliwell Hills (Northern Victoria Land, Continental Antarctica) are investigated, for the first time, applying both culture-dependent and high-throughput sequencing approaches. The study includes all the domains of the tree of life: Eukaryotes, Bacteria and Archaea to give a complete overview of biodiversity and community structure. Furthermore, to explore the geographic distribution of endoliths throughout the Victoria Land (Continental Antarctica), we compared the fungal and bacterial community composition and structure of endolithically colonized rocks, collected in >30 sites in 10 years of Italian Antarctic Expeditions. Compared with the fungi and other eukaryotes, the prokaryotic communities were richer in species, more diverse and highly heterogeneous. Despite the diverse community compositions, shared populations were found and were dominant in all sites. Local diversification was observed and included prokaryotes as members of Alphaproteobacteria and Crenarchaeota (Archaea), the last detected for the first time in these cryptoendolithic communities. Few eukaryotes, namely lichen-forming fungal species as Lecidella grenii, were detected in Helliwell Hills only. These findings suggest that geographic distance and isolation in these remote areas may promote the establishment of peculiar locally diversified microorganisms.

Beyond the extremes: Rocks as ultimate refuge for fungi in drylands

In an era of rapid climate change and expansion of desertification, the extremely harsh conditions of drylands are a true challenge for microbial life. Under drought conditions, where most life forms cannot survive, rocks represent the main refuge for life. Indeed, the endolithic habitat provides thermal buffering, physical stability, and protection against incident ultraviolet (UV) radiation and solar radiation and, to some extent, ensures water retention to microorganisms. The study of these highly specialized extreme-tolerant and extremophiles may provide tools for understanding microbial interactions and processes that allow them to keep their metabolic machinery active under conditions of dryness and oligotrophy that are typically incompatible with active life, up to the dry limits for life. Despite lithobiontic communities being studied all over the world, a comprehensive understanding of their ecology, evolution, and adaptation is still nascent. Herein, we survey the fungal component of these microbial ecosystems. We first provide an overview of the main defined groups (i.e., lichen-forming fungi, black fungi, and yeasts) of the most known and studied Antarctic endolithic communities that are almost the only life forms ensuring ecosystem functionality in the ice-free areas of the continent. For each group, we discuss their main traits and their diversity. Then, we focus on the fungal taxonomy and ecology of other worldwide endolithic communities. Finally, we highlight the utmost importance of a global rock survey in order to have a comprehensive view of the diversity, distribution, and functionality of these fungi in drylands, to obtain tools in desert area management, and as early alarm systems to climate change.

Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica

Cold environments impose challenges to organisms. Polyextremophile microorganisms can survive in these conditions thanks to an array of counteracting mechanisms. Naganishia vishniacii, a yeast species hitherto only isolated from McMurdo Dry Valleys, Antarctica, is an example of a polyextremophile. Here we present the first draft genomic sequence of N. vishniacii. Using comparative genomics, we unraveled unique characteristics of cold associated adaptations. 336 putative genes (total: 6183) encoding solute transfers and chaperones, among others, were absent in sister species. Among genes shared by N. vishniacii and its closest related species we found orthologs encompassing possible evidence of positive selection (dN/dS > 1). Genes associated with photoprotection were found in agreement with high solar irradiation exposure. Also genes coding for desaturases and genomic features associated with cold tolerance (i.e. trehalose synthesis and lipid metabolism) were explored. Finally, biases in amino acid usage (namely an enrichment of glutamine and a trend in proline reduction) were observed, possibly conferring increased protein flexibility. To the best of our knowledge, such a combination of mechanisms for cold tolerance has not been previously reported in fungi, making N. vishniacii a unique model for the study of the genetic basis and evolution of cold adaptation strategies.

Assessment of microbiota present on a Portuguese historical stone convent using high-throughput sequencing approaches

The study performed on the stone materials from the Convent of Christ revealed the presence of a complex microbial ecosystem, emphasizing the determinant role of microorganisms on the biodecay of this built cultural heritage. In this case study, the presence of Rubrobacter sp., Arthrobacter sp., Roseomonas sp., and Marinobacter sp. seems to be responsible for colored stains and biofilm formation while Ulocladium sp., Cladosporium sp., and Dirina sp. may be related to structural damages. The implementation of high-throughput sequencing approaches on the Convent of Christ's biodecay assessment allowed us to explore, compare, and characterize the microbial communities, overcoming the limitations of culture-dependent techniques, which only identify the cultivable population. The application of these different tools and insights gave us a panoramic view of the microbiota thriving on the Convent of Christ and signalize the main biodeteriogenic agents acting on the biodecay of stone materials. This finding highlighted the importance of performing metagenomic studies due to the improvements and the reduced amount of sample DNA needed, promoting a deeper and more detailed knowledge of the microbiota present on these dynamic repositories that support microbial life. This will further enable us to perform prospective studies in quarry and applied stone context, monitoring biogenic and nonbiogenic agents, and also to define long-term mitigation strategies to prevent biodegradation/biodeterioration processes.

Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica

A draft genome sequence was assembled and annotated of the basidiomycetous yeast Rhodotorula sp. strain CCFEE 5036, isolated from Antarctic soil communities. The genome assembly is 19.07 megabases and encodes 6,434 protein-coding genes. The sequence will contribute to understanding the diversity of fungi inhabiting polar regions.

A draft genome sequence was assembled and annotated of the basidiomycetous yeast Rhodotorula sp. strain CCFEE 5036, isolated from Antarctic soil communities. The genome assembly is 19.07 megabases and encodes 6,434 protein-coding genes. The sequence will contribute to understanding the diversity of fungi inhabiting polar regions.

Fungal evolution: major ecological adaptations and evolutionary transitions

Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.

Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes

Endolithic growth is one of the most spectacular microbial adaptations to extreme environmental constraints and the predominant life-form in the ice-free areas of Continental Antarctica. Although Antarctic endolithic microbial communities are known to host among the most resistant and extreme-adapted organisms, our knowledge on microbial diversity and composition in this peculiar niche is still limited. In this study, we investigated the diversity and structure of the fungal assemblage in the cryptoendolithic communities inhabiting sandstone using a meta-barcoding approach targeting the fungal Internal Transcribed Sequence region 1 (ITS1). Samples were collected from 14 sites in the Victoria Land, along an altitudinal gradient ranging from 1,000 to 3,300 m a.s.l. and from 29 to 96 km distance to coast. Our study revealed a clear dominance of a 'core' group of fungal taxa consistently present across all the samples, mainly composed of lichen-forming and Dothideomycetous fungi. Pareto-Lorenz curves indicated a very high degree of specialization (F0 approximately 95%), suggesting these communities are highly adapted but have limited ability to recover after perturbations. Overall, both fungal community biodiversity and composition did not show any correlation with the considered abiotic parameters, potentially due to strong fluctuations of environmental conditions at local scales.

Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities

Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors. Sandstone rocks were collected in Victoria Land, Antarctica along an altitudinal gradient from 834 to 3100 m a.s.l.; differently sun-exposed rocks were selected to test the influence of this parameter on endolithic settlement. Metabarcoding targeting the fungal internal transcribed spacer region 1 (ITS1) was used to catalogue the species found in these communities. Functional profile of guilds found in the samples was associated to species using FUNGuild and variation in functional groups compared across sunlight exposure and altitude. Results revealed clear dominance of lichenized and stress-tolerant fungi in endolithic communities. The main variations in composition and abundance of functional groups among sites correlated to sun exposure, but not to altitude.

Mixed Infection of Respiratory Tract in a Dog Caused by Rhodotorula mucilaginosa and Trichosporon jirovecii: A Case Report

This report describes the isolation of two environmental fungi: Rhodotorula mucilaginosa and Trichosporon jirovecii accompanied by Pseudomonas aeruginosa and Escherichia coli from a dog with bronchotracheitis. All microorganisms were isolated routinely from a mucopurulent discharge, obtained during bronchoscopy from laryngotracheal area. The initial identification of yeasts was confirmed by API Candida and by molecular analysis of internal transcribed spacer region. Administered antimicrobial treatment with Marbofloxacin and Canizol has brought the improvement in the dogs’ health status. The final results of control mycological culture were negative. Most probably underlying hypothyroidism and the use of steroids were the factors predisposing this patient to opportunistic infection of mixed aetiology. As far as we are concerned, this is the first case of dogs’ respiratory tract infection caused by R. mucilaginosa and T. jirovecii.

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities

A wide sampling of rocks, colonized by microbial epi-endolithic communities, was performed along an altitudinal gradient from sea level to 3600 m asl and sea distance from the coast to 100 km inland along the Victoria Land Coast, Antarctica. Seventy-two rock samples of different typology, representative of the entire survey, were selected and studied using denaturing gradient gel electrophoresis to compare variation in fungal diversity according to environmental conditions along this altitudinal and sea distance transect. Lichenized fungi were largely predominant in all the samples studied and the biodiversity was heavily influenced even by minimal local variations. The n-MDS analysis showed that altitude and sea distance affect fungal biodiversity, while sandstone allows the communities to maintain high biodiversity indices. The Pareto-Lorenz curves indicate that all the communities analyzed are highly adapted to extreme conditions but scarcely resilient, so any external perturbation may have irreversible effects on these fragile ecosystems.

Living strategy of cold-adapted fungi with the reference to several representative species

Our planet is dominant with cold environments that harbour enormously diverse cold-adapted fungi comprising representatives of all phyla. Investigation based on culture-dependent and independent methods has demonstrated that cold-adapted fungi are cosmopolitan and occur in diverse habitants and substrates. They live as saprobes, symbionts, plant and animal parasites and pathogens to perform crucial functions in different ecosystems. Pseudogymnoascus destructans caused bat white-nose syndrome and Ophiocordyceps sinensis as Chinese medicine are the representative species that have significantly ecological and economic significance. Adaptation to cold niches has made this group of fungi a fascinating resource for the discovery of novel enzymes and secondary metabolites for biotechnological and pharmaceutical uses. This review provides the current understanding of living strategy and ecological functions of cold-adapted fungi, with particular emphasis on how those fungi overcome the extreme low temperature and perform their ecological function.

Description of Taphrina antarctica f.a. sp. nov., a new anamorphic ascomycetous yeast species associated with Antarctic endolithic microbial communities and transfer of four Lalaria species in the genus Taphrina

In the framework of a large-scale rock sampling in Continental Antarctica, a number of yeasts have been isolated. Two strains that are unable to grow above 20 °C and that have low ITS sequence similarities with available data in the public domain were found. The D1/D2 LSU molecular phylogeny placed them in an isolated position in the genus Taphrina, supporting their affiliation to a not yet described species. Because the new species is able to grow in its anamorphic state only, the species Taphrina antarctica f.a. (forma asexualis) sp. nov. has been proposed to accommodate both strains (type strain DBVPG 5268(T), DSM 27485(T) and CBS 13532(T)). Lalaria and Taphrina species are dimorphic ascomycetes, where the anamorphic yeast represents the saprotrophic state and the teleomorph is the parasitic counterpart on plants. This is the first record for this genus in Antarctica; since plants are absent on the continent, we hypothesize that the fungus may have focused on the saprotrophic part of its life cycle to overcome the absence of its natural host and adapt environmental constrains. Following the new International Code of Nomenclature for Algae, Fungi and Plants (Melbourne Code 2011) the reorganization of Taphrina-Lalaria species in the teleomorphic genus Taphrina is proposed. We emend the diagnosis of the genus Taphrina to accommodate asexual saprobic states of these fungi. Taphrina antarctica was registered in MycoBank under MB 808028.