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

Diversity of endophytic bacterial and fungal microbiota associated with the medicinal lichen Usnea longissima at high altitudes

Endophytic microbial communities of lichen are emerging as novel microbial resources and for exploration of potential biotechnological applications. Here, we focused on a medicinal lichen Usnea longissima, and investigated its bacterial and fungal endophytes. Using PacBio 16S rRNA and ITS amplicon sequencing, we explored the diversity and composition of endophytic bacteria and fungi in U. longissima collected from Tibet at five altitudes ranging from 2,989 to 4,048 m. A total of 6 phyla, 12 classes, 44 genera, and 13 species of the bacterial community have been identified in U. longissima. Most members belong to Alphaproteobacteria (42.59%), Betaproteobacteria (33.84%), Clostridia (13.59%), Acidobacteria (7%), and Bacilli (1.69%). As for the fungal community, excluding the obligate fungus sequences, we identified 2 phyla, 15 classes, 65 genera, and 19 species. Lichen-related fungi of U. longissima mainly came from Ascomycota (95%), Basidiomycota (2.69%), and unidentified phyla (2.5%). The presence of the sequences that have not been characterized before suggests the novelty of the microbiota. Of particular interest is the detection of sequences related to lactic acid bacteria and budding yeast. In addition, the possible existence of harmful bacteria was also discussed. To our best knowledge, this is the first relatively detailed study on the endophytic microbiota associated with U. longissima. The results here provide the basis for further exploration of the microbial diversity in lichen and promote biotechnological applications of lichen-associated microbial strains.

Distinct Taphrina strains from the phyllosphere of birch exhibiting a range of witches' broom disease symptoms

The phyllosphere is an important microbial habitat and reservoir of organisms that modify plant health. Taphrina betulina is the causal agent of birch witches' broom disease. Taphrina species are dimorphic, infecting hosts in the filamentous form and residing in the host phyllosphere as non-infectious yeast. As such, they are expected to be found as resident yeasts on their hosts, even on healthy tissues; however, there is little experimental data supporting this supposition. With the aim of exploring the local infection ecology of T. betulina, we isolated yeasts from the phyllosphere of birch leaves, using three sample classes; infected leaves inside symptom-bearing branches, healthy leaves from symptom-free branches on symptom-bearing trees and leaves from symptom-free branches on symptom-free trees. Isolations yielded 224 yeast strains, representing 11 taxa, including T. betulina, which was the most common isolate and was found in all sample classes, including symptom-free samples. Genotyping revealed genetic diversity among these T. betulina isolates, with seven distinct genotypes differentiated by the markers used. Twenty-two representative T. betulina strains were selected for further study, revealing further phenotypic differences. These findings support that T. betulina is ubiquitous on birch and that individual trees host a diversity of T. betulina strains.

Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications

Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat's physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.

A Novel Yeast Genus and Two Novel Species Isolated from Pineapple Leaves in Thailand: Savitreella phatthalungensis gen. nov., sp. nov. and Goffeauzyma siamensis sp. nov

Four yeast strains, representing one genus and two novel anamorphic yeast species, were isolated from pineapple leaves collected in Thailand. Analysis of the sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions showed the two strains (DMKU-PAL186 and DMKU-PAL178) were closely related to the type strains of the Protomyces and Taphrina species, but with high nucleotide divergence. Two strains (DMKU-PAL39 and DMKU-PAL18) were found to be closely related to the type strains of Goffeauzyma iberica, but with eight nucleotide substitutions in the D1/D2 domains and 26 nucleotide substitutions in the ITS regions. In phylogenetic analyses, the strains DMKU-PAL186 and DMKU-PAL178 formed a well-separated lineage from Protomyces and Taphrina genera, confirming that they represented a distinct genus, while the strains DMKU-PAL39 and DMKU-PAL18 represented a species in the genus Goffeauzyma, which was phylogenetically distinct from other recognized species of the genus. Based on molecular analyses and phenotypic characteristics, the names Savitreella gen. nov. (Taphrinomycetes, Ascomycota) and Savitreella phatthalungensis sp. nov. are proposed to accommodate the strains DMKU-PAL186 and DMKU-PAL178, and the name Goffeauzyma siamensis sp. nov. (Tremellomycetes, Basidiomycota) is proposed to accommodate the strains DMKU-PAL39 and DMKU-PAL18.

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

Illumina Sequencing of 18S/16S rRNA Reveals Microbial Community Composition, Diversity, and Potential Pathogens in 17 Turfgrass Seeds

The increasing need for turfgrass seeds is coupled with the high risk of dangerous microbial pathogens being transmitted through the domestic and international trade of seeds. Concerns continue to be raised about seed safety and quality. Here, we show that next-generation sequencing (NGS) of DNA represents an effective and reliable tactic to monitor the microbial communities within turfgrass seeds. A comparison of DNA sequence data with reference databases revealed the presence of 26 different fungal orders. Among them, serious plant disease pathogens such as Bipolaris sorokiniana, Boeremia exigua, Claviceps purpurea, and Rhizoctonia zeae were detected. Seedborne bacteria, including Erwinia persicina and Acidovorax avenae, were identified from different bacterial orders. Our study indicated that the traditional culturing method and the NGS approach for pathogen identification complement each other. The reliability of culturing and NGS methods was further validated by PCR with specific primers. The combination of these different techniques ensures maximum sensitivity and specificity for turfgrass seed pathogen testing assay.

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.

Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land

The endolithic niche represents an ultimate refuge to microorganisms in the Mars-like environment of the Antarctic desert. In an era of rapid global change and desertification, the interest in these border ecosystems is increasing due to speculation on how they maintain balance and functionality at the dry limits of life. To assure a reliable estimation of microbial diversity, proper sampling must be planned in order to avoid the necessity of re-sampling as reaching these remote locations is risky and requires tremendous logistical and economical efforts. In this study, we seek to determine the minimum number of samples for uncovering comprehensive bacterial and fungal diversity, comparing communities in strict vicinity to each other. We selected three different locations of the Victoria Land (Continental Antarctica) at different altitudes and showing sandstone outcrops of a diverse nature and origin-Battleship promontory (834 m above sea level (a.s.l.), Southern VL), Trio Nunatak (1,470 m a.s.l., Northern VL) and Mt New Zealand (3,100 m a.s.l., Northern VL). Overall, we found that a wider sampling would be required to capture the whole amplitude of microbial diversity, particularly in Northern VL. We concluded that the inhomogeneity of the rock matrix and the stronger environmental pressure at higher altitudes may force the communities to a higher local diversification.

Yeasts producing zeatin

The present paper describes the first screening study of the ability of natural yeast strains to synthesize in culture the plant-related cytokine hormone zeatin, which was carried out using HPLC-MS/MS. A collection of 76 wild strains of 36 yeast species (23 genera) isolated from a variety of natural substrates was tested for the production of zeatin using HPLC-MS/MS. Zeatin was detected in more than a half (55%) of studied strains and was more frequently observed among basidiomycetous than ascomycetous species. The amount of zeatin accumulated during the experiment varied among species and strains. Highest zeatin values were recorded for basidiomycete Sporobolomyces roseus and ascomycete Taphrina sp. that produced up to 8,850.0 ng and 5,166.4 ng of zeatin per g of dry biomass, respectively. On average, the ability to produce zeatin was more pronounced among species isolated from the arctic-alpine zone than among strains from tropical and temperate climates. Our study also demonstrated that epiphytic strains and pigmented yeast species, typically for phyllosphere, are able to more often produce a plant hormone zeatin than other yeasts.

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.

Cold-adapted enzymes produced by fungi from terrestrial and marine Antarctic environments

Antarctica is the coldest, windiest, and driest continent on Earth. In this sense, microorganisms that inhabit Antarctica environments have to be adapted to harsh conditions. Fungal strains affiliated with Ascomycota and Basidiomycota phyla have been recovered from terrestrial and marine Antarctic samples. They have been used for the bioprospecting of molecules, such as enzymes. Many reports have shown that these microorganisms produce cold-adapted enzymes at low or mild temperatures, including hydrolases (e.g. α-amylase, cellulase, chitinase, glucosidase, invertase, lipase, pectinase, phytase, protease, subtilase, tannase, and xylanase) and oxidoreductases (laccase and superoxide dismutase). Most of these enzymes are extracellular and their production in the laboratory has been carried out mainly under submerged culture conditions. Several studies showed that the cold-adapted enzymes exhibit a wide range in optimal pH (1.0-9.0) and temperature (10.0-70.0 °C). A myriad of methods have been applied for cold-adapted enzyme purification, resulting in purification factors and yields ranging from 1.70 to 1568.00-fold and 0.60 to 86.20%, respectively. Additionally, some fungal cold-adapted enzymes have been cloned and expressed in host organisms. Considering the enzyme-producing ability of microorganisms and the properties of cold-adapted enzymes, fungi recovered from Antarctic environments could be a prolific genetic resource for biotechnological processes (industrial and environmental) carried out at low or mild temperatures.

Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats

In cold environments such as polar regions, microorganisms play important ecological roles, and most of our knowledge about them comes from studies of cultivable microorganisms. Metagenomic technologies are powerful tools that can give a more comprehensive assessment of microbial communities, and the amplification of rDNA followed by next-generation sequencing has given good results in studies aimed particularly at environmental microorganisms. Culture-independent studies of microbiota in terrestrial habitats of Antarctica, which is considered the driest, coldest climate on Earth, are increasing and indicate that micro-diversity is much higher than previously thought. In this work, the microbial diversity of terrestrial habitats including eight islands of the South Shetland Archipelago, two islands on the Antarctic Peninsula and Union Glacier, was studied by amplicon-metagenome analysis. Molecular analysis of the studied localities clustered together the islands of the South Shetland Archipelago, except Greenwich Island, and separated them from the Litchfield and Lagotellerie islands and Union Glacier, which is in agreement with the latitudinal difference among them. Among fungi, 87 genera and 123 species were found, of which species belonging to 37 fungal genera not previously cultivated from Antarctica were detected. Phylogenetic analysis, including the closest BLAST-hit sequences, clustered fungi in 11 classes being the most represented Lecanoromycetes and Eurotiomycetes.

Yeasts from macroalgae and lichens that inhabit the South Shetland Islands, Antarctica

Antarctic terrestrial ecosystems are largely dominated by lichens, while shallow coastal environments are mainly covered by macroalgae. The aim of this study was to isolate and to evaluate the diversity of yeasts in different species of macroalgae and lichens collected in South Shetland Islands, Antarctica. A total of 405 yeasts were recovered (205 from macroalgae and 200 from lichens). The yeast community from macroalgae was most diversity than the yeast community from lichen. The dominance index was similar for both substrates. A total of 24 taxa from macroalgae and 18 from lichens were identified, and only 5 were common to both substrates. Metschnikowia australis, Mrakia sp., Rhodotorula glacialis and Glaciozyma litorale were the most abundant yeasts in macroalgae and Cryptococcus victoriae, Rhodotorula laryngis, Rhodotorula arctica, Trichosporon sp. 1 and Mrakia sp. were the most abundant in lichens. Based on molecular and phylogenetic analyses, four yeast from macroalgae and six from lichens were considered potential new species. This is the first study to report the yeast communities from the Antarctic macroalgae Himantothallus grandifolius and lichen Ramalina terebrata. Results suggest that Antarctic phyco and lichensphere represent a huge substrate for cold-adapted yeasts and enhanced the knowledge of the microbiota from extreme environments.