Publications by authors named "Silvano Onofri"

58 Publications

Insights into the Survival Capabilities of Hydrated Colonies after Exposure to Fe Particle Radiation.

J Fungi (Basel) 2021 Jun 22;7(7). Epub 2021 Jun 22.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

The modern concept of the evolution of Mars assumes that life could potentially have originated on the planet Mars, possibly during the end of the late heavy bombardment, and could then be transferred to other planets. Since then, physical and chemical conditions on Mars changed and now strongly limit the presence of terrestrial-like life forms. These adverse conditions include scarcity of liquid water (although brine solutions may exist), low temperature and atmospheric pressure, and cosmic radiation. Ionizing radiation is very important among these life-constraining factors because it damages DNA and other cellular components, particularly in liquid conditions where radiation-induced reactive oxidants diffuse freely. Here, we investigated the impact of high doses (up to 2 kGy) of densely-ionizing (197.6 keV/µm), space-relevant iron ions (corresponding on the irradiation that reach the uppermost layer of the Mars subsurface) on the survival of an extremophilic terrestrial organism--in liquid medium and under atmospheric conditions, through different techniques. Results showed that it survived in a metabolically active state when subjected to high doses of Fe ions and was able to repair eventual DNA damages. It implies that some terrestrial life forms can withstand prolonged exposure to space-relevant ion radiation.
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http://dx.doi.org/10.3390/jof7070495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8304246PMC
June 2021

Growth Forms and Functional Guilds Distribution of Soil Fungi in Coastal Versus Inland Sites of Victoria Land, Antarctica.

Biology (Basel) 2021 Apr 11;10(4). Epub 2021 Apr 11.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

In Victoria Land, Antarctica, ice-free areas are restricted to coastal regions and dominate the landscape of the McMurdo Dry Valleys. These two environments are subjected to different pressures that determine the establishment of highly adapted fungal communities. Within the kingdom of fungi, filamentous, yeasts and meristematic/microcolonial growth forms on one side and different lifestyles on the other side may be considered adaptive strategies of particular interest in the frame of Antarctic constraints. In this optic, soil fungal communities from both coastal and Dry Valleys sites, already characterized thorough ITS1 metabarcoding sequencing, have been compared to determine the different distribution of phyla, growth forms, and lifestyles. Though we did not find significant differences in the richness between the two environments, the communities were highly differentiated and Dry Valleys sites had a higher evenness compared to coastal ones. Additionally, the distribution of different growth forms and lifestyles were well differentiated, and their diversity and composition were likely influenced by soil abiotic parameters, among which soil granulometry, pH, P, and C contents were the potential main determinants.
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http://dx.doi.org/10.3390/biology10040320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070035PMC
April 2021

Microbial activity in alpine soils under climate change.

Sci Total Environ 2021 Aug 10;783:147012. Epub 2021 Apr 10.

Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy. Electronic address:

Soil enzymatic activity was assessed in the Stelvio Pass area (Italian Central Alps) aiming to define the possible effects of climate change on microbial functioning. Two sites at two different elevations were chosen, a subalpine (2239 m) and an alpine belt (2604-2624 m), with mean annual air temperature differing by almost 3 °C, coherent with the worst future warming scenario (RCP 8.5) by 2100. The lower altitude site may represent a proxy of the potential future situation at higher altitude after the upward shift of subalpine vegetation due to climate change. Additionally, hexagonal open top chambers (OTCs) were installed at the upper site, to passively increase by about 2 °C the summer inner temperature to simulate short term effects of warming before the vegetation shift takes place. Soil physicochemical properties and the bacterial and fungal abundances of the above samples were also considered. The subalpine soils showed a higher microbial activity, especially for hydrolytic enzymes, higher carbon, ammonium and hydrogen (p < 0.001) contents, and a slightly higher PO content (p < 0.05) than alpine soils. Bacterial abundance was higher than fungal abundance, both for alpine and subalpine soils. On the other hand, the short term effect, which increased the mean soil temperature during the peak of the growing season in the OTC, showed to induce scarcely significant differences for edaphic parameters and microbial biomass content among the warmed and control plots. Using the manipulative warming experiments, we demonstrated that warming is able to change the enzyme activity starting from colder and higher altitude sites, known to be more vulnerable to the rising temperatures associated with climate change. Although five-years of experimental warming does not allow us to make bold conclusions, it appeared that warming-induced upwards vegetation shift might induce more substantial changes in enzymatic activities than the short-term effects, in the present vegetation context.
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http://dx.doi.org/10.1016/j.scitotenv.2021.147012DOI Listing
August 2021

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

J Fungi (Basel) 2021 Mar 16;7(3). Epub 2021 Mar 16.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

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, 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.
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http://dx.doi.org/10.3390/jof7030213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8001563PMC
March 2021

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages.

Microbiome 2021 03 19;9(1):63. Epub 2021 Mar 19.

Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098, San Michele all'Adige, Italy.

Background: Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.).

Results: A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The "Candidatus Jiangella antarctica" has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa.

Conclusions: Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life. Video abstract.
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http://dx.doi.org/10.1186/s40168-021-01021-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7980648PMC
March 2021

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

Environ Microbiol 2021 Feb 4. Epub 2021 Feb 4.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.

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.
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http://dx.doi.org/10.1111/1462-2920.15419DOI Listing
February 2021

Metabolomics of Dry Versus Reanimated Antarctic Lichen-Dominated Endolithic Communities.

Life (Basel) 2021 Jan 27;11(2). Epub 2021 Jan 27.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

Cryptoendolithic communities are almost the sole life form in the ice-free areas of the Antarctic desert, encompassing among the most extreme-tolerant organisms known on Earth that still assure ecosystems functioning, regulating nutrient and biogeochemical cycles under conditions accounted as incompatible with active life. If high-throughput sequencing based studies are unravelling prokaryotic and eukaryotic diversity, they are not yet characterized in terms of stress adaptations and responses, despite their paramount ecological importance. In this study, we compared the responses of Antarctic endolithic communities, with special focus on fungi, both under dry conditions (i.e., when dormant), and after reanimation by wetting, light, and optimal temperature (15 °C). We found that several metabolites were differently expressed in reanimated opposite sun exposed communities, suggesting a critical role in their success. In particular, the saccharopine pathway was up-regulated in the north surface, while the spermine/spermidine pathway was significantly down-regulated in the shaded exposed communities. The carnitine-dependent pathway is up-regulated in south-exposed reanimated samples, indicating the preferential involvement of the B-oxidation for the functioning of TCA cycle. The role of these metabolites in the performance of the communities is discussed herein.
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http://dx.doi.org/10.3390/life11020096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7911838PMC
January 2021

Iron Ion Particle Radiation Resistance of Dried Colonies of Embedded in Martian Regolith Analogues.

Life (Basel) 2020 Nov 24;10(12). Epub 2020 Nov 24.

Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.

Among the celestial bodies in the Solar System, Mars currently represents the main target for the search for life beyond Earth. However, its surface is constantly exposed to high doses of cosmic rays (CRs) that may pose a threat to any biological system. For this reason, investigations into the limits of resistance of life to space relevant radiation is fundamental to speculate on the chance of finding extraterrestrial organisms on Mars. In the present work, as part of the STARLIFE project, the responses of dried colonies of the black fungus Culture Collection of Fungi from Extreme Environments (CCFEE) 515 to the exposure to accelerated iron (LET: 200 keV/μm) ions, which mimic part of CRs spectrum, were investigated. Samples were exposed to the iron ions up to 1000 Gy in the presence of Martian regolith analogues. Our results showed an extraordinary resistance of the fungus in terms of survival, recovery of metabolic activity and DNA integrity. These experiments give new insights into the survival probability of possible terrestrial-like life forms on the present or past Martian surface and shallow subsurface environments.
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http://dx.doi.org/10.3390/life10120306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761078PMC
November 2020

The Responses of the Black Fungus to High Doses of Accelerated Helium Ions Radiation within Martian Regolith Simulants and Their Relevance for Mars.

Life (Basel) 2020 Jul 31;10(8). Epub 2020 Jul 31.

Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.

One of the primary current astrobiological goals is to understand the limits of microbial resistance to extraterrestrial conditions. Much attention is paid to ionizing radiation, since it can prevent the preservation and spread of life outside the Earth. The aim of this research was to study the impact of accelerated He ions (150 MeV/n, up to 1 kGy) as a component of the galactic cosmic rays on the black fungus when mixed with Antarctic sandstones-the substratum of its natural habitat-and two Martian regolith simulants, which mimics two different evolutionary stages of Mars. The high dose of 1 kGy was used to assess the effect of dose accumulation in dormant cells within minerals, under long-term irradiation estimated on a geological time scale. The data obtained suggests that viable Earth-like microorganisms can be preserved in the dormant state in the near-surface scenario for approximately 322,000 and 110,000 Earth years within Martian regolith that mimic early and present Mars environmental conditions, respectively. In addition, the results of the study indicate the possibility of maintaining traces within regolith, as demonstrated by the identification of melanin pigments through UltraViolet-visible (UV-vis) spectrophotometric approach.
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http://dx.doi.org/10.3390/life10080130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459982PMC
July 2020

sp. nov. and sp. nov., two novel basidiomycetous yeast species isolated from cold environments.

Int J Syst Evol Microbiol 2020 Aug 22;70(8):4704-4713. Epub 2020 Jul 22.

Department of Agricultural, Food and Environmental Sciences & Industrial yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy.

Five yeast strains were isolated from soil and sediments collected from Alps and Apennines glaciers during sampling campaigns carried out in summer 2007 and 2017, respectively. Based on morphological and physiological tests and on phylogenetic analyses reconstructed with ITS and D1/D2 sequences, the five strains were considered to belong to two related but hitherto unknown species within the genus , in an intermediate position between and . The names (holotype DBVPG 10734) and (holotype DBVPG 10736) are proposed for the two novel species and a detailed description of their morphological, physiological and phylogenetic features are presented. Both species fermented glucose, sucrose and trehalose, which is an uncommon feature in basidiomycetous yeasts, and showed septate hyphae with teliospore formation.
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http://dx.doi.org/10.1099/ijsem.0.004336DOI Listing
August 2020

Expansion of shrubs could result in local loss of soil bacterial richness in Western Greenland.

FEMS Microbiol Ecol 2020 08;96(8)

Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Leiden, The Netherlands.

Climate warming in Greenland is facilitating the expansion of shrubs across wide areas of tundra. Given the close association between plants and soil microorganisms and the important role of soil bacteria in ecosystem functioning, it is of utmost importance to characterize microbial communities of arctic soil habitats and assess the influence of plant edaphic factors on their composition. We used 16S rRNA gene amplicons to explore the bacterial assemblages of three different soil habitats representative of a plant coverage gradient: bare ground, biological soil crusts dominated by mosses and lichens and vascular vegetation dominated by shrubs. We investigated how bacterial richness and community composition were affected by the vegetation coverage, and soil pH, moisture and carbon (C), nitrogen (N) and phosphorus (P) contents. Bacterial richness did not correlate with plant coverage complexity, while community structure varied between habitats. Edaphic variables affected both the taxonomic richness and community composition. The high number of Amplicon Sequence Variants (ASVs) indicators of bare ground plots suggests a risk of local bacterial diversity loss due to expansion of vascular vegetation.
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http://dx.doi.org/10.1093/femsec/fiaa089DOI Listing
August 2020

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

Microorganisms 2020 Jun 23;8(6). Epub 2020 Jun 23.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

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.
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http://dx.doi.org/10.3390/microorganisms8060942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356261PMC
June 2020

Intra- and inter-cores fungal diversity suggests interconnection of different habitats in an Antarctic frozen lake (Boulder Clay, Northern Victoria Land).

Environ Microbiol 2020 08 30;22(8):3463-3477. Epub 2020 Jun 30.

Department of Theoretical and Applied Sciences, Insubria University, Varese, Italy.

A perennially frozen lake at Boulder Clay site (Victoria Land, Antarctica), characterized by the presence of frost mounds, have been selected as an in situ model for ecological studies. Different samples of permafrost, glacier ice and brines have been studied as a unique habitat system. An additional sample of brines (collected in another frozen lake close to the previous one) was also considered. Alpha- and beta-diversity of fungal communities showed both intra- and inter-cores significant (p < 0.05) differences, which suggest the presence of interconnection among the habitats. Therefore, the layers of frost mound and the deep glacier could be interconnected while the brines could probably be considered as an open habitat system not interconnected with each other. Moreover, the absence of similarity between the lake ice and the underlying permafrost suggested that the lake is perennially frozen based. The predominance of positive significant (p < 0.05) co-occurrences among some fungal taxa allowed to postulate the existence of an ecological equilibrium in the habitats systems. The positive significant (p < 0.05) correlation between salt concentration, total organic carbon and pH, and some fungal taxa suggests that a few abiotic parameters could drive fungal diversity inside these ecological niches.
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http://dx.doi.org/10.1111/1462-2920.15117DOI Listing
August 2020

Specific adaptations are selected in opposite sun exposed Antarctic cryptoendolithic communities as revealed by untargeted metabolomics.

PLoS One 2020 27;15(5):e0233805. Epub 2020 May 27.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.

Antarctic cryptoendolithic communities are self-supporting borderline ecosystems spreading across the extreme conditions of the Antarctic desert and represent the predominant life-form in the ice-free areas of McMurdo Dry Valleys, accounted as the closest terrestrial Martian analogue. Components of these communities are highly adapted extremophiles and extreme-tolerant microorganisms, among the most resistant known to date. Recently, studies investigated biodiversity and community composition in these ecosystems but the metabolic activity of the metacommunity has never been investigated. Using an untargeted metabolomics, we explored stress-response of communities spreading in two sites of the same location, subjected to increasing environmental pressure due to opposite sun exposure, accounted as main factor influencing the diversity and composition of these ecosystems. Overall, 331 altered metabolites (206 and 125 unique for north and south, respectively), distinguished the two differently exposed communities. We also selected 10 metabolites and performed two-stage Receiver Operating Characteristic (ROC) analysis to test them as potential biomarkers. We further focused on melanin and allantoin as protective substances; their concentration was highly different in the community in the shadow or in the sun. These results clearly indicate that opposite insolation selected organisms in the communities with different adaptation strategies in terms of key metabolites produced.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233805PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253227PMC
August 2020

Multidisciplinary characterization of melanin pigments from the black fungus Cryomyces antarcticus.

Appl Microbiol Biotechnol 2020 Jul 24;104(14):6385-6395. Epub 2020 May 24.

Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100, Viterbo, Italy.

Melanin is a natural pigment present in almost all biological groups, and is composed of indolic polymers and characterized by black-brown colorization. Furthermore, it is one of the pigments produced by extremophiles including those living in the Antarctic desert, and is mainly involved in their protection from high UV radiation, desiccation, salinity and oxidation. Previous studies have shown that melanized species have an increased capability to survive high level of radiation compared with the non-melanized counterpart. Understanding the molecular composition of fungal melanin could help to understand this peculiar capability. Here, we aimed to characterize the melanin pigment extracted from the Antarctic black fungus Cryomyces antarcticus, which is a good test model for radioprotection researches, by studying its chemical properties and spectral data. Our results demonstrated that, in spite of having a specific type of melanin as the majority of fungi, the fungus possesses the ability to produce both 1,8-dihydroxynaphthalene (DHN) and L 3-4 dihydroxyphenylalanine (L-DOPA) melanins, opening interesting scenarios for the protection role against radiation. Researches on fungal melanin have a huge application in different fields, including radioprotection, bioremediation, and biomedical applications. KEY POINTS: • Isolation and characterization by multidisciplinary approaches of fungal melanins. • Discovery that pathways for producing DOPA and DHN are both active even in its extreme habitat. • Hypothesis supporting the possibility of using melanin pigment for radioprotection.
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http://dx.doi.org/10.1007/s00253-020-10666-0DOI Listing
July 2020

Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus.

Fungal Biol 2020 05 31;124(5):458-467. Epub 2020 Jan 31.

Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA. Electronic address:

Friedmanniomyces endolithicus is a highly melanized fungus endemic to the Antarctic, occurring exclusively in endolithic communities of the ice-free areas of the Victoria Land, including the McMurdo Dry Valleys, the coldest and most hyper-arid desert on Earth and accounted as the Martian analog on our planet. F. endolithicus is highly successful in these inhospitable environments, the most widespread and commonly isolated species from these peculiar niches, indicating a high degree of adaptation. The nature of its extremo tolerance has not been previously studied. To investigate this, we sequenced genome of F. endolithicus CCFEE 5311 to explore gene content and genomic patterns that could be attributed to its specialization. The predicted functional potential of the genes was assigned by similarity to InterPro and CAZy domains. The genome was compared to phylogenetically close relatives which are also melanized fungi occurring in extreme environments including Friedmanniomyces simplex, Baudoinia panamericana, Acidomyces acidophilus, Hortaea thailandica and Hortaea werneckii. We tested if shared genomic traits existed among these species and hyper-extremotolerant fungus F. endolithicus. We found that some characters for stress tolerance such as meristematic growth and cold tolerance are enriched in F. endolithicus that may be triggered by the exposure to Antarctic prohibitive conditions.
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http://dx.doi.org/10.1016/j.funbio.2020.01.005DOI Listing
May 2020

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

Microbiol Resour Announc 2020 Apr 2;9(14). Epub 2020 Apr 2.

Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA

A draft genome sequence was assembled and annotated of the basidiomycetous yeast 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.
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http://dx.doi.org/10.1128/MRA.00020-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118180PMC
April 2020

Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.

Microbiol Resour Announc 2020 Mar 5;9(10). Epub 2020 Mar 5.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.

Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes.
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http://dx.doi.org/10.1128/MRA.01599-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171226PMC
March 2020

Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica.

Life (Basel) 2020 Feb 6;10(2). Epub 2020 Feb 6.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

The microbial communities that inhabit lithic niches inside sandstone in the Antarctic McMurdo Dry Valleys of life's limits on Earth. The cryptoendolithic communities survive in these ice-free areas that have the lowest temperatures on Earth coupled with strong thermal fluctuations, extreme aridity, oligotrophy and high levels of solar and UV radiation. In this study, based on DNA metabarcoding, targeting the fungal Internal Transcribed Spacer region 1 (ITS1) and multivariate statistical analyses, we supply the first comprehensive overview onto the fungal diversity and composition of these communities sampled over a broad geographic area of the Antarctic hyper-arid cold desert. Six locations with surfaces that experience variable sun exposure were sampled to compare communities from a common area across a gradient of environmental pressure. The Operational Taxonomic Units (OTUs) identified were primarily members of the Ascomycota phylum, comprised mostly of the Lecanoromycetes and Dothideomycetes classes. The fungal species , endemic to Antarctica, was found to be a marker species to the harshest conditions occurring in the shady, south exposed rock surfaces. Analysis of community composition showed that sun exposure was an environmental property that explained community diversity and structured endolithic colonization.
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http://dx.doi.org/10.3390/life10020013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175349PMC
February 2020

Vegetation, pH and Water Content as Main Factors for Shaping Fungal Richness, Community Composition and Functional Guilds Distribution in Soils of Western Greenland.

Front Microbiol 2019 11;10:2348. Epub 2019 Oct 11.

Biodiversity Dynamics, Naturalis Biodiversity Center, Leiden, Netherlands.

Fungi are the most abundant and one of the most diverse components of arctic soil ecosystems, where they are fundamental drivers of plant nutrient acquisition and recycling. Nevertheless, few studies have focused on the factors driving the diversity and functionality of fungal communities associated with these ecosystems, especially in the scope of global warming that is particularly affecting Greenland and is leading to shrub expansion, with expected profound changes of soil microbial communities. We used soil DNA metabarcoding to compare taxonomic and functional composition of fungal communities in three habitats [bare ground (BG), biological soil crusts (BSC), and vascular vegetation (VV) coverage] in Western Greenland. Fungal richness increased with the increasing complexity of the coverage, but BGs and BSCs samples showed the highest number of unique OTUs. Differences in both fungal community composition and distribution of functional guilds identified were correlated with edaphic factors (mainly pH and water content), in turn connected with the different type of coverage. These results suggest also possible losses of diversity connected to the expansion of VV and possible interactions among the members of different functional guilds, likely due to the nutrient limitation, with potential effects on elements recycling.
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http://dx.doi.org/10.3389/fmicb.2019.02348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797927PMC
October 2019

Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities.

Environ Microbiol Rep 2019 10 26;11(5):718-726. Epub 2019 Aug 26.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.

Endolithic growth within rocks is a critical adaptation of microbes living in harsh environments where exposure to extreme temperature, radiation, and desiccation limits the predominant life forms, such as in the ice-free regions of Continental Antarctica. The microbial diversity of the endolithic communities in these areas has been sparsely examined. In this work, diversity and composition of bacterial assemblages in the cryptoendolithic lichen-dominated communities of Victoria Land (Continental Antarctica) were explored using a high-throughput metabarcoding approach, targeting the V4 region of 16S rDNA. Rocks were collected in 12 different localities (from 14 different sites), along a gradient ranging from 1000 to 3300 m a.s.l. and at a sea distance ranging from 29 to 96 km. The results indicate Actinobacteria and Proteobacteria are the dominant taxa in all samples and defined a 'core' group of bacterial taxa across all sites. The structure of bacteria communities is correlated with the fungal counterpart and among the environmental parameters considered, altitude was found to influence bacterial biodiversity, while distance from sea had no evident influence.
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http://dx.doi.org/10.1111/1758-2229.12788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8057506PMC
October 2019

Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus .

Microbiol Resour Announc 2019 May 9;8(19). Epub 2019 May 9.

Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA

A 30.43-Mb draft genome sequence with 10,355 predicted protein-coding genes was produced for the ascomycete fungus strain CCFEE 6314, a black yeast isolated from Antarctic cryptoendolithic communities. The sequence will be of importance for identifying differences among extremophiles and mesophiles and cataloguing the global population diversity of this organism.
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http://dx.doi.org/10.1128/MRA.00142-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509517PMC
May 2019

Limits of Life and the Habitability of Mars: The ESA Space Experiment BIOMEX on the ISS.

Astrobiology 2019 02;19(2):145-157

20 Extremophile Research & Biobank CCCryo, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.

BIOMEX (BIOlogy and Mars EXperiment) is an ESA/Roscosmos space exposure experiment housed within the exposure facility EXPOSE-R2 outside the Zvezda module on the International Space Station (ISS). The design of the multiuser facility supports-among others-the BIOMEX investigations into the stability and level of degradation of space-exposed biosignatures such as pigments, secondary metabolites, and cell surfaces in contact with a terrestrial and Mars analog mineral environment. In parallel, analysis on the viability of the investigated organisms has provided relevant data for evaluation of the habitability of Mars, for the limits of life, and for the likelihood of an interplanetary transfer of life (theory of lithopanspermia). In this project, lichens, archaea, bacteria, cyanobacteria, snow/permafrost algae, meristematic black fungi, and bryophytes from alpine and polar habitats were embedded, grown, and cultured on a mixture of martian and lunar regolith analogs or other terrestrial minerals. The organisms and regolith analogs and terrestrial mineral mixtures were then exposed to space and to simulated Mars-like conditions by way of the EXPOSE-R2 facility. In this special issue, we present the first set of data obtained in reference to our investigation into the habitability of Mars and limits of life. This project was initiated and implemented by the BIOMEX group, an international and interdisciplinary consortium of 30 institutes in 12 countries on 3 continents. Preflight tests for sample selection, results from ground-based simulation experiments, and the space experiments themselves are presented and include a complete overview of the scientific processes required for this space experiment and postflight analysis. The presented BIOMEX concept could be scaled up to future exposure experiments on the Moon and will serve as a pretest in low Earth orbit.
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http://dx.doi.org/10.1089/ast.2018.1897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383581PMC
February 2019

Survival and redox activity of Friedmanniomyces endolithicus, an Antarctic endemic black meristematic fungus, after gamma rays exposure.

Fungal Biol 2018 12 23;122(12):1222-1227. Epub 2018 Oct 23.

College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada.

Despite living organisms are not exposed to acute ionizing radiation under natural conditions, some exhibit a high radiation resistance. Understanding this phenomenon is important for assessing the impact of radiation-related accidents, occupational exposures and space missions. In this context, in this study we analyzed the effect of gamma rays on the Antarctic cryptoendolithic melanized fungus Friedmanniomyces endolithicus CCFEE 5208 and demonstrated its resistance to acute doses of gamma radiation (up to 400 Gy), accompanied by increase in metabolic activity.
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http://dx.doi.org/10.1016/j.funbio.2018.10.002DOI Listing
December 2018

Survival, DNA, and Ultrastructural Integrity of a Cryptoendolithic Antarctic Fungus in Mars and Lunar Rock Analogs Exposed Outside the International Space Station.

Astrobiology 2019 02 30;19(2):170-182. Epub 2018 Oct 30.

4 Astrobiological Laboratories, Institute of Planetary Research, Management and Infrastructure, German Aerospace Center (DLR) Berlin, Berlin, Germany.

The search for life beyond Earth involves investigation into the responses of model organisms to the deleterious effects of space. In the frame of the BIOlogy and Mars Experiment, as part of the European Space Agency (ESA) space mission EXPOSE-R2 in low Earth orbit (LEO), dried colonies of the Antarctic cryptoendolithic black fungus Cryomyces antarcticus CCFEE 515 were grown on martian and lunar analog regolith pellets, and exposed for 16 months to LEO space and simulated Mars-like conditions on the International Space Station. The results demonstrate that C. antarcticus was able to tolerate the combined stress of different extraterrestrial substrates, space, and simulated Mars-like conditions in terms of survival, DNA, and ultrastructural stability. Results offer insights into the habitability of Mars for future exploration missions on Mars. Implications for the detection of biosignatures in extraterrestrial conditions and planetary protection are discussed.
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http://dx.doi.org/10.1089/ast.2017.1728DOI Listing
February 2019

Responses of the Black Fungus Cryomyces antarcticus to Simulated Mars and Space Conditions on Rock Analogs.

Astrobiology 2019 02 1;19(2):209-220. Epub 2018 Aug 1.

1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy.

The BIOMEX (BIOlogy and Mars Experiment) is part of the European Space Agency (ESA) space mission EXPOSE-R2 in Low-Earth Orbit, devoted to exposing microorganisms for 1.5 years to space and simulated Mars conditions on the International Space Station. In preparing this mission, dried colonies of the Antarctic cryptoendolithic black fungus Cryomyces antarcticus CCFEE 515, grown on martian and lunar analog regolith pellets, were subjected to several ground-based preflight tests, Experiment Verification Tests, and Science Verification Tests (SVTs) that were performed to verify (i) the resistance of our model organism to space stressors when grown on extraterrestrial rock analogs and (ii) the possibility of detecting biomolecules as potential biosignatures. Here, the results of the SVTs, the last set of experiments, which were performed in ultraviolet radiation combined with simulated space vacuum or simulated martian conditions, are reported. The results demonstrate that C. antarcticus was able to tolerate the conditions of the SVT experiment, regardless of the substratum in which it was grown. DNA maintained high integrity after treatments and was confirmed as a possible biosignature; melanin, which was chosen to be a target for biosignature detection, was unambiguously detected by Raman spectroscopy.
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http://dx.doi.org/10.1089/ast.2016.1631DOI Listing
February 2019

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

Front Microbiol 2018 29;9:1392. Epub 2018 Jun 29.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.

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 consistently present across all the samples, mainly composed of lichen-forming and Dothideomycetous fungi. Pareto-Lorenz curves indicated a very high degree of specialization (F 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.
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http://dx.doi.org/10.3389/fmicb.2018.01392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033990PMC
June 2018

Integrity of the DNA and Cellular Ultrastructure of Cryptoendolithic Fungi in Space or Mars Conditions: A 1.5-Year Study at the International Space Station.

Life (Basel) 2018 Jun 19;8(2). Epub 2018 Jun 19.

Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.

The black fungi and are highly melanized and are resilient to cold, ultra-violet, ionizing radiation and other extreme conditions. These microorganisms were isolated from cryptoendolithic microbial communities in the McMurdo Dry Valleys (Antarctica) and studied in Low Earth Orbit (LEO), using the EXPOSE-E facility on the International Space Station (ISS). Previously, it was demonstrated that and survive the hostile conditions of space (vacuum, temperature fluctuations, and the full spectrum of extraterrestrial solar electromagnetic radiation), as well as Mars conditions that were simulated in space for a 1.5-year period. Here, we qualitatively and quantitatively characterize damage to DNA and cellular ultrastructure in desiccated cells of these two species, within the frame of the same experiment. The DNA and cells of exhibited a higher resistance than those of . This is presumably attributable to the thicker (melanized) cell wall of the former. Generally, DNA was readily detected (by PCR) regardless of exposure conditions or fungal species, but the DNA had been more-extensively mutated. We discuss the implications for using DNA, when properly shielded, as a biosignature of recently extinct or extant life.
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http://dx.doi.org/10.3390/life8020023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027225PMC
June 2018

Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities.

Life (Basel) 2018 Jun 2;8(2). Epub 2018 Jun 2.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.

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.
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http://dx.doi.org/10.3390/life8020019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027399PMC
June 2018
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