Search Results (19)

The Antarctic continent hosts highly specialized microbial ecosystems, particularly within endolithic habitats, where microorganisms colonize the interior of rocks in order to withstand conditions that otherwise cannot support life. Previous studies have characterized the composition and abundance of these communities, as well as their different degrees of stress power; furthermore, the effect of different lithic substrates in shaping their associated bacterial assemblages has been extensively investigated. By contrast, how rock typology exerts fungal endolithic colonization still remains unexplored. In this study, we have considered and compared fungal communities inhabiting granite and sandstone rocks collected across Victoria Land, Antarctica, using high-throughput sequencing of the Internal Transcribed Spacer (ITS) region. Our analyses revealed that both rock types were dominated by Ascomycota, with a marked prevalence of lichen-forming fungi, particularly within the class Lecanoromycetes. However, granite-supported communities exhibited significantly higher species richness, likely driven by the structural heterogeneity of the substrate and the presence of fissures enabling chasmoendolithic colonization. In contrast, sandstone communities were more specialized and dominated by strict cryptoendolithic taxa capable of surviving within the rock’s pore spaces. Differential abundance analysis identified key species associated with each substrate, including the lichen Buellia frigida in granite and the black fungus Friedmanniomyces endolithicus in sandstone, two endemic species in Antarctica. Moreover, the use of presence/absence- versus abundance-based diversity metrics revealed contrasting ecological patterns; substrate type had a stronger influence on species presence, whereas geographic location more significantly shaped abundance profiles, highlighting the complex interplay between both factors in determining fungal community composition. Additionally, alpha diversity analyses showed significantly higher species richness in granite compared to sandstone, suggesting that structural heterogeneity and chasmoendolithism may promote a more diverse fungal assemblage. Full article

In restoration practice, direct methods become necessary when indirect methods fail and when aesthetic, chemical, or physical biodeteriorative effects threaten the integrity and legibility of the artifact. More effective methods that prioritize the health of workers and the environment are essential for the outdoor stone monument’s conservation. Although several low-impact methods have been proposed, more case studies are needed to address different biopatina types, products, and lithic substrates. Within the COLLINE Project we focused on peperino, a dark volcanic stone widely used in central Italy since the 7th century BCE, because it has been poorly investigated in terms of diversity of biodeteriogens and low-impact methods for their removal. Direct observation, culture methods, and molecular identification have been applied for the identification of biodeteriogens with particular attention to black meristematic fungi. Three low-impact products, namely a dimethyl sulfoxide (DMSO)-based gel, BioTersus^® (essential oil-based), and Nasier (enzyme-based) were tested in ex situ (on a colonized slab) and in situ trials (on the pulpit of the S. Francesco alla Rocca Basilica, Viterbo, Italy). Three analytical methods, namely reflectance spectroradiometry, laser-induced fluorescence (LIF), and hypercolorimetric multispectral imaging (HMI) were used to test the cleaning efficacy. Results evidenced the strong influence of direct irradiation and water availability in the balance and distribution of phototrophs, fungi, and lichens. The low-impact cleaning methods, particularly the DMSO-based gel and BioTersus^®, effectively remove biodeteriogens from peperino stone while preserving its integrity, offering sustainable solutions for cultural heritage conservation. The instrumental analyses showed that reflectance spectroradiometry and LIF effectively validated the cleaning efficacy, albeit with different sensibility, while HMI, despite spatial constraints, confirmed the three tested cleaning methods do not interfere with peperino stone. Full article

Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions. Full article

The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering through microbial activity, rendering them far from pristine and challenging the quest for biomarkers in ancient sedimentary rocks. In addressing this challenge, a comprehensive analysis utilizing Gas Chromatography Mass Spectrometry (GC-MS) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) was conducted on a 520-Ma-old Cambrian rock. This investigation revealed a diverse molecular assemblage with comprising alkanols, sterols, fatty acids, glycerolipids, wax esters, and nitrogen-bearing compounds. Notably, elevated levels of bacterial C₁₆, C₁₈ and C₁₄ fatty acids, iso and anteiso methyl-branched fatty acids, as well as fungal sterols, long-chained fatty acids, and alcohols, consistently align with a consortium of bacteria and fungi accessing complex organic matter within a soil-type ecosystem. The prominence of bacterial and fungal lipids alongside maturity indicators denotes derivation from heterotrophic activity rather than ancient preservation or marine sources. Moreover, the identification of long-chain (>C22) n-alkanols, even-carbon-numbered long chain (>C20) fatty acids, and campesterol, as well as stigmastanol, provides confirmation of plant residue inputs. Furthermore, findings highlight the ability of contemporary soil microbiota to inhabit rocky substrates actively, requiring strict contamination controls when evaluating ancient molecular biosignatures or extraterrestrial materials collected. Full article

Rock-inhabiting fungi (RIF) are usually extremely tolerant or extremophilic, as they can survive on natural and artificial rocks despite being exposed to stressful conditions. RIF have serious negative effects on the appearance and cohesion of rocky substrates, causing the alteration and decomposition of building materials, but also on human and animal health, as they can act as opportunistic pathogens. Their identification is therefore of great importance, especially in urban areas. In the present study, culturing techniques for isolating fungi, and a polyphasic taxonomic approach to their identification, were used to assess the diversity of micromycetes that darken the surfaces of buildings in various villages and cities in Tarragona Province (Spain). Sixty-four species of RIF belonging to forty-one genera were identified, including a new genus (Coccodomyces) and the following six new fungal species: Coccodomyces pleiosporus, Exophiala caementiphila, Exophiala multiformis, Neocatenulostroma spinulosum, Neodevriesia longicatenispora, and Paradevriesia holothallica. Thus, we have established that building materials are ecological niches where a high biodiversity of RIF can develop. Full article

Saxispiralis lemnorum MUM 23.14 is an extremotolerant microcolonial black fungus, originally isolated from a biodeteriorated limestone artwork in Portugal. This recently introduced species belongs to the Aeminiaceae family, representing the second member of this monophyletic clade. This fungus exhibits a unique set of characteristics, including xerophily, cold tolerance, high UV radiation tolerance, and an exceptional ability to thrive in NaCl concentrations of up to 30% while also enduring pH levels ranging from 5 to 11. To gain insights into its genomic traits associated with stress resistance mechanisms, specialization, and their potential implications in stone biodeterioration, we conducted a comprehensive genome sequencing and analysis. This draft genome not only marks the first for the Saxispiralis genus but also the second for the Aeminiaceae family. Furthermore, we performed two comparative genomic analyses: one focusing on the closest relative within the Aeminiaceae family, Aeminium ludgeri, and another encompassing the genome of different extremotolerant black fungi. In this study, we successfully achieved high genome completeness for S. lemnorum and confirmed its close phylogenetic relationship to A. ludgeri. Our findings revealed traits contributing to its extremophilic nature and provided insights into potential mechanisms contributing to stone biodeterioration. Many traits are common to both Aeminiaceae species and are shared with other black fungi, while numerous unique traits may be attributed to species-specific characteristics. Full article

The Badami Caves are a significant example of ancient Indian rock-cut architecture, dating back to the 6th century. These caves are situated in the Malaprabha River valley and are part of the candidate UNESCO World Heritage Site known as the “Evolution of Temple Architecture—Aihole-Badami-Pattadakal”, which is considered to be the cradle of temple architecture in India. Our study aimed to investigate the diversity, distribution, and biodeterioration phenomena of the fungal communities present on the cave surfaces. The study also conducted a comprehensive analysis of fungal biodeterioration on the cave carvings. Utilizing specialized techniques, the dissolution of calcite, alterations in pH levels, and biomineralization capabilities of isolated fungal strains were monitored. Additionally, this study analyzed fungal acid production using high-performance liquid chromatography (HPLC). Our findings revealed that the major genera of fungi found on the cave surfaces included Acremonium, Curvularia, Cladosporium, Penicillium, and Aspergillus. These isolated fungi were observed to produce acids, leading to the dissolution of calcium carbonate and subsequent decrease in pH values. Notably, the dominant genus responsible for acid production and the promotion of biomineralization was Aspergillus. These discoveries provide valuable insight into the ecology and functions of fungi inhabiting stone surfaces, contributing to our understanding of how to preserve and protect sculptures from biodeterioration. Full article

With an impressive ability to survive in harsh environments, black fungi are an ecological group of melanized fungi that are widely recognized as a major contributor to the biodeterioration of stone cultural heritage materials. As part of the ongoing efforts to study the fungal diversity thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, two isolates of an unknown microcolonial black fungus were retrieved. These isolates were thoroughly studied through a comprehensive analysis based on a multi-locus phylogeny of a combined dataset of ITS rDNA, LSU, and rpb2, along with morphological, physiological, and ecological characteristics. Based on the data obtained from this integrative analysis, we propose a new genus, Saxispiralis gen. nov., and a new species, Saxispiralis lemnorum sp. nov., in the recently described Aeminiaceae family (order Mycosphaerellales). Prior to this discovery, this family only had one known genus and species, Aeminium ludgeri, also isolated from deteriorated limestone. Additionally, considering the isolation source of the fungus and to better understand its potential contribution to the overall stone monument biodeterioration, its in vitro biodeteriorative potential was also evaluated. This work represents a significant contribution to the understanding of the fungal diversity involved in the biodeterioration of limestone heritage. Full article

Cyanobacteria represent a cosmopolitan group of oxyphototrophic bacteria. Although free-living cyanobacteria thriving in aquatic habitats as well as cyanobacteria in terrestrial symbiotic systems (lichens) have been extensively studied in Finland, the diversity of terrestrial rock-inhabiting cyanobacteria is overlooked. As part of an ongoing effort to study terrestrial epilithic cyanobacteria from Finland, we isolated two Pseudanabaena-like cyanobacterial strains and characterized them using a polyphasic approach. Although the two strains were firmly placed within the Pseudanabaena clade in the 16S rRNA phylogenetic analyses, relationships among species were better resolved when phylogenetic analyses were based on a concatenate alignment of 16S rRNA gene and 16S–23S Internal Transcribed Spacer (ITS) region. In addition, 16S–23S ITS percent dissimilarity proved to be more useful for species discrimination in Pseudanabaena compared to secondary structures of conserved 16S–23S ITS domains (D1–D1′, box B, V2 and V3 helices). Considering morphological, molecular and ecological information, we describe P. epilithica sp. nov. and P. suomiensis sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. Neither toxins nor antimicrobial metabolites were detected during LC-MS analysis or antimicrobial susceptibility testing, respectively. Lastly, our phylogenetic analyses revealed that many Pseudanabaena strains are misidentified and highlight the need for taxonomic revision in this poorly studied cyanobacterial genus. Full article

Meristematic black fungi are a highly damaging group of microorganisms responsible for the deterioration of outdoor exposed monuments. Their resilience to various stresses poses significant challenges for removal efforts. This study focuses on the community of meristematic fungi inhabiting the external white marble of the Cathedral of Santa Maria del Fiore, where they contribute to its darkening. Twenty-four strains were isolated from two differently exposed sites of the Cathedral, and their characterization was conducted. Phylogenetic analysis using ITS and LSU rDNA regions revealed a wide diversity of rock-inhabiting fungal strains within the sampled areas. Eight strains, belonging to different genera, were also tested for thermal preferences, salt tolerance, and acid production to investigate their tolerance to environmental stressors and their interaction with stone. All tested strains were able to grow in the range of 5–30 °C, in the presence 5% NaCl, and seven out of eight strains were positive for the production of acid. Their sensitivities to essential oils of thyme and oregano and to the commercial biocide Biotin T were also tested. The essential oils were found to be the most effective against black fungi growth, indicating the possibility of developing a treatment with a low environmental impact. Full article

Black fungi are an ecological group of melanized fungi specialized in extremotolerance and assumed to be among the most stress-resistant eukaryotes on Earth. Multi-omics studies have provided significant evidence that they have a peculiar response to stress that differs considerably from that of common mesophilic hyphomycetes. Survival strategies displayed by these organisms have situated them as attractive models for astrobiology and, in general, for studies directed towards the definition of the actual limits for life. Moreover, the ascertained aptitude of black fungi for degradation of hazardous volatile pollutants and for plastic breakdown suggests prospective application of several species. Full article

Microbial endolithic communities are the main and most widespread life forms in the coldest and hyper-arid desert of the McMurdo Dry Valleys and other ice-free areas across Victoria Land, Antarctica. There, the lichen-dominated communities are complex and self-supporting assemblages of phototrophic and heterotrophic microorganisms, including bacteria, chlorophytes, and both free-living and lichen-forming fungi living at the edge of their physiological adaptability. In particular, among the free-living fungi, microcolonial, melanized, and anamorphic species are highly recurrent, while a few species were sometimes found to be associated with algae. One of these fungi is of paramount importance for its peculiar traits, i.e., a yeast-like habitus, co-growing with algae and being difficult to propagate in pure culture. In the present study, this taxon is herein described as the new genus Antarctolichenia and its type species is A. onofrii, which represents a transitional group between the free-living and symbiotic lifestyle in Arthoniomycetes. The phylogenetic placement of Antarctolichenia was studied using three rDNA molecular markers and morphological characters were described. In this study, we also reappraise the evolution and the connections linking the lichen-forming and rock-inhabiting lifestyles in the basal lineages of Arthoniomycetes (i.e., Lichenostigmatales) and Dothideomycetes. Full article

About 90% of Cynorkis species are endemic to the biodiversity hotspot of Madagascar. This terrestrial habitat-specific genus received little study for fungal diversity to support conservation. We evaluated the diversity of culturable fungi of 11 species and soil characteristics from six sites spanning a >40 km radius in and along the region’s inselbergs. Peloton-forming fungi were grown in vitro from root/protocorm slices and positively identified using DNA sequencing. The fungal diversity was then correlated with soil pH, NO₃^-N, P, and K. All species harbored either putative mycorrhizal associates in the Rhizoctonia complex or Hypocreales fungi. Tulasnella Operational Taxonomic Units (OTUs) were most prevalent in all soil types while Serendipita OTUs were found in species inhabiting granite/rock outcrops in moist soil (seepage areas). Most Cynorkis species were present in soil with low NO₃^-N and P levels with diversity of mycorrhizal fungi inversely correlated to NO₃^-N levels. Of the different orchid life stages sampled, only one species (Cynorkis fastigiata) yielded putative mycorrhizal fungi from juvenile stages. As diversity of mycorrhizal fungi of Cynorkis spp. was negatively correlated with NO₃^-N, and majority of the studied taxa were found in soils with low NO₃^-N and P contents, reintroduction studies must include analysis of N and P in detail. For the first time, we showed that the assemblage of culturable fungi in the roots of habitat-specific species of Cynorkis (Orchidaceae) are intimately tied to specific soil characteristics. Full article

Most of the rock-inhabiting fungi are meristematic and melanized microorganisms often associated with monument biodeterioration. In previous microbial profiling of the Egyptian Djoser pyramid, a Pseudotaeniolina globosa isolate was found. The current study aimed to characterize the P. globosa isolated from the Djoser pyramid compared with an Italian isolate at morphological, physiological, and molecular levels. Experiments were carried out to test temperature, salinity, and pH preferences, as well as stress tolerance to UV radiation and high temperature, in addition to a multi-locus genotyping using ITS, nrSSU or 18S, nrLSU or 28S, BT2, and RPB2 markers. Morphological and molecular data confirmed the con-specificity of the two isolates. However, the Egyptian isolate showed a wider range of growth at different environmental conditions being much more tolerant to a wider range of temperature (4–37 °C) and pH values (3.0–9.0 pH) than the Italian (10–30 °C, 4.0–6.0 pH), and more tolerant to extreme salinity levels (5 M NaCl), compared to the lowest in the Italian isolate (0.2 M NaCl). Besides, the Egyptian isolate was more tolerant to high temperature than the Italian isolate since it was able to survive after exposure to up to 85 °C for 5 min, and was not affected for up to 9 h of UV exposure, while the Italian one could not regrow after the same treatments. The Pseudotaeniolina globosa species was attributed to the family Teratosphaeriaceae of the order Capnodiales, class Dothideomycetes. Our results demonstrated that the Egyptian isolate could be considered an ecotype well adapted to harsh and extreme environments. Its potential bio-deteriorating effect on such an important cultural heritage requires special attention to design and conservation plans and solutions to limit its presence and extension in the studied pyramid and surrounding archaeological sites. Full article

The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the “Shed light in The daRk lineagES of the fungal tree of life” (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments. Full article