Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

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.

Climate change not only affects the biodiversity of natural habitats, but also the flora and fauna within cities. An increase in average temperature and changing precipitation, but additionally extreme weather events with heat waves and flooding, are forecast. The climate in our cities and, thus, also inside buildings is influenced by the changing outdoor climate and urban heat islands. A further challenge to ecosystems is the introduction of new species (neobiota). If these species are pests, they can cause damage to stored products and materials. Much cultural heritage is within buildings, so changes in the indoor climate also affect pests (insect and fungi) within the museums, storage depositories, libraries, and historic properties. This paper reviews the literature and presents an overview of these complex interactions between the outdoor climate, indoor climate, and pests in museums. Recent studies have examined the direct impact of climate on buildings and collections. The warming of indoor climates and an increased frequency or intensity of extreme weather events are two important drivers affecting indoor pests such as insects and fungi, which can severely damage collections. Increases in activity and new species are found, e.g., the tropical grey silverfish Ctenolepisma longicaudatum has been present in many museums in recent years benefitting from increased indoor temperatures.

The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO₃ and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph’s deterioration.

The knowledge of the atmospheric degradation reactions affecting the stability of modern materials is still of current interest. In fact, environmental parameters, such as relative humidity (RH), temperature, and pollutant agents, often fluctuate due to natural or anthropogenic climatic changes. This study focuses on evaluating analytical and statistical strategies to investigate the degradation processes of acrylic and styrene-acrylic paints after exposure to ozone (O₃) and RH. A first comparison of FTIR and Py-GC/MS results allowed to obtain qualitative information on the degradation products and the influence of the pigments on the paints’ stability. The combination of these results represents a significant potential for the use of data fusion methods. Specifically, the datasets obtained by FTIR and Py-GC/MS were combined using a low-level data fusion approach and subsequently processed by principal component analysis (PCA). It allowed to evaluate the different chemical impact of the variables for the characterization of unaged and aged samples, understanding which paint is more prone to ozone degradation, and which aging variables most compromise their stability. The advantage of this method consists in simultaneously evaluating all the FTIR and Py-GC/MS variables and describing common degradation patterns. From these combined results, specific information was obtained for further suitable conservation practices for modern and contemporary painted films.