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.

Petroglyph sites exist all over the world. They are one of the earliest forms of mankind’s expression and a precursor to art. Despite their outstanding value, comprehensive research on conservation and preservation of rock art is minimal, especially as related to biodeterioration. For this reason, the main objective of this study was to explore the factors involved in the degradation of petroglyph sites in the Negev desert of Israel, with a focus on biodegradation processes. Through the use of culture-independent microbiological methods (metagenomics), we characterized the microbiomes of the samples, finding they were dominated by bacterial communities, in particular taxa of Actinobacteria and Cyanobacteria, with resistance to radiation and desiccation. By means of XRF and Raman spectroscopies, we defined the composition of the stone (calcite and quartz) and the dark crust (clay minerals with Mn and Fe oxides), unveiling the presence of carotenoids, indicative of biological colonization. Optical microscopy and SEM–EDX analyses on thin sections highlighted patterns of weathering, possibly connected to the presence of biodeteriorative microorganisms that leach the calcareous matrix from the bedrock and mobilize metal cations from the black varnish for metabolic processes, slowly weathering it.