Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.

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.

Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data.

Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as "microbial dark matter" (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of "unknown microorganisms" that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments-a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as "microbial dark matter sequences" (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results.

Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel.

Throughout the Negev Desert highlands, thousands of ancient petroglyphs sites are susceptible to deterioration processes that may result in the loss of this unique rock art. Therefore, the overarching goal of the current study was to characterize the composition, diversity and effects of microbial colonization of the rocks to find ways of protecting these unique treasures. The spatial organization of the microbial colonizers and their relationships with the lithic substrate were analysed using scanning electron microscopy. This approach revealed extensive epilithic and endolithic colonization and close microbial-mineral interactions. Shotgun sequencing analysis revealed various taxa from the archaea, bacteria and some eukaryotes. Metagenomic coding sequences (CDS) of these microbial lithobionts exhibited specific metabolic pathways involved in the rock elements' cycles and uptake processes. Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes. These damaging actions may contribute to the deterioration of this extraordinary rock art and thus threaten this valuable heritage. Shotgun metagenomic sequencing, in conjunction with the in situ scanning electron microscopy study, can thus be considered an effective strategy to understand the complexity of the weathering processes occurring at petroglyph sites and other cultural heritage assets.

Silica-stabilized gold island films for transmission localized surface plasmon sensing.

Ultrathin gold films prepared by evaporation of sub-percolation layers (typically up to 10 nm nominal thickness) onto transparent substrates form arrays of well-defined metal islands. Such films display a characteristic surface plasmon (SP) absorption band, conveniently measured by transmission spectroscopy. The SP band intensity and position are sensitive to the film morphology (island shape and inter-island separation) and the effective dielectric constant of the surrounding medium. The latter has been exploited for chemical and biological sensing in the transmission localized surface plasmon resonance (T-LSPR) mode. A major concern in the development of T-LSPR sensors based on Au island films is instability, manifested as change in the SP absorbance following immersion in organic solvents and aqueous solutions. The latter may present a problem in the use of Au island-based transducers for biological sensing, usually carried out in aqueous media. Here, we describe a facile method for stabilizing Au island films while maintaining a high sensitivity of the SP absorbance to analyte binding. Stabilization is achieved by coating the Au islands with an ultrathin silica layer, ca. 1.5 nm thick, deposited by a sol-gel procedure on an intermediate mercaptosilane monolayer. The silica coating is prepared using a modified literature procedure, where a change in the reaction conditions from room temperature to 90 degrees C shortened the deposition time from days to hours. The system was characterized by UV-vis spectroscopy, ellipsometry, XPS, HRSEM, AFM, and cyclic voltammetry. The ultrathin silica coating stabilizes the optical properties of the Au island films toward immersion in water, phosphate buffer saline (PBS), and various organic solvents, thus providing proper conditions where the optical response is sensitive only to changes in the effective dielectric constant of the immediate environment. The silica layer is thin enough to afford high T-LSPR sensitivity, while the hydroxyl groups on its surface enable chemical modification for binding of receptor molecules. The use of silica-encapsulated Au island films as a stable and effective platform for T-LSPR sensing is demonstrated.