Elucidating the ecological networks in stone-dwelling microbiomes

Metagenome-resolved functional traits of Rubrobacter species implicated in rosy discoloration of ancient frescoes in two Georgian Cathedrals

Pink biofilm formation on stone monuments and mural paintings poses serious harm to cultural heritage preservation. Pink biofilms are globally widespread and recalcitrant to eradication, often causing recurrences after restoration. Yet, the ecological drivers of pink biofilm formation and the metabolic functions sustaining the growth of pigment-producing biodeteriogens remain unclear. In this study, a combined approach integrating physicochemical investigations, scanning electron microscopy, 16S rRNA sequence-based analysis of the prokaryotic community, metagenomic deep sequencing, and metabolic profiling, was applied to determine the etiology of rosy discoloration of ancient frescoes in the Gelati and the Martvili Cathedrals (Georgia). Martvili samples showed greater diversity than Gelati samples, though Actinomycetota predominated in both samples. Rubrobacter-related sequences were detected in all sampling sites, showing an overwhelming abundance in Gelati samples. Reconstruction of metagenome-assembled genomes (MAGs) and phylogenetic analyses highlighted significant intra-genus diversity for Rubrobacter-related sequences, most of which could not be assigned to any formally described Rubrobacter species. Metabolic profiling of the Gelati metagenomes suggests that carbon-fixing autotrophic bacteria and proteinaceous substances in the plaster could contribute to sustaining the chemoorganotrophic members of the community. Complete pathways for β-carotene and bacterioruberin synthesis were identified in Rubrobacter MAGs, consistent with the Raman spectroscopy-based detection of these pigments in fresco samples. Gene clusters for the synthesis of secondary metabolites endowed with antibiotic activity were predicted from the annotation of Rubrobacter MAGs, along with genes conferring resistance to several antimicrobials and biocides. In conclusion, genome-resolved metagenomics provided robust evidence of a causal relationship between contamination by Rubrobacter-related carotenoid-producing bacteria and the rosy discoloration of Georgian frescoes, with relevant implications for rational biodeteriogen-targeted restoration strategies.

Lithic bacterial communities: ecological aspects focusing on Tintenstrich communities

Tintenstrich communities (TCs) mainly comprise Cyanobacteria developing on rock substrates and forming physical structures that are strictly connected to the rock itself. Endolithic and epilithic bacterial communities are important because they contribute to nutrient release within run-off waters flowing on the rock surface. Despite TCs being ubiquitous, little information about their ecology and main characteristics is available. In this study, we characterized the bacterial communities of rock surfaces of TCs in Switzerland through Illumina sequencing. We investigated their bacterial community composition on two substrate types (siliceous rocks [SRs] and carbonate rocks [CRs]) through multivariate models. Our results show that Cyanobacteria and Proteobacteria are the predominant phyla in this environment. Bacterial α-diversity was higher on CRs than on SRs, and the β-diversity of SRs varied with changes in rock surface structure. In this study, we provide novel insights into the bacterial community composition of TCs, their differences from other lithic communities, and the effects of the rock substrate and structure.

Metagenomic insight into the pathogenic-related characteristics and resistome profiles within microbiome residing on the Angkor sandstone monuments in Cambodia

To reveal the characteristics of indigenous microbiome including the pathogenic-related ones on Angkor monuments in Cambodia and the distribution pattern of resistome at different locations, several sites, namely Angkor Wat, Bayon of Angkor Thom, and Prasat Preah Vihear with different exposure levels to tourists were selected to conduct the metagenomic analysis in this study. The general characteristics of the microbiome on these monuments were revealed, and the association between the environmental geo-ecological feature and the indigenous microbiome was delineated. The most common microbial groups included 6 phyla, namely Acidobacteria, Actinobacteria, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia on the monuments, but Firmicutes and Chlamydiae were the most dominant phyla found in bats droppings. The taxonomic family of Chitinophagaceae could serve as a signature microbial group for Preah Vihear, the less visited site. More importantly, the pathogenic-related characteristics of the microbiome residing on Angkor monuments were uncovered. A set of specific antibiotic resistance genes (ARGs) with cross-niches dispersal capacity (between the environmental microbiome and the microbiome within warm blood fauna) was identified to be high by the source tracking analysis based on ARGs profile varies in this study. Among the 10 ARG-types detected in this study, 6 of them are confined to resistance mechanism of antibiotic efflux-pump. The findings of this study provide new a new direction on public health management and implication globally at archaeological sites for tourism.

Pretty in pink? Complementary strategies for analysing pink biofilms on historical buildings

Salt-weathering is a deterioration mechanism affecting building materials that results from repetitive cycles of salt crystallisation-dissolution in the porous mineral network under changing environmental conditions, causing damage to surfaces. However, an additional biodeterioration phenomenon frequently associated with salt efflorescence is the appearance of coloured biofilms, comprising halotolerant/halophilic microorganisms, containing carotenoid pigments that cause pinkish patinas. In this work, two Austrian historical salt-weathered buildings showing pink biofilms, the St. Virgil's Chapel and the Charterhouse Mauerbach, were investigated. Substrate chemistry (salt concentration/composition) was analysed by ion chromatography and X-ray diffraction to correlate these parameters with the associated microorganisms. Microbiomes were analysed by sequencing full-length 16S rRNA amplicons using Nanopore technology. Data demonstrates that microbiomes are not only influenced by salt concentration, but also by its chemical composition. The chapel showed a high overall halite (NaCl) concentration, but the factor influencing the microbiome was the presence/absence of K+. The K+ areas showed a dominance of Aliifodinibius and Salinisphaera species, capable of tolerating high salt concentrations through the "salt-in" strategy by transporting K+ into cells. Conversely, areas without K+ showed a community shift towards Halomonas species, which favour the synthesis of compatible solutes for salt tolerance. In the charterhouse, the main salts were sulphates. In areas with low concentrations, Rubrobacter species dominated, while in areas with high concentrations, Haloechinothrix species did. Among archaea, Haloccoccus species were dominant in all samples, except at high sulphate concentrations, where Halalkalicoccus prevailed. Finally, the biological pigments visible in both buildings were analysed by Raman spectroscopy, showing the same spectra in all areas investigated, regardless of the building and the microbiomes, demonstrating the presence of carotenoids in the pink biofilms. Comprehensive information on the factors affecting the microbiome associated with salt-weathered buildings should provide the basis for selecting the most appropriate desalination treatment to remove both salt efflorescence and associated biofilms.

Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments

The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.

Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia

A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1  ω8c and C18 : 1  ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.

Diversity and Composition of Culturable Microorganisms and Their Biodeterioration Potentials in the Sandstone of Beishiku Temple, China

Microbial colonization on stone monuments leads to subsequent biodeterioration; determining the microbe diversity, compositions, and metabolic capacities is essential for understanding biodeterioration mechanisms and undertaking heritage management. Here, samples of epilithic biofilm and naturally weathered and exfoliated sandstone particles from different locations at the Beishiku Temple were collected to investigate bacterial and fungal community diversity and structure using a culture-based method. The biodeterioration potential of isolated fungal strains was analyzed in terms of pigmentation, calcite dissolution, organic acids, biomineralization ability, and biocide susceptibility. The results showed that the diversities and communities of bacteria and fungi differed for the different sample types from different locations. The population of culturable microorganisms in biofilm samples was more abundant than that present in the samples exposed to natural weathering. The environmental temperature, relative humidity, and pH were closely related to the variation in and distribution of microbial communities. Fungal biodeterioration tests showed that isolated strains four and five were pigment producers and capable of dissolving carbonates, respectively. Their biomineralization through the precipitation of calcium oxalate and calcite carbonate could be potentially applied as a biotechnology for stone heritage consolidation and the mitigation of weathering for monuments. This study adds to our understanding of culturable microbial communities and the bioprotection potential of fungal biomineralization.

Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins

Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.

High-Quality Genome Sequences of Six Actinobacterial Strains Isolated from Granite, Granodiorite, and Tourmaline Rock Surfaces Sampled from Tamil Nadu, India, and New England, United States

Here, we announce four contiguous and two high-quality draft genome sequences of six actinobacterial strains (Blastococcus, Georgenia, Nocardioides, Allobranchiibius, Yimella, and Williamsia) that were isolated from rock samples obtained from Indian historical ruins and colonial building stones in New England, United States. These new sequences expand the genome datasets recovered from stone-dwelling microbes and will allow the prediction of their potential role in the stone microbiome.

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.

Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times

Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.

Draft Genomes Sequences of 11 Geodermatophilaceae Strains Isolated from Building Stones from New England and Indian Stone Ruins found at historic sites in Tamil Nadu, India

Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria including Geodermatphilaceae. A culture-dependent approach was performed as a companion study with this culture-independent metagenomic analysis of these stone samples and resulted in the isolation of eleven Geodermatphilaceae strains (2 Geodermatophilus and 9 Blastococcus strains). The genomes of the 11 Geodermatphilaceae strains were sequenced and analyzed. The genomes for the two Geodermatophilus isolates, DF1-2 and TF2-6, were 4.45 and 4.75 Mb, respectively, while the Blastococcus genomes ranged in size from 3.98 to 5.48 Mb. Phylogenetic analysis, digital DNA:DNA hybridization (dDDH), and comparisons of the average nucleotide identities (ANI) suggest the isolates represent novel Geodermatophilus and Blastococcus species. Functional analysis of the Geodermatphilaceae genomes provides insight on the stone microbiome niche.

Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes

Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.

Community assembly, potential functions and interactions between fungi and microalgae associated with biodeterioration of sandstone at the Beishiku Temple in Northwest China

Fungi, cyanobacteria and algae are specific microbial groups associated with the deterioration and safety of stone monuments. In this study, high-throughput sequencing analysis was used to investigate the diversity, distributions, ecological functions, and interaction patterns of both the fungal and microalgal (including cyanobacteria and algae) communities on sandstone in the Beishiku Temple, located on the ancient Silk Road. The results showed that the core phyla of fungi were affiliated with unclassified Lecanoromycetes, Engyodontium, Knufia, Epicoccum, Endocarpon, and Cladosporium of Ascomycota whereas the phyla of microalgae were dominated by prokaryotic Cyanobacteria and eukaryotic Chlorophyta. The environmental factors of temperature, relative humidity, and light intensity were monitored simultaneously. The structure of the microbial communities was much more strongly shaped by soluble Cl^-, Na⁺, NO₃^- ions than by the light intensity, moisture content or temperature, especially for the weathered sandstone located outside the caves. The co-occurrence network analysis suggested that a more stable community structure was evident outside the caves than inside. The stronger positive connections and coexistence patterns that were detected indicate a strong adaptability of fungi and microalgae to the distinct oligotrophic microhabitats on sandstone. The metacommunity co-occurrence network exhibited the ecological predominance of fungi, and most of the functional fungi in the biofilms outside the caves belonged to the Lichenized group, based on the FUNGuild prediction. These findings highlight the ecology and functions of stone-inhabiting microorganisms to further advance the current understanding and knowledge of sandstone biodeterioration for protection and management.

Enhancing fluoroglucocorticoid defluorination using defluorinated functional strain Acinetobacter. pittii C3 via humic acid-mediated biotransformation

Defluorination is a key factor in reducing biologically accumulated carcinogenic and teratogenic toxicity of fluoroglucocorticoids (FGCs). To enhance defluorination efficiency, a highly efficient defluorination-degrading strain Acinetobacter. pittii C3 was isolated, and the promotion mechanism through humic acid (HA)-mediated biotransformation was investigated. Optimal biodegradation conditions for Acinetobacter sp. pittii C3 were pH of 7.0, temperature of 25 ℃, and HA content of 5.5 mg/L, according to response surface methodology analysis. The attenuation rate constant and maximum defluorination percentage of triamcinolone acetonide (TA) in HA-mediated biotransformation system (HA-C3) were 3.99 × 10^-2 and 96%, respectively, which were 2.22 and 1.24 times higher than those in the unitary C3 biodegradation system (U-C3), respectively. The major defluorination pathways included elimination, hydrolysis, and hydrogenation, with contributions of 24.5%, 32.4%, and 43.1%, respectively. The bio-reductive hydrodefluorination rate was enhanced by 1.89 times that of HA-mediated, while the other two defluorination pathways exhibited insignificant changes. HA, as the congeries of negatively charged microbes and hydrophobic TA, accelerates the electron transfer rate between Acinetobacter. pittii C3 and TA through the quinone groups. Furthermore, the mutual conversion between the functional groups of hydroxyl oxidation and ketone reduction of HA provided electron donors for TA reductive defluorination and hydrogenation and electron acceptors for TA oxidation. This study provides an effective strategy for FGC-enhanced detoxification using natural HA.

Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities

Airborne microbiome alterations, an emerging global health concern, have been linked to anthropogenic activities in numerous studies. However, these studies have not reached a consensus. To reveal general trends, we conducted a meta-analysis using 3226 air samples from 42 studies, including 29 samples of our own. We found that samples in anthropogenic activity-related categories showed increased microbial diversity, increased relative abundance of pathogens, increased co-occurrence network complexity, and decreased positive edge proportions in the network compared with the natural environment category. Most of the above conclusions were confirmed using the samples we collected in a particular period with restricted anthropogenic activities. Additionally, unlike most previous studies, we used 15 human-production process factors to quantitatively describe anthropogenic activities. We found that microbial richness was positively correlated with fine particulate matter concentration, NH₃ emissions, and agricultural land proportion and negatively correlated with the gross domestic product per capita. Airborne pathogens showed preferences for different factors, indicating potential health implications. SourceTracker analysis showed that the human body surface was a more likely source of airborne pathogens than other environments. Our results advance the understanding of relationships between anthropogenic activities and airborne bacteria and highlight the role of airborne pathogens in public health.

A Multi-Analytical Approach to Infer Mineral–Microbial Interactions Applied to Petroglyph Sites in the Negev Desert of Israel

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.

A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces

There is growing concern surrounding the aesthetic and physical effects of microbial biofilms on heritage buildings and monuments. Carboniferous stones, such as limestone and marble, are soluble in weak acid solutions and therefore particularly vulnerable to biocorrosion. This paper aims to determine the differences and commonalities between the microbiome of physically damaged and undamaged Lincolnshire limestone, an area of research which has not been previously studied. A lack of information about the core microbiome has resulted in conflicting claims in the literature regarding the biodeteriorative potential of many microorganisms. To address this, we used metagenomics alongside traditional microbiological techniques to produce an in-depth analysis of differences between the bacterial microbiomes found on deteriorated and undamaged external limestone surfaces. We demonstrate there is a core microbiome on Lincolnshire limestone present on both damaged and undamaged surfaces. In addition to the core microbiome, significant differences were found between species isolated from undamaged compared to damaged surfaces. Isolated species were characterised for biofilm formation and biodeteriorative processes, resulting in the association of species with biodeterioration that had not been previously described. Additionally, we have identified a previously undescribed method of biofilm-associated biomechanical damage. This research adds significant new understanding to the field, aiding decision making in conservation of stone surfaces.

Draft Genome Sequences of 6 Actinobacterial Strains Isolated from Rock Surfaces Obtained from Indian Stone Ruins in Tamil Nadu, India, and Rocks from New England, United States

Here, we report the draft genome sequences obtained for 6 actinobacterial strains isolated from stone surfaces acquired from New England and Indian ruins. These strains were sequenced to determine their potential functional roles in the stone microbiome. The strains belong to the genera Allobranchiibius, Agrococcus, Dermococcus, Leifsonia, and Mycobacterium.

From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China

Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.

Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions

The surfaces of historical stone monuments are visibly covered with a layer of colonizing microorganisms and their degradation products. In this study, a metadata analysis was conducted using the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential and functionality of the stone microbiome on important world cultural heritage sites under four different climatic conditions. The retrieved stone microbial community composition in these metagenomes shows a clear association between climate types of the historical monuments and the diversity and taxonomic composition of the stone microbiomes. Shannon diversity values showed that microbial communities on stone monuments exposed to dry climate were more diverse than those under humid ones. In particular, functions associated with photosynthesis and UV resistance were identified from geographical locations under different climate types. The distribution of key microbial determinants responsible for stone deterioration was linked to survival under extreme environmental conditions and biochemical capabilities and reactions. Among them, biochemical reactions of the microbial nitrogen and sulfur cycles were most predominant. These stone-dwelling microbiomes on historical stone monuments were highly diverse and self-sustaining driven by energy metabolism and biomass accumulation. And metabolic products of the internal geomicrobiological nitrogen cycling on these ancient monuments play a unique role in the biodeterioration of stone monuments. These results highlight the significance of identifying the essential microbial biochemical reactions to advance the understanding of stone biodeterioration for protection management.

Improvement of Medicago sativa Crops Productivity by the Co-inoculation of Sinorhizobium meliloti-Actinobacteria Under Salt Stress

Biotic and abiotic stresses are severely limiting plant production and productivity. Of notable importance is salt stress that not only limits plant growth and survival, but affects the soil fertility and threatens agricultural ecosystems sustainability. The problem is exacerbated in fragile arid and semi-arid areas where high evaporation, low precipitation and the use of salty water for irrigation is accelerating soil salinization. Legumes, considered very nutritious foods for people and providing essential nutrients for ecosystems are a fundamental element of sustainable agriculture. They can restore soil health by their ability to fix nitrogen in a symbiotic interaction with the rhizobia of the soil. However, salt stress is severely limiting productivity and nitrogen fixation ability in legumes. Plant growth-promoting rhizobacteria (PGPR) and mainly actinobacteria promote plant growth by producing phytohormones, siderophores, antibiotics and antifungal compounds, solubilizing phosphate and providing antagonism to phytopathogenic microorganisms. In addition, actinobacteria have beneficial effects on nodulation and growth of legumes. In this study, actinobacteria isolated from different niches and having PGP activities were used in co-inoculation experiments with rhizobia in Medicago sativa plants rhizosphere submitted to salt stress. The results indicate that drought- and salinity-tolerant Actinobacteria with multiple PGP traits can potentially increase alfalfa growth under saline conditions, in the presence or absence of symbiotic rhizobial bacteria. Actinobacteria discovered in this study can, therefore, be suitable biofertilizers in the formulation of agricultural products improving plant development, health and productivity in saline soils, a necessary alternative for modern agriculture and sustainable development.

Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India

Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.

The Bad and the Good-Microorganisms in Cultural Heritage Environments-An Update on Biodeterioration and Biotreatment Approaches

Cultural heritage objects constitute a very diverse environment, inhabited by various bacteria and fungi. The impact of these microorganisms on the degradation of artworks is undeniable, but at the same time, some of them may be applied for the efficient biotreatment of cultural heritage assets. Interventions with microorganisms have been proven to be useful in restoration of artworks, when classical chemical and mechanical methods fail or produce poor or short-term effects. The path to understanding the impact of microbes on historical objects relies mostly on multidisciplinary approaches, combining novel meta-omic technologies with classical cultivation experiments, and physico-chemical characterization of artworks. In particular, the development of metabolomic- and metatranscriptomic-based analyses associated with metagenomic studies may significantly increase our understanding of the microbial processes occurring on different materials and under various environmental conditions. Moreover, the progress in environmental microbiology and biotechnology may enable more effective application of microorganisms in the biotreatment of historical objects, creating an alternative to highly invasive chemical and mechanical methods.

Influence of Environment on Microbial Colonization of Historic Stone Buildings with Emphasis on Cyanobacteria

Microbial cells that produce biofilms, or patinas, on historic buildings are affected by climatic changes, mainly temperature, rainfall and air pollution, all of which will alter over future decades. This review considers the colonization of stone buildings by microorganisms and the effects that the resultant biofilms have on the degradation of the structure. Conservation scientists require a knowledge of the potential effects of microorganisms, and the subsequent growth of higher organisms such as vascular plants, in order to formulate effective control strategies. The vulnerability of various structural materials (“bioreceptivity”) and the ways in which the environmental factors of temperature, precipitation, wind-driven rain and air pollution influence microbial colonization are discussed. The photosynthetic microorganisms, algae and cyanobacteria, are acknowledged to be the primary colonizers of stone surfaces and many cyanobacterial species are able to survive climate extremes; hence special attention is paid to this group of organisms. Since cyanobacteria require only light and water to grow, can live endolithically and are able to survive most types of stress, they may become even more important as agents of stone cultural property degradation in the future.

Extremophilic microbial communities on photovoltaic panel surfaces: a two-year study

Solar panel surfaces can be colonized by microorganisms adapted to desiccation, temperature fluctuations and solar radiation. Although the taxonomic and functional composition of these communities has been studied, the microbial colonization process remains unclear. In the present work, we have monitored this microbial colonization process during 24 months by performing weekly measurements of the photovoltaic efficiency, carrying out 16S rRNA gene high-throughput sequencing, and studying the effect of antimicrobial compounds on the composition of the microbial biocenosis. This is the first time a long-term study of the colonization process of solar panels has been performed, and our results reveal that species richness and biodiversity exhibit seasonal fluctuations and that there is a trend towards an increase or decrease of specialist (solar panel-adapted) and generalist taxa, respectively. On the former, extremophilic bacterial genera Deinococcus, Hymenobacter and Roseomonas and fungal Neocatenulostroma, Symmetrospora and Sporobolomyces tended to dominate the biocenosis; whereas Lactobacillus sp or Stemphyllium exhibited a decreasing trend. This profile was deeply altered by washing the panels with chemical agents (Virkon), but this did not lead to an increase of the solar panels efficiency. Our results show that solar panels are extreme environments that force the selection of a particular microbial community.