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

Thermal environment driving specific microbial species to form the visible biofilms on the UNESCO World Heritage Dazu Rock Carvings

The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m3 and 23.4 °C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.

Biopatinas on Peperino Stone: Three Eco-Friendly Methods for Their Control and Multi-Technique Approach to Evaluate Their Efficacy

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.

Cast from the Past? Microbial Diversity of a Neolithic Stone Circle

We studied the microbial diversity colonizing limestone rock pools at a Neolithic Monument (Arbor Low, Derbyshire, England). Five pools were analyzed: four located at the megaliths of the stone circle and one pool placed at the megalith at the Gib Hill burial mound 300 m distant. Samples were taken from rock pool walls and sediments, and investigated through molecular metabarcoding. The microbiome consisted of 23 phyla of bacteria (831 OTUs), 4 phyla of archaea (19 OTUs), and 27 phyla of microbial eukarya (596 OTUs). For bacteria, there were statistically significant differences in wall versus sediment populations, but not between pools. For archaea and eukarya, significant differences were found only between pools. The most abundant bacterial phylum in walls was Cyanobacteriota, and Pseudomonadota in sediments. For archaea and microbial eukarya, the dominant phyla were Euryarcheota and Chlorophyta, respectively, in both wall and sediments. The distant pool (P5) showed a markedly different community structure in phyla and species, habitat discrimination, and CHN content. Species sorting and dispersal limitation are discussed as mechanisms structuring the microbiome assemblages and their spatial connectivity. The Arbor Low microbiome is composed of terrestrial representatives common in extreme environments. The high presence of Cyanobacteriota and Chlorophyta in the Arbor Low stones is troubling, as these microorganisms can induce mechanical disruption by penetrating the limestone matrix through endolithic/chasmoendolithic growth. Future research should focus on the metabolic traits of strains to ascertain their implication in bioweathering and/or biomineralization.

Metagenomic study of the microbiome and key geochemical potentials associated with architectural heritage sites: a case study of the Song Dynasty city wall in Shou County, China

Historical cultural heritage sites are valuable for all of mankind, as they reflect the material and spiritual wealth of by nations, countries, or specific groups during the development of human civilization. The types and functions of microorganisms that form biofilms on the surfaces of architectural heritage sites influence measures to preserve and protect these sites. These microorganisms contribute to the biocorrosion of architectural heritage structures through the cycling of chemical elements. The ancient city wall of Shou County is a famous architectural and cultural heritage site from China's Song Dynasty, and the protection and study of this site have substantial historical and cultural significance. In this study, we used metagenomics to study the microbial diversity and taxonomic composition of the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study covered three main topics: (1) examining the distribution of bacteria in the biofilm on the surfaces of the Song Dynasty city wall in Shou County; (2) predicting the influence of bacteria involved in the C, N, and S cycles on the corrosion of the city wall via functional gene analysis; and (3) discussing cultural heritage site protection measures for biocorrosion-related bacteria to investigate the impact of biocorrosion on the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study revealed that (1) the biofilm bacteria mainly belonged to Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes, which accounted for more than 70% of the total bacteria in the biofilms. The proportion of fungi in the microbial community of the well-preserved city wall was greater than that in the damaged city wall. The proportion of archaea was low-less than 1%. (2) According to the Shannon diversity index, the well-preserved portion of the ancient city wall had the highest diversity of bacteria, fungi, and archaea, and bacterial diversity on the good city wall was greater than that on the corroded city wall. (3) Bray-Curtis distances revealed that the genomes of the two good city walls were similar and that the genomes of the corroded city wall portions were similar. Researchers also detected human intestine-related bacteria in four locations on the city walls, with the proportion of these bacteria in the microbial community being greater on good city walls than on bad city walls. (4) KEGG functional analysis revealed that the energy metabolism and inorganic ion transport activities of the bacterial community on the corroded city wall were greater than those of the good city wall. (5) In the carbon cycle, the absence of active glycolysis, the ED pathway, and the TCA cycle played significant roles in the collapse of the east city wall. (6) The nitrogen cycling processes involved ammonia oxidation and nitrite reduction to nitrate. (7) In the sulfur cycle, researchers discovered a crucial differential functional gene, SoxY, which facilitates the conversion of thiosulfate to sulfate. This study suggests that, in the future, biological approaches can be used to help cultural heritage site protectors achieve targeted and precise protection of cultural relics through the use of microbial growth inhibition technology. The results of this study serve as a guide for the protection of cultural heritage sites in other parts of China and provide a useful supplement to research on the protection of world cultural heritage or architectural heritage sites.

Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China

Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.

Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation

SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.

Diversity and composition of microbial communities in Jinsha earthen site under different degree of deterioration

Earthen sites are the important cultural heritage that carriers of human civilization and contains abundant history information. Microorganisms are one of important factors causing the deterioration of cultural heritage. However, little attention has been paid to the role of biological factors on the deterioration of earthen sites at present. In this study, microbial communities of Jinsha earthen site soils with different deterioration types and degrees as well as related to environmental factors were analyzed. The results showed that the concentrations of Mg2+ and SO42- were higher in the severe deterioration degree soils than in the minor deterioration degree soils. The Chao1 richness and Shannon diversity indices of bacteria in different type deterioration were higher in the summer than in the winter; the Chao1 and Shannon indices of fungi were lower in the summer. The differences in bacterial and fungal communities were associated with differences in Na+, K+, Mg2+ and Ca2+ contents. Based on both the relative abundances in amplicon sequencing and isolated strains, the bacterial phyla Actinobacteria, Firmicutes and Proteobacteria, and the Ascomycota genera Aspergillus, Cladosporium and Penicillium were common in all soils. The OTUs enriched in the severe deterioration degree soils were mostly assigned to Actinobacteria and Proteobacteria, whereas the Firmicutes OTUs differentially abundant in the severe deterioration degree were all depleted. All bacterial isolates produced alkali, implying that the deterioration on Jinsha earthen site may be accelerated through alkali production. The fungal isolates included both alkali and acid producing strains. The fungi with strong ability to produce acid were mainly from the severe deterioration degree samples and were likely to contribute to the deterioration. Taken together, the interaction between soil microbial communities and environment may affect the soil deterioration, accelerate the deterioration process and threaten the long-term preservation of Jinsha earthen site.

Microbiome of seventh-century old Parsurameswara stone monument of India and role of desiccation-tolerant cyanobacterium Lyngbya corticicola on its biodeterioration

The Parsurameswara stone monument, built in the seventh century, is one of the oldest stone monuments in Odisha, India. Metagenomic analysis of the biological crust samples collected from the stone monument revealed 17 phyla in the microbiome, with Proteobacteria being the most dominant phylum, followed by cyanobacteria. Eight cyanobacteria were isolated. Lyngbya corticicola was the dominant cyanobacterium in all crust samples and could tolerate six months of desiccation in vitro. With six months of desiccation, chlorophyll-a decreased; however, carotenoid and cellular carbohydrate contents of this organism increased in the desiccated state. Resistance to desiccation, high carotenoid content, and effective trehalose biosynthesis in this cyanobacterium provide a distinct advantage over other microbiomes. Comparative metabolic profiles of the biological crust and L. corticicola show strongly corrosive organic acids such as dichloroacetic acid, which might be responsible for the biocorrosion of stone monuments.

Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China

Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.

Spatial and temporal changes in microclimate affect disease distribution in two ancient tombs of Southern Tang Dynasty

Two tombs of the Southern Tang Dynasty (Qinling Tomb and Shunling Tomb), the most important cultural heritages in China, were built for emperors 1000 years ago and decorated with murals and stone sculptures. After their excavation in the 1950s, it was found that drastic fluctuations in the environment within the tombs had caused multiple diseases, such as salt efflorescence, powdering, and biodeterioration, which led to irreversible damage to the murals. This research comprised long-term (yearly) environmental monitoring and short-term (monthly) investigation into the distribution of salt crystallization and microbial growth within the two tombs. The objective was to unveil the relationship between the temporal and spatial distributions of the mural diseases and environmental characteristics while proposing a promising environmental regulation strategy for relic conservation. The results showed a gradual reduction in temperature fluctuation from the entrance to the back chamber and a distinct vertical stratification in relative humidity. The relative humidity in the upper areas of the tombs reached 100% during summer, while it averaged around 40-50% in the lower areas during winter. Consequently, significant condensation was observed on the ceiling in summer, whereas salt crystallization occurred on the murals in the lower space in winter. The distribution of these diseases was influenced by the airflow exchange between the interior and exterior. Furthermore, the structural disparities between the two tombs contributed to higher relative humidity and greater microorganism coverage in the Shunling Tomb compared to the Qinling Tomb. From the abovementioned findings, we suggest that microclimate control is essential for mitigating mural deterioration and should be paid more attention in the future.

Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments

Epilithic biofilms colonising outdoor stone monuments can intensify the deterioration processes of the stone materials and pose great challenges to their protection. In this study, biodiversity and community structures of the epilithic biofilms colonising the surfaces of five outdoor stone dog sculptures were characterised by high-throughput sequencing. Although they are exposed to the same envrionment in a small yard, the analysis of their biofilm populations revealed high biodiversity and species richness as well as great differences in community compostions. Interestingly, populations responsible for pigment production (e.g., Pseudomonas, Deinococcus, Sphingomonas and Leptolyngbya) and for nitrogen (e.g., Pseudomonas, Bacillus, and Beijerinckia) and sulfur cycling (e.g., Acidiphilium) were the core common taxa in the epilithic biofilms, suggesting the potential biodeterioration processes. Furthermore, significant positive corrolections of metal elements rich in stone with biofilm communities showed that epilithic biofilms could take in minerals of stone. Importantly, geochemical properties of soluble ions (higher concentration of SO₄^2- than NO₃^-) and slightly acidic micro-environments on the surfaces suggest corrosion of biogenic sulfuric acids as a main mechanism of biodeterioration of the sculptures. Interestingly, relative abundacne of Acidiphilium showed a positive correlation with acidic micro-environments and SO₄^2- concentrations, implying they could be an indicator of sulfuric acid corrosion. Together, our findings support that micro-environments are inportant to community assembly of epilithic biofilms and the biodeterioration processes involved.

New frontiers review of some recent conservation techniques of organic and inorganic archaeological artefacts against microbial deterioration

The information on the advances and technology of some recent conservation methods (2020–2023) of organic and inorganic archaeological objects against microbial deterioration is recorded. An outline of comparative new protective methods for conserving plant-origin organic artefacts {Fibers (manuscripts, textile) and wood}, animal-origin organic artefacts (painting, parchment and mummies) and inorganic stone artefacts were investigated. The work not only contributes to the development of safe revolutionary ways for more efficient safe conservation of items of historical and cultural worth but also serves as a significant diagnostic signature for detecting the sorts of microbial identification and incidents in antiques. Biological technologies (environmentally friendly green biocides) are the most used recent, efficient and safe strategy acceptable as alternatives to stop microbial deterioration and prevent any potential interactions between the biological agent and the artefacts. Also, a synergistic effect of combining natural biocides with mechanical cleaning or chemical treatments was suggested. The recommended exploration techniques should be considered for future applications.

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.

Symbiotic microbiota and odor ensure mating in time for giant pandas

To achieve reproduction, male solitary mammals need to locate females using chemical communication with high levels of precision. In the case of giant pandas, the total estrus period of females was usually 15 days each year, however, successful mating activity is finished within 3 days from respective home range. The mating pattern of giant pandas, where multiple males compete for each female requires females employ efficient systems to communicate their estrus phases. To verifying whether the scent secretions of giant pandas changes by gender and estrus progression, the microbiota and compounds in 29 anogenital gland samples from 14 individuals during estrus were analyzed by 16S rRNA sequencing and GC-MS. We show that the microbiota communities covary by gender with 4 particular compounds of scent secretions. Among 597 genera, 34 were identified as biomarkers that could be used to distinguish between different estrus phases. By bacterial-compounds co-analysis, 3 fatty ester acids and squalene compounds covaried with the development of estrus in the bacterial communities of female giant pandas. This study helps clarify how a large, solitary mammal expresses accurate information to improve the likelihood of successful reproduction by changing the composition of microbiota and odor compounds of anogenital glands during estrus.

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.

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.