A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues

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.

Microbial fingerprints reveal interaction between museum objects, curators, and visitors

Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.

Culturable and unculturable potential heterotrophic microbiological threats to the oldest pyramids of the Memphis necropolis, Egypt

A large percentage of the world's tangible cultural heritage is made from stone; thus, it deteriorates due to physical, chemical, and/or biological factors. The current study explored the microbial community inhabiting two prehistoric sites with high cultural value in the Memphis necropolis of Egypt (Djoser and Lahun Pyramids) using amplicon-based metabarcoding and culture-dependent isolation methods. Samples were examined by epifluorescent microscopy for biological signs before environmental DNA extraction and in vitro cultivation. The metabarcoding analysis identified 644 bacterial species (452 genera) using the 16S rRNA and 204 fungal species (146 genera) using ITS. In comparison with the isolation approach, an additional 28 bacterial species (13 genera) and 34 fungal species (20 genera) were identified. A total of 19 bacterial and 16 fungal species were exclusively culture-dependent, while 92 bacterial and 122 fungal species were culture-independent. The most abundant stone-inhabiting bacteria in the current study were Blastococcus aggregatus, Blastococcus saxobsidens, and Blastococcus sp., among others. The most abundant rock-inhabiting fungi were Knufia karalitana and Pseudotaeniolina globosa, besides abundant unknown Sporormiaceae species. Based on previous reports, microorganisms associated with biodeterioration were detected on color-altered sites at both pyramids. These microorganisms are potentially dangerous as physical and chemical deterioration factors and require proper conservation plans from a microbiological perspective.

Insight on bacteria communities in outdoor bronze and marble artefacts in a changing environment

Epilithic bacteria play a fundamental role in the conservation of cultural heritage (CH) materials. On stones, bacterial communities cause both degradation and bioprotection actions. Bronze biocorrosion in non-burial conditions is rarely studied. Only few studies have examined the relationship between bacteria communities and the chemical composition of patinas (surface degradation layers). A better comprehension of bacterial communities growing on our CH is fundamental not only to understand the related decay mechanisms but also to foresee possible shifts in their composition due to climate change. The present study aims at (1) characterizing bacterial communities on bronze and marble statues; (2) evaluating the differences in bacterial communities' composition and abundance occurring between different patina types on different statues; and (3) providing indications about a representative bacterial community which can be used in laboratory tests to better understand their influence on artefact decay. Chemical and biological characterization of different patinas were carried out by sampling bronze and marble statues in Bologna and Ravenna (Italy), using EDS/Raman spectroscopy and MinION-based 16SrRNA sequencing. Significant statistical differences were found in bacterial composition between marble and bronze statues, and among marble patinas in different statues and in the same statue. Marble surfaces showed high microbial diversity and were characterized mainly by Cyanobacteria, Proteobacteria and Deinococcus-Thermus. Bronze patinas showed low taxa diversity and were dominated by copper-resistant Proteobacteria. The copper biocidal effect is evident in greenish marble areas affected by the leaching of copper salts, where the bacterial community is absent. Here, Ca and Cu oxalates are present because of the biological reaction of living organisms to Cu ions, leading to metabolic product secretions, such as oxalic acid. Therefore, a better knowledge on the interaction between bacteria communities and patinas has been achieved.

Biocontamination and diversity of epilithic bacteria and fungi colonising outdoor stone and mortar sculptures

Microbial communities colonising outdoor sculptures form intricate and dynamic ecosystems, which can accelerate the deterioration processes of the artworks and pose challenges to their conservation. In this study, the bacterial and fungal communities colonising the surfaces of five contemporary outdoor sculptures were characterised by high-throughput sequencing. The sculptures, made of marble, granite, Ançã limestone and mortar, are in urban parks and squares in the district of Porto, Portugal. The analysis of the microbial populations revealed great taxonomic diversity and species richness, including in well-preserved sculptures showing few visible traces of contamination. Proteobacteria, namely the genera Pseudomonas and Sphingomonas, were the core taxa common to all the sculptures, while Massilia and Aureobasidium were dominant only in granite. An abundance of pigment-producing microorganisms, such as Deinococcus, Methylobacterium, Rhodotorula and Sporobolomyces, was also found in granite. These are relevant taxonomic groups that can negatively impact stone and mortar artworks. The study was complemented with colourimetric analyses and bioluminescence assays to measure the adenosine triphosphate (ATP) content of samples collected from specific contaminated areas of the sculptures. The characterisation of the microbiomes of sculptures can provide further knowledge on the deterioration risks of this type of artwork in the region and help outline future targeted conservation strategies. KEY POINTS: • Rich and abundant microbiomes expose sculptures' vulnerability to deterioration. • Well-preserved sculptures are at risk of deterioration by pigment-producing taxa. • ATP and colourimetry quickly identified the most relevant contaminated areas.

Benefits of applying organic amendments from recycled wastes for fungal community growth in restored soils of a limestone quarry in a semiarid environment

Applying organic amendments to recover physical, chemical, and biological qualities of soil may enable recovery of soils degraded by mining in semiarid climates. This study's aim was to investigate the development and changes in the composition of fungal communities in restored soils with five different types of organic amendments (two types of vegetable compost and sewage sludge compost, and a mixture of both) compared with unamended soils and surrounding natural soils and to examine the relationships between the fungal taxa, the new physico-chemical and biological soil properties of technosoils after 18 months of restoration, and natural soils. Restoration improved soil quality and fungal diversity, placing these soils in an intermediate position between unrestored soils (with no fungi present) and undisturbed reference soils, which were the most fungal diverse. Sewage-treated soils and their mixtures showed high nitrogen and carbohydrate content as well as high basal respiration and fatty acid content, suggesting that they provided readily biodegradable organic matter. In contrast, greenhouse compost-treated soils showed high total organic carbon and polyphenol content, whereas garden compost-treated soils showed intermediate values. The biological soil properties of both composts showed were similar to those of the reference soils, suggesting that composts contained more resilient organic matter. Organic amendments of dissimilar origin caused significantly different fungal soil communities at the genus level among the restored soils. Results indicated that soil pH, electrical conductivity, total nitrogen content, soil basal respiration, fungi/bacteria-PLFA ratio, and dehydrogenase and β-glucosidase activities, together with Pearson's correlations, revealed that these properties and nutrient content (total organic carbon, C/N ratio, carbohydrates, and polyphenols) influenced 40 soil fungal taxa. Therefore, the organic amendments led to changes in soil properties that favoured plant cover by promoting the soil fungal community growth beneficial to the carbon cycle and symbiotic with plants.

MinION technology for microbiome sequencing applications for the conservation of cultural heritage

The MinION single-molecule sequencing system has been attracting the attention of the community of microbiologists involved in the conservation of cultural heritage. The use of MinION for the conservation of cultural heritage is extremely recent, but surprisingly the only few applications available have been exploring many different substrates: stone, textiles, paintings and wax. The use of MinION sequencing is mainly used to address the metataxonomy (with special emphasis on non-cultivable microorganisms) with the effort to identify species involved in the degradation of the substrates. In this review, we show the current applications available on different artworks, showing how this technology can be a useful tool for microbiologists and conservators also in light of its low cost and the easy chemistry.

The Microbiome of Leonardo da Vinci's Drawings: A Bio-Archive of Their History

Seven emblematic Leonardo da Vinci’s drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic documentation and to infer the nature of the micro-objects removed from the surface of the drawings. The Nanopore generated microbiomes can be used as a “bio-archive” of the drawings, offering a kind of fingerprint for current and future biological comparisons. This information might help to create a biological catalog of the drawings (cataloging), a microbiome-fingerprint for each single analyzed drawing, as a reference dataset for future studies (monitoring) and last but not least a bio-archive of the history of each single object (added value). Results showed a relatively high contamination with human DNA and a surprising dominance of bacteria over fungi. However, it was possible to identify typical bacteria of the human microbiome, which are mere contaminants introduced by handling of the drawings as well as other microorganisms that seem to have been introduced through vectors, such as insects and their droppings, visible through the SEM analyses. All drawings showed very specific bio-archives, but a core microbiome of bacteria and fungi that are repeatedly found in this type of material as true degraders were identified, such as members of the phyla Proteobacteria, Actinobacteria, and Firmicutes among bacteria, and fungi belonging to the classes Sordariomycetes and Eurotiomycetes. In addition, some similarities were observed that could be influenced by their geographical location (Rome or Turin), indicating the influence of this factor and denoting the importance of environmental and storage conditions on the specific microbiomes.

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value

This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology. In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.