Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study

Autofluorescence for the Visualization of Microorganisms in Biodeteriorated Materials in the Context of Cultural Heritage

Microorganisms, including fungi, bacteria, cyanobacteria, and algae, frequently colonize the surfaces of cultural heritage materials. These biological agents can cause biodeterioration through various mechanisms, resulting in aesthetic alteration, physical disruption, or compromise of mechanical integrity. To assess the presence and diversity of microorganisms, a combination of microscopy techniques is commonly used in conjunction with results from both culture-dependent and culture-independent methods. However, microbial populations are often underestimated. To address this issue, microorganisms can be detected by their intrinsic fluorescence, which can be observed via fluorescence microscopy. This approach facilitates the mapping of the spatial arrangement of microorganisms and the understanding of colonization patterns, thereby complementing established imaging techniques and providing insight into the interactions of microbial communities with the substrate. Given the limited research in this area, we examine the potential of microorganism autofluorescence as a molecular tool for investigating biodeterioration in artistic and architectural heritage, with a particular focus on paper and stone materials. Identifying and understanding the diverse microbiota that may be present is crucial for developing tailored and effective preventive measures and conservation treatments, as some of the species discovered may pose significant risks to both artifacts and human health.

Fungal Biodeterioration Risk in Monastic Libraries without Climate Control

Fungi have always posed an unquestionable threat to heritage collections worldwide. Now, in a future of climate change, biological risk factors may have to be considered even more than before. Models and simulations to assess possible impacts a changing outdoor climate will have on indoor environments and, in turn, on biodeterioration are still underdeveloped and require a more substantial data basis. This study aimed at filling some of these knowledge gaps through a broad-based approach combining microclimatic and microbiological monitoring in four historic libraries in Austria with an uncontrolled indoor climate: Altenburg Abbey, Melk Abbey, Klosterneuburg Monastery and the Capuchin Monastery in Vienna. Data were generated from thermohygrometric sensors, cultivation-dependent air- and surface sampling and further surface dust sampling for cultivation-independent analyses. Results gave insights on the status quo of microbiological loads in the libraries and outdoor-indoor relationships. Influences of the geographic location and room-use on corresponding indoor fungal profiles were identified. Lower fungal diversities were found at the most rural site with the strongest climatic fluctuations and extreme values than in the most urban, sheltered library with a very stable climate. Further, the humidity-stabilizing potential of large collections of hygroscopic materials, such as books, was also examined. Implications for a sustainable approach to prevent future biodeterioration are discussed, supporting the long-term preservation of these valuable historic collections.

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.

Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts

Historical paper documents are susceptible to complex degradation processes, including biodeterioration, which can progressively compromise their aesthetic and structural integrity. This study analyses seventeenth century handwritten historical letters stored at the Correr Museum Library in Venice, Italy, exhibiting pronounced signs of biodeterioration. The techniques used encompassed traditional colony isolation on agar plates and proteomics analyses, employing nanoscale liquid chromatography coupled with high-resolution mass spectrometry (nano-LC-MS). Fluorescence microscopy was used for the first time in the historical paper biodeterioration context to supplement the conventional stereoscopic, optical, and scanning electron microscopic imaging techniques. This method enables the visualisation of microorganisms beyond and beneath the paper's surface through their natural intrinsic autofluorescence in a non-invasive and non-destructive way. The results demonstrate a diverse, complex, and abundant microbiota composed of coexisting fungal and bacterial species (Ascomycota, Mucoromycota, Basidiomycota, Proteobacteria, and Actinobacteria), along with mite carcasses, insects, parasites, and possibly protists. Furthermore, this study reveals certain species that were not previously documented in the biodeterioration of historical paper, including human pathogens, such as Histoplasma capsulatum, Brucella, Candida albicans, and species of Aspergillus (A. flavus, A. fumigatus, A. oryzae, A. terreus, A. niger) known to cause infections or produce mycotoxins, posing substantial risk to both artefacts and humans.

Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts

This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.

Colored stains: Microbial survey of cellulose-based and lignin rich papers

During the centuries diverse types of paper were produced and were characterized by a different ratio of natural macromolecules, mainly lignin and cellulose. Handmade paper has a higher content of cellulose respect to the early machine-made paper, where the lignin is the other important component. Microorganisms are able to colonize and deteriorate both types of papers. They can release on their surfaces pigments and colorants which produced anesthetic stains. The microbiota colonising 17 stains on handmade and machine-made paper surfaces together with that in library and archive environments was analyzed. Combination of microbiological and high-throughput sequencing (HTS) approaches were applied. The culture-dependent methodology comprised: isolation, DNA identification, hydrolytic and paper staining assays. The HTS was performed by MinION platform and for the mycobiome a more suitable bioinformatics analysis pipeline, MetONTIIME based on QIIME2 framework, was applied. The paper model staining assay permitted the direct recognition of colorizing isolates which in combination with sequencing data evidenced a complex microbial community able to stain the two types of paper. Staining abilities were confirmed by frequently isolated and detected fungi and also by new ones such as Roussoella euonymi and Achaetomium. We have also evidenced the staining ability of several bacteria.

Biodeterioration of carbographic ribbon: Isolation, identification of causal agents and forensic implications

This study is part of a comprehensive investigation that was performed in regard to a case of alterations on a carbographic ribbon used in a typewriter that was found and seized by inner security operations of the Arma dei Carabinieri, Italy. Thirty-six coded scripts possessing potentially and criminally liable content were present on the tape; however, only the 6th and 7th scripts exhibited alterations of an uncertain nature. The study included sampling that was performed under sterile conditions of a large surface area of carbographic ribbons. A protocol based on physico-chemical, microbiological, and biomolecular tools was established. Preliminary results revealed the presence of fungal contamination that was primarily located on the inner surface of the 6th and 7th scripts on the black carbographic ribbon. One fungal strain was isolated and identified by universal ITS-PCR primer and rDNA sequencing as Alternaria infectoria strain NIS4. Fungal growth was monitored for 3 weeks in the laboratory under different environmental conditions (temperature, open-closed system, and substrate). The A. infectoria NIS4 strain exhibited the best growth at 28°C under a closed system with RH near saturation. We also noted that the fungal growth was abundant at 15°C. Moreover, this fungus (a potential human pathogen) possessed the ability to colonize the surface of the new carbographic ribbon even when using mineral medium; however, this only occurred in a closed system environment and not in open systems due to rapid desiccation. Under our experimental conditions, the A. infectoria NIS4 strain could degrade gelatin as an organic matter present in trace amounts that are often used as a binder in a carbographic ribbon emulsions. The results revealed that the isolated microorganism was the major biological candidate capable of altering the investigated carbographic ribbon; however, these alterations could only occur under favourable environmental conditions.

AIMS

Identify the cause of microbial alterations on a carbographic ribbon in a typewriter used in a hypogean Italian criminal house named "covo."

METHODS AND RESULTS

The isolation and identification of biodeteriogens (Alternaria infectoria NIS4) were performed using both culture-dependent and-independent methods, including ITS regions-primed PCR and rDNA techniques. Environmental scanning electron microscopy (ESEM) and optical observations were also performed. Growth tests and biodeterioration simulation tests on carbographic ribbons at the lab scale were performed under different environmental conditions. The A. infectoria NIS4 strain exhibited biodeterioration activity on carbographic ribbons under environmental conditions that were extremely favourable for growth. A high ability to colonize carbographic ribbon surfaces with fast and abundant growth at both 15°C and 28°C under lab-scale conditions at RH near saturation was observed.

CONCLUSIONS

In this forensic case study, the ability of the isolated micromycetes A. infectoria NIS4 strain to colonize and induce alterations and degradation in a carbographic ribbon stored under indoor environmental conditions was examined. When favourable conditions change over time, the risk of microbial colonization and the damage produced by the fungal biodeterioration processes on the synthetic material objects has been confirmed.

SIGNIFICANCE AND IMPACT OF STUDY

The current study contributes to the knowledge of biodeterioration processes in carbographic ribbon and the responsible agents, and our study provides an example of how environmental microbiology can also aid in forensic studies.

3′-Amino modifications enhance the antifungal properties of N4-alkyl-5-methylcytidines for potential biocides

A set of 3′-modified N4-alkyl-5-methyl-2′-deoxycytidines has been synthesized and evaluated for biological activity. The replacement of the 3′-hydroxyl group with amino, aminoethyl and dialkylamino groups significantly enhances antifungal activity.

Corrigendum: Application of a Medical Diode Laser (810 nm) for Disinfecting Small Microbiologically Contaminated Spots on Degraded Collagenous Materials for Improved Biosafety in Objects of Exceptional Historical Value From the Auschwitz-Birkenau State Museum and Protection of Human Health

[This corrects the article DOI: 10.3389/fmicb.2020.596852.].

Application of a Medical Diode Laser (810 nm) for Disinfecting Small Microbiologically Contaminated Spots on Degraded Collagenous Materials for Improved Biosafety in Objects of Exceptional Historical Value From the Auschwitz-Birkenau State Museum and Protection of Human Health

The research aim was to optimize the operating parameters of a diode laser irradiation for the effective disinfection of degraded collagenous materials. Historical leather shoes stored at the Auschwitz-Birkenau State Museum in Oświęcim (Poland) were the main study objects. Surfaces of contaminated small spots occurring on the degraded materials were sampled with moistened swabs and microbiologically examined using the molecular techniques MALDI-TOF MS, 16S rRNA, and NGS sequencing. The surfaces were colonized by bacteria with 10⁶ CFU/100 cm² and 10⁴ CFU/100 cm² by fungi, on average. Microorganisms of the genera Bacillus and Penicillium were predominant. The effectiveness of the laser treatment was assessed for the new and degraded collagenous materials against isolated environmental strains using four variants of exposure time and number of repetitions. 0.3 W/CW 2 × 2 min variant was the most effective and also did not noticeably change the color of the treated samples. The variant caused a reduction in the numbers of microorganisms by 96–100%. After 1 month, four types of leather were subjected to comprehensive physico-chemical analyses. SEM and FTIR techniques confirmed that laser irradiation in the selected optimal variant did not affect the surface morphology and collagen structure, while XPS technique enabled detection of subtle changes in non-historical protective coatings on the surfaces of tested degraded historical materials.

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.

Preliminary Studies on Fungal Contamination of Two Rupestrian Churches from Matera (Southern Italy)

The Sassi, a UNESCO World Heritage Site and its rupestrian churches, are richly decorated and visited by thousands of visitors every year. It is important to preserve this heritage which shows signs of deterioration due to abiotic and/or biotic factors. Aiming to carry out in the future an environmental-friendly restoration, a screening of the fungi present on walls and frescoes of two rupestrian churches “Santa Lucia alle Malve” and “La Madonna dei derelitti” located, respectively, in the “Sasso Caveoso” and in the “Sasso Barisano” was performed. Isolation and characterization of fungal species from investigated sites was carried out. Total genomic DNA (gDNA) was extracted from pure fungal cultures and subsequently utilized in PCRs using primers that amplify a portion of the ribosomal DNA (ITS5/ITS4) or the β-tubulin gene (Bt2a/Bt2b). The amplicons were directly sequenced. Obtained nucleotide sequences were compared to those present in the GenBank (NCBI) showing a very high similarity (99–100%) with the following species: Parengyodontium album, Alternaria alternata, Cladosporium cladosporioides, Lecanicillium psalliotae, Meyerozyma guilliermondii and Botryotrichum atrogriseum. All sequences from this study were deposited in the EMBL database. Detailed knowledge about fungi isolated from stone is indispensable not only to counter/reduce the structural and aesthetic damage but also to protect the health of both guardians and visitors who may develop different pathologies due to the spores diffused in the environment.

Detection of potential biodeterioration risks for tempera painting in 16th century exhibits from State Tretyakov Gallery

In this study, we investigated biodeterioration of materials used in tempera painting by analyzing the structure of the microbiome in ancient tempera paintings exhibited in State Tretyakov Gallery, Moscow, Russia. Samples were obtained from 16^th-century paintings, including a grand Russian Orthodox icon “The Church Militant” (all exhibits were without visible signs of biodeterioration), and from surrounding walls and ceilings (with vast zones of visible microbial growth). A number of microorganisms isolated from visible signs of environmental bio-damage were also detected in tempera paintings kept in temperature- and humidity-controlled conditions unfavorable for the growth of microflora. To determine the biodegrading potential of the microbiome for tempera paintings, we developed a set of mock layers from paintwork materials used in tempera painting of 16^th century and their modern analogues and inoculated them with cultures containing filamentous fungi and bacteria. The susceptibility to microbial degradation of individual tempera painting materials was examined by micro-Fourier Transform Infrared (FTIR) spectroscopy, which enabled detection of even invisible signs of biodeterioration. The results indicate that the microorganisms isolated from paintings and surrounding areas in the museum are capable of causing significant damage of various tempera materials, among which varnishes were the most resistant; however, the addition of antiseptic (sodium pentachlorophenolate) can inhibit microbial growth on sturgeon glue.

Comparative genomics of Bacteria commonly identified in the built environment

BACKGROUND

The microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles.

RESULTS

Here, we selected bacterial genera commonly identified in the BE (or "Common BE genomes") and compared them against other prokaryotic genera ("Other genomes"). The "Common BE genomes" were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the "Common BE genomes" were statistically larger than those of the "Other genomes" but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the "Common BE genomes" compared to the "Other genomes."

CONCLUSION

Of the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.

Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study

Paper documents in archives, libraries, and museums often undergo biodeterioration by microorganisms. Fungi and less often bacteria have been described to advance paper staining, so called “foxing” and degradation of paper substrates. In this study, for the first time, the fungal and bacterial diversity in biodeteriorated paper documents of Hellenic General State Archives dating back to the 19th and 20th century has been assessed by culture‐dependent and independent methods. The internally transcribed spacer (ITS) region and 16S rRNA gene were amplified by PCR from fungal and bacterial isolates and amplicons were sequenced. Sequence analysis and phylogeny revealed fungal phylotypes like Penicillium sp., Cladosporium sp., Penicillium citrinum, Alternaria infectoria, Alternaria alternata, Epicoccum nigrum, and Penicillium chrysogenum which are often implicated in paper deterioration. Bacterial phylotypes closely related to known biodeteriogenic bacteria such as Bacillus spp., Micrococcus spp., Kocuria sp. in accordance with previous studies were characterized. Among the fungal phylotypes described in this study are included well‐known allergens such as Penicillium spp., Alternaria spp., and Cladosporium spp. that impose a serious health threat on staff members and scholars. Furthermore, fungal isolates such as Chalastospora gossypii and Trametes ochracea have been identified and implicated in biodeterioration of historical paper manuscripts in this study for the first time. Certain new or less known fungi and bacteria implicated in paper degradation were retrieved, indicating that particular ambient conditions, substrate chemistry, or even location might influence the composition of colonizing microbiota.