Disclosing a crypt: microbial diversity and degradation activity of the microflora isolated from funeral clothes of Cardinal Peter Pázmány

Microbial degradation mechanism of historical silk revealed by proteomics and metabolomics

Archaeological silk undergoes destructive and irreversible changes during the natural process of decay. However, in-depth studies on the influence of this biological factor are still lacking. Here, a combination of proteomics and metabolomics is proposed for the first time to explore the interaction between bacteria and historical silk during biodegradation, which provides information on changes at the molecular level of proteins and bacterial metabolites. Morphological observation revealed biofilms produced by Stenotrophomonas maltophilia and Pseudomonas alcaligenes when cultured in the stationary phase and confirmed severe deterioration of silk. Proteomics showed that S. maltophilia had an unbiased effect on silk fibroin, indicating its ability to disrupt both heavy and light chains, as well as other proteins, while P. alcaligenes showed an affinity for more disordered proteins. Analysis of bacterial metabolites showed that overall activity reduction and significant accumulation of fatty acid and phenol metabolites occurred after silk addition, suggesting that the presence of silk may inhibit the activity of an individual strain. This study provides a new insight into the microbial degradation mechanism of archaeological silk.

Dynamics of microbial community composition during degradation of silks in burial environment

The silk residues in the soil formed the unique niche, termed "silksphere." Here, we proposed a hypothesis that silksphere microbiota have great potential as a biomarker for unraveling the degradation of the ancient silk textiles with great archaeological and conservation values. To test our hypothesis, in this study, we monitored the dynamics of microbial community composition during silk degradation via both indoor soil microcosmos model and outdoor environment with amplicon sequencing against 16S and ITS gene. Microbial community divergence was evaluated with Welch two sample t-test, PCoA, negative binomial generalized log-linear model and clustering, etc. Community assembly mechanisms differences between silksphere and bulk soil microbiota were compared with dissimilarity-overlap curve (DOC) model, Neutral model and Null model. A well-established machine learning algorithm, random forest, was also applied to the screening of potential biomarkers of silk degradation. The results illustrated the ecological and microbial variability during the microbial degradation of silk. Vast majority of microbes populating the silksphere microbiota strongly diverged from those in bulk soil. Certain microbial flora can serve as an indicator of silk degradation, which would lead to a novel perspective to perform identification of archaeological silk residues in the field. To sum up, this study provides a new perspective to perform the identification of archaeological silk residue through the dynamics of microbial communities.

Phototrophic and fungal communities inhabiting the Roman cryptoporticus of the national museum Machado de Castro (UNESCO site, Coimbra, Portugal)

Caves are oligotrophic environments, characterized by constant temperatures, high humidity and low natural light. However, microbial shifts can still happen in such environments, especially with the increase in tourist activity and implementation of artificial lights, making caves even more susceptible to environmental changes. As a result, proliferation of phototrophic organisms can increase dramatically, leading to their settlement on stone surfaces, which in turn facilitates the development of heterotrophic organisms, such as fungi and bacteria. The Roman Cryptoporticus of the National Museum Machado de Castro, erected by the Romans in the 1st or second century, is one of the most emblematic buildings in the city of Coimbra. However, the majority of the rooms that constitute this monument show signs of biodeterioration by microalgae and cyanobacteria as well as of fungi. The aim of this study was to characterize the phototrophic and fungal communities at this site, employing culture-dependent and-independent methodologies. Culture-dependent results showed that the phototrophic communities were mainly composed of green microalgae, whereas the culture-independent showed that cyanobacteria were the most dominant. As to the fungal communities, both approaches identified various entomopathogenic fungal species. In addition, the culture-independent analysis also allowed to verify the presence of animal reads, suggesting the hypothesis that animal vectored dispersion can play an important role in the development of fungi at this environment.

Accumulation of microorganisms on work clothes of workers collecting different types of waste - A feasibility study

Electrostatic dust cloths have previously been used to study microorganisms in settled dust by placing the cloths horizontally on surfaces (called Electrostatic Dust Collectors, EDC). In this study, we investigate whether the same cloths, henceforth called 'E-Cloths', can be used to study accumulation of microorganisms and endotoxin on workers' clothes. This was studied as current methods have limitations. It was examined for waste collection workers, as their work environment is associated with elevated exposure to microorganisms and endotoxin. Each worker received a kit with a T-shirt with an attached E-Cloth on the front, a instruction letter, and a questionnaire. Workers wore the T-shirts during the next two workdays. Unaffected by waste type collected, it was possible to measure the accumulation of bacteria, fungi, and endotoxin from the work environment on the E-Cloths. Geometric mean concentration of 9 × 10⁶ CFU bacteria/m², 1 × 10⁷ CFU fungi/m², and 4 × 10⁴ endotoxin units/m² were found. In total, 100 different bacterial and 25 fungal species were found. The genus Bacillus (with 18 species) and Brevibacterium aurantiacum were among the dominating bacteria. For fungi, Penicillium brevicompactum, P. commune, Penicillium italicum, and Aspergillus niger were most often found. Importantly, mainly environmental bacteria and fungi had accumulated on the E-Cloths and only few skin-related bacterial species were present, showing that accumulation had happened from the work exposure and not workers' skin. In conclusion, the T-shirts with an E-Cloth can be used as a self-administered method for measurement of accumulation of microorganisms and endotoxin from the work environment on waste collection workers' clothes.

Sustainable Packaging Material Based on PCL Nanofibers and Lavandula luisieri Essential Oil, to Preserve Museological Textiles

The connection with textiles is one of the oldest traditions in humanity, and in the historical scenario, textiles and clothing deal with material culture. Therefore, preservation is of the utmost importance to keep this important heritage. Packaging and protection of museological textiles is imperative due to the risks that these articles suffer, mainly concerning the attack of microorganisms that promote the acceleration of their degradation, and it is still necessary to create a proper packing material. In the present work we describe a bibliographic review about the museological scenario, focused on the packaging for preservation of textile articles, as well as the techniques usually used in preventive material conservation. Future perpsctives for the improvement in the conservation of museological textiles are also given. This research aims to produce a sustainable material based on polycaprolactone (PCL), with and without antimicrobial function by incorporating Lavandula luisieri essential oil (EO), in the form of a non-woven substrate for museological packaging. A comparison was made with the most frequently used materials, such as raw cotton and a non-woven polyester. The results demonstrated that both PCL and PCL + EO obtained a good characterization for museological application with good breaking strength and excellent whiteness index. In addition, PCL + EO showed a high bacterial reduction when compared with other protective materials frequently used in museums. Therefore, these findings emphasize the potential use of this material as an innovative protective antibacterial museological packaging solution, able to safeguard and preserve textile museum and clothing collections for longer and for future generations.

Multi-Technique Investigation of Grave Robes from 17th and 18th Century Crypts Using Combined Spectroscopic, Spectrometric Techniques, and New-Generation Sequencing

The textile fragments of the funeral clothes found in the 17th and 18th century crypts were subjected to spectroscopic, spectrometric, and microbial investigation. The next-generation sequencing enabled DNA identification of microorganisms at the genus and in five cases to the species level. The soft hydrofluoric acid extraction method was optimized to isolate different classes of dyes from samples that had direct contact with human remains. High-performance liquid chromatography coupled with diode matrix and tandem mass spectrometry detectors with electrospray ionization (HPLC-DAD-ESI-MS/MS) enabled the detection and identification of 34 colourants that are present in historical textiles. Some of them are thus far unknown and uncommon dyes. Indigo, madder, cochineal, turmeric, tannin-producing plant, and young fustic were identified as sources of dyes in textiles. Scanning electron microscopy with energy-dispersive X-ray detector (SEM-EDS) and Fourier transform infrared spectroscopy (FT-IR) were used to identify and characterize fibres and mordants in funeral gowns. Of the 23 textile samples tested, 19 were silk while the remaining four were recognized as wool. The presence of iron, aluminium, sodium, and calcium suggests that they were used as mordants. Traces of copper, silica, and magnesium might originate from the contaminants. The large amount of silver indicated the presence of metal wire in one of the dyed silk textiles. SEM images showed that textile fibres were highly degraded.

Taphonomy of experimental burials in Taphos-m: The role of fungi

BACKGROUND

The fungi present in the decaying remains enable a better understanding of the processes of decomposition after death. There are not many studies about fungi on decaying bodies and it is not known which fungal sampling methods are effective.

AIMS

The main objective of this study was to find the best method for sampling fungi in carcasses, prove the effectiveness of this method and identify the fungal colonies in animal carcasses from experimental burials.

METHODS

Samples from 13 carcasses of Sus scrofa domestica, from the experimental project Taphos-m, were taken with different materials: spatula, sterile swabs and RODAC contact plates.

RESULTS

RODAC contact plates with the RBA culture medium showed higher proliferation of fungal colonies. Thirty genera of fungi were isolated from different substrates (bone, tissue, lime). Most of the fungi genera or groups identified have been described before in the literature, but the substrates they came from were different in some cases.

CONCLUSIONS

Sampling with RODAC contact plates was found to be the most effective method, as it provides a nutritional culture medium that may allow growth since the moment of sampling. Fungi colonies grew better in RBA culture medium because bacterial growth is inhibited. Most of the observed fungi are related to the environment but some others have been found related to decomposing bodies for the first time.

Current Knowledge on the Fungal Degradation Abilities Profiled through Biodeteriorative Plate Essays

Fungi are known to contribute to the development of drastic biodeterioration of historical and valuable cultural heritage materials. Understandably, studies in this area are increasingly reliant on modern molecular biology techniques due to the enormous benefits they offer. However, classical culture dependent methodologies still offer the advantage of allowing fungal species biodeteriorative profiles to be studied in great detail. Both the essays available and the results concerning distinct fungal species biodeteriorative profiles obtained by amended plate essays, remain scattered and in need of a deep summarization. As such, the present work attempts to provide an overview of available options for this profiling, while also providing a summary of currently known fungal species putative biodeteriorative abilities solely obtained by the application of these methodologies. Consequently, this work also provides a series of checklists that can be helpful to microbiologists, restorers and conservation workers when attempting to safeguard cultural heritage materials worldwide from biodeterioration.

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.

Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century

A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event.

First case of a dog infected with Aspergillus (Phialosimplex) caninus in Australasia

Case history: A 2-year-old Rottweiler dog from Perth (WA, Australia) was referred for assessment of a chronic productive cough and weight loss.Clinical findings: Severely enlarged bilateral superficial cervical lymph nodes and severely enlarged abdominal organs were present. The body condition score was poor and there was moderate muscle wasting. Thoracic and abdominal computed tomography images revealed severe diffuse enlargement of thoracic and abdominal lymph nodes, hepatomegaly and diffuse splenomegaly. A diffuse bronchial pattern with severe multifocal saccular bronchiectasis was identified in the lungs.Diagnostic findings: Fungal organisms were seen within macrophages on cytological preparations and on histopathological sections of biopsies of the superficial cervical lymph node. Macrophages contained intracytoplasmic, non-filamentous round-to-ovoid organisms, which varied in size from 5-30 µm in diameter with variable morphology. Budding was not observed, and no hyphae were present. Fungal culture of lymph node tissue resulted in growth of Aspergillus (Phialosimplex) caninus which was confirmed by amplification and sequencing of a segment of the 16S-23S rRNA internal transcribed spacer. Concurrent bacterial bronchitis was diagnosed on culture of broncho-alveolar fluid.Diagnosis: Disseminated aspergillosis caused by Aspergillus caninus.Clinical relevance: This is believed to be the first report of infection caused by A. caninus in a dog in Australasia. The dog was treated with itraconazole for 7 months and was still alive 7 months after the start of treatment.

Long-Term Treatment and Survival in Three Apparently Immunocompetent Dogs with Disseminated Fungal Infection Caused by Phialosimplex caninus

Disseminated fungal infections cause morbidity and mortality in dogs. The prognosis varies depending on the infecting agent. Phialosimplex caninus is a recently recognized type of hyalohyphomyces. Knowledge regarding the clinical course of P caninus infection in dogs is limited to two previous case reports. The clinical features, diagnostic findings, responses to medical therapy, and long-term outcomes of three dogs with disseminated P caninus are presented in this study. All dogs had improved quality of life once itraconazole administration, with or without terbinafine, was instituted. Long-term disease remission was maintained even after discontinuation of antifungal therapy in a single dog.

Improving biomass and starch accumulation of bioenergy crop duckweed (Landoltia punctata) by abscisic acid application

Duckweed is a valuable feedstock for bioethanol production due to its high biomass and starch accumulation. In our preliminary experiment, we found that abscisic acid (ABA) could simultaneously increase starch and biomass accumulation of duckweed, but the mechanisms are still unclear. The results showed that the biomass production of duckweed reached up to 59.70 and 63.93 g m⁻² in 6 days, respectively, with an increase of 7% (P < 0.05) compared to the control. The starch percentage increased from 2.29% up to 46.18% after 14 days of treatment, with a total of starch level 2.6-fold higher than that of the control. Moreover, the level of endogenous ABA, zeatin-riboside (ZR) and indole-3-acetic acid (IAA) increased, while gibberellins (GAs) decreased. Notably, ABA content in treated samples reached 336.5 mg/kg (fresh weight), which was 7.5-fold greater than that of the control. Importantly, the enzyme activities involved in starch biosynthesis increased while those catalyzing starch degradation decreased after ABA application. Taken together, these results indicated that ABA can promote biomass and starch accumulation by regulating endogenous hormone levels and the activity of starch metabolism related key enzymes. These results will provide an operable method for high starch accumulation in duckweed for biofuels production.

Aspergillus subgenus Polypaecilum from the built environment

Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.

Microbial Life and Death in a Foxing Stain: a Suggested Mechanism of Photographic Prints Defacement

The gelatin-silver halide black and white prints represent an enormous photography heritage with a great value. Unaesthetic phenomena, the foxing stains that are caused by microbial growth on surface, have been described in stamps, drawings, books, and tissues but, until now, scarcely for photographic materials. In this study, a combination of various techniques, including culture-dependent and culture-independent approaches (RNA and DNA analysis), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and μ-Raman spectroscopy supported by X-ray fluorescence analysis (XRF), permitted to describe the microbial contamination dynamics of foxing stains present on the surface of two gelatin-silver halide photographs. The investigation provided also information on the effects of microbial activity on the materials' chemistry of the two prints. The action of microbial community resulted locally in either (a) formation of mixed aluminum-iron-potassium phosphate compounds that could be attributed to the hydrolytic activity of bacteria, (b) leaching of barite,

Application of solid-phase microextraction with gas chromatography and mass spectrometry for the early detection of active moulds on historical woollen objects

The goal of this work was to determine the microbial volatile organic compounds emitted by moulds growing on wool in search of particular volatiles mentioned in the literature as indicators of active mould growth. The keratinolytically active fungi were inoculated on two types of media: (1) samples of wool placed on broths, and (2) on broths containing amino acids that are elements of the structure of keratin. All samples were prepared inside 20 mL vials (closed system). In the first case (1) the broths did not contain any sources of organic carbon, nitrogen, or sulfur, i.e. wool was the only nutrient for the moulds. A third type of sample was historical wool prepared in a Petri dish without a broth and inoculated with a keratinolytically active mould (open system). The microbial volatiles emitted by moulds were sampled with the headspace solid-phase microextraction method. Volatiles extracted on solid-phase microextraction fibers were analyzed in a gas chromatography with mass spectrometry system. Qualitative and quantitative analyses of chromatograms were carried out in search of indicators of metabolic activity. The results showed that there are three groups of volatiles that can be used for the detection of active forms of moulds on woollen objects.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum,Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereuss train was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days.

Microbial communities affecting albumen photography heritage: a methodological survey

This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19^th and early 20^th centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

A combined approach to assess the microbial contamination of the archimedes palimpsest

A combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the Archimedes Palimpsest, an unusual parchment manuscript. SEM analyses revealed the microbial damage to the collagen fibers and the presence of characteristic cell chains typical of filamentous bacteria and fungal spores. Molecular analysis confirmed a homogeneous bacterial community colonizing the manuscript. The phyla Proteobacteria and Actinobacteria were associated with this ancient parchment; the sequences were most related to uncultured clones detected in the human skin microbiome and in ephitelium, and to cultivated species of the genera Acinetobacter and Nocardiopsis. Nevertheless, a great variation was observed among the different sampled areas indicating fungal diversity. Blumeria spp. dominated in the healthy areas of the parchment while degraded areas showed disparate fungal communities, with dominant members of the genera Mucor and Cladosporium. In addition, the quantification of the β-actin gene by real-time PCR analyses (qPCR) revealed a higher fungal abundance on degraded areas than on the healthy ones.

Microbial deterioration of cultural heritage and works of art--tilting at windmills?

Microorganisms (bacteria, archaea and fungi), in addition to lichens and insect pests, cause problems in the conservation of cultural heritage because of their biodeteriorative potential. This holds true for all types of historic artefacts, and even for art made of modern materials, in public buildings, museums and private art collections. The variety of biodeterioration phenomena observed on materials of cultural heritage is determined by several factors, such as the chemical composition and nature of the material itself, the climate and exposure of the object, in addition to the manner and frequency of surface cleaning and housekeeping in museums. This study offers a review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials. The decontamination of infected artefacts, exhibition rooms and depots incurs high expenditure for museums. Nevertheless, the question has to be raised: whether the process of biodeterioration of cultural heritage can or should be stopped under all circumstances, or whether we have to accept it as a natural and an implicit consecution of its creation. This study also highlights critically the pros and cons of biocide treatments and gives some prominent examples of successful and unsuccessful conservation treatments. Furthermore, an outlook on the future research needs and developments in this highly interesting field is given.

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air

The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and – as a result of salt emanating from the walls – on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors.