Edited by: Massimiliano Marvasi, University of Florence, Italy
Reviewed by: Jay Prakash Verma, Banaras Hindu University, India; Giovanna Cristina Varese, University of Turin, Italy
†Present address: Katja Sterflinger, Institute of Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna, Austria
This article was submitted to Microbiotechnology, a section of the journal Frontiers in Microbiology
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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
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Our cultural heritage is an asset that we must protect and monitor in order to pass it on to our future generations. One of the greatest pleasures is its contemplation in various permanent or temporary exhibitions. Most valuable graphic art pieces are displayed or stored in a particular museum, library or exhibition site under optimal conditions for their conservation and safety. However, it is common for these objects to be loaned out for certain thematic exhibitions in other museums or exhibition halls around the world. In this context, it is necessary to devise a method to monitor the risks of microbial contamination that may occur during packaging, transport and/or exhibition at the other sites and to allow a comparison before and after these trips. This monitoring is carried out by restorers and experts from the various institutions that provide and receive the object in question, but also by experts from renowned third-party institutions, which apply conventional technologies such as visual inspection, microscopy, but also introducing molecular technologies in order to achieve a detailed assessment of the risk of biological contamination posed by this type of transfer.
Conservators have long since started using new technologies such as miniaturized environmental condition recorders that keep track of how an object is stored during a move or an exhibition, away from the usual storage environment (
Molecular techniques, including DNA-based fingerprinting techniques in addition to cloning and Sanger sequencing, have been largely applied to investigate and monitor the biological colonization on art objects since more than two decades (
Third generation sequencing technologies offer an intelligent solution to the limitations mentioned above (
Although molecular techniques are not completely free from bias (
In the present study we apply the Nanopore sequencing technology in combination with a whole genome amplification (WGA) protocol to survey some of Leonardo da Vinci’s most emblematic drawings. This strategy was applied as the only diagnostic method or in combination with SEM analyses, in order to explore the nature of contaminants deposited on the surfaces of the drawings. The sampling strategy, based on a very delicate micro-aspiration, was aimed primarily at collecting dust particles, microbial cells and other debris from small areas of surfaces. The aim was to create a bio-archive of the dust and other collectable material deposited on the drawings, in order to monitor their conservation status and thus be able to use them for possible comparisons in the future. The sampling was not used to assess the percentage of living propagules, however, the molecular strategy adopted could theoretically indicate the presence of fungal or bacterial cells with an anomalous abundance, compared to typical indoor dust composition. Furthermore, the information contained in this bio-archive is an added value for the drawings, that can in turn help to understand some issues related to the history of storage of the investigated drawings. This study represents one more example of how the Nanopore technology, in this case in combination with microscopy techniques, can be a practical tool for the rapid biological diagnosis and monitoring in priceless objects.
Seven emblematic drawings from Leonardo da Vinci were selected for the analysis of their microbiomes (
The Leonardo da Vinci’s drawings investigated. The drawings currently housed in the Royal Library of Turin are: “
Conservators of the ICPAL (Istituto Centrale per la Patologia degli Archivi e del Libro) collected samples from the
The total number of membranes used for sampling varied between the drawings, ranging from 10 to 36 membranes per drawing (depending on the size of the drawing). Each single used membrane was immediately introduced in a single sterile Eppendorf tube and appropriately labeled for the storage of the samples until DNA extraction analyses. The same kind of membranes was used for SEM observation of the particulate sampled from the drawings and its chemical analysis.
The DNA was extracted using the FastDNA SPIN Kit for soil (MP Biomedicals, Illkrich, France) as recommended by the manufacturers. DNA extraction was performed directly from the membranes by grouping a maximum of four membranes per reaction tube. DNA extracted from each single reaction tube was pooled per sample to obtain a single microbiome from each drawing. The DNA concentrations were assessed by using the Qubit 2.0 fluorometer (Invitrogen Corporation), with the Qubit dsDNA HS Assay Kit.
Whole genome amplification (WGA) and template preparation was performed following the “Premium whole genome amplification protocol” available in the Oxford Nanopore community. For WGA, all reactions were executed in a BioRad C1000 Thermal Cycler using the REPLI-g Midi Kit (Qiagen), which uses the innovative Multiple Displacement Amplification (MDA) technology. The libraries were performed using the Ligation Sequencing kit 1D SQK-LSK109 and the Flow cell Priming kit EXP-FLP001 (Oxford Nanopore Technologies). All steps performed for library preparation were performed as described by
Details of the sequencing runs performed on seven drawings of Leonardo da’Vinci using the MinIon (Nanopore sequencing technology).
“ |
1518 | 1,775,691 | 1,543,693 | 166,129 | 7.7 Gb | 8.77 | 4.34 | |
“ |
1639 | 1,354,462 | 1,168,117 | 123,072 | 5.0 Gb | 9.26 | 3.71 | |
“ |
1706 | 2,796,008 | 2,408,671 | 1,009,200 | 12.4 Gb | 9.08 | 4.44 | |
“ |
1558 | 2,857,065 | 2,461,722 | 317,761 | 13.9 Gb | 9.09 | 4.86 | |
“ |
1570 | 3,168,743 | 2,796,829 | 414,016 | 16.8 Gb | 9.51 | 5.31 | |
“ |
1512 | 1,710,990 | 1,514,255 | 65,343 | 6.8 Gb | 10.94 | 3.97 | |
“ |
1523 | 2,732,413 | 2,376,913 | 183,811 | 14.2 Gb | 10.38 | 5.19 |
Resulting fast5 data files were basecalled using the Nanopore GPU basecalling with GUPPY 3.0.3 on UBUNTU 16.04 (Nanopore Community Platform). Once the Fastq files were generated, the data were compared with databases using one of the available pipelines for data analyses of the Nanopore Community Platform, following the steps recommended by manufacturers. The selected workflow chosen was “What’s in my pot” (WIMP), which is an EPI2ME workflow for taxonomic classification of basecalled sequences (reads) generated by Nanopore sequencing. WIMP initially filters FASTQ files with a mean q-score below a minimum threshold (defaults to 7).
Relative abundances, taxonomic clustering, correspondence analysis and alpha diversity analysis were performed using the R packages taxonomic, phyloseq and microbiome for the R version 4.0.0. (
The sequences obtained by the metagenomic analysis are deposited and publicly available under the BioProject ID:
Features of interest in the drawings were documented with a Leica MZ16 stereoscopic microscope fitted with low-temperature optic fiber lights. The system was equipped with a digital camera connected with a computer and software (Leica Application Suite, LAS, Leica Microsystems GmbH Wetzlar, Germany) that allowed the acquisition of images at different magnifications.
The micro-objects removed from the drawings, fibers and membranes used to sample the drawings were analyzed using a variable pressure SEM instrument (EVO50, Carl-Zeiss Electron Microscopy Group) equipped with a detector for backscattered electron diffraction (BSD). After SEM imaging using Variable Pressure mode, some of the samples were covered with gold for further analysis in High Vacuum mode.
The samples were placed on a sulfur-free carbon adhesive (Spectrotabs AGG3358, Agar Scientific) glued onto an aluminum stub (1.25 cm diameter, Agar Scientific). Chemical analysis was performed by means of EDS (INCA 250, Oxford Instruments). The SEM was fitted with a tungsten filament and operated at 20 keV, with an average working distance of 12.5 mm, with a chamber pressure between 30 and 150 Pa, chosen to keep unaltered micro-structures. The electron beam current was adjusted (∼400 pA) to generate sufficient X-rays to allow reliable identification of EDS peaks, minimize spectral artifacts and achieve detector dead times < 20%. The beam spot size was 5–30 nm in diameter. Acquisition live time for single analysis was set at 50 s. We performed EDS analyses of several types. Some were point analyses, and some consisted of the approximate entire surface of fibers and particles. Conventional ZAF correction (for atomic number Z, absorption and fluorescence) was applied, integrated into the Oxford INCA 250 microanalysis software used.
The EDS measurements were analyzed using statistical tests to evaluate the relationships between variables and the significance of the differences between samples. One-way analysis of the variance (ANOVA) was applied and the significance of the differences was tested at 95% confidence. The ANOVA model used was “unbalanced” because the number of observations within each category was not the same. ANOVA was followed by a
Seven outstanding drawings by Leonardo da Vinci were investigated (
The results showed that the proportion of the analyzed reads that could finally be phylogenetically assigned using the Nanopore WIMP workflow was different for each drawing (
Alpha diversity of drawings calculated from the rarefied classified abundance data using the R package phyloseq.
Relative abundance of eukaryotes, bacteria, archaea, and viruses in the microbiomes of all seven investigated drawings.
Concerning bacteria (
Relative abundance of the bacterial communities of all seven investigated drawings:
Relative abundance of the eukaryotic communities of all seven investigated drawings at the phylum level.
Each drawing owned a very specific microbiome, showing an independent molecular profile or “biological pedigree.”
Heatmap reporting the relative abundance (%) of genera in each of the investigated drawings; the genera shown represent greater than 0.5% abundance in at least one sample.
The bacterial communities dominated over the eukaryotic communities in all the drawings. The most dominant phylum showed to be the
In contrast, members of the
The Actinobacteria were the second most represented phylum within the bacteria, with all members identified belonging to the
The phylum Firmicutes was mainly represented by members of the
The same occurred with the
First of all, it is important to note that an average of 34% of the eukaryotic sequences that could be identified in the drawings showed to be affiliated with the
Only a few taxa of the phylum Ascomycota represented more than 0.5% of the total reads in the microbiomes of the drawings (
Canonical correspondence analysis was used as an ordination method, providing a spatial representation of the relationship of taxa and samples. In the first CA axis of the bacterial community (
Canonical correspondence analysis plot of the first and second CA axis for bacterial
For obvious reasons of relevance, fragility and uniqueness of the objects studied, the microscopic analysis of the drawings was mainly aimed at acquiring photographic documentation using non-invasive techniques, using above all a stereoscopic microscope with fiber optic illumination. The nature of micro-objects that the restorers were able to remove from the surface without causing damage could then be explored further by SEM-EDS. These were mostly particles superimposed on the fibers without any apparent historical value. In addition, some of the membranes used to remove dust from the surface of the designs undergoing molecular investigation were analyzed with SEM-EDS mainly to assess the effectiveness of the sampling method applied.
On many of the drawings analyzed, roundish waxy brown incrustations were specifically observed, often surrounded by greasy looking halos on the underlying fibers. These recurrent “objects” have been documented and in some cases removed and chemically analyzed.
Insects’ droppings. Waxy brown incrustations documented on the fibers of drawing L4 (
EDS analysis of three insects’ droppings removed and analyzed from drawing L4 (“
L4.1 | 75.41a | 4.66bc | 14.10b | 0.70a | 0.24c | 0.65b | 2.45a | 1.32b | 0.41b | 0.06b |
L4.2 | 67.68b | 8.58bc | 15.89b | 0.51b | 0.48c | 1.25b | 2.50a | 2.10a | 0.83b | 0.18ab |
L4.3 | 56.03c | 23.96a | 15.48b | 0.38c | 0.28c | 0.62b | 1.69b | 1.12b | 0.41b | 0.04b |
L2.1 | 57.35c | 0.00c | 31.23a | 0.08e | 1.13a | 3.12a | 0.86c | 0.13c | 5.63a | 0.48a |
L2.2 | 59.29c | 0.00c | 30.70a | 0.20d | 0.90b | 3.31a | 0.58c | 0.00c | 5.02a | 0.00b |
L2.3 | 54.49c | 12.63b | 26.44a | 0.02e | 0.43c | 1.05b | 0.51c | 0.16c | 3.89a | 0.38ab |
Pr > F (Model) | <0.0001 | <0.0001 | <0.0001 | <0.0001 | <0.0001 | <0.0001 | <0.0001 | <0.0001 | <0.0001 | 0.02 |
Significant | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
SEM imaging and EDS analysis of the membranes used for sampling the airborne material deposited on the drawings between the fibers and destined to outline their genetic “pedigree,” showed the effectiveness of the suction system which, without contact with the drawing, made it possible to recover significant micro-objects including fungal spores.
SEM images of the surface of a membrane used to sample the surface of the drawing L3 (
In this study we investigated for the first time some of Leonardo da Vinci’s most emblematic drawings using third generation sequencing technology. One of the most limiting steps found when investigating these invaluable objects, namely the sampling, was carried out using a filtering suction system with small nitrocellulose membranes, which allowed a precise and representative sampling of the total surface of the drawings to obtain all the microbiome on their surfaces.
Furthermore, the tiny nitrocellulose membranes offered the advantage of being easily pooled and used directly for DNA extraction. The total DNA extracted from each drawing was subjected to a metagenomic approach to amplify the entire genomes using the MinION Nanopore sequencing technology. This molecular strategy was already tested by our working group on cultural heritage objects and was shown to be easy for the operator to handle, fast and of a relatively low cost, in comparison with other NGS technologies (
A somewhat surprising result was the higher proportion of bacteria relative to fungi in all the drawings, as fungi were thought to be always dominant in the microbial communities that colonized cultural heritage objects made or supported on paper (
Concerning the first point, the sampling of visibly biodeteriorated paper often lead to the identification of fungi actively growing and using either cellulose or other compounds. In the case of the Leonardo’s drawings no visible biodeterioration, apart from the foxing stains, could be detected. The high proportion of bacteria in relation to fungi could be an index of the type of deposition and the quality of the storage environment. Bacteria in dust are particularly associated with finer dust particles (
Regarding the second point, the technologies employed so far could have biased the results in favor of fungi, either through culture-dependent techniques, due to their rapid germination in the appropriate culture medium, or even through molecular techniques. The molecular techniques used so far in paper-based objects, whether of first- (
The microbiomes derived from the drawings showed a high biodiversity, with the exception of drawing L4, whose microbiome was heavily contaminated with human sequences, this contamination being perhaps due to its greater handling. In fact, the L4 drawing had massive traces of modern adhesive that required a prolonged conservation work, which was carried out with the aid of a magnification apparatus and various manipulations to which the other drawings were not subjected. This may have resulted in greater removal of surface dust, but at the same time in greater human contamination. Another element to consider in this drawing is the very different nature of its support. The drawing was analyzed with Infrared False Color Photography and Fiber Optics Reflectance Spectroscopy and results showed that the paper was treated with layers of lead white [basic lead carbonate 2PbCO3 × Pb(OH)2] mixed with indigo (
The results derived from bacteria showed a dominance of
Members of the
The genus
The
The
The Actinobacteria were the second most represented phylum within the bacteria. The genus
The phylum Firmicutes was mainly represented by members of the order
Members of the order
Regarding the members of other phyla relatively less abundant in the microbiomes of the drawings, such as
It is important to note that it is difficult to compare the data generated in this study with those published in the literature, due to the different technologies applied. As mentioned above, there are not many studies focused on the detection of bacteria on paper-materials and even fewer conducting culture-independent approaches. However, the data generated in this study through third-generation sequencing analyses are somewhat consistent with previous studies where first- and second-generation sequencing was performed. The core microbiome found in this study includes mainly bacteria belonging to the phyla
To summarize our data, the bacterial species detected in this study can be roughly grouped according to their origin on the paper-support of the drawings. A first group is formed by bacteria that are mainly contaminants introduced by human manipulation, mainly species of the genera
Among the detected fungi, only some members of the
Members of the
Within the
Members of the
In summary, most of the fungi detected in this study have been previously identified in other studies focused on paper-supported materials and include species of the genera
A previous study of the L2 drawing performed in 2012 showed that both the recto and verso had been affected by a fungal attack by the species
The incrustations analyzed so far were found to be insect droppings (
Finally, we would like to make a general discussion about the conservation over the centuries of these unique and very fragile objects, in terms of the need to remove insect excrements, dust and the remains of fungi and bacteria, since they are all substances rich in nitrogen, and chemically reactive compounds, capable of oxidizing and degrading the paper fibers. Microorganisms that are still viable also pose other risks, as they can proliferate and cause much more serious damage under certain environmental conditions. However, the manipulation of the drawings could also lead to possible additional contamination, as demonstrated in this study by the presence of bacteria from the human microbiome and the abundant human DNA. However, thanks to the “dirt” found on these heritage objects it has been possible to study their history and to draw a distinctive profile that forms part of the drawings themselves and describes them. The information obtained in this study comes from samples that would be eliminated in a routine conservative treatment. Incrustations, amorphous particles, pieces of glue and remains of supporting cardboard are materials that have been removed by restorers up to now. However, in light of what can be discovered from their meticulous study, the process of conserving certain artistic objects probably needs to be reconsidered because part of their history is written in their “dirt”.
This study shows for the first time the complete microbiomes of some of Leonardo da Vinci’s most emblematic drawings. The strategy applied for their research, namely the Nanopore sequencing technology, is one of the most advanced so far to investigate all the phylogenetic groups included in each of the microbiomes. In addition, the complementation with SEM analysis allowed the visualization of insect droppings in some of the drawings, which are directly correlated with many of the microorganisms found on their surfaces.
The results show a surprising dominance of bacteria over fungi. This fact is partly due to the sampling strategy used, aimed at sampling mainly the dust deposited on the surface of the drawings, but also to the source of contamination to which they have been subjected in the recent past, resulting in a high proportion of bacteria typical of the human microbiome, introduced by intensive handling of the drawings during restoration works, in addition to other microorganisms that have obviously been introduced as contaminants through vectors, such as insects and their excrements.
It is important to clarify that, unlike other case studies that point to visible paper damage caused by fungi, often also associated with bacteria, no clear damage apart from foxing was observed in this study. The sensitivity of the Nanopore sequencing method, which provides information on the abundance of the different taxa in each sample, could have an advantage over other methods for monitoring an ongoing deterioration process, because it allows the assessment of quantitative relationships between taxa and also the deduction of variations in these relationships due to detrimental situations.
In general, the biological information contained in the investigated drawings showed very specific microbiomes, which can be used as a bio-archive of the history the objects, providing a kind of fingerprint for current and future comparisons. However, some similarities were observed that could be influenced by the geographical location of the drawings. Some taxa were only detected in the drawings stored in the Royal Library of Turin, while other taxa were only detected in the drawings stored in the Corsinian Library in Rome.
The results show a high proportion of human DNA, especially in drawing L4, which indicates an inadequate manipulation of this drawing, most probably during the previous restoration processes. This result indicates that restoration techniques should be continually reviewed based on scientific evidence and that monitoring studies in the field of conservation and restoration should be encouraged.
Finally, in order to maximize the value of the samples that can be obtained from unique artworks, it is critical to optimize the analytical processes through protocols that allow the conservation and reuse of the samples in various analyses. Analytical techniques based on the study of environmental DNA will enable the maximum exploitation of natural bio-archives represented by dust, biofilm or other traces of past events present in the works. In perspective, it is possible to imagine a pipeline of measures aimed at obtaining the maximum information from samples taken from unique objects, such as Leonardo’s drawings, which allow very little sampling. Measuring the vitality and activity of individual microbial cells present in materials is probably the next challenge. There are techniques that have already been consolidated in other fields of biology, such as cytofluorimetric measures and single-cell RNA sequencing, which examines the sequence information of individual cells with optimized NGS technologies, which would allow a better understanding of the function of an individual microorganism in the context of its microenvironment. In the light of the new research techniques and their resolving power, some considerations on the impact that cleaning and consolidation techniques may have on the information content of ancient materials are now really urgent. Likewise, new methods and protocols are needed, both for the documentation and for the recovery of these natural “bio-archives” that accompany all the unique objects of our artistic and cultural heritage, without weighing down the already arduous work of conservators and restorers.
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below:
GP conceived the design of the study, conducted molecular analyses, processed sequencing data, and wrote the manuscript. MSc and PC conducted sampling and participated in SEM analyses. FP performed and analyzed SEM and SEM-EDS and contributed to the writing of the manuscript. AG analyzed the sequencing data and contributed to the writing of the manuscript. MSe and KS conceived and contributed to the design of the study and supervised the project. All authors approved the final version for submission.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
We thank the ICPAL staff and the restorers who helped to sample the drawings.
The Supplementary Material for this article can be found online at: