Bacteria isolated from rock art paintings: the case of Atlanterra shelter (south Spain)

Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints

Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.

Ecological strategies of bacterial communities in prehistoric stone wall paintings across weathering gradients: A case study from the Borana zone in southern Ethiopia

Rock art paintings represent fragile ecosystems supporting complex microbial communities tuned to the lithic substrate and climatic conditions. The composition and activity of these microbial communities associated with different weathering patterns affecting rock art sites remain unexplored. This study aimed to explore how bacterial communities adapt their ecological strategies based on substrate weathering, while also examining the role of their metabolic pathways in either biodeterioration or bioprotection of the underlying stone. SEM-EDS investigations coupled with 16S rRNA gene sequencing and PICRUSt2 analysis were applied on different weathered surfaces that affect southern Ethiopian rock paintings to investigate the relationships between the current stone microbiome and weathering patterns. The findings revealed that samples experiencing low and high weathering reached a climax stage characterized by stable microenvironments and limited resources. This condition favored K-strategist microorganisms, leading to reduced α-biodiversity and a community with a positive or neutral impact on the substrate. In contrast, moderately-weathered samples displayed diverse microhabitats, resulting in the prevalence of r-strategist bacteria, increased α-biodiversity, and the presence of specialist microorganisms. Moreover, the bacterial communities in moderately-weathered samples demonstrated the highest potential for carbon fixation, stress responses, and complete nitrogen and sulfur cycles. This bacterial community also showed the potential to negatively impact the underlying substrate. This research provided valuable insights into the little-understood ecology of bacterial communities inhabiting deteriorated surfaces, shedding light on the potential role of these microorganisms in the sustainable conservation of rock art.

The Sustainability of Rock Art: Preservation and Research

Rock art is a widespread cultural heritage, representing an immovable element of the material culture created on natural rocky supports. Paintings and petroglyphs can be found within caves and rock shelters or in open-air contexts and for that reason they are not isolated from the processes acting at the Earth surface. Consequently, rock art represents a sort of ecosystem because it is part of the complex and multidirectional interplay between the host rock, pigments, environmental parameters, and microbial communities. Such complexity results in several processes affecting rock art; some of them contribute to its destruction, others to its preservation. To understand the effects of such processes an interdisciplinary scientific approach is needed. In this contribution, we discuss the many processes acting at the rock interface—where rock art is present—and the multifaceted possibilities of scientific investigations—non-invasive or invasive—offered by the STEM disciplines. Finally, we suggest a sustainable approach to investigating rock art allowing to understand its production as well as its preservation and eventually suggest strategies to mitigate the risks threatening its stability.

On the Biodiversity and Biodeteriogenic Activity of Microbial Communities Present in the Hypogenic Environment of the Escoural Cave, Alentejo, Portugal

Hypogenic caves represent unique environments for the development of specific microbial communities that need to be studied. Caves with rock art pose an additional challenge due to the fragility of the paintings and engravings and to microbial colonization which may induce chemical, mechanical and aesthetic alterations. Therefore, it is essential to understand the communities that thrive in these environments and to monitor the activity and effects on the host rock in order to better preserve and safeguard these ancestral artforms. This study aims at investigating the Palaeolithic representations found in the Escoural Cave (Alentejo, Portugal) and their decay features. These prehistoric artworks, dating back up to 50,000 B.P., are altered due to environmental conditions and microbial activity inside the cave. Microbial cultivation methods combined with culture-independent techniques, biomarkers’ viability assays and host rock analysis allowed us to better understand the microbial biodiversity and biodeteriogenic activity within the hypogenic environment of this important cave site. This study is part of a long-term monitoring program envisaged to understand the effect of this biocolonisation and to understand the population dynamics that thrive in this hypogean environment.

Geomicrobial Investigations of Colored Outer Coatings from an Ethiopian Rock Art Gallery

The open rock shelter of Yabelo in Ethiopia hosts diverse Holocene paintings of great cultural importance. The paintings are characterized by the presence of different mineral coatings, whose features have not been studied yet. Our goal was to understand whether different rock samples from the Yabelo paintings collected in close proximity may reveal coatings with different minerology and biology. Thus, elemental analyses combined with microscopic and molecular investigations were performed on two coatings, one whitish (sample 1) and one reddish (sample 2). Although both samples were dominated by heterotrophic bacteria, the two coatings showed distinct mineralogical and microbiological characteristics. Sample 1 contained higher amounts of Ca and P than sample 2, which was likely related to the presence of organic matter. Sample 1 hosted bacterial genera that are potentially involved in biomineralization processes, metal redox cycles and metal resistance. In contrast, sample 2 showed mainly pathogenic and commensal bacteria that are characteristic of animal and human microbiota, and other microorganisms that are involved in nitrogen and metal biogeochemical cycles. Overall, our results indicated that the bacterial communities were particular to the coating mineralogy, suggesting a potential role of the biological components in the crust genesis.

Proteomic and metagenomic insights into prehistoric Spanish Levantine Rock Art

The Iberian Mediterranean Basin is home to one of the largest groups of prehistoric rock art sites in Europe. Despite the cultural relevance of prehistoric Spanish Levantine rock art, pigment composition remains partially unknown, and the nature of the binders used for painting has yet to be disclosed. In this work, we present the first omic analysis applied to one of the flagship Levantine rock art sites: the Valltorta ravine (Castellón, Spain). We used high-throughput sequencing to provide the first description of the bacterial communities colonizing the rock art patina, which proved to be dominated by Firmicutes species and might have a protective effect on the paintings. Proteomic analysis was also performed on rock art microsamples in order to determine the organic binders present in Levantine prehistoric rock art pigments. This information could shed light on the controversial dating of this UNESCO Cultural Heritage, and contribute to defining the chrono-cultural framework of the societies responsible for these paintings.

Laboratory-induced endolithic growth in calcarenites: biodeteriorating potential assessment

This study is aimed to assess the formation of photosynthetic biofilms on and within different natural stone materials, and to analyse their biogeophysical and biogeochemical deterioration potential. This was performed by means of artificial colonisation under laboratory conditions during 3 months. Monitoring of microbial development was performed by image analysis and biofilm biomass estimation by chlorophyll extraction technique. Microscopy investigations were carried out to study relationships between microorganisms and the mineral substrata. The model applied in this work corroborated a successful survival strategy inside endolithic microhabitat, using natural phototrophic biofilm cultivation, composed by cyanobacteria and algae, which increased intrinsic porosity by active mineral dissolution. We observed the presence of mineral-like iron derivatives (e.g. maghemite) around the cells and intracellularly and the precipitation of hausmannite, suggesting manganese transformations related to the biomineralisation.

Microbial diversity in paleolithic caves: a study case on the phototrophic biofilms of the Cave of Bats (Zuheros, Spain)

The biological colonization of rocks in the Cave of Bats (Cueva de Los Murciélagos, Zuheros, Spain) was studied in order to reveal the diversity of microorganisms involved in the biofilm formation. The culturable, metabolically active fraction of biodeteriogens present on surfaces was investigated focusing on morphological, ultrastructural, and genetic features, and their presence related to the peculiar environmental conditions of the underground site. PCR-ITS analysis and 16S rDNA sequences were used to clusterize and characterize the isolated strains. The presence of bacterial taxa associated to the photosynthetic microflora and fungi within the biofilm contributed to clarify the relationships inside the microbial community and to explain the alteration observed at the different sites. These results will contribute to the application of more successful strategies for the preventive conservation of subterranean archaeological sites.

Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma)

Bacterial diversity in caves is still rarely investigated using culture-independent techniques. In the present study, bacterial communities on Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma) were analyzed, using 16S rDNA-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. Results revealed complex bacterial communities consisting of a high number of novel 16S rDNA sequence types and indicated a high biodiversity of lithotrophic and heterotrophic bacteria. Identified bacteria were related to already cultured bacteria (39 clones) and to environmental 16S rDNA clones (46 clones). The nearest phylogenetic relatives were members of the Proteobacteria (41.1%), of the Acidobacterium division (16.5%), Actinobacteria (20%), Firmicutes (10.6%), of the Cytophaga/Flexibacter/Bacteroides division (5.9%), Nitrospira group (3.5%), green non-sulfur bacteria (1.2%), and candidate WS3 division (1.2%). Thirteen of these clones were most closely related to those obtained from the previous studies on Tito Bustillo Cave. The comparison of the present data with the data obtained previously from Altamira and Tito Bustillo Caves revealed similarities in the bacterial community components, especially in the high abundance of the Acidobacteria and Rhizobiaceae, and in the presence of bacteria related to ammonia and sulfur oxidizers.

Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona

Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year-1) and compared to samples taken from areas designated as having medium (30-40 visitors year-1) and low (2-3 visitors year-1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations.

Bacillus decolorationis sp. nov., isolated from biodeteriorated parts of the mural paintings at the Servilia tomb (Roman necropolis of Carmona, Spain) and the Saint-Catherine chapel (Castle Herberstein, Austria)

Microbial growths causing discoloration on the Roman wall paintings of the Servilia tomb at the necropolis of Carmona (Spain) and the medieval wall paintings of the Saint-Catherine chapel at Castle Herberstein (Austria) were investigated and from four different samples, a group of ten strains with similar characteristics was isolated. The isolates were characterized in a polyphasic taxonomic study, including 16S rDNA sequence analysis, (GTG)5-PCR genomic fingerprinting, DNA-DNA hybridization, DNA base ratio, fatty acid analysis, morphological and biochemical characterization. The data obtained attribute the isolates to a novel species of the genus Bacillus, for which the name Bacillus decolorationis sp. nov. is proposed. The type strain is strain LMG 19507T (=DSM 14890T).

Altamira cave Paleolithic paintings harbor partly unknown bacterial communities

Since it has been reported that microorganisms can affect painting pigments, Paleolithic painting microbiology deserves attention. The present study is the first report on the bacterial colonization of the valuable Paleolithic paintings in the famous Altamira cave (Spain). One sample taken from a painting area in the Polychromes Hall was analyzed culture-independently. This was the first time microbiologists were allowed to take sample material directly from Altamira paintings. Identification methods included PCR amplification of 16S rRNA genes (16S rDNA) and community fingerprinting by denaturing gradient gel electrophoresis (DGGE). The applied approach gave insight into a great bacterial taxonomic diversity, and allowed the detection of unexpected and unknown bacteria with potential effects on the conservation of the painting. Regarding the number of 29 visible DGGE bands in the community fingerprint, the numbers of analyzed clones described about 72% of the phylogenetic diversity present in the sample. Thirty-eight percent of the sequences analyzed were phylogenetically most closely related to cultivated bacteria, while the majority (62%) were most closely related to environmental 16S rDNA clones. Bacteria identified in Altamira were related with sequence similarities between 84.8 and 99.4% to members of the cosmopolitan Proteobacteria (52.3%), to members of the Acidobacterium division (23.8%), Cytophaga/Flexibacter/Bacteroides phylum (9.5%), green non-sulfur bacteria (4.8%), Planctomycetales (4.8%) and Actinobacteria (4.8%). The high number of clones most closely related to environmental 16S rDNA clones showed the broad spectrum of unknown and yet to be cultivated bacteria in Altamira cave.

16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain)

Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates.

Microbiological study of the dripping waters in Altamira cave (Santillana del Mar, Spain)

The culturable microbial populations in dripping waters from Altamira cave were studied and compared with those of the ceiling rock. Water communities have low proportions of gram-positive bacteria, and are mainly composed of gram-negative rods and cocci (Enterobacteriaceae and Vibrionaceae), while those of ceiling rocks are mainly Streptomyces spp. The community differences are probably related to environmental cave conditions: high humidity, relatively low and stable temperature, water pH close to neutrality and nature of the organic matter. All these factors seem to favor colonization and long-term growth of actinomycetes over other heterotrophic bacteria on ceiling rocks.