Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel

Abstract

The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO4) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO3)2 and Mg(NO3)2) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out. Key points • Poorly (CaSO4) and highly (Ca(NO3)2, Mg(NO3)2) soluble salts were detected • Halophilic and mineral weathering microorganisms reveal ecological impacts of salts • Microbial communities involved in nitrate and sulfate cycles were detected

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

“…Pavlović and colleagues [25] analyzed various genes (ITS and 16S rDNA region; and the nitrite reductase (nirK), sulfite reductase (dsr), the sox enzyme system for sulfur oxidation (soxB) and the ammonia monooxygenase (amoA) genes) to study a salt-contaminated twelfth century granite-built chapel. The authors contributed to the knowledge of the role of microorganisms in the presence of salt and damp stains, by founding a well-defined relationship between the microbiome and soluble salts, and consequently the biodeterioration phenomena affecting these chapels.…”

Unraveling disparate roles of organisms, from plants to bacteria, and viruses on built cultural heritage

“…Dark and wet heritage sites, such as caves and chapels, can act as reservoirs of pathogenic organisms. In a recent study, Pavlović et al ( 2022 ) detected, for the first time, the dangerous amphibian fungal parasite Batrachochytrium on paving stones in a historical European chapel. A high proportion of the massive decline in amphibians worldwide has been associated with this pathogen, and human-mediated translocation of the fungus is the main cause of the widespread distribution of the disease (Rollins-Smith 2020 ).…”

“…Likewise, long-term protection and the permanence of active organisms should be considered; e.g., live Pseudomonas stutzeri cells should be allowed to remain in treated areas of stonework to continue their nitrate biocleaning function (Pavlović et al 2022 ).…”

MinION Whole-Genome Sequencing in Resource-Limited Settings: Challenges and Opportunities

“…MinION sequencing has been successfully applied in the context of fungal detection in the developed world for various applications such as de novo genome assemblies of yeasts like Saccharomyces cerevisiae [69,70], genome assembly from PCR products [29], detection of fungi using metagenomics [71,72], fungal ecology studies [73], epidemiological outbreaks of Candida species [74], and diagnosis of fungal pathogens in plants [27,28,30]. However, in resource-limited settings, application of MinION sequencing technologies has not been yet applied, thus providing opportunities to explore the utilization of this technology in mycology.…”