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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<jats:italic>nirK<\/jats:italic>,<jats:italic>dsr<\/jats:italic>, and<jats:italic>soxB<\/jats:italic>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 (CaSO<jats:sub>4<\/jats:sub>) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO<jats:sub>3<\/jats:sub>)<jats:sub>2<\/jats:sub>and Mg(NO<jats:sub>3<\/jats:sub>)<jats:sub>2<\/jats:sub>) 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Key points<\/jats:title><jats:p>\u2022<jats:italic>Poorly (CaSO<\/jats:italic><jats:sub><jats:italic>4<\/jats:italic><\/jats:sub><jats:italic>) and highly (Ca(NO<\/jats:italic><jats:sub><jats:italic>3<\/jats:italic><\/jats:sub><jats:italic>)<\/jats:italic><jats:sub><jats:italic>2<\/jats:italic><\/jats:sub><jats:italic>, Mg(NO<\/jats:italic><jats:sub><jats:italic>3<\/jats:italic><\/jats:sub><jats:italic>)<\/jats:italic><jats:sub><jats:italic>2<\/jats:italic><\/jats:sub><jats:italic>) soluble salts were detected<\/jats:italic><\/jats:p><jats:p>\u2022<jats:italic>Halophilic and mineral weathering microorganisms reveal ecological impacts of salts<\/jats:italic><\/jats:p><jats:p>\u2022<jats:italic>Microbial communities involved in nitrate and sulfate cycles were detected<\/jats:italic><\/jats:p><\/jats:sec>","DOI":"10.1007\/s00253-022-11961-8","type":"journal-article","created":{"date-parts":[[2022,5,21]],"date-time":"2022-05-21T04:03:01Z","timestamp":1653105781000},"page":"4297-4314","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel"],"prefix":"10.1007","volume":"106","author":[{"given":"Jelena","family":"Pavlovi\u0107","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pilar","family":"Bosch-Roig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena","family":"Ruskov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matej","family":"Plan\u00fd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domenico","family":"Pangallo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5733-8833","authenticated-orcid":false,"given":"Patricia","family":"Sanmart\u00edn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,5,21]]},"reference":[{"key":"11961_CR1","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1007\/s002489900174","volume":"38","author":"P Albertano","year":"1999","unstructured":"Albertano P, Urz\u00ec C (1999) Structural interactions among epilithic cyanobacteria and heterotrophic microorganisms in Roman hypogea. 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