Natural stone can undergo disaggregation from various causes, including physical actions such as freeze–thaw cycles, temperature and humidity variations, chemical actions such as the solubilization of minerals by organic and inorganic acids, as well as biological actions due to the colonization of organisms that can produce biocorrosion and biomineralization. This research investigates the impact of microclimatic conditions and microbial activity on the physical and chemical integrity of stone heritage, particularly the biodeterioration caused by fungi in the case of a Romanian rock church. Various analytical techniques were employed, including macroscopic and optical microscopy, Raman spectroscopy, X-ray diffraction, and culture-based identification methods, to characterize the mineral composition and microbial contamination of the rock samples. The analyses revealed that the sandstone consists primarily of quartz (over 90%), muscovite (5–10%), and feldspars. The identified fungi included Cladosporium herbarium, Aspergillus niger, and Mortierella hyalina. The SEM images showed fungal hyphae and spores within the kaolinite–illite matrix, indicating significant microbial colonization and its role in rock deterioration. Additionally, microclimatic data collected over a 12-week period highlighted the substantial fluctuations in temperature and relative humidity within the church, which contribute to the physical and chemical weathering of the stone. This study also noted high levels of particulate matter (PM2.5 and PM10) and volatile organic compounds, which can exacerbate microbial growth and stone decay. The comprehensive analysis underscores the need for targeted preservation strategies that consider both microclimatic factors and microbial colonization to effectively conserve stone heritage sites, ensuring their longevity and structural integrity.
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