Identification of keystone taxa shaping biocrust formation and biodeterioration of limestone monuments in the Xiaoling Tomb of the Ming Dynasty

Abstract The limestone monuments of the Rectangular Tower in the Xiaoling Tomb of the Ming Dynasty, created in the mid-14th century, are biodeteriorating due to environmental exposure, leading to the formation of black biocrusts. However, the microbiomes shaping biocrust formation and the biodeterioration involved remain unclear, which largely challenges the conservation of stone monuments at this archaeological site. Here, we systematically investigated the physicochemical properties and microbial communities of biocrusts to identify keystone taxa that shape their formation and biodeterioration. Physicochemical analysis showed that biological crusts contribute to substantial calcium loss of the limestone monuments. Microscopy and spectroscopy indicated that microbial interactions with limestone promote the formation of biological crusts. High-throughput sequencing revealed that two photosynthetic bacterial phyla, Cyanobacteria and Chloroflexi, predominated in the biocrusts, suggesting that photosynthesis might be a crucial process involved in biocrust formation. Moreover, fungal communities in the biological crusts mainly consisted of Ascomycota, Basidiomycota, and Chytridiomycota, with archaeal communities purely dominated by Crenarchaeota. Microbial co-occurrence network and correlation analyses identified 12 keystone taxa across 11 genera that shape biocrust formation. Importantly, Scytonema could provide organic carbon and nitrogen fixation for Spirosomaceae , and Cyanobacteriia , Setophaeosphaeria , Agaricomycetes , and Plectosphaerella are likely the keystone taxa responsible for both biocrust formation and the associated biodeterioration. Additionally, two predominant ammonia-oxidizing archaea, Nitrososphaeraceae and Candidatus_ Nitrocosmicus, could support chemolithoautotrophic growth in the microbiome by oxidizing ammonia and fixing carbon dioxide. Together, these findings underscore the need for targeted conservation strategies to mitigate microbial biodeterioration of stone monuments during biocrust formation.