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

The limestone monuments of the Rectangular Tower in the Xiaoling Tomb of the Ming Dynasty, created in the mid-fourteenth century, are biodeteriorating from environmental exposure, resulting in the formation of black biocrusts. However, the microbiomes that shape biocrust formation and the biodeterioration processes involved remain unclear, significantly challenging 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 indicated that biological crusts are associated with calcium mobilization and redistribution of the limestone monuments. Microscopy and spectroscopy indicated that microbial interactions with limestone promote the formation of biological crusts. Importantly, we observed the significant predominance of Cyanobacteria and/or Chloroflexi in biocrusts, suggesting that photosynthesis may be a crucial process in biocrust formation. Fungal communities in biocrusts were dominated by Ascomycota, Basidiomycota, and Chytridiomycota, while archaeal communities were dominated solely by Nitrososphaerota. Microbial co-occurrence network and correlation analyses identified 12 keystone taxa across 11 genera that shape biocrust formation. Importantly, Scytonema spp. could provide organic carbon and nitrogen for Spirosomaceae spp., and members of the classes Cyanobacteriia and Agaricomycetes, as well as the genera Setophaeosphaeria and Plectosphaerella, are likely the keystone taxa responsible for both biocrust formation and the associated biodeterioration. Additionally, two predominant ammonia-oxidizing archaeal families (i.e., 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.