Potential Environmental Drivers of Fossil Bones Degradation—A Metabarcoding Approach in Two Carpathian Caves

Abstract Studies on fossil bone microbial communities are scarce; even fewer studies were performed in cave deposits. For our research, sediments and fossil bones were sampled, and the whole community 16S rRNA gene-based metabarcoding analyses were performed on samples from Muierilor and Ursilor caves, some of Romania’s most important archaeological and paleontological sites. Most of the identified taxa belong to Bacteria, with Proteobacteria, Acidobacteriota, Bacteroidota, and Actinobacteriota amongst the most abundant phyla in bone samples from both caves. The sediment samples presented similar composition, with Proteobacteria and Acidobacteriota being the most abundant phyla. The inferred bacteriomes indicated the presence of environment-specific bacteria, typical bone colonizers, and bacteria found in soils and decomposing human remains or archaeological profiles as well as phosphate-solubilizing and organotrophic bacteria. Diversity indices indicated a higher diversity in bone samples from Muierilor Cave than in Ursilor Cave samples and sediment samples from both caves. Environmental conditions, especially air relative humidity, were also considered in explaining the bacteriome diversity in different cave settings. These findings help to understand fossil bones’ deposition and degradation in various environmental conditions. Furthermore, this is the first attempt to relate microenvironments and bacteria to preserving fossil bones from caves.