Bone is used extensively as a source of information in biological and archaeological research as it is, together with tooth, usually the only mineralised tissue preserved on an archaeological site. Bonecontains important information which can answer questions about mobility, ancestry, diet or diagenetic processes to name a few. Environmental parameters such as temperature, pH, oxygen and soil hydrology, as well as biological factors such as microbes play a major role in bone diagenesis. Characterising the depositional environment and the microbial community is crucial in understanding the deterioration processes of bone material. The rapid evolution of DNA sequencing platforms continually pushes the boundary for which questions can be answered by this tool. By applying Next-Generation Sequencing (NGS) tools to study the structure of the microbial community, it is possible to improve our understanding of the bone bioerosion process, which is traditionally only characterised using visualisation analysis of the damage pattern on the bone microstructure. In this study we have conducted a series of burial experiments using modern pig bone fragments at well-characterised depositional sites, and applied NGS tools to study the endogenous pig DNA as well as the microbial community both within the degrading bones and in the surrounding environment. In the first chapter an updated review on the chemical composition and structure of bone (and tooth) is presented, and discuss the different processes involved in mineralised tissue degradation as well as the different environmental factors which are known to influence the degradation processes. When extracting DNA from old or degraded bone a substantial part of the genetic output is microbial DNA. However, traditionally this microbial portion is often considered contamination, and little research exists with focus on extracting this part of the genetic pool. The second chapter explores different laboratory protocols aimed at extracting the microbial component of the bone’s DNA content. The third and fourth chapters relate to data analysis on bone samples that were subjected to a series of burial experiments, in which we have examined bone diagenesis at the initial stages of deposition. Specifically, the third chapter explores the endogenous DNA degradation, whereas the focus in the last chapter is on the microbial community and how this is influenced by the depositional environment, and how the microbial community changes over time after deposition.
Ph.d.-afhandling. Københavns Universitet, 2019.