Bone biodeterioration-The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community.

Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone fragments (femur and humeri) deposited at different well-defined environments in Denmark. The bacterial community in the bone fragments and surrounding depositional environment were studied over one year, and correlated with the bioerosion damage patterns observed microscopically in the bones. We observed that the bacterial communities within the bones were heavily influenced by the local microbial community, and that the general bone microbial diversity increases with time after exposure. We found the presence of several known collagenase producing bacterial groups, and also observed increases in the relative abundance of several of these in bones with tunneling. We anticipate that future analyses using shotgun metagenomics on this and similar datasets will be able to provide insights into mechanisms of microbiome driven bone degradation

Diagenesis of archaeological bone and tooth

An understanding of the structural complexity of mineralised tissues is fundamental for exploration into the field of diagenesis. Here we review aspects of current and past research on bone and tooth diagenesis using the most comprehensive collection of literature on diagenesis to date. Environmental factors such as soil pH, soil hydrology and ambient temperature, which influence the preservation of skeletal tissues are assessed, while the different diagenetic pathways such as microbial degradation, loss of organics, mineral changes, and DNA degradation are surveyed. Fluctuating water levels in and around the bone is the most harmful for preservation and lead to rapid skeletal destruction. Diagenetic mechanisms are found to work in conjunction with each other, altering the biogenic composition of skeletal material. This illustrates that researchers must examine multiple diagenetic pathways to fully understand the post-mortem interactions of archaeological skeletal material and the burial environment

Releasing the microbes from old bones: the effect of different DNA extraction protocols on microbial community profiling

DNA-based characterisation of microbial communities can enable those interested in bone diagenesis to address questions relating to the complexity and diversity of said microbial communities. We explored whether biases could be introduced due to differences in the DNA extraction methods used. We investigated the effect of four alternative approaches on the extraction of DNA from bone, in order to examine the resulting effect on the bacterial and fungal OTUs recovered using metabarcoding. We found that the different extraction methods resulted in differences in the microbial OTU profiles generated, both when looking at the fungal and the bacterial communities within the bone. Our results emphasise the need for consistency when working with DNA extraction if comparison of results between different research groups are to be valid. Furthermore, it is clear that future efforts will be needed to determine which methods may provide the most accurate representation of the microbial community in bones