Innovative metagenomic approaches for detection of microbial communities involved in biodeteriorattion of cultural heritage

Abstract

Microorganisms can colonize any known environment and modify it due to their extremely wide and versatile metabolism. From the microorganisms point of view, cultural heritage (CH) objects represent a series of very heterogeneous habitats (from historical stones to paints or archaeological wood) where they can grow as well as in natural habitats. Aesthetical and/or structural modifications of CH materials due to microbial growth and activities are referred as biodeterioration. In most cases biodeterioration is not due to a single species of microorganisms, but is the results of the activities of a composite microbial community at some stage of its development on the artwork. The knowledge of microbial community composition and its metabolic potential is essential to individuate the microorganisms mainly responsible for deterioration and take the appropriate measures to control their growth. Microbial communities can be investigated by two different methods: culture-dependent (based on the cultivation of microorganisms) and culture-independent (based on the analysis of diagnostic molecules, mainly nucleic acids). Even if culture-dependent methods allow to study the physiology and metabolism of the isolated microorganisms, they provide limited information on the diversity of complex microbial communities since the vast majority of microorganisms (approximately 99% for environmental samples) are not yet culturable. Microbiology applied to Conservation is a relatively young branch of environmental microbiology. For many years methods used to detect microorganisms inhabiting CH objects have been culture-dependent while molecular techniques developed from microbial ecology have been adopting only in recent years. Here we discuss the potential application of innovative metagenomics approaches, to investigate microbial communities on CH. Metagenomics approaches can be divided in targeted and untargeted methods. The targeted methods amplify and sequence marker regions of the ribosomal DNA to obtain a genus level picture of the microorganisms present in different substrates. The untargeted approaches can provide strain level information of the genes and the biochemical functions present in a microbial community. This review emphasizes the importance of applying metagenomics based, culture-independent techniques, in combination with the culture-dependent ones, to assess the biodiversity of microorganisms colonizing CH objects and take proper actions for their conservation.