Biodeterioration of organic substrates is a process involving several types of micro/organisms and represents a ravelled problem particularly for confined environments (archives, libraries, hypogeal, museum), where microbial growth depends on a combination of factors such as relative humidity, indoor temperature fluctuation, water activity, chemical and physical properties of materials surface (Else et al., 2003; Gallo et al., 1999; Valentin, 2003). Both water condensation phenomena and poor ventilation, that allow micro-climate formation suitable for the development of microorganisms for fungi and bacteria that may release toxins with human health damaging proprieties, that may persist in the environment (Singh et al., 1995; Peltola et al., 2001). Studies on microbial communities structure in indoor environment reported an high contamination of bacteria such as Bacillus, Micrococcus, Streptomyces, Actinomycetes, among fungi as Penicillum, Cladosporium, Aspergillus, Alternaria, Trichoderma, Rhizopus, (Valentin, 2003).
It is well known that ribosomal RNA genes are essential for all organisms, representing ideal loci for microbial characterization, for phylogenic study and for strains differentiation even within species (Cardinale et al., 2004; Gonzales, 2003). In this study we report a new sampling method and microbial identification strategies, based on PCR and microarray analysis, that can identify bacterial and fungal as biodeteriogens for works of art and/or pathogens for human, focalising our attention on microbial populations, present in the bioaerosol and on works of art surface