## 3 Microbiome Analysis by Culture-Independent Methods
### Genomic DNA vs. RNA  
The total microbial biomass is a useful indicator of microbial population and contamination on solid surfaces, but the viable microbes are important estimators of microbial activity and metabolic potential. The expression analysis of genes can yield detailed information about the metabolically-active members and microbial metabolic state of the microbiome and about the microbe-mediated biodeterioration process and potential, for example, following the microbial metabolic activities of ammonia oxidation by bacteria and archaea [32; 85] and sulfur oxidation [60; 61] on cultural relics with RNA. Assessment of the metabolically-active members or groups in the microbial community is a more selective and specific approach to identifying the specific culprits than the overall information recovered from the genomic DNA of samples.  
Currently, it is necessary to determine the level of metabolic or physiological activity of specific functional microflora in biofilm or microbiome on cultural heritage because this information is the basis for conservators and scientists to gain a deeper understanding of the biodeterioration processes, to monitor the effectiveness and success of the conservation treatments, and to develop alternative and non-toxic conservation strategies to inhibit or slow down microbe-mediated biodeterioration (Figure 4). Although real-time quantitative PCR (RT qPCR) is currently a routine tool for solving many scientific problems, it is not useful for routine monitoring of biodeterioration and has been used only occasionally on samples of cultural heritage. In a recent study, the community of ammonia-oxidizing microorganisms as a biodeterioren on the Angkor monuments, the ammonia-oxidizing archaea (AOA), were determined to be the more active members over ammonia-oxidizing bacteria (AOB) in the nitrifying reaction of the microbiome on Angkor monuments. They can play an important role in biodeterioration according to the results from the RT qPCR analyzing the expression of _amoA_ gene of samples [32]. Further confirmation of the biochemical capabilities are still expected to establish the microbial transformation processes responsible for destruction of materials (see next section).  
Gene-by-gene molecular analysis is too time-consuming and requires a high level of technical skill in conservation science. As a result, it is not cost-effective in application. Recent metatranscriptomics approaches that rely on NGS platforms offer more possibilities for understanding the metabolic pathways and the activity of the specific metabolic processes within microbial communities [30; 83; 87]. However, metatranscriptomics approaches applied to the study of biodeterioration of cultural heritage are still in their infancy and their application in conservation science is not yet widely available. In general, the costs for molecular analysis are going down rapidly and operational issues with RNA protection and extraction are also improving. Bioinformatics tools to process the metatranscriptome datasets are also becoming routine for processing to microbial communities and gene assembly associated with biodeterioration.