In situ monitoring of bacterial presence and activity

The transfer of molecular biology methods and concepts to environmental microbiology and microbial ecology has provided new insights into microbial complexity and activity in many different types of natural settings, and the rapidly expanding genomic databases have further accelerated the development. Comparative genomics, meta-genomes, techniques for in situ metabolic activity monitoring, and DNA chips for rapid identification of hundreds of species as well as for transcriptomic investigations are tools which have recently been added to those of fluorescent in situ hybridization (FISH) and reporter gene techniques. This chapter reviews the application of some of these in situ methods and tools in the context of mucosal colonization, after which one specific example—monitoring of quorum sensing-based cell-cell communication in colonized lungs of cystic fibrosis (CF) animal models. The first fluorescent protein to be useful as a tool for gene expression was the green fluorescent protein (GFP) from the jellyfish Aequorea victoria. The last 10 years of development of new molecular tools for microscopic investigations, along with the rapid development and dispersal of advanced fluorescence microscopy methods, have resulted in greatly improved techniques for studies of microbial performance in very complex settings, including those found in connection with both commensal and pathogenic bacteria in animals and even human patients.