Whole cell probing with fluorescently labelled probes for in situ analysis of microbial populations

Until 1965, microbiologists struggled with simplicity of bacterial morphology and phenotypic characters in an attempt to construct a phylogenetic division for the prokaryotes. Then, it was found that molecular sequences were the source of much evolutionary information. Consequently, the way from phenotypic to genotypic characteristics for evolutionary inference was clear. Ribosomes within biological cells are the sites of protein synthesis. They are composed of a mixture of nucleic acids [ribosomal RiboNucleic Acids (rRNA)] and proteins and have an average size of 70s in bacteria. Because of their role in cell survival, maintenance and reproduction, rRNAs and their genes are described as being evolutionally conserved. Other genes can also be used to infer evolutionary relationships, and phylogenies inferred from all these molecules tend to concur. Comparative analyses of small subunit rRNA gene sequences were used in the 1980s to create a phylogeny or natural division for life on earth. It is composed of three domains - Bacteria, Archaea and Eucarya. The database of small subunit rRNA sequences is very large and allowed this broad comparative analysis to be done. In addition, the databases of these gene sequences are cumulative and constitute a growing resource available by modern communication channels to all researchers. The phylogenetic information has been used to clarify classification and taxonomic anomalies in the Bacteria and Archaea. Within the Bacteria, the small subunit rRNA is the 16S rRNA and the genes that code for this molecule are 16S rDNAs. In most cases, the 16S rDNA is exactly transcribed to form the 16S rRNA - i.e. the primary nucleic acid sequences of these two molecules are the same. Additionally, ribosomes of Bacteria contain the larger 23S rRNA (genes = 23R rDNAs), and sequence information from 23S rDNAs is also used to address evolutionary relationships between different Bacteria