Bacterial diversity, ecology, and evolution

Toward a problem of how to recognize bacterial species in situ

Abstract

Increasing 16S rRNA gene sequence analyses have greatly advanced our knowledge of the phylogeny and diversity of bacterial species. Bacterial taxonomic systems are being reconstructed along the phylogenetic lines based on 16S rRNA sequence data. Ribosomal RNA approaches such as rRNA-targeted fluorescent in situ hybridization and PCR cloning of environmental 16S rRNA genes are now widely used to evaluate phylogenetic structures of bacterial communities and to identify bacterial species in situ without any cultivation and isolation. The current knowledge of bacterial diversity based on the molecular data and the rRNA and biomarker approaches to in situ species identification are reviewed.