Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity.

Our perspective on microbial diversity has improved enormously over the past few decades. In large part this has been due to molecular phylogenetic studies that objectively relate organisms. Phylogenetic trees based on gene sequences are maps with which to articulate the elusive concept of biodiversity. Thus, comparative analyses of small-subunit rRNA (16S or 18S rRNA) and other gene sequences show that life falls into three primary domains, Bacteria, Eucarya, and Archaea (51, 52). Based on rRNA trees, the main extent of Earth’s biodiversity is microbial. Our knowledge of the extent and character of microbial diversity has been limited, however, by reliance on the study of cultivated microorganisms. It is estimated that .99% of microorganisms observable in nature typically are not cultivated by using standard techniques (1). Recombinant DNA and molecular phylogenetic methods have recently provided means for identifying the types of organisms that occur in microbial communities without the need for cultivation (see references 1, 20, and 35 for reviews). Results from application of these methods to a number of diverse environments confirm that our view of microbial diversity was limited and point to a wealth of novel and environmentally important diversity yet to be studied (34). It is the aim of this review to collate, compare, and incorporate the results of the environmental sequence-based studies into the context of known bacterial diversity. We discuss the sequence data at the taxonomic level of the phylogenetic division because divisions constitute first-order clades for describing the breadth of bacterial diversity. Although we have yet to determine even the outlines of the bacterial tree, common threads are beginning to emerge that revise our current views of bacterial diversity and distribution in the environment.