Exploring prokaryotic diversity in the genomic era

Abstract

Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples.

Figure 1

Pie charts showing the phylum-level distribution of prokaryotic isolates (a) in the Australian Collection of Microorganisms [11] and (b) in the prokaryote genome sequences completed or in progress as of 20 August 2001 [29].

Figure 2

'Full-cycle' rRNA approach to characterizing microorganisms in their natural settings without the need for cultivation. Access to whole genomes of uncultivated organisms is also possible using the same basic approach but with large-insert cloning vectors, such as BACs, which remove the need for PCR.

Figure 3

Evolutionary distance dendrograms of (a) bacterial and (b) archaeal diversity derived from comparative analysis of 16S rRNA gene sequences. The trees were constructed using the ARBsoftware package and a sequence database modified from the March 1997 ARB database release [39] using 50% consensus sequence filters for each domain and the Olsen correction and neighbor-joining options. This modified database will be available from the Ribosomal Database Project [40] user-submitted alignments download site [41]. Major lineages (phyla) are shown as wedges with horizontal dimensions reflecting the known degree of divergence within that lineage. Phyla with cultivated representatives are in gray and, where possible, named according to the taxonomic outline of Bergey's Manual [8]. Phyla known only from environmental sequences are in white; because they are not formally recognized as taxonomic groups, they are usually named after the first clones found from within the group [14,20]. Note that environmental groups E2 and E3 defined in [20] are part of the Thermoplasmata phylum in the archaeal tree in (b). The number of genome sequences completed or in progress for each phylum is given in brackets after the phylum name, with the exception of Methanopyrus kandleri, which is not included in the tree because it is represented by a single sequence. The scale bar represents 0.1 changes per nucleotide.