Culture-dependent studies indicate that representatives of some bacterial divisions are cosmopolitan in the environment, whereas others appear restricted to certain habitats (39
). Culture-independent studies so far conducted reflect and expand this view. Table summarizes the environmental distribution of sequences by habitat type, compiled from most of the available 16S rRNA-based clonal analyses: 86 studies contributing nearly 3,000 sequences. An expanded version of this table that details division-level representation in the individual studies is available at http://crab2.berkeley.edu/pacelab/176.htm
. Table includes only divisions for which representatives have been detected in at least two independent studies and for which at least one near-complete 16S rRNA gene sequence is known. Table is, therefore, not an exhaustive listing of potential division-level diversity for all studies.
TABLE 1 Summary of 16S rRNA-based clonal analyses of diversity of uncultivatedbacteriaa
Sequence representatives of several bacterial divisions have been identified in a wide range of habitats, suggesting the cosmopolitan or ubiquitous distribution of the corresponding organisms in the environment and, potentially, their broad metabolic capabilities. Some of these cosmopolitan divisions are well-known from cultivation studies; however, others are little known or have not yet been detected by cultivation. Figure summarizes the representation of selected cosmopolitan divisions by sequences of cultivated and uncultivated organisms. The Proteobacteria (purple photosynthetic bacteria and relatives), Cytophagales (Bacteroides-Cytophaga-Flexibacter group), and the two gram-positive divisions, Actinobacteria and low-G+C gram-positive bacteria, are well represented by cultivated organisms and therefore are familiar to us in principle. These four divisions account for 90% of all cultivated bacteria characterized by 16S rRNA sequences and approximately 70% of the environmental sequences collated in Table . By contrast, other cosmopolitan divisions revealed by clonal analyses, such as Acidobacterium, Verrucomicrobia, GNS bacteria, and OP11, are poorly represented by sequences from cultivated organisms (Fig. ) and consequently are little known with regard to their general properties. Although many of the bacterial divisions occur widely, others seem to occupy a more limited range of habitats (Table ). All cultivated representatives of Aquificales, for instance, are thermophilic hydrogen metabolizers, and all environmental sequences of Aquificales have been obtained only from high-temperature environments. This suggests a specialized habitat niche for this group. Alternatively, the apparently limited environmental distribution may simply reflect a sampling or methodological artifact and representatives of such divisions may be present in a wider range of habitats, but not yet detected.
Relative representation in selected cosmopolitan bacterial divisions of 16S rRNA sequences from cultivated and uncultivated organisms. Results were compiled from 5,224 and 2,918 sequences from cultivated and uncultivated organisms, respectively.
The database of environmental rRNA sequences is compromised in resolving some phylogenetic issues by a large number of relatively short sequences. More than half of the sequences collated in Table are less than 500 nucleotides (nt) long, which represents only one-third of the total length of 16S rRNA. This is due to an unfortunate trend in many environmental studies of sequencing only a portion of the gene in the belief that a few hundred bases of sequence data is sufficient for phylogenetic purposes. Indeed, 500 nt is sufficient for placement if some longer sequence is closely related (>90% identity in homologous nucleotides) to the query sequence. In the case of novel sequences, <85% identical to known sequences, however, <500 nt is usually insufficient comparative information to place the sequence accurately in a phylogenetic tree and can even be misleading.
Since all but 4 (40
) of the 86 studies collated in Table were conducted using PCR to amplify rDNA from extracted environmental DNA, the question arises as to whether molecular analyses accurately reflect the division-level diversity that occurs in the environment. It is well established that PCR-associated artifacts such as differential amplification of different rDNA templates (36
), sensitivity to rRNA gene copy number (12
), PCR primer specificity (48
), sensitivity to template concentration (6
), amplification of contaminant rDNA (45
), and formation of chimeric sequences (23
) may skew our assessment of microbial diversity. Most of the studies collated in Table , however, analyzed tens to hundreds of clones, so it seems likely that these studies have sampled the main types of sequences in the communities examined. We believe, acknowledging the caveats of the methodology, that the clonal analyses collated in Table probably include the most abundant (metabolically active) bacterial sequence types in the samples analyzed, likely representing the members of the communities that are involved in the principal metabolic activities, such as carbon cycling.