Construction of rarefaction curves for each phylum enabled us to compare the extent of sampling of each phylum at various taxonomic levels and their relative richness. For example, we compared rarefaction curves from OP11 (Fig.
2A), which currently has no cultured representatives (
11),
Acidobacterium (Fig.
2B), which is one of the most abundant phyla in soil but is difficult to culture (
13), and γ-
Proteobacteria (Fig.
2C), which is the most well-sampled and well-studied phylum, whose members include
Pseudomonas spp. and
E. coli (
10). Each of these rarefaction curves indicates that the rate of discovering new sequences remains high for all phyla considered, although we are much further along in sampling the γ-
Proteobacteria than any other phylum. As the likelihood of finding new sequences decreases, new methods of isolating sequences will be needed or new environments must be sampled to determine the completeness of the census.
Although the bacterial phyla have been sampled to various extents and contain different numbers of sequences, it is possible to use rarefaction to determine differences in relative richness between phyla that would be observed if current sampling practices continued. OP11, which was recently shown to have a patchy distribution in various environments and is relatively sparse within those samples (
9), has a relative species richness higher than that of the
Acidobacteria but lower than that of the γ-
Proteobacteria. We base this on the observation that the 178 sequences in the OP11 phylum contained 134 different species, and after the same sampling effort, the
Acidobacteria sequences represented between 100 and 114 species (95% confidence interval) and the γ-
Proteobacteria sequences contained between 143 and 162 species (
P < 0.05). The relative species richness of the OP11 phylum is not significantly different from that of the β-
Proteobacteria (95% confidence interval = 112 to 135 OTUs) and
Planctomyces (95% confidence interval = 125 to 144 OTUs) phyla (
P > 0.05) for the same sampling effort. Using similar reasoning, we found the relative species richness among the
Acidobacteria and
Cyanobacteria phyla to be similar. Finally, although the γ-
Proteobacteria phylum contains the largest number of sequences, the
Firmicutes,
Verrucomicrobia,
Bacteroidetes, and sequences that were not classified into a phylum each contain greater relative species richness. Rarefaction curves and data files for all of the bacterial phyla are available (
http://plantpath.wisc.edu/∼pds/rdpproject.html ).