Species Numbers in Bacteria

Abstract

A modified biological species definition (BSD), i.e., that bacteria exchange genes within a species, but not usually between species, is shown to apply to bacteria. The formal definition of bacterial species, which is more conservative than the modified BSD, is framed in terms of DNA hybridization. From this I estimate there are a million species of bacteria in 30 grams of rich forest topsoil and propose that there will be at least a billion species worldwide.

Figure 1

Plot of codon bias by sequence divergence between genes found in E. coli and Salmonella. CAI (Codon Adaptation Index) is a measure of codon bias. Ks is the number of substitutions per synonymous sites, where the distance is corrected for multiple hits using the Kimura two-parameter model (Kimura 1980). This figure is modified from Figure 1 of Sharp 1991. Codon bias explains 50% of the variation in synonymous site divergence. The open circles are the genes that might have been laterally transferred after the species split.

Figure 2

DNA rehybridization kinetics. This figure is a modification of Figure 3 of Torsvek, et al. (1990a). The E. coli genome is about 4.5 megabases and the unique DNA in cows is about 1,000 times larger as is human. Thus the initial hybridization of the soil bacterial DNA at same point that the calf thymus starts to re-hybridize suggests that the most common species in the soil is about one tenth of one percent of the total number. The line at the far right is the re-association kinetics for a homogenous sample like the calf thymus DNA, shifted so it has the same Cot as the soil bacteria at 50% re-association. This shows that the different species of DNA from the soil have very different frequencies.