Not So Simple After All: Bacteria, Their Population Genetics, and Recombination

Abstract

The pervasive nature of bacterial recombination has become clear. Despite this, the population genetics of bacteria persist in being viewed as simple. Here, I argue against that characterization. After summarizing the history of the topic, I survey the evidence for remarkable and unexplained variation in recombination rate among and within bacterial species. I finally argue that despite recent assertions that recombination means bacterial genes are "public goods," in bacteria the level of selection is the gene, and genes can be understood to have niches with dimensions including the other contents of the genome in which they find themselves.

Figure 1.

A typical figure contrasting the complexity of the prokaryotic cell (left) with that of the eukaryote (right). This example is drawn from Wikimedia Commons, but similar images decorate many textbooks, with especially nice examples being found in Lodish (2003) among others. (From the Science Primer, a work of the National Center for Biotechnology Information, part of the National Institutes of Health. As a work of the U.S. Federal government, the image is in the public domain.)

Figure 2.

The tree of life determined by analysis of 16S rRNA sequences. The three taxa circled are those representing plants, animals, and fungi. As can be seen, the great majority of diversity, at least as assessed by this metric, lies elsewhere. (From Pace 1997; modified, with permission, from The American Association for the Advancement of Science © 1997.)

Figure 3.

Three of the >90 loci that encode serologically distinct capsules in the pneumococcus. The three capsules shown range from 13,844 to 30,298 bp in size. The three examples shown include a fraction of the genes contributing to pneumococcal serotype diversity. Loci are colored according to function and named according to homology groups, for details see the original publication (Bentley et al. 2006).

Figure 4.

The impact of homologous recombination on genotypic diversity. Density is measured here as D, the probability of randomly picking the same genotype twice. θ and ρ are, respectively, the population mutation and recombination rates. The positions of Streptococcus pneumoniae (S.pn), Neisseria meningitidis (N.m), Staphylococcus aureus (S.a), Helicobacter pylori (H.p), Streptococcus pyogenes (S.py), Burkholderia pseudomallei (B.p), and Bacillus cereus (B.c), based on parameters estimated from all data for those species in the corresponding multilocus sequence typing (MLST) databases, are shown. (From Hanage et al. 2006; modified, with permission, from the author.)