Bacteria gone native vs. bacteria gone awry?: plasmidic transfer and bacterial evolution.

Abstract

Despite the importance, abundance, and diversity of bacteria, we are just beginning to understand their evolutionary biology. Sex, understood as genetic exchange, is one of the keystone issues in bacterial evolution. Most bacteria reproduce by binary fission, and genetic exchange is independent of reproduction (1). If there is little or no genetic exchange among clones, each strain evolves as an independent lineage, and standard population genetics concepts, such as allelic frequencies and changes of these frequencies in populations, are not applicable (2). On the other hand, if recombination is common among related bacterial lineages (i.e., within bacterial species), we may analyze bacterial populations like most other organisms using standard population genetics methods (2). Recently, Maynard-Smith et al. (3), using detailed analyses based on multilocus linkage disequilibrium, have shown that there is a wide range of bacterial sexualities, ranging from lineages with little or no recombination (like Salmonella ) to others that are almost panmictic (like Neisseria gonorrhoeae ), and some with intermediate (and more complicated) sexualities: localized recombination among closely related strains ( Rhizobium meliloti ) or apparently very clonal populations, due to few very successful strains, have a structure called “epidemic” (e.g., Neisseria meningitidis ) (3). These analyses are mainly based on multilocus enzyme electrophoresis data from chromosomal genes. But bacteria have a fascinating complication; they usually present accessory genes, in the form of smaller chromosomes, known as plasmids (4, 5). Plasmids usually encode specific functions, such as conjugation, antibiotic resistance, sugar utilization, colicin activity, and nitrogen fixation (5–8). Some plasmids are small and cryptic (i.e, without any known function, if any), whereas others are large and more complex (5, 9). Plasmidic genes are not only dynamic, due to rearrangements and duplications within and among them (9, 10), they are also capable of moving among strains, among related bacterial …