Submitted to: Symbiosis
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 24, 2004
Publication Date: September 24, 2004
Citation: Van Berkum, P.B., Eardly, B. 2004. Use of population genetic structure to define species limits in the rhizobiaceae. Symbiosis 38: 109-122.
Interpretive Summary: The microbial world profoundly influences agriculture because members either can be beneficial or be harmful. Among microbes, the most predominant are bacteria and archae, which are distinguished from all other life forms by the absence of a membrane bound nucleus containing the genetic material of the cell. Because of their importance in industry, medicine, and agriculture, bacterial molecular and evolutionary biology is a predominant approach used to uncover novel beneficial species and to track virulent pathogens. The most common method of classifying bacteria is to use the small ribosomal gene sequence to portray bacterial genealogy and from this to develop a functional taxonomy from which to extrapolate potential presence of desirable or undesirable characters. The assumption is that genetic traits are passed along by descent from parent to offspring, represented by ribosomal gene inheritance, while genetic variability results from mutation and selection. However, we demonstrate that ribosomal genes in extant bacteria are products of gene exchange and recombination between diverse and sometimes unrelated organisms. Therefore, current methods used to portray bacterial evolutionary relationships are invalid and the evidence in support for the description of taxonomic groups is unsupportable. This information is useful to scientists with interest in bacterial identification, taxonomy and evolutionary biology.
Symbiotic bacteria of the family Rhizobiaceae are currently defined using a consensus or polyphasic approach, where emphasis in determining species limits is based on the quantification of genotypic and phenotypic similarity. In the first part of this review some of the limitations of this approach are examined. In the second part an alternative population-based approach is considered. The primary assumption underlying this approach is that ecological selection is the dominant force constraining genetic diversity in bacterial populations. Practical methods for assessing the range and extent of this diversity are described, along with an example of how such information has been used to provide evidence for two symbiotic nitrogen-fixing species within the genus Sinorhizobium.