|Van Berkum, Peter|
Submitted to: Nitrogen Fixation International Congress
Publication Type: Book / Chapter
Publication Acceptance Date: 1/30/2005
Publication Date: 1/30/2005
Citation: Van Berkum, P.B., Eardly, B.D. 2005. Impact of genomics on the reconstruction of evolutionary relationships of nitrogen-fixing bacteria and implications for taxonomy. Nitrogen Fixation International Congress. Chapter 13, p. 201-219.
Interpretive Summary: The microbial world profoundly influences the environment and numerous human activities. 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, it is essential that we understand bacterial molecular and evolutionary biology in order to track virulent pathogens or to identify novel cultures that show a potential application or that pose a new threat. In this report we review the literature regarding bacterial evolution and methods of bacterial taxonomy. It is generally accepted that the mechanisms by which all species evolve are identical. These mechanisms include the emergence of mutations to furnish genetic variability, transfer of genomes and newly acquired variability to progeny and subsequent selection for the most competent descendants. In this review the evidence for evolution by hierarchical descent in bacteria is evaluated. Of special importance are genomic islands that possess genes to confer pathogenicity or symbiosis in otherwise very similar genetic backgrounds. We suggest that bacterial evolution should be viewed as a web rather than the standard 'tree of life'. It is of critical importance that agricultural and medical scientists understand the evolution of these genomic islands and their exchange. This information is of particular importance to scientists interested in following the inheritance and transfer of genomic islands and to taxonomists attempting to refine and improve bacterial classification.
Technical Abstract: Advances in genomic characterization methods, such as genomic sequencing and multilocus sequence typing have made it possible to envisage a global DNA sequence-based framework upon which to base future taxonomic decisions. In the implementation of this type of approach however, important issues will need to be addressed, e.g., which genomes should be sequenced and which species concept would be most relevant? Cot curve analyses used to examine the diversity of bacterial species in soils, have led to estimates that more than one billion bacterial species may inhabit the biosphere. Even if this figure is a gross overestimate and the efficiency of DNA sequencing continues to improve, it is still likely that within the foreseeable future it will only be possible to sequence a tiny fraction of the genomes present on the planet. Consequently, if the breadth of bacterial species diversity is to be catalogued, it will require a much more efficient means of estimating genomic diversity. The problem of how to best define a bacterial species also will probably persist into the foreseeable future. Although it is encouraging that both population geneticists and taxonomists agree that phylogenetic relatedness should be a central guiding principle, the present lack of a method for reconstructing complex networks of relationships among recombining bacterial lineages presents a significant and perhaps even intractable problem for all except for the most clonal of species. For this reason, existing methods for estimating phylogenetic relationships, such as those based on comparative 16S rRNA gene sequence analyses, will probably continue to enjoy popularity among taxonomists, in spite of the inherent risks of inferring the evolutionary history of an entire genome from the analysis of a single, perhaps unrepresentative, gene.