Abstract
Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea, the four lineages within the genus, as well as its sister-genus Tatumella. This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella, various traits involved in nutrient cycling were identified within Pantoea, providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.
Highlights
Since the early twentieth century scientists have recognized the value of phylogenetic inferences in determining natural relationships between taxa, which is essential for both taxonomy and evolutionary studies (Woese, 1987)
At the intra-generic level, these sets were comparable in the sizes of the gene sets (Figure 2), with the exception of the P. rodasii lineage
The gene sets for the four lineages consisted of 2844 genes for the P. agglomerans lineage, 2924 genes for the P. ananatis lineage, 3599 genes for the P. rodasii lineage and 2872 genes for the P. dispersa lineage (Figure 3)
Summary
Since the early twentieth century scientists have recognized the value of phylogenetic inferences in determining natural relationships between taxa, which is essential for both taxonomy and evolutionary studies (Woese, 1987). The move toward a more natural classification system by these early bacteriologists, based on phylogenetics, proved exceedingly difficult as traditionally used morphological traits were not variable enough to group taxa reliably (Stanier and Van Niel, 1941; Woese, 1987; Woese et al, 1990) This led to the use of physiological. Biological Processes that Differentiate Bacteria characters, some researchers already argued early on that such data would not be suitable for developing evolutionary hypotheses They emphasized that physiological traits would generally not be phylogenetically informative as long as there were no clear understanding of their genetic basis and overall biological importance (Stanier and Van Niel, 1941). Scholars mostly abandoned the field of bacterial systematics until more reliable characters became available with the advent of nucleic acid-based molecular phylogenetics in the 1970s (Woese, 1987, 1994, 1998; Woese et al, 1990; McInerney et al, 2011)
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