Gene transfer between and among Bacteria and Archaea can occur through a variety of mechanisms, including transformation, transduction and conjugation. It is estimated that about 1% of bacteria are able to undergo natural transformation in which reasonably large segments of the DNA can be potentially available for recombination (Thomas & Nielsen 2005
). Since all organisms studied have been found to harbour phages, it is probable that transduction is one of the most widespread mechanisms known to effect gene transfer. The transfer of plasmids, which may involve large segments of the DNA, appears to be less common.
Conceptually, the bacterial species is in a state of dynamic genetic flux. First and foremost to these organisms is that they must, on the one hand, adapt to their niche, while on the other hand, be prepared to move into another. Therefore, genes may enter or leave the organism as long as they do not result in rapidly displacing the organism from its niche, which could lead to their untimely extinction. Indeed, recombinant mobile genetic elements may provide the recipient organism with some advantage in a changing environment, as the new genes may proffer a selective advantage that enables the organism to evolve to adjust its niche and improve its fitness.
For example, two polycyclic aromatic hydrocarbon (PAH)-degrading organisms of the Gammaproteobacteria, Neptunomonas naphthovorans
and a Pseudoalteromonas
sp. that are located at the same marine site, have been shown to harbour a dioxygenase whose sequence indicates that they are clearly related to each other (Hedlund & Staley 2006
). Since this creosote-contaminated, US Environmental Protection Agency Superfund Site contains PAH compounds, the logical inference is that these bacteria have been able to incorporate and express the genes involved in PAH degradation, most probably via plasmid transfer from one to the other or from another PAH-degrading organism. However, the housekeeping genes of the organism have probably remained unchanged and will continue to be useful for classification by the GPSC as ecospecies or, in this example, ‘ecogenera’ using the MLSA approach. Eventually, however, the strong selective pressure of this environment may result in the evolution of the capabilities of these organisms towards novel species that are better suited to this recently changed environment.
Even interdomain gene transfers have been reported in the literature. One notable example of this was the discovery of six formaldehyde oxidation genes in two groups, the methanogens of the Archaea and the methanotrophs of the Proteobacteria. Recently, however, another phylum of the Bacteria, the Planctomycetes were found to harbour these same genes and furthermore, all six of the Planctomycetes proteins involved in formaldehyde oxidation exhibited an intermediate phylogeny between that of the Proteobacteria and the Archaea (Chistoserdova et al. 2004
). This could be interpreted in a variety of ways, some of which do not involve interdomain HGT. Therefore, simply because some evidence may suggest interdomain HGT, it does not necessarily mean that it is the actual explanation, inasmuch as the simple vertical transfer of these genes with loss from some taxa could explain the data equally well.
Although the mechanisms by which DNA can be transferred from one bacterium to another are known, their effect at great distances is poorly understood. How probable is it that a bacterium wafted in the air or carried by water currents thousands of kilometres around Earth will serve as a vector to transfer genes through transduction, transformation or conjugation? Is it possible that phages are the principal agents involved in long-distance transfers?
Recent evidence indicates that homologous recombination (HR) of small segments of the genome containing less than 1000
bp is occurring across considerable geographical distances. Thus, evidence from the hot springs genera, Thermotoga
(Nesbo et al. 2006
) and Sulfolobus
) indicates that this process is significant. Perhaps, phages are responsible for the transfer. This is consistent with what has been reported for genomes, also, such as Prochlorococcus
species (genera?) that reside at higher and lower depths in the marine water column (Coleman et al. 2006
). For Thermotoga
, evidence was also provided for HR of large gene fragments. However, as the authors state, it is uncertain whether these came from organisms at global scales or rather from the local environments owing to inadequate local sampling (Nesbo et al. 2006
Although the data are not extensive at this time, these patterns suggest that the genomes of resident bacteria at one locale may be markedly affected by genes arising from a distant location. If so, this could be a major driving force for bacterial evolution in that the genomes of bacteria endemic to one area can be impacted by a distant genetic source. As long as these transfers are not extensive, they should not override the core genome of a bacterium. In that case, the phylogeographic pattern of the endemic bacterium can be discerned and the taxonomy of the organism can be determined by the GPSC. Clearly, however, much more extensive work will be needed to understand the genetic diversity of species within and between locations.
Recent MLSA work on 770 strains of the highly recombinant genus, Neisseria
indicates that the individual species, N. meningitidis
, N. lactamica
and N. gonorrhoeae
can all be identified using concatenated sequences of seven housekeeping loci (Hanage et al. 2005
). A few strains arose from a branch separating N. meningitidis
from N. lactamica
. These strains were regarded as ‘fuzzy species’ or incipient species.
Interestingly, when highly recombinant bacteria are considered, it could be argued that they fulfil the definition of a pseudo-biological species concept in which sexuality plays the major role in speciation. However, it must be recognized that within animal species all the genes are transferred; the transfer is only intraspecies, it is the sole means of reproduction and fertile progeny are produced. None of these criteria fully apply to the Bacteria and Archaea ().
Differences in sexual exchange between Bacteria and Archaea versus animal species according to the biological species concept (BSC).
Therefore, the primary challenge of a GPSC for Bacteria and Archaea is that it cannot apply to bacteria which are so highly recombinant that the phylogeny cannot be discerned. The highly recombinant types that cannot be phylogenetically resolvable would need to be considered as sub-specific varieties. On the other hand, if further evidence indicates that recombination is the driving as well as cohesive force in the speciation of some groups of highly recombinant bacteria, then a recombinant species concept for these Bacteria and Archaea may be more appropriate.