Whitehead, Dion;Dress, Andreas - The Influence of Environment on Horizontal Gene Transfer

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Title: The Influence of Environment on Horizontal Gene Transfer	P175
Whitehead, Dion; Dress, Andreas dion.whitehead@uni-bielefeld.de Centre of Biotechnology (CeBiTec) Faculty of Technology, University Bielefeld

Introduction
In the world of bacterial and archaea, assimilating genes from different species appears to be a relatively frequent phenomenon. Horizontal gene transfer (HGT) between microbes seems to be a major force in thier evolution. But our knowledge doesn't go much further than knowing that HGT occurs, and more in some species than others, and that "operational" genes are transferred more often than "informational" genes(Jain, Rivera & Lake, 1999). One of the reasons is the difficulty of verifying HGT, then delineating its history. Since most of these events happened millions of years ago and left no record except within the genome, prediction is based on the gene in question being, in some way, different to the rest of the genome(Koonin, Makarova & Aravind, 2001).
One of the general questions of HGT, relevant in this time of uncertainties over GM foods and antibiotic resistant pathogens, is about constraints. Does the pattern of HGT follow constraints, or is the process a wild free-for-all, with genes randomly diffusing between genomes? Specifically, is spatial and environmental distance a measurable constraint?

Discussion
One of the constraints of HGT might be the physical habitat, or biotope, of the microbe. For example, archaea living in the strange environment of deep sea thermal vents would have little physical contact with a stomach commensal of a sheep, and therefore little chance of HGT, and even if microbes could move between these two biotopes, few from either would survive in the new biotope. This example is obvious, but with finer ecological resolution interesting questions are raised. How much exchange goes on between those microbes living in our intestines and the ubiquitous soil bacteria, compared with our intestinal bacteria and an external pathogen e.g. M. genitalium. For it is clear that bacteria sharing close biotopes of similar character exchange genes readily(Davison, 1999). Is the pattern of HGT related, in some measurable way, to the distribution and proximity of biotopes?

To look for a relationship between genes and biotopes a method must be constructed to be able to meaningfully compare these two types of data. Put simply, we want to compare genetic distance of sets of orthologs, to environmental distance of those orthologs.
However, attributing numbers to ecological distances is not straightforward. Firstly, although we know some habitats of many microbes, we do not know their complete range of suitable environments. For some microbes, e.g. obligate intracellular parasites, this is not a problem, as the microbe cannot survive much beyond a very narrow range of environments. However for those metabolically versatile species, e.g. P. aeruginosa, it is more problematic. Defining a list of habitats where P. aeruginosa is found and not found requires some educated guesses. Secondly, attributing numerical distances between biotopes is also guesswork. Some biotopes are separated by geography and character, e.g. deep-sea vents and the mammalian lung, and the likelihood of microbe movement and survival is obviously very low. For others the distinction is less sharp, i.e. the mammal intestine and soil. There is constant movement between these biotopes through defecation and the consumption of plant and animal material from the ground. Because of these uncertainties, a coarse biotope model has initially been constructed. This gives a matrix of distances between biotopes, and corrospondingly, a distance matrix between microbes. This is being compared to a distance matrix from a set of orthologs.

Two problems have arisen. Firstly, how do we separate vertical descent from horizontal transfer for a given set of orthologs? Secondly, how to meaningfully compare two independent, non-symmetric matrices?

[1] Davison J. (1999) Genetic exchange between bacteria in the environment. Plasmid, 42, 73-91.
[2] Jain R., Rivera M.C. & Lake J.A. (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A, 96, 3801-3806.
[3] Koonin E.V., Makarova K.S. & Aravind L. (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol, 55, 709-742.