The role of horizontal gene transfer in the evolution of microbial me resistance

Horizontal gene transfer (HGT) is the process through which microbes, organisms that reproduce asexually, exchange genes. This mechanism facilitate rapid adaptation to changing and pollution impacted environments. Studies have revealed that HGT is not a marginal phenomenon, as it has been thought of for many years, but a common process which revolutionizes our view of the “tree of life” (see figure below), where frequent gene transfer during the evolution of life has modified the tree to resemble more a “net of life” by the horizontal movement of genes from one “branch” to the other.

There are three major mechanisms of gene transfer between microorganisms. These are illustrated in the adjoining figure. Our current research is focused on transfer of metal resistance genes on bacterial plasmids among bacteria in subsurface soils and how this process enables life in metal and radionuclide contaminated aquifers.                           This cartoon depicts the three major mechanisms of gene transfer as they occur in the environments where these processes are known to affect the fitness of the microbial community to the environment. Our lab is actively studying conjugation in soils and its affects the ability of the community to withstand metal stress

This study is important because the deep subsurface has been contaminated with metals and radionuclide due to the production of nuclear weapons and energy. This raises a public health concern with the mobilization of toxic metals and radionuclides to groundwater. The most feasible approach to controlling this problem is the stimulation of microbes whose activities reduce mobility of these contaminants in the soil. These microbes however are exposed to high concentrations of toxic metals and therefore their metal resistance is critical to the immobilization of metals and radionuclides. HGT of metal resistance genes in subsurface microbial communities is therefore a mechanism that enhances resistance to metals and therefore bioremediation.

Initial studies conducted in our lab by Dr. Jonna Coombs showed that some but no all genes for resistance to the toxic metal lead in subsurface bacteria have evolved by HGT. Jonna used a combination of PCR amplifications, DNA sequencing, and bioinformatic analyses in her work. Click here if you would like to read more about Dr. Coombs's studies (1, 2)

To explore the possible involvement of conjugation in the documented HGT among subsurface bacteria a graduate student, Aspa Chatziefthimiou, is using an oligonucleotide microarray hybridization to show that metal resistance genes are located on plasmids that were extracted from the subsurface bacteria as shown in the figure below. Plasmids labeled with a fluorescence dye are hybridized with the array to produce signals with those probes for which homologous genes are present on the plasmid. The DNA of such plasmids are then sequenced and analyzed for the presence of elements known to mediate gene transfer.

This figure illustrates our protocol for DNA microarray hybridization that identifies metal resistance genes on plasmids. First, plasmid DNA is separated by gel electrophoresis (left). Second, the isolated plasmid DNA is labeled with fluorescent dye and hybridizated to the probes arrayed on a glass slide (center); the colored circle indicates a probe with a significant signal. Third, the signals are quantitated and plotted (right). Strain Bacillus sp. Y7 is one of the subsurface strains that Aspa has been studying. It has at least six different plasmids (left) and one among them, designated Y7-5 carries lead resistance gene as indicated by the circled hybridization signal (center) and the pink bar (right).

These studies are being conducted in collaboration with Dr. Patty Sobecky from Georgia Tech, Dr. Søren Sørensen from the University of Copenhagen , and Dr. Niels Kroer from the National Environmental Research Institute, Denmark with support from the NABIR program of the Dept. of Energy.