To better understand those traits bacteria require for growth and survival on leaves we have done extensive work to address the nature of the "microhabitats" in which bacteria live on leaves. We have shown that measures of such factors as carbon source abundance on a leaf as a whole are not predictive of the environment of bacteria at the very small scales at which they live. To address this we have developed new tools for the study of the expression of bacterial genes while bacteria reside in natural habitats such as on leaves or in the soil. I have shown that bacterial ice nucleation genes have properties that make them excellent reporters of the transcriptional activity of other genes to which they are fused. I thus have advanced the application of "reporter genes" to the study of microbial ecology in natural habitats.
For example, by fusing environmentally-responsive promoters to ice nucleation or gfp reporter genes in bacteria to produce "biosensors" we can assess the response of individual bacteria to its local environment. This work has led us to make the descriptions of the actual concentration of important nutrients such as ferric iron, fructose, ammonium ions, nitrate, and sucrose on plants at the scale of individual bacterial cells. Our recent use of use of modified gfp reporter genes with altered stability in cells, in particular, has provided unprecedented insight into the world of microbes in natural habitats. We are finding that a given habitat such as a leaf or root is extraordinarily diverse in the number of sites where resources such as sugars are available as well as the amounts of such resources at a site. In essence we find that a given root or leaf harbors thousands of individual "universes" where bacteria live in isolation of other microbes and where they compete only locally with one another. It is through understanding of such small-scale spatial processes that we should be able to progress toward understanding how we can change the normal microbial communities on leaves to avoid plant pathogenic bacteria and ice nucleation active bacteria that can be harmful to plants. Clearly, patterns of competition and secondary metabolite production are much more complex than others had anticipated.
Several other such studies on the nature of plant habitats at small scales are underway. These will continue to be a major focus of the lab in the near future since they should provide useful information to better understand the natural world at the very small scale in which cells live in natural habitat