Evolutionary genetics, speciation, adaptive radiation and biogeography of bacteria. Model systems: Bacillus from Death Valley, Cyanobacteria from Yellowstone, and plastic-degrading bacteria from local landfills.
Our lab aims to identify the ecologically distinct bacterial groups (ecotypes) within a community and to determine what differences allow them to coexist; we also aim to identify the processes by which one ecotype splits to become two irreversibly separate lineages. Much of our recent research has aimed to develop a theory of bacterial species and speciation, for the purpose of identifying and characterizing these ecotypes and their origins. For the purposes of our studies in speciation, we define an ecotype as an ecologically homogeneous group of closely related bacteria and we consider each ecotype to be a species.
We are using Bacillus from desert soils in Death Valley as a model system to study the origins of bacterial species. In particular, we are studying Bacillus isolated along a salinity gradient and from rhizospheres of various plants and at different elevations to study central issues of bacterial speciation.
First, we are aiming to identify the ecotypes that are adapted to different organic resources and/or are adapted to different physical conditions. We are whole-genome analyses to hypothesize ecotype demarcations, using Ecotype Simulation (which our lab developed and is continuing to improve) and other sequence-based ecotype-demarcating algorithms. We are also identifying ecotypes by their unique microhabitat associations, as determined by soil chemistry and physical structure as well as by rhizosphere and elevation associations. Finally, we are identifying ecotypes by their genome content, in particular with regard to genes most likely to determine ecological function.
Second, we are aiming to determine the ecological dimensions by which ecotypes diverge. Of particular interest is whether newly divergent species have most frequently diverged with respect to the organic resources they utilize or instead by the physical conditions that they can tolerate.
Third, we are testing alternative theories of bacterial speciation. Of particular interest are the Stable Ecotype model (where ecotypes are long-standing and are recurrently purged of diversity by periodic selection), the Species-Less model (where ecotypes are not subject to cohesive forces), and the Nano-Niche model (where most-closely-related ecotypes are only quantitatively different in their ecological niches).
Fourth, we are developing a systematics of Bacillus at the ecotype level. Here we are naming and describing the ecotypes within a recognized species. We see this as a model system to encourage other microbial ecologists and systematists to describe the many ecologically distinct, infraspecific lineages they discover within the recognized bacterial species.
Finally, we are working to develop bacterial bioremediators of environmental plastic. We have developed a novel approach to enriching for plastic-degrading soil bacteria, and we have discovered a dozen novel phyla as well as hundreds of novel genera. We aim to describe these novel organisms following the SeqCode approach to classifying bacteria using only their genome sequences.
Our recent papers may be accessed here (not up to date): https://fcohan.faculty.wesleyan.edu/publications-2/