The Cohan Lab at Wesleyan University studies the origins of ecological diversity in bacteria, using the Bacillus of Death Valley soils as a model system. We are also exploring the diversity of bacteria that can help bioremediate environmental plastic. Finally, we are studying the evolution of sporulation and germination behavior in Bacillus.
Bacillus genomes and ecology. (This is the work of a team of Masters’ and undergraduate students, mentored by me and my colleague Danny Krizanc.) We are exploring the origins of bacterial species, using Death Valley Bacillus as a model system. Our approach is to identify the most newly divergent “ecotypes,” which have species-like properties, and to investigate what is genetically and ecologically distinct about them. We are analyzing several hundred genomes of strains we have isolated from Death Valley, covering various elevations from the valley floor (below sea level) to higher elevations, from 900 to 3000 meters, with samples from rhizosphere soil (root soil) and bulk soil (not attached to roots). We have used the genomes to produce an evolutionary tree for each of three focal species, based on the set of shared genes throughout the genome. We have used our algorithm, Ecotype Simulation, to hypothesize the demarcations of ecotypes. We are now exploring whether we have fully enumerated the ecotypes within our focal Bacillus species.
We are on the path toward fully describing these ecotypes and adding them to the lexicon of bacterial systematics. First (and this part is completed), we have shown that the ecotypes differ in their associations with habitats. That is, some ecotypes are specialized on lower elevations and others on higher elevations, while some are specialized to rhizosphere and others to free soil. This involved developing a novel algorithm for taking into account the phylogenetic structure of the tree when analyzing habitat differences. We are now describing the ecotypes based on their preferred habitats and their gene content.
Plastic bioremediation. (This is the work of my PhD student, Fatai Olabemiwo, and his team of undergraduates.) We are aiming to develop Bacillus strains with the dual functions of promoting the growth of agricultural plants while also degrading nanoplastics on agricultural fields. This project began with our discovery that some but not all plant-growth-promoting Bacillus strains we studied can utilize plastic in their growth. We then aimed to improve the ability of the plastic-degrading strains (dubbed plastivores) to degrade plastics more fully. Our approach was to subject these strains to laboratory culture where plastics are among their potential resources. We have developed plant-growth-promoting Bacillus strains with improved plastic degradation.
Another direction of the plastivore project has been to identify and characterize plastic-degrading bacteria that we have collected from the nearby Portland, Connecticut landfill. We have developed a novel approach (a modified Winogradsky column) for enriching for plastic-degrading bacteria, and we have shown that our approach is indeed successful at increasing the yields of genes involved in plastic degradation. We have isolated over 200 strains of bacteria from our modified Winogradsky columns, and we have shown that many of them have the capacity to oxidize plastics in the environment. We have produced metagenomes (a way to sequence many of the genes from a community without cultivating the bacteria) from the landfill bacteria. The metagenomes have enabled us to produce full genome sequences of the most abundant species (metagenome-assembled genomes, or MAGs). We were delighted to find that, through the metagenomes, we have discovered and genome-sequenced three novel bacteria phyla, as well as dozens of novel genera, all with the capacity for plastic degradation. We are working to introduce them into the systematics of bacteria.
Finally, we are analyzing the metatranscriptomes from the landfill bacteria. The metatranscriptomes are giving us the full set of gene expression from the landfill’s bacterial community, comparing when the bacteria are cultured on plastic versus when they are cultured on glucose. Our hope is that we will discover novel genes involved in plastic degradation in this way, and this approach has given us thousands of genes not previously known to be involved in plastic degradation. We suspect that a small fraction of these genes are directly involved in plastic degradation, while most are probably adaptations to living in a plastic-enriched environment.
Genome tiling. (This is the work of my undergraduate student, Jocelyn Wang, mentored by me and my colleague Danny Krizanc.) We are beginning a new project, which we call the Genome Tiling project, aimed to find whether bacterial species form sequence clusters based on their genomes’ shared genes. Some of our colleagues have previously made a case that bacterial species form discrete clusters based on their genome sequences, but the previous work may be biased by including only the most abundant and easily cultured species. We have an unbiased plan to utilize our isolates and MAGs from the Portland landfill to compare genomes against the uncultivated members of their own communities.
Evolution of sporulation and germination behavior in Bacillus. (This is the PhD project of my PhD student, Katie Sagarin, and her team of undergraduates.) The spore stage allows Bacillus to endure heat and desiccation during long, hot droughts of the desert, and it is particularly important to note that the bacteria must “decide” to form spores or to germinate in an uncertain, stochastic environment. We have challenged the bacteria to adapt to an environment that has predictable and constant changes, using a batch culture approach. Here, bacteria are inoculated into a rich medium and then are cultured for a constant number of hours, and then are diluted into fresh medium. We have shown that the length of time that the bacteria must live in used, spent medium has a dramatic effect on their sporulation and germination behavior.