Research Topics

Genetics, Genomics, Microbial Ecology, Molecular Evolution

B.S. Ecology Ethology and Evolution, University of Illinois, 2000
PhD Plant Biological Sciences, University of Minnesota, 2002-2007
Postdoc, University of Toronto, 2007-2009

Evolutionary genetics of plant-microbe symbiosis

The organisms we observe in the world around us are awash in symbiosis. Each plant, animal, or fungus we can see is really a mixed community of its own cells and a diverse community of microbes that live in and on it. These microbes can have beneficial effects wherein they increase host fitness, or they can decrease host fitness, or even have little effect. We study plants, bacteria, and fungi and the symbiotic interactions among them from several evolutionary, genetic/genomic, and ecological angles. One of our key systems is the nitrogen-fixing symbiosis between leguminous plants and rhizobial bacteria (Figure 1). This symbiosis is critical in earth’s nutrient cycles: rhizobia are the main source of fixed nitrogen on land (aside from industrial fertilizers), and legume crops and nitrogen fixing bacteria are important components of sustainable agriculture. Despite over 100 years of investigation, many questions remain about how these mutualistic partners interact, how their interactions vary across different abiotic and biotic environments, and how this variation leads to different evolutionary outcomes. Because all organisms are symbiotic by nature, understanding how symbiosis evolves is of utmost importance, particularly in light of global change, which is rapidly altering the selective environments for so many organisms. Rhizobial bacteria are a diverse and interesting group of bacteria that live dual lives, residing in the soil sometimes and forming symbiosis with host plants sometimes. For this reason, they have rather large, multi-part genomes whose dynamics are interesting in their own right. We are trying to integrate these interesting dynamics (plasmid transfer and other recombination events) into our understanding of symbiosis evolution.

Some big research questions that motivate research in the Heath lab:

• What is the molecular basis of symbiosis variation: what naturally-occurring allelic variation results in the phenotypic variation on which natural selection acts in natural populations? Is this variation regulatory, structural, both?
• For rhizobia, which often have housekeeping and symbiosis genes on separate genome elements, do coevolutionary dynamics occur between the plasmid(s) and chromosome, and how do these dynamics influence symbiosis with plants?
• How do the benefits exchanged in mutualistic symbiosis evolve: and how do these interactions remain beneficial through millions of years of (co)evolution?
• What aspects of the environment alter mutualism evolution: Nutrient environment? Presence of additional mutualists or antagonists?
• How do different plant symbionts (bacteria and fungi above and belowground) interact with each other to affect plant health, including resistance to pathogens?
• How do plant hosts evolve to modulate interactions with multiple microbial partners, particularly given pleiotropy in the plant signaling genes that mediate different symbioses?

To answer our research questions, our lab takes an integrative approach that combines top-down (phenotype-focused) and bottom-up (genome-focused) methods in evolutionary genetics including:

• Population genomics: Whole genome re-sequencing of bacterial and plant genomes from natural populations.
• Quantitative genetics: common garden experiments in the field, incubator, growth chamber, or greenhouse.
• Host inoculations: Manipulative cross-inoculation experiments in the field and greenhouse to study the effects of microbes and their interactions on plant health.
• Trait mapping: Developing a genotype-phenotype map of symbiotic phenotypes using QTL and GWAS mapping approaches to discover the allelic variants that control important traits.
• Transcriptomics and metabolomics: Using RNAseq and metabolite analysis to understand the physiological basis of symbiosis variation.

286 Morrill Hall
505 S. Goodwin Ave
Urbana, IL 61801