My research is broadly motivated by the desire to understand how abiotic and biotic factors shape organismal evolution and phenotypic expression. My work spans scales of inquiry ranging from genes to communities and I use a diverse set of tools including manipulative experiments, mathematical modeling, and genomics/transcriptomics. To date, I have leveraged two model genetic systems to explore ecological and evolutionary questions:

  1. A rhizobium/legume system where the genes underlying the resource mutualism between these two organisms have been extensively studied
  2. Arabidopsis thaliana a genetic model organism where the gene networks underlying life-cycle transitions have been intensively studied

Evolutionary ecology of the rhizobia/legume mutualism


When living in symbiosis with legume hosts, rhizobial bacteria convert atmospheric nitrogen into a plant-available form. In exchange, rhizobia receive carbon in the form of dicarboxylates and a favorable environment for reproduction. Rhizobia do not always live in symbiosis and the majority of the population at any given time are free-living microbes in the soil. Little is known about how adaptation to the free-living environment affects the stability of the mutualism or the extent to which host genotype mediates competitive outcomes between closely related microbial strains.


  • Novel ‘Select and Re-sequence’ methodology to:
    • Measure rhizobial fitness in symbiotic and free-living environments and use them to infer the strength of selection and fitness tradeoffs (Burghardt et al. 2018, PNAS)
      • Measure rhizobial interactions with closely related strains
      • Identify key drivers of mutualism evolution
      • Study bacterial adaptation to abiotic factors and microbiome manipulations
    • Genomic basis of host-strain specificity (w/ Diana Trujillo & Nevin Young)
    • Test evolutionary and ecological consequences of host/free-living environmental cycles (Burghardt et al. in review, Evolution)
  • The transcriptomic basis of host genome by symbiont genome interactions in Medicago truncatula nodules (Burghardt et al. 2017, Molecular Ecology)
  • GWAS to determine the genetic architecture of and identify natural genetic variation underlying rhizobial fitness, plant benefit, stress and metabolic tolerance traits (Burghardt et al. 2018, PNAS; Epstein, Burghardt et al. 2018, mSphere)
  • Generation of mutants and validation of bacterial candidate genes from the GWAS (w/ Mike Sadowsky and Ping Wang)
  • Agricultural Applications:
    • Evolution-enabled management of beneficial inoculants
    • Symbiont-informed legume crop development
    • Use of cover crops for soil health for maintenance of specific rhizobial strains

Life cycle phenology of Arabidopsis thaliana: environmental and genetic contributions across landscapes

In annual plants, the timing of germination, flowering, and seed dispersal define the life cycle and the timing of these developmental transitions (phenology) exhibits plasticity in response to altered climatic conditions, whether caused by climate change or by dispersal into new locations. The timing of these transitions is critical because for these sessile organisms they define the seasonal conditions that each life stage must survive through. What factors shape when organisms transition from life stage to life stage? How do these transitions function together across the range of a species to determine life cycles?  How will climate change and long-distance/human-mediated dispersal influence life cycles? And ultimately, how does changing life-cycle expression change fitness? Further, as the word life cycle itself emphasizes, life cycles are inherently cyclical and yet they are often studied linearly in ways that de-emphasize connections between generations. How important are these trans-generational connections for life-cycle expression?



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