Research

The Marx laboratory uses experimental evolution as an approach to address the selective pressures and varied outcomes of adaptation of microbial populations. Current projects include:

  • Systems-level physiological basis of selection and epistasis in adaptation of strains bearing engineered horizontal gene transfers. Can we move toward being able to quantitatively predict the probability of various evolutionary outcomes, and how the mutations along these trajectories interact?
  • Experimental evolution of multi-species, synthetic consortia to integrate studies of the physiological, ecological and evolutionary aspects of cooperation and coevolution in microbial communities. Can metabolic models guide predictions as to the function and adaptation of novel assemblages, particularly conditions where costly cooperation is selectively advantageous?
  • Distribution of fitness effects, identity and interaction of beneficial mutations available for adaptation. How can we characterize the raw material available for adaptation and how this changes as adaptation to a particular environment slows down?
  • Investigation of fitness tradeoffs and adaptive diversifications associated with specialist vs. generalist lifestyles. Can we predict when to utilize more than one substrate simultaneously vs. forming independent ecotypes?
  • Transposable elements as key variation in adaptation. What roles do mobile elements play in the evolution of laboratory and natural populations?
  • Balance of costs and benefits associated with gene expression and codon usage. What drives selection upon codon usage in genomes?
  • Physiological function of hopanoids in Methylobacterium. What role do these key geological biomarkers play in this present-day model organism, and what inferences can thus be drawn about ancient environments?

Funding Resources:

  • 2010-2013       National Science Foundation: “Hopanoid Physiology: Implications for Microbial Life on the Early Earth” (co-PI: Ann Pearson, Harvard, EAR-1024723)
  • 2010-2013       Department of Energy: “An open source platform for multi-scale spatially distributed simulations of microbial ecosystems” (PI: Daniel Segrè, Boston U., co-PI: Nathaniel C. Cady, U. Albany, DE-SC0004962)
  • 2009-2014       National Science Foundation: “CAREER: Distribution of Fitness Effects, Identity and Interaction of Beneficial Mutations Available for Adaption.” (DEB-0845893)
  • 2009-2011       National Institutes of Health: ARRA Supplement to “Systems-level physiological basis of selection and epistasis in adaptation.” (3R01 GM078209-03S1)
  • 2007-2012       National Institutes of Health: “Systems-level physiological basis of selection and epistasis in adaptation.” (co-PI: Daniel Segrè, Boston U., 1R01 GM078209-01A1)
  • 2006-2007       The Clark/Cooke Fund: “Evolution of metabolic specialization and tradeoffs in laboratory populations.”
  • 2006-2007       National Science Foundation: Microbial Biology Special Starter Grant: “Adaptation, tradeoffs and specialized metabolism in experimental and natural populations.” (IOB-0612591)
  • 2006                The William F. Milton Fund: “Influence of environmental factors on the emergence of cooperation and coevolution in defined, multi-species microbial consortia.”