People and Contact Information
Principal Investigator
Research Assistant
Paige Swanson
paigekswanson@gmail.com
As a research technician and lab manager, I do many different things in the Marx Lab. Currently, I am working with former postdoc Alex Bradley and graduate student Nigel Delaney to answer questions about Methylobacterium populations that have been evolved experimentally in our lab. I am a recent transplant from Colorado, where I studied Evolutionary Biology at the University of Colorado at Boulder. When not in the lab, you’ll typically find me in the kitchen.
Postdoctoral Fellows
Lon Chubiz
lchubiz (at) fas.harvard.edu
My focus in the Marx Lab is in understanding the genetic and physiological basis underlying adaption. Particularly, how does underlying pleiotropy and epistasis constrain the adaptive trajectories available to an organism challenged with a new environment? Cellular metabolism provides an ideal framework to address this question. Using the aerobic methylotrophMethylobacterium extorquens as model system allows this question to be approached from the perspective of metabolic specialization. By understanding the mechanistic basis for observed phenotypes in evolved populations, I believe answering this question is possible.
Sean Michael Carroll
scarroll (at) oeb.harvard.edu
My work explores how various mechanisms of adaptation lead to improved growth in Methylobacterium extorquens AM1, a model microbe for studies of one-carbon (C1) metabolism and microbial evolution. I study at a systems-level the mechanisms by which strains acclimate and adapt to an engineered C1 metabolism: using whole-genome sequencing, microarray analyses, and quantification of metabolites to connect genotypes to higher-order properties such as growth rate and fitness. In a complementary approach, I use a regulated promoter system to directly modulate the activity of key C1 enzymes and measure the effect of these “idealized mutations” on growth rate and fitness. And with the help of students from this year’s OEB100 (2012) class, I am documenting the genomic and phenotypic changes that our model microbe has undergone during fifty years of life in the lab. Together, I hope to help illuminate how factors such as epistasis, pleiotropy, and clonal interference influence adaptive trajectories and shape microbial functions in the lab, in the wild, or in human health and disease.
William Harcombe
wharcombe (at) oeb.harvard.edu
Microbes are capable of incredible metabolic feats, acquiring energy from a diverse array of compounds. I am interested in how evolution shapes these metabolic capabilities. At the single species level I study how bacteria adapt to acquisition of a novel metabolic pathway. At the multi-species level I study how adaptation alters the productivity of model consortia. Metabolism of various compounds often depends on a complex network of interacting bacteria. I use model microbial assemblages (combinations of E. coli,Salmonella, and Methylobacterium) to test how ecological and evolutionary processes influence community composition and function.
Joshua Michener
michener(at)fas.harvard.edu
I study adaptation following horizontal gene transfer, seeking to understand the co-evolutionary process as a pathway adapts to its new host and a host to its new pathway. Specifically, I’m looking at the growth of Methylobacterium extorquens on a toxic pollutant, dichloromethane. A pathway for dichloromethane utilization exists in one strain of M. extorquens, but does not function when transferred to a closely related strain. I’m using experimental evolution to evolve the pathway in its new host, exploring the adaptive mechanisms and trajectories.
Graduate Students
Dipti Nayak
dnayak (at) oeb.harvard.edu
My research focuses on using experimental evolution to understand microbial physiology. For my PhD I am trying to understand the physiological basis of formaldehyde stress response as well as the genetics of the N-methyl glutamate pathway for methylamine utilization in Methylobacterium extorquens using experimental evolution.
José Rojas Echenique
rojasechenique@fas.harvard.edu
I’m interested in the possible forms that the organisms in a population can take on as they evolve. Conceptually we organize these forms according to their fitness and mutational distance from one another on a fitness landscape. I’m working towards an understanding of the physiological traits and interactions that make up a model fitness landscape: the central carbon metabolism of Methylobacterium extorquens.
http://www.people.fas.harvard.edu/~rojasechenique/
Sarah Douglas
sdouglas@mcb.harvard.edu
“Costly cooperation between unrelated organisms presents a Darwinian dilemma: if natural selection favors individuals with the highest relative fitness, why should an organism increase the fitness of its neighbors? Using a unique bacterial system that allows the de novo evolution of cooperation, I am characterizing the ecological dynamics and molecular mechanisms underlying the rise of this social behavior. I also study how selection sorts variations in cooperative strategies within a population, and how this variation affects resistance to cheater invasion. Knowing how mutational diversity impacts cooperative phenotypes, and how selection acts upon phenotypic variety, will lead to a more accurate understanding of dynamic, ecologically complex systems of cooperation.”
Nicholas Leibyleiby (at) fas.harvard.edu
I’m a PhD student in Systems Biology. I study E. coli evolving over long periods in laboratory conditions, and the tradeoffs that occur in metabolic flexibility in order to optimize for the present environment.
Ying Zhang
zhangying3409 (at ) gmail.com
I’m a PhD student and visiting scholar in the Marx Lab. My research focuses on evolving syntrophic communities that link fermentation to metal reduction. Particularly, iron reducing bacteria that oxidize substrates-generally organic acid produced from fermenting bacteria-to various Fe(Ⅲ)-bearing minerals as terminal electron accepters. I am interested in using “biostimulation” as a strategy to directly spur the metabolic activity of metal reducing bacteria. As the first step, I am now concentrating my effort to find a synthetic consortium comprised of a fermenter and a metal reducing bacteria who are friendly to each other.
Laboratory Assistant
Chris Engles
cengles (at) fas.harvard.edu
When I’m not sterilizing glassware, ordering lab supplies or updating WordPress sites, I’m taking pictures or shooting movies. On weekends I can typically be found at my satellite office.
Former Postdocs:
Alexander S. Bradley (2008-12, now Assistant Professor, Earth and Planetary Sciences, Washington U., MO) http://bradleylab.wustl.edu
Jessica Purswani (2011-12, now postdoctoral fellow, U. Granada, Spain)
Deepa Agashe (2008-11, now Fellow (PI), Ecology and Evolution, National Centre for Biological Sciences, Bangalore, India) http://ncbs.res.in/dagashe
Completed Ph.D. theses:
Nigel F. Delaney (2012, now postdoctoral fellow, Broad Institute, Cambridge, MA)
Ming-Chun “Miki” Lee (2010, now postdoctoral fellow, Biochemistry, U. Hong Kong)
Hsin-Hung “David” Chou (2009, now an EMBO postdoctoral fellow, Inst. Of Molecular Systems Biology, ETH, Zürich)
Visiting Erasmus Mundus M.S. thesis:
Alex Betts (2012-2013, future Ph.D. student, Oxford University)
Özden Baltekin (2011-12, now Ph.D. student, Uppsala U., Sweden)
Completed B.A. theses:
Lewis M. Ward (2010, future Ph.D. student, Geological and Planetary Sciences, CalTech, CA)
David G. Robinson (2009, now Ph.D. student, Quantitative and Computational Biology, Princeton, NJ)
Other former rotation/collaborating graduate students: Zain Ali, Anthony Blair, Hsiao-Han Chang, Delbert “Andre” Green, Arnon Levy, Tami Lieberman, Niall Mangan, Jue Wang
Other former undergraduates: Earl “Alex” Pickett, Chris Ding, Dan Lorenzana, Sherif Gerges, David Guernsey, Ed Kogan, Jessica Berger, Julia Berthet, Kiahana Brooks, Lela Sims, Lucy Liu, Roxana Tarnita, Samantha Parker, Vicky Wu, Will Polachek
Former high school student: Jaya Gandhi
Former technicians: Anthony Blair, Maggie Chen, Melissa Derby, Maryska Kaczmarek(now Ph.D. student, Integrative Biology, U. Texas, Austin)