My initial training as a biological engineer kindled my interest in trying to understand environmental processes by unraveling the molecular machinery at their basis. Based on this background and the appreciation of the important roles of microbes in nature’s geochemical cycles, my current research focuses on the connection between microbial genome evolution and altered ecological behavior. Improved insights into how microbial communities function and respond to change might inform microbial resource management strategies, particularly in the context of climate change mitigation. Increasing evidence, including from my own work, indicates that subtle genetic variation between closely related microbial populations can significantly affect their environmental distribution, and alter their response to perturbations. These observations lead to the question at what level of resolution microbial communities need to be studied to draw meaningful correlations between ecological phenomena and system function. Yet, studies within ecosystem context that focus on the effects of strain dynamics on function remain scarce.
Work in my laboratory focuses on questions at the interface of evolution and ecology:
(i) How do fine-scale evolutionary processes impact ecological differentiation?
(ii) What is the impact of strain-level ecological differentiation on community functioning?
(iii) how does human disturbance of the local and global environment drive microbial evolutionary trajectories?
Denef V.J., J.F. Banfield. 2012. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336(6080):462-6
Morowitz, M.J., V.J. Denef, E. Costello, B. Thomas, D.A. Relman, J.F. Banfield. 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A 108(3): 1128–1133
Denef, V.J., Mueller, R.S., and Banfield J.F. 2010. Winogradsky review: AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J. 4(5):599-610.
Denef, V.J., L. Kalnejais, P., Mueller, R.S., Wilmes, B. Baker, Brian C. Thomas, N.C. VerBerkmoes, R.L. Hettich, and J.F. Banfield. 2010. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A 107(6):2383-90.
Denef, V.J., N.C. VerBerkmoes, M.B. Shah, P. Abraham, M. Lefsrud, R.L. Hettich, and J.F. Banfield. 2009. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol. 11(2), 313-325.