The School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign

Bacteria and Archaea represent the vast majority of biodiversity on Earth. In fact, the closer we look at microbial populations, the more diversity we see. For example, microbial environmental genomics, is uncovering patterns of sequence variation (microdiversity) within species that were once assumed to be homogeneous. Making sense of this diversity will require identifying the ways that dynamic ecological and evolutionary processes interact in the natural microbial world. Because microorganisms are integral parts of all ecosystems on earth, understanding these interactions will have great implications across basic and applied biological systems.

My lab focuses on the evolutionary ecology of microbial populations. We combine field sampling of natural populations with culture and non-culture based genetic and genomic analyses. Currently we are working on understanding how the interactions between basic population genetic parameters (mutation, selection, recombination and genetic exchange, neutral genetic drift, and biogeography) shape diversity, promote ecological differentiation, and lead to speciation in the microbial world. Ultimately we will develop a comparative approach, describing natural population dynamics of different species across spatial and temporal scales, with a particular interest in how population structures reflect the unique biology and ecology of organisms in the Archaeal domain.

        Typical Sulfolobus Habitat                          Sampling in Lassen National Park

Current Projects:

Population genomics of Sulfolobus islandicus.

We are investigating the tempo and mode of archaeal genome evolution through comparative genomics of eight closely related Sulfolobus islandicus strains from biogeographically isolated geothermal environments. We are using this data to quantify the rate of horizontal gene transfer and other genome level dynamics over geologically-defined time scales.

We welcome you to explore these genomes yourself at http://www.life.illinois.edu/sulfolobus_islandicus/

Recombination in S. islandicus

We have completely sequenced 12 new genomes of Sulfolobus from the same environment in order to quantify rates of recombination, identify genes under selection and determine the effects of virus-host co-evolutionary dynamics within a single population.

Coevolutionary interactions between Sulfolobus islandicus and its viruses.

We are investigating local adaptation in the coevolutionary interactions between Sulfolobus islandicus and mobile genetic elements such as plasmids, viruses and transposable elements. We are identifying to what extent the biogeographic distribution of mobile elements is determined by the biogeography of its hosts. We are investigating variation in the Sulfolobusimmune systems that may be responsible for defining the patterns of coevolutionary interactions.

Effects of disturbance on microbial populations.

Lake ecosystems are primary indicators of ecosystem health and response to climate change. We are investigating the population dynamics of bacterial and archaeal species in humic bogs in northern Wisconsin. We are using molecular tools to study how disturbances are introduced by seasonal mixing of the water column in fall and spring effect diversity within and between lake populations. We are investigating the balance between immigration and adaptation in microbial populations and how microbial population diversity relates to community diversity through a collaborative Microbial Observatory grant with other research labs at the University of Illinois and the University of Wisconsin.

North Sparkling Bog Minocqua, Wisconsin

Listen to an interview with Dr. Whitaker featured on MicrobeWorld – Meet the Scientist MTS8. February 18, 2009. http://www.microbeworld.org.

Learn more about Microbial Ecology and Evolution at Illinois at http://mcb.illinois.edu/microecology

Representative Publications

Hinsby Cadillo-Quiroz, Xavier Didelot, Nicole L. Held, Alfa Herrera, Aaron Darling, Michael L. Reno, David J. Krause, Rachel J. Whitaker. 2012. Patterns of Gene Flow Define Species of Thermophilic Archaea. PLoS Biol 10(2): e1001265. doi:10.1371/journal.pbio.1001265 [FULL TEXT]

Lauren Childs, Nicole L. Held, Mark I. Young, Rachel J. Whitaker * and Joshua S. Weitz *. Multi-scale Model of CRISPR-induced Co-evolutionary Dynamics: Diversification at the Interface of Lamarck and Darwin. (in press Journal of Evolution).* co-corresponding authors.

Rachel J. Whitaker. A new age of naturalists. 2011. Microbe Magazine. (in press).

Rachel J. Whitaker. Crystal Ball-2011: An appreciation for natural variation. 2011. Environmental Microbiology. Volume 3, Issue 1, Pages: 1–26.

N.L. Held, A. Herrera, H. Cadillo-Quiroz, R.J. Whitaker. CRISPR associated diversity within a natural population of Sulfolobus islandicus. (2010) PLoS ONE. 5(9): p. e12988.

K. Milferstedt, N. Youngblut and R.J. Whitaker. Spatial scaling and persistence in methanogen populations from humic bog lakes. ISME Journal (2010) 4(6): 764-776. [Abstract]

R.J. Whitaker.  Evolution: spatial scaling of microbial interactions.  Current Biology. (2009) 19 (20). R954-6. [Abstract]

M.L. Reno, N.L. Held, C.J. Fields, P.V. Burke and R.J. Whitaker. Biogeography in the pan-genome of Sulfolobus islandicus. Proceedings of the National Academy of Sciences U.S.A (2009) 106 (21) 8605-8610. [Abstract]

N.L. Held and R.J. Whitaker. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environmental Microbiology (2009) 11:457-466. [Abstract]

J.L. Green, B.J.M. Bohannan and R.J. Whitaker. Microbial Biogeography: Taxonomy to Traits. Science (2008) 320 (5879): 1039-43. [Abstract.]

E.E. Allen, G.W. Tyson, R.J. Whitaker, C. Detter, P. Richardson and J.F. Banfield. Recent evolutionary modes deduced by isolate vs. strain population comparative genomics. Proceedings of the National Academy of Sciences U.S.A. (2007) 104(6): 1883-8. [Abstract]

R.J. Whitaker. Allopatric origins of microbial species. Philosophical Transactions of the Royal Society B (2006) doi:10.1098/rstb.2006.1927. [Abtract]

R.J. Whitaker and J.F. Banfield. Population genomics in natural microbial communities. Trends in Ecology and Evolution (2006) 21(9):508–16. dio:10.10.16/j.tree..2006.07.001. [Abstract]

R.J. Whitaker and J.F. Banfield. Population dynamics through the lens of extreme environments. Molecular Geomicrobiology, Reviews in Minerology, and Geochemistry (2005) 59: 259–277. [Abstract]

R.J. Whitaker, D.W. Grogan and J.W. Taylor. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Molecular Biology and Evolution (2005) 22:2354–61. [Abstract]

R.J. Whitaker, D.W. Grogan and J.W. Taylor. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science (2003) 301: 976–8. [Abstract]

Complete Publications List