Vaughn Cooper, Ph.D.

Vaughn Cooper

   Associate Professor

    Rudman Hall, Room 212
    (603) 862-3422
    Lab Webpage

     Educational Background:

     Ph.D., Michigan State University, 2000
     B.A., Amherst College, 1994


Courses Taught:

General Microbiology (MICR 503); Genomes and Bioinformatics (MICR 711/811); Problems in Microbiology (MICR 795); Microbial Ecology and Evolution (MICR/GEN 713/813); Molecular Evolution (GEN 715/815);  Microbiology Seminar (MICR 997); Current Topics in Microbiology (MICR 905); Hot Topics in Microbiology (MICR 906); Fundamentals of Genetics (GEN 604) 

General Area of Interest and/or Specialty:

 Microbial evolutionary genetics: Microbial Population Biology; Mechanisms of pathogenic adaptation 

Research Foci - Environmental Microbiolgy

1.  Adaptation to life in biofilms

As introduction, please see our recent publication (Poltak and Cooper ISME J. 2010) that describes our system for studying long-term evolution in biofilms and the forces governing community assembly. Populations of Burkholderia cenocepacia, known to cause severe infections in patients with cystic fibrosis, underwent more than 1,500 generations of biofilm selection. Diverse communities were more productive in mixture than any single genotype; this synergy was caused by cross-feeding and the partitioning of biofilm space that produce mutualistic interactions.

We are now characterizing the molecular and functional bases of biofilm adaptation as well as the population genetic dynamics by sequencing whole-population metagenomes on the Illumina platform, which allowed us to infer the frequency of adaptive alleles on the basis of their read depth. Notably, some evolved alleles occur in homologs commonly found to mutate in isolates of P. aeruginosa from CF infections, which suggests that biofilm adaptation may occur along conserved pathways.

Some questions that we are currently pursuing include:

  • How and why do Pseudomonas aeruginosa biofilms evolve exceptional diversity?  
  • How do biofilm niche breadth and evolutionary history combine to affect evolvability? How do molecular mechanisms of plasticity evolve?
  • Are similar ecotypes evolved in different biofilm communities functionally interchangeable?
  • Do mixed-species biofilms also evolve similar ecotypes that also enhance community productivity?
  • How does biofilm diversity affect the resilience and pathogenicity of the community in a range of host models?

2.  What is the distribution of pleiotropic effects among beneficial mutations? (NSF CAREER award)

The rare fraction of mutations that are beneficial in any given environment is poorly understood. Even less certain is how these mutations tend to influence fitness in other environments: mutational effects could be limited to a single condition or have widespread consequences in many environments. This project collects many single beneficial mutations from bacterial populations and precisely quantifies their fitness in the selective environment. The pleiotropic (correlated) effects of these mutants are then measured by exposing them to a range of foreign conditions. This project seeks to define the relationship between adaptation and changes in niche breadth and to characterize the biological networks that link genetics, physiology, and ecology.

An important benefit of our approach is that it allows high school and college students to study “evolution in action” and explore the widespread effects of single mutations. We are currently collaborating with three area high schools to develop our protocols. With higher-throughput methods for measuring fitness and identifying mutations, we are now poised to produce the best and most nuanced database of adaptive mutations to address numerous basic problems in evolutionary genetics.

3. How does the environment, both internal and external, determine the effects of beneficial mutations? (A collaborative NSF award with Tim Cooper, Houston and Paco Moore, Akron)

The genetic mutations that underlie adaptation can have different effects depending on the external environment (phenotypic plasticity), their genetic environment (epistasis) or both. We are studying how external and genetic environments affect the contribution of adaptive mutations to an organism's phenotype. We focus on the first five adaptive mutations that fixed in an experimentally evolved E. coli population. We manipulate the external environment by altering the growth-limiting resource, and the genetic environment by introducing the same adaptive mutations into different strains of E. coli within a known phylogenetic context. To test candidate mechanisms underlying interactions between adaptive mutations and their external and genetic environments, we measure fitness and the transcriptome of constructed strains in a common environment. 

4. Ecological population structure of Vibrios and the oyster microbiome - (A collaboration with C. Whistler and S. Jones, UNH).

Changing climate and land use patterns increase the frequency of conditions favorable for Vibrio in estuaries and thus increase the probability of human infections from shellfish consumption. We now must better understand ecological dynamics that drive Vibrio abundance and risk of illness. This project, which uses cutting-edge population genetics and genomics, focuses on how physical factors, such as temperature, salinity, and dissolved nutrients, affect vibrios within the context of other resident microbes within oysters. We hope to use these data to aid development of sensitive and accurate typing methods for pathogenic Vibrios in susceptible ecosystems.  More generally, by examining the interplay of physical conditions and microbial community interactions on the emergence of pathogenic biovars, we will be better equipped to predict broader infectious threats and protect human health.


  1. Traverse C.C., Mayo-Smith L.M., Poltak S.R., Cooper V.S. 2013. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. 2013 Jan 15; 110(3):E250-9. doi: 10.1073/pnas.1207025110. Epub 2012 Dec 27.
  2. Ellis C.N., Schuster B.M., Striplin M.J., Jones S.H., Whistler C.A., and Cooper V.S. 2012. Influence of seasonality on the genetic diversity of Vibrio parahaemolyticus in New Hampshire shellfish waters as determined by multilocus sequence analysis.  Appl Environ Microbiol. 2012 May;78(10):3778-82. doi: 10.1128/AEM.07794-11. Epub 2012 Mar 9.
  3. Morrow J.D. and Cooper V.S. 2012. Evolutionary effects of translocations in bacterial genomes. Genome Biol Evol. 2012 Jan;4(12):1256-62. doi: 10.1093/gbe/evs099.
  4. Schuster B.M., Tyzik A.L., Donner R.A., Striplin M.J., Almagro-Moreno S., Jones S.H., Cooper V.S., and Whistler C.A. 2011. Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates. Appl Environ Microbiol. 2011 Nov;77(21):7568-75. doi: 10.1128/AEM.00378-11. Epub 2011 Sep 16.
  5. Abebe, E, F. Abebe-Akele, J. Morrison, V.S. Cooper, and W.K. Thomas. 2011. An insect pathogenic symbiosis between a Caenorhabditis and Serratia. Virulence. 2011 Mar-Apr; 2(2): 158–161.
  6. Poltak, S.R. and V.S. Cooper. 2011. Ecological succession of long-term experimentally evolved biofilm produces synergistic communities. ISME J. 2011 Mar;5(3):369-78. doi: 10.1038/ismej.2010.136. Epub 2010 Sep 2.
  7. Flynn, K.M, S.H. Vohr, P.J. Hatcher and V.S. Cooper*. 2010. Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus. Genome Biol Evol. 2010;2:859-69. doi: 10.1093/gbe/evq068. Epub 2010 Oct 26.
  8. Jones, S., M. Striplin, J. Mahoney, V.S. Cooper and C.E. Whistler. 2010. Incidence and abundance of pathogenic Vibrio species in the Great Bay Estuary, New Hampshire, pp. 127-134, In, Proceedings of the Seventh International Conference on Molluscan Shellfish Safety. Lassus, P. (Ed.). Nantes, France, June 14-19, 2009. Quae Publishing, Versailles, France.
  9. Schuster, B.M., V.S. Cooper, and C.E. Whistler. 2010. Breaking the language barrier: Experimental evolution of non-symbiotic Vibrio fischeri in squid tailors luminescence to the host. Symbiosis 51, 1, 85-96, DOI: 10.1007/s13199-010-0074-2.
  10. Cooper, V.S, S. Vohr, S.C. Wrocklage, and P.J. Hatcher. 2010. Why genes evolve faster on secondary chromosomes in bacteria. PLoS Comput Biol. 2010 Apr 1;6(4):e1000732. doi: 10.1371/journal.pcbi.1000732.
  11. Ellis, C.E. and V.S. Cooper. 2010 Experimental adaptation of Burkholderia cenocepacia to onion medium compromises host range. Appl Environ Microbiol. 2010 Apr;76(8):2387-96. doi: 10.1128/AEM.01930-09. Epub 2010 Feb 12
  12. Cooper, V.S., W.A. Carlson, and J.J. LiPuma. 2009. Susceptibility of Caenorhabditis elegans to Burkholderia infection depends on prior diet and secreted bacterial attractants. PLoS ONE 4(11): e7961. doi:10.1371/journal.pone.0007961
  13. Cooper, V.S. 2007. Experimental evolution of pathogens. Encyclopedia of Infectious Disease, Michel Tibayrenc, editor. Wiley, New York.
  14. Cooper, V. S. 2006. The study of microbial adaptation by long-term experimental evolution. The Evolution of Microbial Pathogens, Hank Seifert and Victor DiRita, editors. ASM Press.
  15. Cooper, V.S. and J.J. LiPuma. 2005. Liquid C. elegans culture for the study of Burkholderia pathogenesis. 10th Annual Meeting, International Burkholderia cepacia Working Group. Oklahoma City, OK.
  16. Cooper, V.S., E. O. Romero, and J.J. LiPuma. VNTR-based typing of Burkholderia cenocepacia. 9th Annual Meeting, International Burkholderia cepacia Working Group. 2004. Vancouver, B.C.
  17. Cooper, V. S. Long-term experimental evolution in Escherichia coli. X. Quantifying the fundamental and realized niche. 2002. BMC Evol Biol. 2002 Aug 22;2:12.
  18. Cooper, V. S., M. H. Reiskind, J. A. Miller, K. A. Shelton, B. A. Walther, J. S. Elkinton, and P. W. Ewald. 2002. Timing of transmission and the evolution of virulence of an insect virus. Proc Biol Sci. 2002 Jun 7;269(1496):1161-5.
  19. Cooper, V. S., A. F. Bennett and R. E. Lenski. 2001. Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment. Evolution 55(5):889-896.
  20. Cooper, V. S., D. Schneider, M. Blot, and R. E. Lenski. 2001. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of E. coli B. J Bacteriol. 2001 May;183(9):2834-41.
  21. Riley, M. S., V. S. Cooper, R. E. Lenski, L. J. Forney and T. L. Marsh. 2001. Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution. Microbiology. 2001 Apr;147(Pt 4):995-1006.
  22. Cooper, V. S. and R. E. Lenski. 2000. The population genetics of ecological specialization in evolving Escherichia coli populations. Nature. 2000 Oct 12;407(6805):736-9.
  23. Turner, P. E., V. S. Cooper, and R. E. Lenski. 1998. Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Evolution 52(2): 315-329.
  24. Elena, S. F., V. S. Cooper, R. E. Lenski. 1996. Mechanisms of punctuated evolution (technical comment). Science 274:1748-1750.
  25. Elena, S. F., V. S. Cooper, R. E. Lenski. 1996. Punctuated evolution caused by selection of rare beneficial mutations. Science 272:1802-1804.