R. Thane Papke

Associate Professor

University of Connecticut
Department of Molecular & Cell Biology
91 North Eagleville Road, Unit 3125
Biology/Physics Building 402
Storrs, CT 06269-3125

Telephone: 860-486-7963
Fax: 860-486-4331

Visit Associate Professor Papke’s Website.


Education: Ph.D.: Department of Microbiology, Montana State University, Bozeman, MT; Postdoctoral Training: Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia

Research Interests: Although we recognize names of microorganisms like Escherichia coli and Bacillus subtilis, our ability to classify strains into “natural kinds” is rigorously tested by the observation that genetic variation is frequently shuttled across so-called species boundaries. Also, much of what we know about species comes from well-studied pathogenic bacteria, which are often classified by the disease that they cause (e.g., Bacillus anthracis or Neisseria gonorrhoeae). This is important to doctors and their patients but the Earth’s biomass and diversity is comprised mainly of prokaryotes, the vast majority of which do not cause disease. Combined, these observations suggest that our understanding of species evolution is relatively shallow and that our current standards of classification are biased and difficult to apply to most microbes. The main goal of our research is to use evolution and ecology theory in combination with approaches like genomics, metagenomics and population genetics to investigate intra and inter species variation, gene flow and genetic relationships for non-pathogenic (e.g., environmental) prokaryotes. We concentrate on hypersaline adapted Archea (Haloarchaea) as model organisms because they live in island-like habits which aid in simplifying or sorting the evolutionary forces that effect their distributions, adaptations and variation.

Selected Publications:

Ram-Mohan, N., Oren, A., and Papke, R.T. (2016) Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizer pond in Eilat, Israel. Extremophiles DOI: 10.1007/s00792-016-0864-4.

Paulina Corral, Rafael R. de la Haba, Cristina Sanchez-Porro, Mohammad Ali Amoozegar, R. Thand Papke, and Antonio Ventosa. (2015) Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake.  IJSEM, doi: 10.1099/ijsem.0.000738

Ventosa, A., De la Haba, R.R., Sánchez-Porro, C. and Papke, R.T. (2015) Microbial diversity of hypersaline environments: a metagenomic approach. Current Opinions in Microbiology.25:80-87

Papke, R.T., Corral, P., Ram-Mohan, N., de la Haba, R.R., Sánchez-Porro, C., Makkay, A. and Ventosa, A. (2015) Horizontal gene transfer, dispersal and haloarchaeal speciation. Life 5:1405-1426.

Chimileski S and Papke RT (2015) Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions. Front. Microbiol. 6:362. doi: 10.3389/fmicb.2015.00362

Ouellette, M., Jackson, L., Chimileski, S. and Papke, R.T. (2015) Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.  Frontiers in Microbiology  doi: 10.3389/fmicb.2015.00251.

Corral, P., de la Haba, R.R., Sánchez-Porro, C., Amoozegar, M.A., Papke, R.T., and Ventosa, A. (2015) Halorubrum persicum sp. nov., an extremely halophilc archeaon isolated from sediment of a hypersaline lake.  IJSEM doi:10.1099/ijs.0.000175.

Fernández, A., Vera-Gargallo, B., Sánchez-Porro, C., Ghai, R., Papke, R.T., Rodriguez-Valera, F., and Ventosa, A. (2014) Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach.  Frontiers in Microbiology.

Chimileski, S., Dolas, K. Naor, A. Gophna, U., and Papke R.T. (2014) Extracellular DNA metabolism in Haloferax volcanii.  Frontiers in Microbiology: 5:57.

Ouellette, M., Makkay, A., and Papke, R.T. (2013) Dihydroxyacetone metabolism in Haloferax volcanii. Frontiers in Microbiology: doi: 10.3389/fmicb.2013.00376.

Papke, R.T., De la Haba, R.R., Infante, C., Perez, D., Sánchez-Porro, C., Lapierre, P, and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Marinobacter lipolyticus strain SM19. Genome Announcements 1:e00379-13.

De al Haba, R.R., Sánchez-Porro, C., León, M.J., Papke, R.T. and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Pseudoalteromonas ruthenica strain CP76. Genome Announcements. 1:e00268-13

Zhaxybayeva, O., Ram Mohan, N., Stepanauskas, R. and Papke, R.T. (2013) Cell sorting analysis of geographically separated hypersaline environments.  Extremophiles. 17:265-275.

Williams, D., Gogarten, J.P. and Papke, R.T. (2012) Quantifying chimerism in haloarchaea: homologous replacement of loci between species.  Genome Biology and Evolution. 4:1223-1244.

Luk, A.W.S., Williams, T.J., Erdman, S., Papke, R.T., and Cavicchioli, R. (2014) Viruses of Haloarchaea. Life. doi:10.3390/life4040681

Chimileski S, Franklin MJ amd Papke RT (2014) Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer. BMC Biology 12:65. doi:10.1186/s12915-014-0065-5

Shannon M. Soucy, Matthew S. Fullmer, R. Thane Papke and Johann Peter Gogarten: Inteins as indicators of gene flow in the halobacteria. Frontiers in  Microbiol ogy  5: 299, 25 June 2014 | doi:10.3389/fmicb.2014.00299

Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, et al. (2014) DNA as a Phosphate Storage Polymer and the Alternative Advantages of Polyploidy for Growth or Survival. PLoS ONE 9(4): e94819. doi:10.1371/journal.pone.0094819 

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT:
Population and genomic analysis of the genus Halorubrum.
Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140

Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP and Papke RT (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front. Microbiol. 5:143. doi: 10.3389/fmicb.2014.00143

Noar, A., Mevarech, M., Lapierre, P., Papke, R.T., and Gophna U. Efficient Interspecies recombination in halophilic Archaea and the formation of recombinant hybrids. Current Biology.

Andam, C.P., Harlow, T.J., Papke, R.T., and Gogarten, J.P. Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales. BMC Evol. Biol.

Papke, R.T. and Gogarten, J.P. (2012) Perspective: Biased exchange groups causes the appearance of prokaryotic lineages. Science 336:45-46.

Ghai, R., Pasic, L. Fernandez, A.B., Martin-Cuadrado, A., Mizuno, C., McMahon, K., Papke, R.T., Stepanauskas, R., Rodriguez-Brito, B., Rohwer, F., Sanchez-Porro, C., Ventosa, A., and Rodriguez-Valera, F. (2011) New abundant microbial groups in aquatic hypersaline environments. Scientific Reports 1:135.

de la Haba, R.R., Marquez, M.C. Papke, R.T. and Ventosa, A. (2011) Multilocus sequence analysis (MLSA) of the family Halomonadaceae. International Journal of Systematic and Evolutionary Microbiology. (published ahead of print April 8, 2011, doi:10.1099/ijs.0.032938-0)

Papke, R.T., White, E., Reddy, P., Weigel, G., Kamekura, M., Minegishi, H., Usami, R., and Ventosa, A. (2011) A multilocus sequence analysis (MLSA) approach to Halobacteriales phylogeny and taxonomy. International Journal of Systematic and Evolutionary Microbiology. 61:2984-2995.

Bahl, J., Lau, M.C.Y., Pointing, S.B. Smith, G.J.D., Vijaykrishna,D., Cary, S.C., Chan, Y. Lacap, D.C., Lee, C.S., Papke, R.T., Warren-Rhodes, K.A., Wong, F.K.Y. and McKay, C.P. (2011) Ancient origins determined global biogeography of hot and cold desert cyanobacteria. Nature Communications. 2:163 DOI:10.1038/ncomms1167.

Naor, A., Lazary, R., Barzel, A., Papke, R.T., Gophna, U. (2011) In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii. PLoS One. 6:1 e15833.

Zhaxybayeva, O. Doolittle, W.F., Papke, R.T. & Gogarten, J.P. (2009) Intertwined evolutionary histories of Marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution, 1:325-339.

Sharma, A.K., Zhaxybayeva, O., Papke, R.T., & Doolittle, W.F. (2008) Actinorhodopsins: relatives of proteorhodopsin found predominantly in nonmarine environments. Environmental Microbiology. 10:1039-1056.

Papke, R.T., Zhaxybayeva, O., Feil, E., Sommerfeld, K., Muise, D. and Doolittle, W.F. (2007) Searching for species in haloarchaea. Proc. Natl. Acad. Sci. U.S.A. 104:14092-14097.

Cuadros-Orellana, S., Legault, B., Martin-Cuadorado, A.-B., D’Auria, G., Zhaxybayeva, O., Papke, R.T. and Rodriguez-Valera, F. (2007) Genomic plasticity in Prokaryotes; the case of the square haloarchaeon. ISME Journal. 1:235-245.

Sharma, A.K., Walsh, D.A., Bapteste, E., Rodriguez-Valera, F., Doolittle, W.F. and Papke, R.T. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evolutionary Biology. 7:79.

Doolittle, W.F. and Papke, R.T. (2006). Genomics and the bacterial species problem. Genome Biology. 7:116.

Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F. and Papke, R.T. (2006). Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Research. 16:1099-1108.

Legault, B., López-López A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodríguez-Valera F. and Papke, R.T. (2006) Environmental genomics of Haloquadratum walsbyi in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics. 7:171.

Mongodin, E.F., Legault, B., Walsh, D.A., Daugherty, S., Nesbø, C.L., Papke, R.T. Shanchez-Perez, G., Sharma, A.K., Charlebois, R.L., Bapteste, E., Nelson, K.E., Doolittle, W.F., and Rodríguez-Valera, F. (2005). The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. U.S.A. 102:18147-18152.

Walsh, D.A., Papke, R.T. and Doolittle, W.F. (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environ. Microbiol. 7:1655-1666.

Papke, R.T., Koenig, J.E., Rodríguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern population of Halorubrum. Science. 306: 1928-1929.

Papke, R.T. and Ward, D.M. (2004) Minireview: The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48:293-303.

Papke, R.T., Ramsing, N.B., Bateson, M.M. and Ward, D.M. (2003) Geographic isolation in thermophilic cyanobacteria. Environ. Microbiol. 5:650-659.

Papke, R.T., Douady, C.J., Doolittle, W.F. and Rodríguez-Valera, F. (2003) Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern. Environ. Microbiol. 5:1039-1045.

Papke, R.T. and Doolittle, W.F. (2003) Phage evolution: new worlds of genomic diversity. Curr. Biol. 13:R606-R607.

Boucher, Y., Douady, C.J., Papke, R.T., Walsh, D.A., Boudreau, M.E.R., Nesbø, C.L., Case, R.J. and Doolittle, W.F. (2003) Lateral gene transfer, adaptation and the origins of prokaryotic groups. Annu. Rev. Genet. 37:283-328.