Emeritus Professor of Microbiology William “Barny” Whitman received his PhD in 1978 from The University of Texas at Austin with Bob Tabita studying the enzyme RuBisCO from Rhodospirillum rubrum. He continued his research on autotrophic prokaryotes during his postdoctoral studies with Ralph Wolfe at the University of Illinois at Urbana. He joined the Department of Microbiology at the University of Georgia in 1982 where his laboratory studies free-living prokaryotes of environmental importance. His research attempts to understand the physiological, molecular biological and biochemical basis for the ecology and systematics of prokaryotes. This integrated approach has been applied to the methane-producing archaeon Methanococcus, the marine roseobacteria, and soil bacteria. Since 2006, he has served as Director of the Editorial Office for Bergeys Manual Trust and has worked on the 2nd edition of Bergey’s Manual of Systematic Bacteriology, volumes 3-5, and the new online journal Bergey’s Manual on Systematics of Archaea and Bacteria. One goal of this work is to reconcile the taxonomy with the phylogeny and understand the biological basis for the prokaryotic groups Education: BS, 1973, Dept Biological Sciences, State Univ of New York at Stony Brook PhD, 1978, Dept Microbiology, Univ of Texas at Austin. Advisor: F. Robert Tabita Postdoctorate, 1978-1982, Dept Microbiology, Univ of Illinois, Advisor: Ralph S. Wolfe Research Research Areas: Bioinformatics and -omics/Computational Biology Microbial Ecology Microbial Physiology Molecular Microbiology Research Interests: Prokaryotes are the dominant form of life on earth, representing an enormous biomass and number of individual cells. They are so diverse that it is misleading to give them a common name. In one way, they are really just what are left after the familiar plants, animals, fungi and protists are named. Nevertheless, they are the engines that make the biosphere and the ancestors to all modern life. Their evolution established the central plan for the living cell and shaped the biogeochemistry of the planet. Research in our laboratory uses an integrated approach to understand the nature of free-living prokaryotes. We believe that studying the ecology, systematics, physiology, biochemistry, and molecular biology together provides the best understanding for microorganisms. Likewise, the history or evolution of an organism provides insight into the modern organism. We have used these approaches to study the carbon and sulfur metabolism of the methane-producing archaeon Methanococcus, the sulfur metabolism of the marine alphaproteobacterium Ruegeria, and the impact of agriculture on soil bacterial communities. Labs (via personnel): William B. Whitman Labs: Whitman Selected Publications Selected Publications: Complete publication list is available here Recent Research Publications Bullock, H.A., C.R. Reisch, A. Burns, M.A. Moran, and W.B. Whitman. 2014. Regulatory and functional diversity of methylmercaptopropionate CoA ligases from the dimethylpropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria. J. Bacteriol.196:1275-1285. Lin, Y.-T., S.-L. Tang, C.-W. Pai, W.B. Whitman, D.C. Coleman, and C.-Y. Chiu. 2014. Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo.Microbiol. Ecol. 67: 421-429. Gutierrez, T., G. Rhodes, S. Mishamandani, D. Berry, W.B. Whitman, P.K. Nichols, K.T. Semple, and M.D. Aitken. 2014. Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. and description of Arenibacter algicola Maitra, N., W.B. Whitman, S. Ayyampalayam, S. Samanta, K. Sarkar, C. Bandopadhyay, M. Aftabuddin, A.P. Sharma, and S.K. Manna. 2014. Draft genome sequence of the aquatic phosphorous-solubilizing and –mineralizing bacterium Bacillus sp. strain CPSM8. Genome Announcements 2: e01265-13. Gutierrez, T., D.H. Green, P.K. Nichols, W.B. Whitman, K.T. Semple, and M.D. Aitken. 2013. Polycyclovorans algicola Sarmiento, F., J. Mrazek, and W.B. Whitman. 2013. Genome scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. U.S.A. 110: 4727-4731.[ ] Tan, D., W.M. Crabb, W.B. Whitman, and L. Tong. 2013. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS ONE 8: e63870. [ Williams, M.A., K. Jangid, S.G. Shanmugam, and W.B. Whitman. 2013.Bacterial communities in soil mimic patterns of vegetative succession and ecosystem climax but are resilent to change between seasons.Soil Biol. Biochem. 57: 749-757. [ Jangid, K., W.B. Whitman, L.M. Condron, B.L. Turner, and M.A. Williams. 2013. Progressive and retrogressive ecosystem development coincide with soil bacterial community change in a dune system under lowland temperate rainforest in New Zealand. Plant Soil. 367: 235-247. [ Jangid, K., W.B. Whitman, L.M. Condron, B.L. Turner, and M.A. Williams. 2013. Soil bacterial community succession during long-term ecosystem development. Mol. Ecol. 22: 3415-3424. [ Sarmiento, F., C.K. Ellison, and W.B. Whitman. 2013. Genetic confirmation of the role of sulfopyruvate decarboxylase in coenzyme M biosynthesis in Methanococcus maripaludis. Archaea 2013: ID185250. [ Reisch, C.R., W.M. Crabb, S.M. Gifford, Q. Teng, M.J. Stoudemeyer, M.A. Moran, and W.B. Whitman. 2013. Metabolism of dimethylsulfoniopropionate by Ruegeria pomeroyi DSS-3. Mol. Microbiol. 89: 774-791. [DOI: 10.1111/mmi.12314] Schuller, D.J., C.R. Reisch, M.A. Moran, W.B. Whitman, and W.N. Lanzilotta. 2012. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelegabacter ubique. Protein Sci. 21: 289-298. Gutierrez, T., P.D. Nichols, W.B. Whitman, and M.D. Aitken. 2012. Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton.Appl. Environ. Microbiol. 78: 628-637. Lin, Y.-T., W.B. Whitman, D.C. Coleman, and C.-Y. Chiu. 2012. Comparison of soil bacterial communities between coastal and inland forests in a subtropical area.Appl. Soil Ecol. 60: 49-55. Lie, T.J., K.C. Costa, B. Lupa, S. Korpole, W.B. Whitman, and J.A. Leigh. 2012. An essential anaplerotic role for the energy-conserving hydrogenase Eha in hydrogenotrophic methanogenesis.Proc. Nat. Acad. Sci. U.S.A.: 109: 15473-15478. Liu, Y., X. Zhu, A. Nakamura, R. Orlando, D. Söll, and W.B. Whitman. 2012. Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis.J. Biol. Chem 287: 36683-36692. Gutierrez, T., D.H. Green, W.B. Whitman, P.K. Nichols, K.T. Semple, and M.D. Aitken. 2012. Algiphilus aromaticivorans gen. nov., sp nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov. Inter. J. System. Evol. Microbiol. 62: 2743-2749. Lin, Y.-T., K. Jangid, W.B. Whitman, D.C. Coleman, and C.-Y. Chiu. 2011. Soil bacterial communities in native and regenerated perhumid montane forests. Appl. Soil Ecol. 47: 111-118. Lin, Y.-T., K. Jangid, W.B. Whitman, D.C. Coleman, and C.-Y. Chiu. 2011. Change in bacterial community structure in response to disturbance of natural hardwood and secondary coniferous forest soils in central Taiwan. Microbial Ecol. 61: 429-437. Lin, Y.-T, W.B. Whitman, D.C. Coleman, and C.-Y. Chiu. 2011. Molecular characterization of soil bacterial community in a perhumid, low mountain forest. Microbes and Environments 26: 325-331. Reisch, C.R., M.J. Stoudemayer, V.A. Varaljay, I.J. Amster, M.A. Moran, and W.B. Whitman. 2011. Novel pathway for assimilation of dimethylsulfoniopropionate widespread in marine bacteria. Nature 473: 208-211. Jangid, K., M.A. Williams, A.J. Franzluebbers, T.M. Schmidt, D.C. Coleman, and W.B. Whitman. 2011.Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties.Soil Biol. Biochem. 43: 2184-2193. Garcia, S.L., K. Jangid, W.B. Whitman, and K.C. Das. 2011. Transition of microbial communities during the adaption to anaerobic digestion of carrot waste. Bioresource Technology 102: 7249-7256. Chaerun, S.K., N.P.D. Pangesti, K. Toyota, and W.B. Whitman. 2011. Changes in microbial functional diversity and activity in paddy soils irrigated with industrial wastewaters in Bandung, West Java Province, Indonesia. Water Air and Soil Pollution 217: 491-502. Recent Reviews and Book Chapters Sutcliffe, I.C., M.E. Trujillo, W.B. Whitman, and M. Goodfellow. 2013. A call to action for the International Committee on Systematics of Prokaryotes. Trends Microbiol. 21: 51-52. Ludwig, W., J. Euzéby, P. Schumann, H.J. Busse, M.E. Trujillo, P. Kämpfer, and W.B. Whitman. 2012. Road map of the Actinobacteria. In: M. Goodfellow, P. Kämpfer, H.J. Busse, M.E. Trujillo, K.-S. Suzuki, W. Ludwig, and W.B. Whitman (eds.). Bergey’s Manual of Systematic Bacteriology 5, 2nd ed., Springer, New York, pp. 1-28. Moran, M.A., C.R. Reisch, R.P. Kiene, and W.B. Whitman (2012) Genomic insights in bacterial DMSP transformations. Ann. Rev. Marine Sci. 4: 523-542. Liu, Y., L.L. Beer, and W.B. Whitman (2012) Methanogenesis: a window into ancient sulfur metabolism. Trends in Microbiology 20: 251-258. Liu, Y., L.L. Beer, and W.B. Whitman. 2012. Sulfur metabolism in archaea reveals novel processes. Environ. Microbiol. 14: 2632-2644. Ludwig, W., J. Euzeby, and W.B. Whitman. 2011. Road Map of the Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. In: N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward, W. Ludwig, and W.B. Whitman (eds.). Bergey’s Manual of Systematic Bacteriology 4, 2nd ed., Springer, New York, pp. 1-20. Sarmiento Boban, F., J.A. Leigh, and W.B. Whitman. 2011. Genetic systems for hydrogenotrophic methanogens. In. A.C. Rosenzweig and S.W. Ragsdale (eds.). Meth. Enzymol. 494, Elsevier, New York, pp. 43-73. Reisch, C.R., M.A. Moran, and W.B. Whitman. 2011. Bacterial catabolism of dimethylsulfoniopropionate (DMSP). Frontiers of Microbiology 2: article 172, doi: 10.3389/fmicb.2011.00172. Whitman, W.B. 2011. Intent of the nomenclatural Code and recommendations about naming new species based on genomic sequences. The Bulletin of BISMiS 2: 135-140. Whitman, W.B. 2011. What’s up with Bergey’s? Australia Microbiology 32: 62-63. Philippot, L., S.G.E. Andersson, T.J. Battin, J.I. Prosser, J.P. Schimel, W.B. Whitman, and S. Hallin. 2010. The ecological coherence of high bacterial taxonomic ranks. Nature Rev. Microbiol. 8: 1-7. Of note: Supervising Editor, Bergey’s Manual Trust, 2006-present Editor, Archaea, 2013-present K-Shuff K-shuff is a powerful computer program designed to identify spatial clustering in a given dataset based on the reduced second moment measure, or K-function. In essence, K-shuff can be adapted for comparing any data from two (or more) samples to understand their relationship with each other. As an example, we adapt this technique to compare 16S rRNA gene sequence libraries from different environmental samples by treating gene sequences as points in space with hundreds of dimensions. Download K-shuff. Click here to download the latest beta version of K-shuff for testing. NOTE: The current version of K-shuff was successfully tested with an input distance matrix of upto 4000 sequences on a Windows-PC with 2.8 GHz processor and 4 GB RAM. Under these conditions, the analysis was completed in less than 25 minutes including random permutations. Run times increase slightly if you have more comparisons, i.e., number of libraries within the same distance matrix size. Download WSCF-dataset. Click here to download the WSCF-dataset used in K-shuff. Download K-shuff User Manual: Click here to download the K-shuff user manual. If you wish to use K-shuff for your research, please contact Prof. William Whitman. Courses Regularly Taught: MIBO 4090/6090 MIBO 8160 MIBO 3000-3000L
