Selected Publications (since 2001):

Keswani, J., and W.B. Whitman (2001) Relationships of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int. J. Syst. Evol. Microbiol. 51:667-678.

Rother, M., A. Resch, W.L. Gardner, W.B. Whitman, and A. Böck (2001) Heterologous expression of archaeal selenoprotein genes directed by the SECIS element located in the 3' non-translated region. Mol. Microbiol. 40: 900-908.

Kayar, S.R., A. Fahlman, W.C. Lin, and W.B. Whitman (2001) Increasing activity of H₂-metabolizing microbes lowers decompression sickness risk in pigs during H₂ dives. J. Appl. Physiol. 91: 2713-2719.

Stathopoulos, C., W. Kim, T. Li, I. Anderson, B. Deutsch, S. Palioura, W. Whitman, and D. Soll. (2001) Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. U.S.A. 98: 14292-14297.

Singleton, D.R., M.A. Furlong, S.L. Rathbun, and W.B. Whitman. (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67: 4374-4376.

Furlong, M.A., D.R. Singleton, D.C. Coleman, and W.B. Whitman. (2002) Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Appl. Environ. Microbiol. 68: 1265-1279.

Yang, Y.L., J.N. Gluska, and W.B. Whitman (2002) Intracellular pyruvate flux in the methane-producing archaeon Methanococcus maripaludis. Arch. Microbiol. 178: 493-498.

Fahlman, A., W.C. Lin, W.B. Whitman, and S.R. Kayar (2002) Modulation of decompression sickness risk in pigs with caffeine during H2 biochemical decompression. J. Appl. Physiol. 93: 1583-1589.

Brigmon, R.L., M. Furlong, and W.B. Whitman (2003) Identification of Thiothrix unzii in two distinct ecosystems. Lett. Appl. Microbiol. 36:88-91.

Hoover, R.B., E.V. Pikuta, A.K. Bej, D. Marsic, W.B. Whitman, J. Tang, and P. Krader (2003) Spirochaeta americana sp. nov., a new haloalkaliphilic, obligately anaerobic spirochete isolated from soda Mono Lake in California. Inter. J. Syst. Evol. Microbiol. 53: 815-821.

Pikuta, E.V., R.B. Hoover, A.K. Bej, D. Marsic, E.N. Detkova, W.B. Whitman, and P. Krader (2003) Tindallia californiensis sp. nov., a new anaerobic, haloalkaliphilic, spore-forming acetogen isolated from Mono Lake in California. Extremophiles 7: 327-334.

Singleton, D.R., M.A. Furlong, A.D. Peacock, D.C. White, D.C. Coleman, and W.B. Whitman (2003) Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones. Inter. J. Syst. Evol. Microbiol. 53: 485-490.

Lin, W.C., Y.L. Yang, and W.B. Whitman (2003) The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch. Microbiol. 179:444-456.

Singleton, D.R., P.F. Hendrix, D.C. Coleman, and W.B. Whitman (2003) Identification of uncultured bacteria tightly associated with the intestine of the earthworm Lumbricus rubellus (Lumbricidae; Oligochaeta) Soil Biol. Biochem. 35: 1547-1555.

González, J.M.., J.S. Covert, W.B. Whitman, J.R. Henriksen, F. Mayer, B. Scharf, R. Schmitt, A. Buchan, J.A. Fuhrman, R.P. Kiene, and M.A. Moran (2003) Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., DMSP demethylating bacteria from marine environments. Inter. J. Syst. Evol. Microbiol. 53: 1261-1269.

Pikuta, E.V., R.B. Hoover, A.K. Bej, D. Marsic, W.B. Whitman, D. Cleland, and P. Krader (2003) Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth. Inter. J. Syst. Evol. Microbiol. 53: 1327-1332.

Farahi, K., W.B. Whitman, and E.T. Kraemer (2003) RED-T: utilizing the Ratios of Evolutionary Distances for determining alternative phylogenetic events. Bioinformatics 19: 2152-2154.

Farahi, K., G.D. Pusch, R. Overbeek, and W.B. Whitman (2004) Detection of lateral gene transfer (LGT) events in the prokaryotic tRNA synthetases by the Ratios of Evolutionary Distances method. J. Mol. Evol. 58: 615-631.

Porat, I., B.W. Waters, Q. Teng, and W.B. Whitman (2004) Two biosynthetic pathways for the aromatic amino acids in the archaeon Methanococcus maripaludis. J. Bacteriol. 186: 4940-4950.

Plaza, G.A., R.Upchurch, R.L. Brigmon, W.B. Whitman, and K. Ulfig (2004) Rapid DNA extraction for screening soil filamentous fungi using PCR amplification. Polish J. Environ. Studies 13: 315-318.

Hendrickson, E.L., R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J.A. Dodsworth, W. Gillett, D.E. Graham, M. Hackett, A.K. Haydock, A. Kang, M.L. Land, R. Levy, T.J. Lie, T.A. Major, B.C. Moore, I. Porat, A. Palmeiri, G. Rouse, C. Saenphimmachak, D. Söll, S. Van Dien, T. Wang, W.B. Whitman, Q. Xia, Y. Zhang, F.W. Larimer, M.V. Olson and J.A. Leigh (2004) Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J. Bacteriol. 186: 6956-69-69.

Lin, W., and W.B. Whitman (2004) The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch. Microbiol. 181: 68-73.

Haydock, A.K., I. Porat, W.B. Whitman, and J.A. Leigh (2004) Continuous culture of Methanococcus maripaludis under defined nutrient conditions. FEMS Microbiol. Lett. 238: 85-91.

Major, T., H. Burd, and W.B. Whitman (2004) Abundance of 4Fe-4S motifs in the genomes of methanogens and other prokaryotes. FEMS Microbiol. Lett. 239: 117-123.

Moran, M. A., A. Buchan, J. M. Gonzalez, J. F. Heidelberg, W. B. Whitman, R. P. Kiene, J. R. Henriksen, G. M. King, R. Belas, C. Fuqua, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pal, J. A. Eisen, E. Rahe, W. M. Sheldon, W. Ye, T. R. Miller, J. Carlton, D.A. Rasko, I. T. Paulsen, Q. Ren, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A. Sullivan, M. J. Rosovitz, D. H. Haft, J. Selengut, and N. Ward (2004) Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432: 910-913.

Sauerwald, A., W. Zhu, T.A. Major, H. Roy, S. Palioura, D. Jahn, W.B. Whitman, J.R. Yates 3rd, M. Ibba, and D. Söll (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307: 1969-1972.

Kim, W., T.A. Major, and W.B. Whitman (2005) Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis. Archaea 1, 375-384.

Porat, I., W. Kim, E.L. Hendrickson, Q. Xia, Y. Zhang, T. Wang, F. Taub, B.C. Moore, I.J. Anderson, M. Hackett, J.A. Leigh, and W.B. Whitman (2006) Disruption of the Ehb hydrogenase operon limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J. Bacteriol. 188: 1373-1380.

Xia, Q., E.L. Hendrickson, Y. Zhang, T. Wang, F. Taub, B.C. Moore, I. Porat, W.B. Whitman, M. Hackett, and J.A. Leigh. 2006. Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol. Cell. Proteomics 5: 868-881.

Howard, E.C., J.R. Henriksen, A. Buchan, C.R. Reisch, H. Büergmann, R. Welsh, W. Ye, J.M. González, K. Mace, S.B. Joye, R.P. Kiene, W.B. Whitman, and M.A. Moran. 2006. Identification of the bacterial gene limiting sulfur flux from surface seawater. Science 314: 649-652.

Porat, I., M. Sieprawska-Lupa, Q. Teng, F.J. Bohanon, R.H. White, and W.B. Whitman. 2006. Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol. Microbiol. 62: 1117-1132.

Kendall, M.M., Y. Liu, M. Sieprawska-Lupa, K.O. Stetter, W.B. Whitman, and D.R. Boone. 2006. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int. J. Syst. Evol. Microbiol. 56: 1525-1529.

Lee, Y.-J., C.S. Romanek, G.L. Mills, R.C. Davis, W.B. Whitman, and J. Wiegel. 2006. Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water. Int. J. Syst. Evol. Microbiol. 56: 2089-2093.

Pikuta, E.V., R.B. Hoover, A.K. Bej, D. Marsic, W.B. Whitman, P.E. Krader, and J. Tang. 2006. Trichococcus patagoniensis sp. nov., a facultative anaerobe that grows at -5 C, isolated from penguin guano in Chilean Patagonia. Int. J. Syst. Evol. Microbiol. 56: 2055-2062.

Pikuta, E.V., T. Itoh, P. Krader, J. Tang, W.B. Whitman, and R.B. Hoover. 2006. Anaerovirgula multivorans gen. nov., sp. nov., a novel spore-forming, alkaliphilic anaerobe isolated from Owens Lake, California, USA. Int. J. Syst. Evol. Microbiol. 56: 2623-2629.

Yuan, J., S. Palioura, J.C. Salazar, D. Su, P. O’Donoghue, M.J. Hohn, A.M. Cardoso, W.B. Whitman, and D. Söll. 2006. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. USA 103:18923-18927.

Ding, Y., K.C. Das, W.B. Whitman, and J.R. Kastner. 2006. Enhanced biofiltration of hydrogen sulfide in the presence of methanol and resultant bacterial diversity. Transactions of the ASABE (American Society of Agricultural and Biological Engineers) 49:2051-2059.

Sokolov, T., J. Hanel, R.U. Onyenwoke, A.-L. Reysenbach, A. Banta, R. Geyer, J.M. González, W.B. Whitman, and J. Wiegel. 2007. Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov. Extremophiles 11: 145-157.

Hendrickson, E.L., A.K. Haydock, B.C. Moore, W.B. Whitman, and J.A. Leigh. 2007. Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. Proc. Natl. Acad. Sci. USA 104: 8930-8934.

Lee, Y.-J., M. Dashti, A. Prange, F.A. Rainey, M. Rohde, W.B. Whitman, and J. Wiegel. 2007. Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite. Int. J. Syst. Evol. Microbiol. 57: 1429-1434.

Upchurch, R., C.-Y. Chiu, K. Everett, G. Dyszynski, D.C. Coleman, and W.B. Whitman. In press. Differences in the composition and diversity of bacterial communities from agricultural and forest soils. Soil Biol. Biochem.

Tarlera, S., K. Jangid, A. Ivester, W.B. Whitman, and M. Williams. In press. Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development. FEMS Microbiology Ecology

Reviews and Book Chapters (since 2001):

Graham, D.E., N. Kyrpides, I.J. Anderson, R. Overbeek, and W.B. Whitman (2001) Genome of Methanocaldococcus (Methanococcus) jannaschii. Meth. Enzymol. 330:40-123.

Whitman, W.B., D.R. Boone, Y. Koga, and J. Keswani (2001) Taxonomy of Methanogenic Archaea. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York., p. 211-213.

Whitman, W.B., D.R. Boone, and Y. Koga (2001) Order Methanococcales. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p. 236.

Whitman, W.B., D.R. Boone, and Y. Koga (2001) Family I. Methanococcaceae. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p. 236..

Whitman, W.B., D.R. Boone, and Y. Koga (2001) Family II. Methanocaldococcaceae. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p. 242-243.

Whitman, W.B. (2001) Genus I. Methanococcus. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p.236-240.

Whitman, W.B. (2001) Genus I. Methanothermococcus. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p. 241-242.

Whitman, W.B. (2001) Genus I. Methanocaldococcus. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p.243-245.

Whitman, W.B. (2001) Genus I. Methanotorris. In: Bergey's Manual of Systematic Bacteriology Bacteriology, 2nd ed. (G.M. Garrity, ed.), Springer, New York, p. 245-246.

Garcia, J.-L., B. Ollivier, and W.B. Whitman (2001) The order Methanomicrobiales. In: The Prokaryotes, A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K. H. Schleifer (eds.), The Prokaryotes, Springer-Verlag, New York.

Whitman, W.B., and C. Jeanthon. (2002) The order Methanococcales In: The Prokaryotes, A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K. H. Schleifer (eds.), The Prokaryotes, Springer-Verlag, New York.

González, J.M., and W.B. Whitman. (2002) Oceanospirillum and related genera. In: The Prokaryotes, A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K. H. Schleifer (eds.), The Prokaryotes, Springer-Verlag, New York.

Stackebrandt, E., W. Frederiksen, G.M. Garrity, P.A.D. Grimont, P. Kampfer,M.C.J. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H.G. Truper, L. Vauterin, A.C. Ward, and W.B. Whitman (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Inter. J. Syst. Evol. Microbiol. 52: 1043-1047.

Whitman, W. B. (2002) Archaea. In: Microbial Life, J. J. Perry, J. T. Staley, and S. Lory (ed.), Sinauer Assoc., Pub., Sunderland, MA, p. 386-408.

Stackebrandt, E., W. Frederiksen, G.M. Garrity, P.A.D. Grimont, P. Kampfer, M.C.J. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H.G. Truper, L. Vauterin, A.C. Ward, and W.B. Whitman (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Inter. J. Syst. Evol. Microbiol. 52: 1043-1047.

Singleton, D.R., S.L. Rathbun, G.E. Dyszynski and W.B. Whitman (2004) LIBSHUFF Comparisons of 16S rRNA Gene Clone Libraries. In: Molecular Microbial Ecology Manual, 2 ed., A.D.L. Akkermans, F.J. de Bruijn, G.A. Kowalchuk, I.M. Head, J.D van Elsas (eds.) Kluywer Academic Pub.

Hedderich, R., and W.B. Whitman (2004) Physiology and biochemistry of the methane-producing archaea. In: The Prokaryotes, A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K. H. Schleifer (eds.), Springer-Verlag, New York.

Coleman, D.C., and W.B. Whitman (2005) Linking species richness, biodiversity and ecosystem function in soil systems. Pedobiologia 49: 479-497.

Johnson, J.L., and W.B. Whitman (2007) Similarity analysis of DNAs. In: Methods for General and Molecular Microbiololgy, 3rd ed., C.A. Reddy (ed.) Am. Soc. Microbiol., Washington D.C., pp. 624-652.

Whitman, W. B. (2007) Archaea. In: J.T. Staley, R.P. Gunsalus, S. Lory, and J.J. Perry (eds.), Microbial life, 2nd ed., Sinauer Ass., Sunderland, MA., pp. 515-543.