Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Harry R. Beller's Publications

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Peer Reviewed Publications

  1. Goh, E.-B., E. E. K. Baidoo, H. Burd, T. S. Lee, J. D. Keasling, H. R. Beller. (In press). Substantial improvements in methyl ketone production in E. coli and insights on the pathway from in vitro studies.  Metabolic Engineering  doi 10.1016/j.ymben.2014.09.003
  2. Beller, H. R., Li Yang, C. Varadharajan, R. Han, H. C. Lim, U. Karaoz, S. Molins, M. A. Marcus, E. L. Brodie, C. I. Steefel, and Peter S. Nico.  (in press) Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products. Environ. Sci. Technol. doi 10.1021/es5016982
  3. Javidpour, P., J. H. Pereira, E.-B. Goh, R. P. McAndrew, S. M. Ma, G. D. Friedland, J. D. Keasling, S. R. Chhabra, P. D. Adams, and H. R. Beller.  2014.  Biochemical and structural studies of NADH-dependent FabG used to increase the bacterial production of fatty acids under anaerobic conditions. Appl. Environ. Microbiol. 80:497-50.
  4. Bi, C., P. Su, J. Müller, Y.-C. Yeh, S. R. Chhabra, H. R. Beller, S. W. Singer, N. J. Hillson.  2013. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production.  Microbial Cell Factories 12:107  doi:10.1186/1475-2859-12-107. 
  5. Beller, H. R., P. Zhou, T. C. Legler, A. Chakicherla, S. Kane, T. E. Letain, P. O'Day.  2013. Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans Frontiers in Microbiology 4:249. doi: 10.3389/fmicb.2013.00249
  6. Müller, J., D. MacEachran, H. Burd, N. Sathitsuksanoh, C. Bi, Y-C. Yeh, T. S. Lee, N. J. Hillson, S. R. Chhabra, S. W. Singer, and H. R. Beller.  2013. Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones.  Appl. Environ. Microbiol. 79:4433-4439.
  7. Beller, H. R., R. Han, U. Karaoz, H. C. Lim, E. L. Brodie.  2013. Genomic and physiological characterization of the chromate-reducing, aquifer-derived firmicute Pelosinus sp. strain HCF1. Appl. Environ. Microbiol. 79:63-73.
  8. Yeh, Y.-C., J. Müller, C. Bi, N. J. Hillson, H. R. Beller, S. R. Chhabra, S. W. Singer.  2013.  Functionalizing bacterial cell surfaces with a phage protein.  Chemical Communications 49:910-912.
  9. Paap, S. M., T. H. West, D. K. Manley, E. J. Steen, H. R. Beller, J. D. Keasling, D. C. Dibble, S. Chang, B. A. Simmons. 2013. Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: analysis of environmental and economic performance.  Biomass and Bioenergy 49:49-62.
  10. Beller, H. R., T. C. Legler, and S. R. Kane.  2012 (Book chapter). "Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans", vol. 881, pp. 99-136, In Microbial Systems Biology: Methods and Protocols [Methods in Molecular Biology series], A. Navid (ed.), Springer Science. DOI 10.1007/978-1-61779-827-6_5.
  11. Pereira, J. H., E.-B. Goh, J. D. Keasling, H. R. Beller, P. D. Adams. 2012. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus. Acta Crystallographica D68:1320-1328.
  12. Han, R., L. Qin, S. T. Brown, J. N. Christensen, H. R. Beller. 2012. Differential isotopic fractionation during Cr(VI) reduction under aerobic versus denitrifying conditions by an aquifer-derived bacterium.  Appl. Environ. Microbiol. 78:2462-2464.
  13. Goh, E.-B., E. E. K. Baidoo, J. D. Keasling, and Beller, H. R.  2012. Engineering of bacterial methyl ketone synthesis for biofuels. Appl. Environ. Microbiol. 78:70-80.
  14. Beller, H. R., E.-B. Goh, and J. D. Keasling. 2011. Definitive alkene identification needed for in vitro studies with Ole (olefin synthesis) proteins.  Journal of Biological Chemistry 286(26):le11.
  15. O. Chertkov, A. Copeland, S. Lucas, A. Lapidus, K. W. Berry, J. C. Detter, T. Glavina Del Rio, N. Hammon, E. Dalin, H. Tice, S. Pitluck, P. Richardson, D. Bruce, L. Goodwin, C. Han, R. Tapia, E. Saunders, J. Schmutz, T. Brettin, F. Larimer, M. Land, L. Hauser, S. Spring, M. Rohde, N. C. Kyrpides, N. Ivanova, M. Göker, H. R. Beller, H.-P. Klenk, and T. Woyke.  2011. Complete genome sequence of Tolumonas auensis type strain (TA 4T).  Standards in Genomic Sciences 5(1), doi:10.4056/sigs.2184986.
  16. Chhabra, S. R., G. Butland, D. Elias, J-M. Chandonia, O-Y Fok, T. Juba, A. Gorur, S. Allen, C.M. Leung, K. Keller, S. Reveco, G. Zane, E. Semkiw, R. Prathapam, B. Gold, M. Singer, M. Ouellet, D. Sazakal, D. Jorgens, M.N. Price, E. Witkowska, H. R. Beller, A.P. Arkin, T.C. Hazen, M.D. Biggin, M. Auer, J.D. Wall, and J. D. Keasling.  2011.  Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.  Appl. Environ. Microbiol. 77:7595-7604.

  17. DeAngelis, K. M., C. H. Wu, H. R. Beller et al. 2011. PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.  Appl. Environ. Microbiol. 77: 6313 - 6322.
  18. Han, R., J. T. Geller, L.Yang, E. L. Brodie, R. Chakraborty, J. T. Larsen, and H. R. Beller.  2010. Physiological and transcriptional studies of Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived pseudomonad.  Environ. Sci. Technol. 44:7491-7497.
  19. Beller, H. R., E.-B. Goh, and J. D. Keasling. 2010. Genes involved in long-chain alkene biosynthesis in Micrococcus luteus. Appl. Environ. Microbiol.  76:1212-1223.
  20. Young, M., V. Artsatbanov, H. R. Beller, et al.  2010. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium.  J. Bacteriol. 192:841-860.
  21. Beller, H. R., T. C. Legler, F. Bourguet, T. E. Letain, S. R. Kane, and M. A. Coleman. 2009.  Identification of c-type cytochromes involved in anaerobic, bacterial U(IV) oxidation. Biodegradation 20:45-53.
  22. Beller, H. R., S. R. Kane, T. C. Legler, J. R. McKelvie, B. Sherwood Lollar, F. Pearson, L. Balser, and D. M. Mackay. 2008.  Comparative assessments of benzene, toluene, and xylene natural attenuation by quantitative polymerase chain reaction analysis of a catabolic gene, signature metabolites, and compound-specific isotope analysis. Environ. Sci. Technol. 42:6065-6072.
  23. Kunapuli, U., C. Griebler, H. R. Beller, and R. U. Meckenstock. 2008. Identification of intermediates formed during anaerobic benzene degradation by an iron-reducing enrichment culture.  Environmental Microbiology 10:1703-1712.
  24. Letain, T. E., S. R. Kane, T. C. Legler, E. P. Salazar, P. G. Agron, and H. R. Beller. 2007. Development of a genetic system for the chemolithoautotrophic bacterium Thiobacillus denitrificans.  Appl. Environ. Microbiol.  73:3265-3271.
  25. Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legler, and M. A. Coleman. 2006.  Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic vs. denitrifying conditions. J. Bacteriol. 188:7005-7015.
  26. Beller, H. R., P. S. G. Chain, T. E. Letain, A. Chakicherla, F. W. Larimer, P. M. Richardson, M. A. Coleman, A. P. Wood, and D. P. Kelly. 2006. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J. Bacteriol. 188:1473-1488.
  27. Beller, H. R.  2005. Anaerobic, nitrate-dependent oxidation of U(IV) oxide minerals by the chemolithoautotrophic bacterium Thiobacillus denitrificans.  Appl. Environ. Microbiol. 71:2170-2174.
  28. McKelvie, J. R., J. E. Lindstrom, H. R. Beller, S. A. Richmond, and B. Sherwood Lollar. 2005.
  29. Analysis of anaerobic BTX biodegradation in a subarctic aquifer using isotopes and benzylsuccinates. Journal of Contaminant Hydrology 81:167-186.
  30. Ulrich, A. C., H. R. Beller, and E. A. Edwards.  2005. Metabolites detected during biodegradation of 13C6-benzene in nitrate-reducing and methanogenic enrichment cultures. Environ. Sci. Technol. 39:6681-6691.
  31. Beller, H. R., V. Madrid, G. B. Hudson, W. W. McNab, and T. Carlsen. 2004. Biogeochemistry and natural attenuation of nitrate in groundwater at an explosives test facility.  Applied Geochemistry 19:1483-1494.
  32. Beller, H. R., S. R. Kane, T. C. Legler, and P. J. J. Alvarez.  2002. A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ. Sci. Technol. 36:3977-3984.
  33. Beller, H. R.  2002. Anaerobic biotransformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by aquifer bacteria using hydrogen as the sole electron donor. Water Research 36: 2533-2540.
  34. Beller, H. R., and K. Tiemeier.  2002. Use of liquid chromatography/tandem mass spectrometry to detect distinctive indicators of in situ RDX transformation in contaminated groundwater. Environ. Sci. Technol. 36: 2060-2066.
  35. Beller, H. R. 2002. Analysis of benzylsuccinates in groundwater by liquid chromatography/ tandem mass spectrometry and its use for monitoring in situ BTEX biodegradation. Environ. Sci. Technol. 36: 2724-2728.
  36. Kane, S. R., H. R. Beller, T. C. Legler, and R. T. Anderson. 2002. Biochemical and genetic evidence of benzylsuccinate synthase in toluene-degrading, ferric iron-reducing Geobacter metallireducens.  Biodegradation 13: 149-154.
  37. Reusser, D. E., J. D. Istok, H. R. Beller, and J. A. Field. 2002.  In situ transformation of deuterated toluene and xylene to benzylsuccinic acid analogs in BTEX-contaminated aquifers. Environ. Sci. Technol. 36: 4127-4134.
  38. Beller, H. R. 2000. Metabolic indicators for detecting in situ anaerobic alkylbenzene degradation.  Biodegradation 11: 125-139.
  39. Beller, H. R., and E. A. Edwards. 2000. Anaerobic toluene activation by benzylsuccinate synthase in a highly enriched methanogenic culture. Appl. Environ. Microbiol. 66: 5503-5505.
  40. Kane, S. R., H. R. Beller, T. C. Legler, C. J. Koester, H. C. Pinkart, R.U. Halden, A.M. Happel. 2001. Aerobic biodegradation of methyl tert-butyl ether by aquifer bacteria from leaking underground storage tank sites. Appl. Environ. Microbiol. 67: 5824-5829.
  41. Koester, C. J., H. R. Beller, and R. U. Halden. 2000. Analysis of perchlorate in groundwater by electrospray ionization mass spectrometry/mass spectrometry.  Environ. Sci. Technol. 34: 1862-1864.
  42. Beller, H. R., and A. M. Spormann. 1999. Substrate range of benzylsuccinate synthase from Azoarcus sp. strain T. FEMS Microbiol. Letters 178: 147-153.
  43. Krieger, C. J., H. R. Beller, M. Reinhard, and A. M. Spormann. 1999. Initial reactions in anaerobic oxidation of m-xylene by the denitrifying bacterium Azoarcus sp. strain T. J. Bacteriol. 181: 6403-6410.
  44. Heider, J., A. M. Spormann, H. R. Beller, and F. Widdel. 1998. Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol. Reviews 22: 459-473.
  45. Beller, H. R., and A. M. Spormann. 1998. Analysis of the novel benzylsuccinate synthase reaction for anaerobic toluene activation based on structural studies of the product. J. Bacteriol. 180: 5454-5457.
  46. Beller, H. R., and A. M. Spormann. 1997. Benzylsuccinate formation as a means of anaerobic toluene activation by sulfate-reducing strain PRTOL1. Appl. Environ. Microbiol. 63: 3729-3731.
  47. Beller, H. R., and A. M. Spormann. 1997. Anaerobic activation of toluene and o-xylene by addition to fumarate in denitrifying strain T. J. Bacteriol. 179: 670-676.
  48. Beller, H. R., A. M. Spormann, P. K. Sharma, J. R. Cole, and M. Reinhard. 1996. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl. Environ. Microbiol. 62: 1188-1196.
  49. Beller, H. R., W.-H. Ding, and M. Reinhard. 1995. Byproducts of anaerobic alkylbenzene metabolism useful as indicators of in situ bioremediation.  Environ. Sci. Technol. 29: 2864-2870.
  50. Beller, H. R., and M. Reinhard. 1995. The role of iron in enhancing anaerobic toluene degradation in sulfate-reducing enrichment cultures. Microb. Ecol. 30:105-114.
  51. Beller, H. R., M. Reinhard, and D. Grbic-Galic. 1992. Metabolic by-products of anaerobic toluene degradation by sulfate-reducing enrichment cultures. Appl. Environ. Microbiol. 58: 3192-3195.
  52. Beller, H. R., D. Grbic-Galic, and M. Reinhard. 1992. Microbial degradation of toluene under sulfate-reducing conditions and the influence of iron on the process.  Appl. Environ. Microbiol. 58:786-793.
  53. Beller, H. R., E. A. Edwards, D. Grbic-Galic, and M. Reinhard.  1991. Microbial degradation of alkylbenzenes under sulfate-reducing and methanogenic conditions.  EPA/600/2-91/027.  Final Report prepared for U.S. Environmental Protection Agency.  National Technical Information Service (publication #PB91-212324),  Springfield, VA.
  54. Beller, H. R., and B. R. T. Simoneit.  1988.  Hexachlorophene distributions in estuarine sediments.  Bull. Environ. Contam. Toxicol.  41:645-650.
  55. Beller, H. R., and B. R. T. Simoneit.  1986.  “Polychlorinated biphenyls and hydrocarbons:  distributions among bound and unbound lipid fractions of estuarine sediments,”  pp. 198-214.  In:  Organic Marine Geochemistry.  M.L. Sohn (ed). ACS Symposium Series No. 305, American Chemical Society, Washington, DC.
  56. Simoneit,  B. R. T., and H. R. Beller. 1987.  “Lipid geochemistry of Cretaceous/Tertiary boundary sediments, Hole 605, Deep Sea Drilling Project Leg 93, and Stevns Klint, Denmark,” pp. 1211-1221.  In:  Initial Reports of the Deep Sea Drilling Project, Vol. 93, pt. 2.  J.E. van Hinte, S. W. Wise, Jr., et al. (eds).  U.S. Government Printing Office, Washington, DC.
  57. Simoneit,  B. R. T., and H. R. Beller. 1985.  “Lipid geochemistry of the Cretaceous/Tertiary boundary sediments, Hole 577, Deep Sea Drilling Project Leg 86,” pp. 671-674.  In:  Initial Reports of the Deep Sea Drilling Project, Vol. 86.  G.R. Heath, L.H. Burckle, et al. (eds).  U.S. Government Printing Office, Washington, DC.

 

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