Environmental

Sciences

Division

2001-Present Publications in Microbial Genomics and Ecology

Publications

1993- 1996

1997-2000

  1. Amonette, J. E., J. Kim, C. K. Russell, A. V. Palumbo, W. L. Daniels. 2003. Fly ash amendments catalyze soil carbon sequestration. In: Proceedings of the Second Annual Conference on Carbon Sequestration. May 5-8, 2003. Alexandria, Va.
  2. Beliaev, A. S., D. K. Thompson, M. W. Fields, L. Y. Wu, D. P. Lies, K. H. Nealson, and J. Z. Zhou 2002. Microarray transcription profiling of a Shewanella oneidensis etrA mutant Journal of Bacteriology. 184:4612-4616.
  3. Gao, H. C., Y. Wang, X. D. Liu, T. F. Yan, L. Y. Wu, E. Alm, A. Arkin, D. K. Thompson, and J. Z. Zhou 2004. Global transcriptome analysis of the heat shock response of Shewanella oneidensis Journal of Bacteriology. 186:7796-7803.
  4. Gruntzig, V., S. C. Nold, J. Z. Zhou, and J. M. Tiedje 2001. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR Applied and Environmental Microbiology. 67:760-768.
  5. Gu, B. H., D. B. Watson, L. Y. Wu, D. H. Phillips, D. C. White, and J. Z. Zhou 2002. Microbiological characteristics in a zero-valent iron reactive barrier Environmental Monitoring and Assessment. 77:293-309.
  6. Hurt, R. A., X. Y. Qiu, L. Y. Wu, Y. Roh, A. V. Palumbo, J. M. Tiedje, and J. H. Zhou 2001. Simultaneous recovery of RNA and DNA from soils and sediments Applied and Environmental Microbiology. 67:4495-4503.
  7. Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Y. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, J. H. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje 2005. Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations Proceedings of the National Academy of Sciences of the United States of America. 102:2099-2104.
  8. Li, Y. L., J. Yang, C. L. L. Zhang, B. L. Deng, and T. J. Phelps 2002. Dissolution of iron-rich clay and sulfur sequestration by a sulfate-reducing bacterium Geochimica Et Cosmochimica Acta. 66:A453-A453.
  9. Liu, X. D., S. M. Tiquia, G. Holguin, L. Y. Wu, S. C. Nold, A. H. Devol, K. Luo, A. V. Palumbo, J. M. Tiedje, and J. Z. Zhou 2003. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico Applied and Environmental Microbiology. 69:3549-3560.
  10. Liu, X. D., C. E. Bagwell, L. Y. Wu, A. H. Devol, and J. H. Zhou 2003. Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats Applied and Environmental Microbiology. 69:6073-6081.
  11. Liu, Y. Q., J. Z. Zhou, M. V. Omelchenko, A. S. Beliaev, A. Venkateswaran, J. Stair, L. Y. Wu, D. K. Thompson, D. Xu, I. B. Rogozin, E. K. Gaidamakova, M. Zhai, K. S. Makarova, E. V. Koonin, and M. J. Daly 2003. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation Proceedings of the National Academy of Sciences of the United States of America. 100:4191-4196.
  12. Liu, Y. Q., W. M. Gao, Y. Wang, L. Y. Wu, X. D. Liu, T. F. Yan, E. Alm, A. Arkin, D. K. Thompson, M. W. Fields, and J. Z. Zhou 2005. Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions Journal of Bacteriology. 187:2501-2507.
  13. Love, L. J., J. F. Jansen, T. E. McKnight, Y. Roh, and T. J. Phelps 2004. A magnetocaloric pump for microfluidic applications Ieee Transactions on Nanobioscience. 3:101-110.
  14. Love, L. J., J. F. Jansen, T. E. McKnight, Y. Roh, T. J. Phelps, L. W. Yeary, and G. T. Cunningham 2005. Ferrofluid field induced flow for microfluidic applications Ieee-Asme Transactions on Mechatronics. 10:68-76.Luo, F., L. Khan, F. Bastani, I. L. Yen, and J. Z. Zhou 2004. A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles Bioinformatics. 20:2605-2617.
  15. Mailloux, B. J., M. E. Fuller, G. F. Rose, T. C. Onstott, M. F. DeFlaun, E. Alvarez, C. Hemingway, R. B. Hallet, T. J. Phelps, and T. Griffin 2003. A modular injection system, multilevel sampler, and manifold for tracer tests Ground Water. 41:816-827.
  16. Martin, M. Z., S. D. Wullschleger, C. T. Garten, and A. V. Palumbo 2003. Laser-induced breakdown spectroscopy for the environmental determination of total carbon and nitrogen in soils Applied Optics. 42:2072-2077.
  17. Martin, M. Z., S. D. Wullschleger, C. T. Garten, A. V. Palumbo, and J. G. Smith 2004. Elemental analysis of environmental and biological samples using laser-induced breakdown spectroscopy and pulsed Raman spectroscopy Journal of Dispersion Science and Technology. 25:687-694.
  18. Moser, D. P., T. C. Onstott, J. K. Fredrickson, F. J. Brockman, D. L. Balkwill, G. R. Drake, S. M. Pfiffner, D. C. White, K. Takai, L. M. Pratt, J. Fong, B. S. Lollar, G. Slater, T. J. Phelps, N. Spoelstra, M. Deflaun, G. Southam, A. T. Welty, B. J. Baker, and J. Hoek 2003. Temporal shifts in the geochemistry and microbial community structure of an ultradeep mine borehole following isolation Geomicrobiology Journal. 20:517-548.
  19. Murray, A. E., D. Lies, G. Li, K. Nealson, J. Zhou, and J. M. Tiedje 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes Proceedings of the National Academy of Sciences of the United States of America. 98:9853-9858.
  20. Onstott, T. C., D. P. Moser, S. M. Pfiffner, J. K. Fredrickson, F. J. Brockman, T. J. Phelps, D. C. White, A. Peacock, D. Balkwill, R. Hoover, L. R. Krumholz, M. Borscik, T. L. Kieft, and R. Wilson 2003. Indigenous and contaminant microbes in ultradeep mines Environmental Microbiology. 5:1168-1191.
  21. Palumbo, A. V., J. C. Schryver, M. W. Fields, C. E. Bagwell, J. Z. Zhou, T. Yan, X. Liu, and C. C. Brandt 2004. Coupling of functional gene diversity and geochemical data from environmental samples Applied and Environmental Microbiology. 70:6525-6534.
  22. Palumbo, A. V., J. F. McCarthy, J. E. Amonette, L. S. Fisher, S. D. Wullschleger, and W. L. Daniels 2004. Prospects for enhancing carbon sequestration and reclamation of degraded lands with fossil-fuel combustion by-products Advances in Environmental Research. 8:425-438.
  23. Palumbo, A. V., S.. M. Pfiffner, L. Fagan, M.McNeilly, S. Rishell, J. E. Kostka, and C. C. Brandt. In press. Substrate and Community Structure Determinants of Uranium Reduction Rates in Subsurface Sediments. Proceedings of the 3rd European Bioremediation Conference, July 4-7, 2005. Crete
  24. Palumbo, A. V., S. Fisher, M. Martin, Z. Yang, J. Tarver, S. D. Wullschleger. 2004. Application of emerging tools and techniques for measuring carbon and microbial communities in reclaimed mine soils. Environmental Management. Vol 33, Supplement 1, pp S518-S527.
  25. Palumbo, A. V., L.S. Fisher, J.R. Tarver, W.L. Daniels, Z. Yang, S.M. Tiquia, L. Wu, J. Zhou, J. Amonette. 2003. Microbial communities, carbon and nitrogen in mine soils reclaimed with fly ash and biosolids amendments (Issues with the Use of Fly Ash for Carbon Sequestration). In: Proceedings of the 2nd Annual Conference on Carbon Sequestration. May 5-8, 2003. Alexandria, V
  26. Pfiffner, S. M., A. V. Palumbo, G. D. Sayles, and D. Gannon 2004. Microbial population and degradation activity changes monitored during a chlorinated solvent biovent demonstration Ground Water Monitoring and Remediation. 24:102-110.
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  27. Phelps, T. J., D. J. Peters, S. L. Marshall, O. R. West, L. Y. Liang, J. G. Blencoe, V. Alexiades, G. K. Jacobs, M. T. Naney, and J. L. Heck 2001. A new experimental facility for investigating the formation and properties of gas hydrates under simulated seafloor conditions Review of Scientific Instruments. 72:1514-1521.
  28. Phelps, T. J., A. V. Palumbo, and A. S. Beliaev 2002. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints Current Opinion in Biotechnology. 13:20-24.
  29. Post, W. M., R. C. Izaurralde, J. D. Jastrow, B. A. McCarl, J. E. Amonette, V. L. Bailey, P. M. Jardine, T. O. West, and J. Z. Zhou 2004. Enhancement of carbon sequestration in US soils Bioscience. 54:895-908.
  30. Powers, L. G., H. J. Mills, A. V. Palumbo, C. L. Zhang, K. Delaney, and P. A. Sobecky 2002. Introduction of a plasmid-encoded phoA gene for constitutive overproduction of alkaline phosphatase in three subsurface Pseudomonas isolates FEMS Microbiology Ecology. 41:115-123.
  31. Qiu, X. Y., L. Y. Wu, H. S. Huang, P. E. McDonel, A. V. Palumbo, J. M. Tiedje, and J. Z. Zhou 2001. Evaluation of PCR-generated chimeras: Mutations, and heteroduplexes with 16S rRNA gene-based cloning Applied and Environmental Microbiology. 67:880-887.
  32. Qiu, X.-Y.,  R.A. Hurt, L.-Y. Wu, C.-H. Chen, J.M. Tiedje and J.-Z. Zhou. 2004. Detection and quantification of copper-denitrifying bacterianext term by quantitative competitive PCR Journal of Microbiological Methods, Volume 59:199-210.
  33. Qi Ye, Y.Roh, S.L. Carroll, B.Blair, J. Zhou, C.L. Zhang, and M. W. Fields. 2004. Alkaline Anaerobic Respiration: Isolation and Characterization of a Novel Alkaliphilic and Metal-Reducing Bacterium. Appl. Envir. Microbiol. 70: 5595-5602.
  34. Qiu, X, G. W. Sundin, L. Wu, J. Zhou, and J. M. Tiedje. 2005. Comparative Analysis of Differentially Expressed Genes in Shewanella oneidensis MR-1 following Exposure to UVC, UVB, and UVA Radiation  J. Bacteriol. 2005 187: 3556-3564
  35. Rhee, S. K., X. D. Liu, L. Y. Wu, S. C. Chong, X. F. Wan, and J. Z. Zhou 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays Applied and Environmental Microbiology. 70:4303-4317.
  36. Riestenberg, D., O. West, S. Lee, S. McCallum, and T. J. Phelps 2003. Sediment surface effects on methane hydrate formation and dissociation Marine Geology. 198:181-190.
  37. Roh, Y., R. J. Lauf, A. D. McMillan, C. Zhang, C. J. Rawn, J. Bai, and T. J. Phelps 2001. Microbial synthesis and the characterization of metal-substituted magnetites Solid State Communications. 118:529-534.
  38. Roh, Y., S. V. Liu, G. S. Li, H. S. Huang, T. J. Phelps, and J. Z. Zhou 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado Applied and Environmental Microbiology. 68:6013-6020.
  39. Roh, Y., C. L. Zhang, H. Vali, R. J. Lauf, J. Zhou, and T. J. Phelps 2003. Biogeochemical and environmental factors in Fe biomineralization: Magnetite and siderite formation Clays and Clay Minerals. 51:83-95.
  40. Romanek, C. S., C. L. L. Zhang, Y. L. Li, J. Horita, H. Vali, D. R. Cole, and T. J. Phelps 2003. Carbon and hydrogen isotope fractionations associated with dissimilatory iron-reducing bacteria Chemical Geology. 195:5-16.
  41. Schryver, J.C., C. C. Brandt, S. M. Pfiffner, A. V. Palumbo, J. S. Almeida, A. D. Peacock, D.C. White, J. P. McKinley, and P.E. Long. In press. Community Structure of UMTRA Site Groundwater as Assessed by Nonlinear Analyses. Microbial Ecology.
  42. Schut, G. J., J. Z. Zhou, and M. W. W. Adams 2001. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex Journal of Bacteriology. 183:7027-7036.
  43. Sepulveda-Torres, L. D., J. Z. Zhou, C. Guasp, J. Lalucat, D. Knaebel, J. L. Plank, and C. S. Criddle 2001. Pseudomonas sp strain KC represents a new genomovar within Pseudomonas stutzeri International Journal of Systematic and Evolutionary Microbiology. 51:2013-2019.
  44. Stapleton, R. D., Z. L. Sabree, A. V. Palumbo, C. L. Moyer, A. H. Devol, Y. Roh, and J. Z. Zhou 2005. Metal reduction at cold temperatures by Shewanella isolates from various marine environments Aquatic Microbial Ecology. 38:81-91.
  45. Taranenko, N. I., R. Hurt, J. Z. Zhou, N. R. Isola, H. Huang, S. H. Lee, and C. H. Chen 2002. Laser desorption mass spectrometry for microbial DNA analysis Journal of Microbiological Methods. 48:101-106.
  46. Thompson, D. K., A. S. Beliaev, C. S. Giometti, S. L. Tollaksen, T. Khare, D. P. Lies, K. H. Nealson, J. Lim, J. Yates, C. C. Brandt, J. M. Tiedje, and J. Z. Zhou 2002. Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress Applied and Environmental Microbiology. 68:881-892.
  47. Tiquia, S. M., L. Y. Wu, S. C. Chong, S. Passovets, D. Xu, Y. Xu, and J. Z. Zhou 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples Biotechniques. 36:664-+.
  48. Treves, D. S., B. Xia, J. Zhou, and J. M. Tiedje 2003. A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil Microbial Ecology. 45:20-28.
  49. Wan, X. F., N. C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, L. J. Hauser, L. Y. Wu, X. D. Liu, T. F. Yan, A. Leaphart, R. L. Hettich, J. Z. Zhou, and D. K. Thompson 2004. Transcriptomic and proteomic characterization of the fur modulon in the metal-reducing bacterium Shewanella oneidensis Journal of Bacteriology. 186:8385-8400.
  50. Wan, X. F., D. Xu, A. Kleinhofs, and J. Z. Zhou 2004. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes Bmc Evolutionary Biology. 4.
  51. Wightman, P. G., J. B. Fein, D. J. Wesolowski, T. J. Phelps, P. Benezeth, and D. A. Palmer 2001. Measurement of bacterial surface protonation constants for two species at elevated temperatures Geochimica Et Cosmochimica Acta. 65:3657-3669.
  52. Wu, L. Y., D. K. Thompson, G. S. Li, R. A. Hurt, J. M. Tiedje, and J. Z. Zhou 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment Applied and Environmental Microbiology. 67:5780-5790.
  53. Wu, L. Y., D. K. Thompson, X. D. Liu, M. W. Fields, C. E. Bagwell, J. M. Tiedje, and J. Z. Zhou 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications Environmental Science & Technology. 38:6775-6782.
  54. Xia, B. C., D. S. Treves, J. Z. Zhou, and J. M. Tiedje 2001. Soil microbial community diversity and driving mechanisms Progress in Natural Science. 11:818-824.
  55. Xu, D., G. S. Li, L. Y. Wu, J. Z. Zhou, and Y. Xu 2002. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis Bioinformatics. 18:1432-1437.
  56. Yan, T. F., M. W. Fields, L. Y. Wu, Y. G. Zu, J. M. Tiedje, and J. Z. Zhou 2003. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater Environmental Microbiology. 5:13-24.
  57. Ye, Q., M. Fields, J. Zhou, Y. Roh, T. J. Phelps, and C. L. Zhang 2002. Isolation of an alkaliphilic metal-reducing bacterium from a saline pond containing high concentrations of boron Geochimica Et Cosmochimica Acta. 66:A861-A861.
  58. Ye, Q., Y. Roh, S. L. Carroll, B. Blair, J. Z. Zhou, C. L. Zhang, and M. W. Fields 2004. Alkaline anaerobic respiration: Isolation and characterization of a novel alkaliphilic and metal-reducing bacterium Applied and Environmental Microbiology. 70:5595-5602.
  59. Zatsepina, O. Y., D. Riestenberg, S. D. McCallum, M. Gborigi, G. Brandt, B. A. Buffett, and T. J. Phelps 2004. Influence of water thermal history and overpressure on CO2-hydrate nucleation and morphology American Mineralogist. 89:1254-1259.
  60. Zhang, C. L., J. Horita, D. R. Cole, J. Z. Zhou, D. R. Lovley, and T. J. Phelps 2001. Temperature-dependent oxygen and carbon isotope fractionations of biogenic siderite Geochimica Et Cosmochimica Acta. 65:2257-2271.
  61. Zhou, J., S. Liu, B. Xia, C. Zhang, A. V. Palumbo, and T. J. Phelps 2001. Molecular characterization and diversity of thermophilic iron-reducing enrichment cultures from deep subsurface environments Journal of Applied Microbiology. 90:96-105.
  62. Zhou, J. Z., and J. H. Miller 2002. Microbial genomics - Challenges and opportunities: The 9th International Conference on Microbial Genomes Journal of Bacteriology. 184:4327-4333.
  63. Zhou, J. Z., and D. K. Thompson 2002. Challenges in applying microarrays to environmental studies Current Opinion in Biotechnology. 13:204-207.
  64. Zhou, J. Z., and D. K. Thompson 2004. Microarray Technology and Applications in Environmental Microbiology. Advances in Agronomy, Volume 82, 2004, Pages 183-270.
  65. Zhou, J. Z., and J. M. Tiedje 2002. New DOE program expands dramatically beyond microbial Genomics ASM News. 68:110-111.
  66. Zhou, J. Z., B. C. Xia, D. S. Treves, L. Y. Wu, T. L. Marsh, R. V. O'Neill, A. V. Palumbo, and J. M. Tiedje 2002. Spatial and resource factors influencing high microbial diversity in soil Applied and Environmental Microbiology. 68:326-334.
  67. Zhou, J. Z., B. C. Xia, H. S. Huang, D. S. Treves, L. J. Hauser, R. J. Mural, A. V. Palumbo, and J. M. Tiedje 2003. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils Soil Biology & Biochemistry. 35:915-924.
  68. Zhou, J. H. 2003. Microarrays for bacterial detection and microbial community analysis Current Opinion in Microbiology. 6:288-294.
  69. Zhou, X. C., L. Y. Wu, and J. Z. Zhou 2004. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers Langmuir. 20:8877-8885.
  70. Zhou, X. C., and J. Z. Zhou 2004. Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles Analytical Chemistry. 76:5302-5312.
  71. Zhou, J. Z., B. C. Xia, H. Huang, A. V. Palumbo, and J. M. Tiedje 2004. Microbial diversity and heterogeneity in sandy subsurface soils Applied and Environmental Microbiology. 70:1723-1734.

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Anthony V. Palumbo,
Environmental Sciences Division,
P. O. Box 2008,
Oak Ridge National Laboratory,
Oak Ridge, Tennessee 37831-6038
Phone: (865)576-8002
Fax: (865)576-0524
E-mail: palumboav@ornl.gov

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Revised May 15, 2005