**Earth Sciences Division Ecology Department**

**2005--2006**

Abulencia, C.B., D.L. Wyborski, J. Garcia, M. Podar, W. Chen, S.H.
Chang, H.W. Chang, D.B. Watson, E. Brodie, T.C. Hazen, and M. Keller,
Environmental whole-genome amplification to access microbial diversity
in contaminated sediments. *Applied and Environmental Microbiology*,
**72** (5), 3291-3301, LBNL-60416, 2006.

Andersen, G.L., P. Hu, E. Brodie, and H.H. McAdams, Whole genome
transcriptional analysis of toxic metal stresses in Caulobacter
crescentus. Genomes-To-Life workshop. Washington D. C. Washington, D.
C., DOE Genomes-to-Life program. LBNL-60665, 2005.

Balser, T.C., and M.K. Firestone, Linking microbial community
composition and soil processes in a California annual grassland and
mixed-conifer forest. *Biogeochemistry*, **73** (2), 395-415,
LBNL-60675, 2005.

Brodie, E.L., T. DeSantis, D. Joyner, S.M. Baek, J.T. Larsen, G.L.
Andersen, T.C. Hazen, P.M. Richardson, D.J. Herman, T.K. Tokunaga, J.M.
Wan, and M.K. Firestone, Bacterial population dynamics during uranium
reduction and re-oxidation: Application of a novel high density
oligonucleotide microarray approach. *Appl. Environ. Microbiol.*,
**72**(9), 6288-6298, LBNL-59761, 206.

Burns, J.R., and N.W.T. Quinn, Use of geospatial technologies to compare
environmental impacts of wetland delayed drawdown in California\'s San
Joaquin Basin. LBNL-60747, 2006.

Chain, P.S.G., P. Hu, S.A. Malfatti, L. Radnedge, F. Larimer, L.M.
Vergez, P.L. Worsham, M.C. Chu, and G.L. Andersen, Complete genome
sequence of Yersinia Pestis Strains Antiqua and Nepal516: Evidence of
gene reduction in an emerging pathogen. *Journal of Bacteriology*,
**188** (12), 4453-4463, LBNL-60248, 2006.

Chhabra, S.R., Q. He, K. Huang, S.P. Gaucher, E. Alm, Z. He, M.Z. Hadi,
T. Hazen, J. Wall, J. Zhou, A. Arkin, and A. Singh, Global analysis of
heat shock response in Desulfovibrio vulgaris Hildenborough. *J.
Bacteriol*, **188** (5), 1817-1828, LBNL-60298, 2006.

Clark, M. E., Q. He, Z. He, K. H. Huang, E. J. Alm, X. Wan, T. C. Hazen,
A. P. Arkin, J. D. Wall, J. Zhou, and M. W. Fields, Temporal
transcriptomic analysis of Desulfovibrio vulgaris Hildenborough
transition into stationary phase growth during electron donor depletion.
*Appl. Environ. Microbiol.* **72,** 5578-5588, LBNL-60466, 2006.

Clavijo, R.I., C. Loui, G.L. Andersen, W. Riley, and S.W. Lu,
Identification of genes associated with survival of Salmonella enterica
serovar Enteridis in chicken egg albumen. *Applied and Environmental
Microbiology*, **72** (2), 1055-1064, LBNL-60807, 2006.

Codd, R., P. Lay, N.Y. Tsibakhashvili, T.L. Kalabegishvili, I.G.
Murusidze, and H.-Y.N. Holman, Chromium(V) complexes generated in
Arthrobacter oxydans by simulation analysis of EPR spectra. *J. Inorg.
Biochem*, LBNL-61264, in press 2006.

DeAngelis, K.M., P.S. Ji, M.K. Firestone, and S.E. Lindow, Two novel
bacterial biosensors fro detection of nitrate availability in the
rhizosphere. *Applied and Environmental Microbiology*, **71** (12),
8537-8547, LBNL-60817, 2005.

DeSantis, T., E. Brodie, J.P. Moberg, I.X. Zubieta, Y.M. Piceno, and
G.L. Andersen, High-density universal 16S rRNA microarray analysis
reveals broader diversity than typical clone library when sampling the
environment. *Microbial Ecology*, LBNL-59763.

DeSantis, T., K. Hansen, E. Brodie, Y.M. Piceno, J. Bullard, P. Hu, and
G.L. Andersen, Hybridization efficiency analysis of probes targeting 16S
rRNA genes using the Affymetrix GeneChip Format. LBNL-61253 Abs.

DeSantis, T., P. Hugenholtz, N. Larsen, M. Rojas, E. Brodie, K. Keller,
T. Huber, D. Dalevi, P. Hu, and G.L. Andersen, Greengenes:
Chimera-checked 16S rRNA gene database and workbench compatible with
ARB. *Applied and Environmental Microbiology*, **72** (7), 5069-5072,
LBNL-59764, 2006.

DeSantis, T., P. Hugenholtz, N. Larsen, M. Rojas, E. Brodie, K. Keller,
T. Huber, D. Dalevi, P. Hu, Y.M. Piceno, R. Phan, and G.L. Andersen,
Greengenes, The ARB-compatible Chimera-checked 16S rRNA Gene Database,
introduces new online tools including NAST, A flexible massive multiple
sequence alignment tool. LBNL-61252 Abs., 2006.

DeSantis, T.Z., P. Hugenholtz, K. Keller, E.L. Brodie, N. Larsen, Y.M.
Piceno, R. Phan, and G.L. Andersen, NAST: A multiple sequence alignment
server for comparative analysis of 165 rNRA genes. *Nucleic Acids
Research*, **34** (Supplement 2) W394-W399, LBNL-59765, 2006.

DeSantis, T.Z., C.E. Stone, S.R. Murray, J.P. Moberg, and G.L. Andersen,
Rapid quantification and taxonomic classification of environmental DNA
from both prokaryotic and eukaryotic origins using a microarray. *FEMS
Microbiology Letters*, **245** (2), 271-278, LBNL-57331, 2005.

Dunphy Guzman, K.A., M. Taylor, and J.F. Banfield, Environmental risks
of nanotechnology: National nanotechnology initiative funding,
2000-2004. *Environmental Science & Technology*, **40** (5), 1401-1407,
LBNL-59431, 2006.

Ferre, T.P.A., A. Binley, J. Geller, E. Hill, and T. Illangasekare,
Hydrogeophysical methods at the laboratory scale. in *Hydrogeophysics*,
Springer, Dordrecht, The Netherlands, 2005. LBNL-60929. 2005.

Fields, M., C.E. Bagwell, S.L. Carroll, T. Yan, X. Liu, P.M. Jardine,
C.S. Criddle, T.C. Hazen, and J. Zhou, Polyphasic characterization of
microbial communities under stressful conditions and the identification
of different relationships based upon geochemical data or multiple gene
sequences. *Environ. Sci. Technol.*, **40**, 2601-2607, LBNL-60460,
2006.

Hazen, T., and H. Tabak, Developments in bioremediation of soils and
sediments polluted with metals and radionuclides: 2. Field research on
bioremediation of metals and radionuclides. *Environmental Science &
Bio/Technology*, **4** (3), 157-183, LBNL-60264, 2005.

Hazen, T.C., and D. Stahl, Process control in natural and engineered
systems by monitoring microbial stress response. *Current Opinions in
Biotechnology.*, **17**, 285-290, LBNL-60297, 2006.

He, Q., K. Huang, Z. He, E. Alm, M. Fields, T. Hazen, A. Arkin, J. Wall,
and J. Zhou, Energetic consequences of nitrite stress in Desulfovibrio
vulgaris Hildenborough inferred from global transcriptional analysis.
*Applied and Environmental Microbiology*, **72** (6), 4370-4381,
LBNL-60422, 2006.

Hengpraprom, S., C.M. Lee, and R.T. Coates, Sorption of humic acids and
alpha-endosulfan by lay minerals. *Environmental Toxicology And
Chemistry* (25), 11-17, LBNL-60933, 2006.

Holman, H.-Y., K. Bjornstad, M. Martin, E.A. Blakely, and F.G.
Blankenberg, Mid-infrared reflection-absorption spectromicroscopy
(MIRAS) of Atherosclerosis in ApoE(-/-) knockout mice. *Nature
Medicine*, LBNL-61263, submitted 2006.

Holman, H.-Y.N., Synchrotron radiation infrared spectromicroscopy: a
non-invasive molecular probe for biogeochemical processes. *Advances in
Agronomy*, **90**, 79-127, LBNL-60323, 2006.

Hu, P., D. Ballinger, C. Pthiyagoda, K. Pant, T. Torok, and G.L.
Andersen, Genome-wide single nucleotide polymorphism analysis of
salmonella enterica. American Society for Micorbiology Annual
Conference. Orlando, FL, American Society for Microbiology. LBNL-60879
Poster. 2005.

Hu, P., E. Brodie, Y. Suzuki, H.H. McAdams, and G.L. Andersen,
Whole-genome transcriptional analysis of heavy metal stresses in
Caulobacter crescentus. *Journal of Bacteriology*, **187** (24),
LBNL-59011, 2005.

Kalabegishvili, T.L., N.Y. Tsibakhashvili, I.G. Murusidze, D.T.
Pataraya, M.A. Gurielidze, and H.-Y. Holman, Formation of Cr(V) and
Cr(III) in Arthrobacter oxydans exposed to high concentrations of
Cr(VI). in *Modern Multidisciplinary Applied Microbiology,* Wiley-VCH
Verlag GmbH & Co., Germany, 2006. LBNL-61265. 2006.

Koenigsberg, S., T. Hazen, and A.D. Peacock, Environmental
biotechnology: A bioremediation perspective. *Remediation* (Autumn), 5,
LBNL-60459, 2005.

Lin, L.-H., P.-L. Wang, D. Rumble, J. Lippmann-Pipke, B. Sherwood
Lollar, E. Boice, L. Pratt, E. Brodie, T.C. Hazen, G.L. Andersen, T.
DeSantis, D.P. Moser, D. Kershaw, and T. Onstott, Long term
biosustainability in a high energy, low diversity crustal biotome.
*Science*, LBNL-60468, Submitted 2006.

Lin, Z., Y. Zhu, T.L. Kalabegishvili, N.Y. Tsibakhashvili, and H.-Y.
Holman, Effect of chromate action on morphology of basalt-inhabiting
bacteria. *Materials Science and Engineering*, **26** (4), 610--612,
LBNL-61266, 2006.

Monaselidze, J., M. Abuladze, N. Asatiani, E. Kiziria, S. Barbakadze, G.
Majagaladze, M. Iobadze, L. Tabatadze, H.-Y.N. Holman, and N.
Sapojnikova, Characterization of chromium-induced apoptosis in cultured
mammalian cells: A differential scanning calorimetry study.
*Thermochimica Acta*, **441** (1), 8-15, LBNL-60739, 2006.

Mukhopadhyay, A., Z. He, E. Alm, A. Arkin, E.E. Baidoo, S.C. Borglin, W.
Chen, T.C. Hazen, Q. He, H.-Y. Holman, K. Huang, R. Huang, D. Joyner, N.
Katz, M. Keller, P. Oeller, A. Redding, J. Sun, Z. Yang, J. Wall, J.
Wei, H.-C. Yen, J. Zhou, and J. Keasling, Salt stress in Desulfovibrio
vulgaris Hildenborough: An integrated genomics approach. *Genome
Research*, **188** (11), 4068-4078, LBNL-59862, 2006.

Pfiffner, S.M., A.V. Palumbo, T.J. Phelps, J.J. Beauchamp, D.B.
Ringelberg, H.C. Pinkart, D.C. White, and T.C. Hazen, Microbial
monitoring as a measure of success for in situ TCE bioremediation. *FEMS
Microbiology Ecology*, LBNL-45232 JArt, In Review, 2006.

Quinn, N.W.T., Qualitative analysis/discussion of increased contractual
delveries - San Luis Unit. LBNL, Berkeley, CA, 36 pp., LBNL-60612. 2006.

Quinn, N.W.T., M.W. Hanna, J.S. Hanlon, J.R. Burns, C.M. Taylor, D.
Marciochi, S. Lower, V. Woodruff, D. Wright, and T. Poole, Real-time
water quality management in the Grassland Water District. LBNL,
Berkeley, CA, 192 pp., LBNL-56825. 2005.

Quinn, N.W.T., and A. Tulloch, San Joaquin River diversion data
assimilation, drainage estimation and installation of diversion
monitoring stations. LBNL, Berkeley, CA. LBNL-56940. 2005.

Redding, A., A. Mukhopadhyay, D. Joyner, T.C. Hazen, and J. Keasling,
Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using
iTRAQ proteomics. *Briefings in Functional Genomics and Proteomics*,
**5** (2), 133--143, LBNL-59867, 2006.

Shepler, C.G., S.E.H. Gallaher, T.E. Letain, T.C. Hazen, H. Nitsche, and
S.B. Clark, The effect of Bacillus sphaericus on the transformation of
the U(VI) oxyhydroxide metaschoepite to secondary U(VI) solids.
*Radiochemica Acta.*, LBNL-60469, Submitted 2005.

Stroo, H.F., D.V. Nakles, J.P. Kreitinger, R.C. Lohehr, S.B. Hawthorn,
R.G. Luthy, and H.-Y.N. Holman, Improving risk assessments for
manufactured gas plant soils by measuring PAH availability. *Integrated
Environmental Assessment and Management*, **1** (3), 259-266,
LBNL-58445, 2005.

Tsibakhashvili, N.Y., M.V. Frontasyeva, T.I. Kirkesali, N.G. Aksenova,
T.L. Kalabegishvili, I.G. Murusidze, L.M. Mosulishvili, and H.-Y.N.
Holman, Epithermal neutron activation analysis of Cr(VI)-reducer
basalt-inhabiting bacteria. *Analytical Chemistry*, **78** (18),
6285--6290, LBNL-60810, 2006.

Wozei, E., S.W. Hermanowicz, and H.-Y. Holman, Developing a biosensor
for estrogens in water samples: Study of the real-time response of live
cells of the estrogen-sensitive yeast strain RMY/ER-ERE using
fluorescence microscopy. *Biosensors and Bioelectronics*, **21** (8),
1654-1658, LBNL-58194, 2006.