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

Romy Chakraborty's Publications

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Book Reviews

  • Romy Chakraborty and Terry C Hazen. (2006) Environmental Toxicology 2nd edition by Alan Scragg. In The Quarterly Review of Biology 81(3), University Of Chicago Press.

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Book Chapters

  • Coates J.D and Chakraborty R. (2003) Anaerobic Bioremediation - An Emerging Resource for Environmental Cleanup. In, Bioremediation: A Critical Review. Horizon Scientific Press (Editors: I.M. Head, I. Singleton and M. Milner University of Newcastle, UK).
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Publications in Journals

  1. Coates J.D, Chakraborty R, Lack, J.G, O’Connor, S.M, Cole, K.A, Bender K.S, and Achenbach, L.A. (2001) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two novel organisms. Nature 411:1039-1043.
  2. Coates J.D, Chakraborty R, O'Connor, S.M, and Thieme, J. (2001) The geochemical effects of microbial humic substances reduction. Acta hydrochimica et hydrobiologica 28(7): 420-427.
  3. Coates J.D, Cole K.A, Chakraborty R, O’Connor S.M, Achenbach L.A. (2002). The diversity and ubiquity of bacteria utilizing humic substances as an electron donor for anaerobic respiration.  Applied and Environmental Microbiology 68(5): 2445-2452.
  4. Lack J.G, Chaudhuri S. K, Chakraborty R, Achenbach L.A, Coates J.D. (2002) Anaerobic biooxidation of Fe (II) by Dechlorosoma suillum. Microbial Ecology 43: 424-431.
  5. Bender K.S, Chakraborty R, O’Connor S.M, Coates J.D, Achenbach L.A. (2002) Sequencing and Transcriptional Analysis of the Chlorite Dismutase Gene of Dechloromonas agitata and Its Use as a Metabolic Probe. Applied and Environmental Microbiology 68(10): 4820-4826.
  6. Coates J.D, Chakraborty R, McInerney M.J. (2002) Anaerobic benzene biodegradation- a new era. Research in Microbiology 153: 621-628.
  7. Coates J.D and Chakraborty R. (2003) Anaerobic Bioremediation - An Emerging Resource for Environmental Cleanup. In, Bioremediation: A Critical Review. Horizon Scientific Press (Editors: I.M. Head, I. Singleton and M. Milner University of Newcastle, UK).
  8. Chakraborty R and Coates, J.D. (2004) Anaerobic degradation of monoaromatic hydrocarbons. Applied Microbiology and Biotechnology 64: 437-446.
  9. Chakraborty R and Coates J.D. (2005). Hydroxylation and carboxylation – two crucial steps of anaerobic benzene degradation by Dechloromonas strain RCB. Applied and Environmental Microbiology 71(9): 5427-5432.
  10. Bender K. S, Shang C, Chakraborty R, Belchik S.M, Coates J.D, and Achenbach L.A (2005). Identification, characterization, and classification of genes encoding perchlorate reductase. Journal Of Bacteriology. 187: 5090-5096.
  11. Chakraborty R, O’Connor S.M, Chan E, and Coates J. D (2005) Anaerobic degradation of BTEX compounds by Dechloromonas strain RCB. Applied and Environmental Microbiology 71(12): 8649-8655.
  12. Chakraborty R*, Tang Y.J*, Martin H.G, Chu J, Hazen T.C, Keasling J.D (2007) Flux analysis of central metabolic pathways in the Fe (III)-reducing organism Geobacter metallireducens via 13C isotopic labeling. Applied and Environmental Microbiology 73(12): 3859-3864.
  13. Mukhopadhyay A, Redding A.M, Joachimiak M.P, Arkin A.P. Borglin S.E, Dehal P.S, Chakraborty R, Geller J.T, Hazen T.C, He Q, Joyner D.C, Martin V.J.J, Wall J.D, Yang Z.K, Zhou J, Keasling J.D (2007). Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough. Journal Of Bacteriology 189(16): 5996-6010.
  14. Faybishenko, B., Hazen T.C, Long P.E, Brodie E.L, Conrad M.E, Hubbard S.S, Joyner D.C, Borglin S.E, Chakraborty R, Williams K.H, Peterson J.E, Chen J, Tokunaga T.K, Wan J, Firestone M, Newcomer D.L, Resch C.T, Cantrell K.J, Willett A, Koenigsberg S. (2008). In Situ Long-Term Reductive Bioimmobilization of Cr(VI) in Groundwater Using Hydrogen release compund.  Environmental Science and Technology. 42(22): 8478-8485.
  15. Hazen T.C, Chakraborty R, Gregory I.R, Bowman J.P, Jimenez L, Zhang D, Fleming J.M, Sayler G.S, Pfiffner S.M, Brockman F.J. (2009) Use of Gene Probes to Assess the Impact and Effectiveness of Aerobic In Situ Bioremediation of TCE and PCE. Archives of Microbiology 191:221-232.
  16. Hazen T.C, Dubinsky E.A, DeSantis T.Z, Andersen G.L, Piceno Y.M, Singh N, Janssen J.R, Probst A, Borglin S.E, Fortney J.L, Stringfellow W.T, Bill M, Conrad M.S, Tom L.M, Chavarria K.L, Alusi T.R, Lamendella R, Joyner D.C, Spier C, Baelum J, Auer M, Zemla M.L, Chakraborty R, Sonnenthal E.L, D'haeseleer P, Holman HY.N, Osman S, Lu Z, Van Nostrand J.D, Deng Y, ZhouJ, and Mason O.U. (2010). Deep-sea oil plume enriches psychrophilic oil-degrading bacteria causing rapid disappearance of oil. Science. 330(6001): 2004-2008.
  17. Han R, Geller J.T, Yang L, Brodie E.L, Chakraborty R, Larsen J.T, Beller H.R. (2010). Physiological and transcriptional studies of Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived Pseudomonad. Environmental Science and Technology 44(19): 7491-7497.
  18. Chakraborty R, Hazen T.C, Joyner D. C., Kossel K, Singer M. E., Site J, Torok T. (2011). Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris. Journal of Microbiological Methods. 86(2):204-209.
  19. Liu P, Meagher R.J, Light Y.K, Yilmaz S, Chakraborty R, Arkin A.P, Hazen T.C, Singh A.K. (2011). Integrated microfluidic fluorescence in situ hybridization (µFISH) and flow cytometry for environmental bacterial detection. Lab on a Chip. 11(16):2673-9.
  20. DeAngelis K.M, Wu C.H, Beller H.R, Brodie E.L, Chakraborty R, DeSantis T.Z, Fortney J.L, Hazen T.C, Osman S.R, Singer M.E, Tom L.M, Andersen G.L. (2011). PCR amplification-independent methods for detection of microbial communities by high-density microarray. Applied and Environmental Microbiology 77(18): 6313-6322.
  21. Chakraborty R, Wu C.H, Hazen T.C. (2012). Systems Biology Approach Used in Bioremediation. Current Opinions in Biotechnology. 23:1-8.
  22. Bælum J, Borglin S.E., Chakraborty R, Fortney J.L, Lamendella R, Mason O.U, Auer M, Zemla M, Bill M, Conrad M.E, Malfatti S.A, Tringe S.G, Holman H.Y, Hazen T.C, Jansson J.K. (2012). Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environmental Microbiology. 14(9): 2405-2416.
  23. Chakraborty R*, Borglin S.E, Dubinsky E.L, Andersen G.L, Hazen T.C. (2012). Microbial response to the MC252 Oil and Corexit 9500 in the Gulf of Mexico. Frontiers in Microbiology. doi: 10.3389/fmicb.2012.00357
  24. Brown S.D, Utturkar S.M, Arkin A.P, Deutschbauer A.M, Elias D.A, Hazen T.C, Chakraborty R. Draft Genome Sequence for Desulfovibrio africanus strain PCS. (2013). Genome Announcements. 1(2):e00144-13. doi:10.1128/genomeA.00144-13.
  25. Dubinsky E.A, Borglin S.E, Chakraborty R, Hollibaugh J.T, Mason O.U, Piceno Y.M, Reid, F.C, Stringfellow W.T, Tom L, Hazen, T.C, Andersen G.L. (2013). Evolution of Hydrocarbon-Degrading Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico. Environtal Science and Technology. 47(19):10860-7
  26. Louie K.B, Bowen B.P, Cheng X, Berleman J, Chakraborty R, Deutschbauer A.M,  Arkin, A.P, Northen T.R. (2013). ‘Replica-extraction-transfer’ nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Analytical Chemistry. 85 (22): 10856–10862
  27. Lamendella R, Strutt, S, Borglin S.E, Chakraborty R, Tas N, Mason O.U, Hultman J, Prestat E, Hazen T.C, Jansson J.K. Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Frontiers in Microbiology. Accepted, March 2014.



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