Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

Shetty, Ameesha R.; de Gannes, Vidya; Obi, Chioma C.; Lucas, Susan; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Linda; Mikhailova, Natalia; Teshima, Hazuki; Han, Cliff; Tapia, Roxanne; Land, Miriam; Hauser, Loren J.; Kyrpides, Nikos; Ivanova, Natalia; Pagani, Ioanna; Chain, Patrick S.  G.; Denef, Vincent J.; Woyke, Tanya; Hickey, William J.

doi:10.1186/s40793-015-0041-x

Title: Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

Journal Article · Sat Aug 15 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0041-x· OSTI ID:1259495

Shetty, Ameesha R. ^[1]; de Gannes, Vidya ^[2]; Obi, Chioma C. ^[3]; Lucas, Susan ^[4]; Lapidus, Alla ^[5]; Cheng, Jan-Fang ^[4]; Goodwin, Lynne A. ^[6]; Pitluck, Samuel ^[4]; Peters, Linda ^[4]; Mikhailova, Natalia ^[4]; Teshima, Hazuki ^[6]; Han, Cliff ^[6]; Tapia, Roxanne ^[6]; Land, Miriam ^[7]; Hauser, Loren J. ^[7]; Kyrpides, Nikos ^[4]; Ivanova, Natalia ^[4]; Pagani, Ioanna ^[4]; Chain, Patrick S. G. ^[6]; Denef, Vincent J. ^[8] more »

Univ. of Wisconsin, Madison, WI (United States)
Univ. of West Indies, Kingston (Jamaica)
Univ. of Lagos (Nigeria)
DOE Joint Genome INst., Walnut Creek, CA (United States)
St. Petersburg Academic Univ. (Russia)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of Michigan, Ann Arbor, MI (United States)

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin [1] and its genome sequence was determined to gain insights into the mechanisms and pathways of PAH metabolism.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231; CSP795673; AC05-00OR22725

OSTI ID:: 1259495

Alternate ID(s):: OSTI ID: 1265487

Journal Information:: Standards in Genomic Sciences, Vol. 10, Issue 1; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 24 works

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References (29)

Nanopods: A New Bacterial Structure and Mechanism for Deployment of Outer Membrane Vesicles Shetty, Ameesha; Chen, Shicheng; Tocheva, Elitza I. PLoS ONE, Vol. 6, Issue 6 https://doi.org/10.1371/journal.pone.0020725	journal	June 2011
Effects of Outer Membrane Vesicle Formation, Surface-Layer Production and Nanopod Development on the Metabolism of Phenanthrene by Delftia acidovorans Cs1-4 Shetty, Ameesha; Hickey, William J. PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0092143	journal	March 2014
Molecular characteristics of xenobiotic-degrading sphingomonads Stolz, Andreas Applied Microbiology and Biotechnology, Vol. 81, Issue 5 https://doi.org/10.1007/s00253-008-1752-3	journal	November 2008
Insights into the genetic diversity of initial dioxygenases from PAH-degrading bacteria Moser, Ralf; Stahl, Ulf Applied Microbiology and Biotechnology, Vol. 55, Issue 5 https://doi.org/10.1007/s002530000489	journal	May 2001
The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons Hickey, William J.; Chen, Shicheng; Zhao, Jiangchao Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00125	journal	January 2012
Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria Habe, Hiroshi; Omori, Toshio Bioscience, Biotechnology, and Biochemistry, Vol. 67, Issue 2 https://doi.org/10.1271/bbb.67.225	journal	January 2003
A Rapid Method of Total Lipid Extraction and Purification Bligh, E. G.; Dyer, W. J. Canadian Journal of Biochemistry and Physiology, Vol. 37, Issue 8 https://doi.org/10.1139/o59-099	journal	August 1959
Rapid isolation method for lipopolysaccharide and lipid A from Gram-negative bacteria Yi, Eugene C.; Hackett, Murray The Analyst, Vol. 125, Issue 4 https://doi.org/10.1039/b000368i	journal	January 2000
Mineralization of Individual Congeners of Linear Alkylbenzenesulfonate by Defined Pairs of Heterotrophic Bacteria Schleheck, David; Knepper, Thomas P.; Fischer, Karin Applied and Environmental Microbiology, Vol. 70, Issue 7 https://doi.org/10.1128/AEM.70.7.4053-4063.2004	journal	July 2004
The bacterial species definition in the genomic era Konstantinidis, Konstantinos T.; Ramette, Alban; Tiedje, James M. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475 https://doi.org/10.1098/rstb.2006.1920	journal	October 2006
Int-B13, an Unusual Site-Specific Recombinase of the Bacteriophage P4 Integrase Family, Is Responsible for Chromosomal Insertion of the 105-Kilobase clc Element ofPseudomonas sp. Strain B13 Ravatn, Roald; Studer, Sonja; Zehnder, Alexander J. B. Journal of Bacteriology, Vol. 180, Issue 21 https://doi.org/10.1128/JB.180.21.5505-5514.1998	journal	November 1998
Tit-for-Tat: Type VI Secretion System Counterattack during Bacterial Cell-Cell Interactions Basler, Marek; Ho, Brian T.; Mekalanos, John J. Cell, Vol. 152, Issue 4 https://doi.org/10.1016/j.cell.2013.01.042	journal	February 2013
One-Component Styrene Monooxygenases: An Evolutionary View on a Rare Class of Flavoproteins Tischler, Dirk; Gröning, Janosch A. D.; Kaschabek, Stefan R. Applied Biochemistry and Biotechnology, Vol. 167, Issue 5 https://doi.org/10.1007/s12010-012-9659-y	journal	April 2012
Bacterial phenylalanine and phenylacetate catabolic pathway revealed Teufel, R.; Mascaraque, V.; Ismail, W. Proceedings of the National Academy of Sciences, Vol. 107, Issue 32 https://doi.org/10.1073/pnas.1005399107	journal	July 2010
The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications Luengo, Jose M.; Garcia, Jose L.; Olivera, Elias R. Molecular Microbiology, Vol. 39, Issue 6 https://doi.org/10.1046/j.1365-2958.2001.02344.x	journal	March 2001
Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway Harwood, Caroline S.; Burchhardt, Gerhard; Herrmann, Heidrun FEMS Microbiology Reviews, Vol. 22, Issue 5 https://doi.org/10.1111/j.1574-6976.1998.tb00380.x	journal	December 1998
Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440 Jimenez, J. I.; Canales, A.; Jimenez-Barbero, J. Proceedings of the National Academy of Sciences, Vol. 105, Issue 32 https://doi.org/10.1073/pnas.0802273105	journal	August 2008
Characterization of methylhydroquinone-metabolizing oxygenase genes encoded on plasmid in Burkholderia sp. NF100 Tago, Kanako; Sato, Junichi; Takesa, Hideaki Journal of Bioscience and Bioengineering, Vol. 100, Issue 5 https://doi.org/10.1263/jbb.100.517	journal	November 2005
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
Class I. Alphaproteobacteria class. nov. Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/0-387-29298-5_1	book	January 2005
Class II. Betaproteobacteria class. nov. Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/0-387-29298-5_2	book	January 2005
NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969) Willems, A.; De Ley, J.; Gillis, M. International Journal of Systematic Bacteriology, Vol. 41, Issue 3 https://doi.org/10.1099/00207713-41-3-445	journal	July 1991
Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov. Wen, Aimin; Fegan, Mark; Hayward, Chris International Journal of Systematic and Evolutionary Microbiology, Vol. 49, Issue 2 https://doi.org/10.1099/00207713-49-2-567	journal	April 1999
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds Top, Eva M.; Springael, Dirk Current Opinion in Biotechnology, Vol. 14, Issue 3 https://doi.org/10.1016/s0958-1669(03)00066-1	journal	June 2003
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
A Three-Component Enzyme System Catalyzes the O Demethylation of the Herbicide Dicamba in Pseudomonas maltophilia DI-6. Wang, X.; Li, B.; Herman, P. L. Applied and environmental microbiology, Vol. 63, Issue 4 https://doi.org/10.1128/aem.63.4.1623-1626.1997	journal	January 1997
Isolation of Soil Bacteria Adapted To Degrade Humic Acid-Sorbed Phenanthrene Vacca, D. J.; Bleam, W. F.; Hickey, W. J. Applied and Environmental Microbiology, Vol. 71, Issue 7 https://doi.org/10.1128/aem.71.7.3797-3805.2005	journal	July 2005
A Rapid Method of Total Lipid Extraction and Purification Bligh, E. G.; Dyer, W. J. Canadian Journal of Biochemistry and Physiology, Vol. 37, Issue 1 https://doi.org/10.1139/y59-099	journal	January 1959

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Prokaryotic Hydrocarbon Degraders Prince, Roger C.; Amande, Tivkaa J.; McGenity, Terry J. Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes https://doi.org/10.1007/978-3-319-60053-6_15-1	book	January 2018
Mud volcanoes and the presence of PAHs Remizovschi, Alexei; Carpa, Rahela; Forray, Ferenc L. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58282-2	journal	January 2020
Three-dimensional bright-field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms: THREE-DIMENSIONAL BRIGHT-FIELD SCANNING TRANSMISSION Hickey, William J.; Shetty, Ameesha R.; Massey, Randall J. Journal of Microscopy, Vol. 265, Issue 1 https://doi.org/10.1111/jmi.12455	journal	August 2016
Prokaryotic Hydrocarbon Degraders Prince, R. C.; Gramain, A.; McGenity, T. J. Handbook of Hydrocarbon and Lipid Microbiology https://doi.org/10.1007/978-3-540-77587-4_118	book	January 2010

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59 BASIC BIOLOGICAL SCIENCES
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Phenanthrene
polycyclic aromatic hydrocarbons
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Title: Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

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