Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

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

Journal Article · · Standards in Genomic Sciences
 [1];  [2];  [3];  [4];  [5];  [4];  [6];  [4];  [4];  [4];  [6];  [6];  [6];  [7];  [7];  [4];  [4];  [4];  [6];  [8] more »;  [4];  [1] « less
  1. Univ. of Wisconsin, Madison, WI (United States)
  2. Univ. of West Indies, Kingston (Jamaica)
  3. Univ. of Lagos (Nigeria)
  4. DOE Joint Genome INst., Walnut Creek, CA (United States)
  5. St. Petersburg Academic Univ. (Russia)
  6. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  8. Univ. of Michigan, Ann Arbor, MI (United States)
+ Show Author Affiliations
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 by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3’ end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Lastly, determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.
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; AC05-00OR22725
OSTI ID:
1259495
Alternate ID(s):
OSTI ID: 1265487
Journal Information:
Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 10; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (33)

One-Component Styrene Monooxygenases: An Evolutionary View on a Rare Class of Flavoproteins journal April 2012
The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds journal June 2003
Dietary palmitic acid promotes a prometastatic memory via Schwann cells journal November 2021
Rapid isolation method for lipopolysaccharide and lipid A from Gram-negative bacteria journal January 2000
The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications journal March 2001
Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440 journal August 2008
Bacterial phenylalanine and phenylacetate catabolic pathway revealed journal July 2010
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal June 1990
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
NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969) journal July 1991
A Three-Component Enzyme System Catalyzes the O Demethylation of the Herbicide Dicamba in Pseudomonas maltophilia DI-6. journal January 1997
Mineralization of Individual Congeners of Linear Alkylbenzenesulfonate by Defined Pairs of Heterotrophic Bacteria journal July 2004
Isolation of Soil Bacteria Adapted To Degrade Humic Acid-Sorbed Phenanthrene journal July 2005
A Rapid Method of Total Lipid Extraction and Purification journal January 1959
Characterization of methylhydroquinone-metabolizing oxygenase genes encoded on plasmid in Burkholderia sp. NF100 journal November 2005
Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria journal January 2003
The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons journal January 2012
Class I. Alphaproteobacteria class. nov. book January 2005
Class II. Betaproteobacteria class. nov. book January 2005
Molecular characteristics of xenobiotic-degrading sphingomonads journal November 2008
Insights into the genetic diversity of initial dioxygenases from PAH-degrading bacteria journal May 2001
The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds journal June 2003
Tit-for-Tat: Type VI Secretion System Counterattack during Bacterial Cell-Cell Interactions journal February 2013
Gene Ontology: tool for the unification of biology journal May 2000
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. journal April 1999
Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway journal December 1998
A Three-Component Enzyme System Catalyzes the O Demethylation of the Herbicide Dicamba in Pseudomonas maltophilia DI-6. journal January 1997
Mineralization of Individual Congeners of Linear Alkylbenzenesulfonate by Defined Pairs of Heterotrophic Bacteria journal July 2004
Isolation of Soil Bacteria Adapted To Degrade Humic Acid-Sorbed Phenanthrene journal July 2005
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 journal November 1998
A Rapid Method of Total Lipid Extraction and Purification journal August 1959
Nanopods: A New Bacterial Structure and Mechanism for Deployment of Outer Membrane Vesicles 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 journal March 2014

Cited By (4)

Prokaryotic Hydrocarbon Degraders book January 2018
Prokaryotic Hydrocarbon Degraders book January 2010
Mud volcanoes and the presence of PAHs journal January 2020
Three-dimensional bright-field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms: THREE-DIMENSIONAL BRIGHT-FIELD SCANNING TRANSMISSION journal August 2016

Similar Records

Draft Genome Assembly of Delftia acidovorans Type Strain 2167
Journal Article · Wed Sep 03 20:00:00 EDT 2014 · Genome Announcements · OSTI ID:1629333
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis
Journal Article · Wed Apr 07 20:00:00 EDT 2010 · PLoS Genetics · OSTI ID:1627282

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
Delftia acidovorans Cs1-4
Genome
Nanopods
Phenanthrene
Polycyclic aromatic hydrocarbons
phn island
polycyclic aromatic hydrocarbons