title: Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.
abstract: 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. 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.
authors.affiliation: O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison, WI 53706 USA.
authors.forename: Ameesha R
authors.initials: AR
authors.lastname: Shetty
authors.affiliation: Department of Food Production, University of the West Indies, St. Augustine, Trinidad and Tobago.
authors.forename: Vidya
authors.initials: V
authors.lastname: de Gannes
authors.affiliation: Department of Microbiology, University of Lagos, Lagos, Nigeria.
authors.forename: Chioma C
authors.initials: CC
authors.lastname: Obi
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St.Petersburg, Russia.
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA.
authors.forename: Lynne A
authors.initials: LA
authors.lastname: Goodwin
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Samuel
authors.initials: S
authors.lastname: Pitluck
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Linda
authors.initials: L
authors.lastname: Peters
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Mikhailova
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA.
authors.forename: Hazuki
authors.initials: H
authors.lastname: Teshima
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA.
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA.
authors.forename: Roxanne
authors.initials: R
authors.lastname: Tapia
authors.affiliation: Oak Ridge National Laboratory, Oak Ridge, TN USA.
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.affiliation: Oak Ridge National Laboratory, Oak Ridge, TN USA.
authors.forename: Loren J
authors.initials: LJ
authors.lastname: Hauser
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Ioanna
authors.initials: I
authors.lastname: Pagani
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA.
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI USA.
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Denef
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA USA.
authors.forename: Tanya
authors.initials: T
authors.lastname: Woyke
authors.affiliation: O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison, WI 53706 USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Hickey
keywords: Delftia acidovorans Cs1-4; Genome; Nanopods; Phenanthrene; phn island; polycyclic aromatic hydrocarbons