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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

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

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. More... »

PAGES

55

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  • Identifiers

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    http://scigraph.springernature.com/pub.10.1186/s40793-015-0041-x

    DOI

    http://dx.doi.org/10.1186/s40793-015-0041-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1033842776

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26380642


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