Genome Sequence of the 1,4-Dioxane-Degrading Pseudonocardia dioxanivoransStrain CB1190

Sales, Christopher M.; Mahendra, Shaily; Grostern, Ariel; Parales, Rebecca E.; Goodwin, Lynne; Woyke, Tanja; Nolan, Matt; Lapidus, Alla; Chertkov, Olga; Ovchinnikova, Galina; Sczyrba, Alexander; Alvarez‐Cohen, Lisa

doi:10.1128/jb.00415-11

Cited by 56 publications

(44 citation statements)

References 18 publications

(10 reference statements)

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“…This finding is attributed to the high homology of the PHE primer sequences to CB1190 and further supported by the significant positive correlation (r ϭ 0.93, P Ͻ 0.01) between CB1190 16S rRNA genes and PHE abundance in activated sludge. DXMO and ALDH expression profiles were very similar, which was expected since these targets are located within the same gene cluster associated with dioxane or tetrahydrofuran degradation in CB1190 (35), Pseudonocardia tetrahydrofuranoxydans K1 (15), Pseudonocardia sp. strain ENV478 (19), and Rhodococcus sp.…”

Section: Discussionmentioning

confidence: 57%

“…1). Gene concentrations are representative of cell copies, with CB1190 containing 3 copies of the 16S rRNA gene and single copies of the selected monooxygenase and dehydrogenase genes (35). All targets experienced an initial lag phase, exponential growth phase, and subsequent stationary phase until day 6, when dioxane was removed to levels below the detection limit.…”

Section: Discussionmentioning

confidence: 99%

“…Identification of candidate biomarkers was focused on monooxygenase and dehydrogenase genes based on earlier work describing the dioxane degradation pathway for monooxygenase-expressing bacteria (29,36) and expression of dehydrogenase genes in bacteria during utilization of monooxygenase-inducing substrates (37)(38)(39). To facilitate gene selection, an in silico analysis was performed to identify all annotated monooxygenase groups within CB1190 and its associated plasmids (35). Candidate targets were selected from this comprehensive list based on their functional roles in the biological transformation of recalcitrant compounds.…”

Section: Methodsmentioning

confidence: 99%

“…strain ENV478 (19). In addition, the recently completed genomic assembly and annotation of Pseudonocardia dioxanivorans CB1190 (hereafter "CB1190") (35), a bacterium able to use dioxane as the sole source of carbon and energy (18,32), facilitated a comprehensive in silico analysis of genes encoding several multicomponent monooxygenase clusters (35), including a plasmidencoded region containing the entire THF degradation gene cluster from Pseudonocardia sp. strain ENV478.…”

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confidence: 99%

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Identification of Biomarker Genes To Predict Biodegradation of 1,4-Dioxane

Gedalanga

Pornwongthong

Mora³

et al. 2014

Appl Environ Microbiol

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Bacterial multicomponent monooxygenase gene targets in Pseudonocardia dioxanivorans CB1190 were evaluated for their use as biomarkers to identify the potential for 1,4-dioxane biodegradation in pure cultures and environmental samples. Our studies using laboratory pure cultures and industrial activated sludge samples suggest that the presence of genes associated with dioxane monooxygenase, propane monooxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase are promising indicators of 1,4-dioxane biotransformation; however, gene abundance was insufficient to predict actual biodegradation. A time course gene expression analysis of dioxane and propane monooxygenases in Pseudonocardia dioxanivorans CB1190 and mixed communities in wastewater samples revealed important associations with the rates of 1,4-dioxane removal. In addition, transcripts of alcohol dehydrogenase and aldehyde dehydrogenase genes were upregulated during biodegradation, although only the aldehyde dehydrogenase was significantly correlated with 1,4-dioxane concentrations. Expression of the propane monooxygenase demonstrated a time-dependent relationship with 1,4-dioxane biodegradation in P. dioxanivorans CB1190, with increased expression occurring after over 50% of the 1,4-dioxane had been removed. While the fraction of P. dioxanivorans CB1190-like bacteria among the total bacterial population significantly increased with decrease in 1,4-dioxane concentrations in wastewater treatment samples undergoing active biodegradation, the abundance and expression of monooxygenase-based biomarkers were better predictors of 1,4-dioxane degradation than taxonomic 16S rRNA genes. This study illustrates that specific bacterial monooxygenase and dehydrogenase gene targets together can serve as effective biomarkers for 1,4-dioxane biodegradation in the environment.

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Section: Discussionmentioning

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Identification of Biomarker Genes To Predict Biodegradation of 1,4-Dioxane

Gedalanga

Pornwongthong

Mora³

et al. 2014

Appl Environ Microbiol

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“…strain Tü6071, sequence accession AFHJ01000000 [94] Bifidobacterium breve UCC2003, sequence accession CP000303 [95] Propionibacterium acnes, sequence accession CP002815 [96] Amycolicicoccus subflavus DQS3-9A1 T , sequence accession CP002786 (chromosome), CP002787 (plasmid pAS9A-1), and CP002788 (plasmid pAS9A-2). [97] Gordonia neofelifaecis NRRL B-59395, sequence accession AEUD01000000 [98] Pseudonocardia dioxanivorans strain CB1190, sequence accession NC_015312-4 and CP002595-7 [99] Bifidobacterium longum subsp. longum KACC 91563, sequence accession CP002794 to CP002796 [100] Streptomyces cattleya NRRL 8057, sequence accession FQ859185 (chromosome) and FQ859184 (megaplasmid) [101] Rhodococcus sp.…”

Section: Tenericutesmentioning

confidence: 99%

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011

Nelson

2011

Stand. Genomic Sci.

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Practical Perspectives of 1,4‐Dioxane Investigation and Remediation

Chiang

Anderson

Wilken

et al. 2016

Remediation Journal

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1,4‐Dioxane (dioxane) is a contaminant of emerging concern that is classified by the U.S. Environmental Protection Agency as a likely human carcinogen. Dioxane has been used as a minor or major ingredient in many applications, and is also generated as an unwanted by‐product of industrial processes associated with the manufacturing of polyethylene, nonionic surfactants, and many consumer products (cosmetics, laundry detergents, shampoos, etc.). Dioxane is also a known stabilizer of chlorinated solvents, particularly 1,1,1‐trichloroethane, and has been commonly found comingled with chlorinated solvent plumes. Dioxane plumes at chlorinated solvent sites can complicate site closure strategies, which to date have not typically focused on dioxane. Aggressive treatment technologies have greatly advanced and are clearly capable of achieving lower parts per billion cleanup criteria using ex situ advanced oxidation processes and sorption media. In situ chemical oxidation has also been demonstrated to effectively remediate dioxane and chlorinated solvents. Other in situ remedies, such as enhanced bioremediation, phytoremediation, and monitored natural attenuation, have been studied; however, their ability to achieve cleanup levels is still somewhat questionable and is limited by co‐occurring contaminants. This article summarizes and provides practical perspectives on dioxane analysis, plume stability relative to other contaminants, and the development of investigation tools and treatment technologies.

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Genome Sequence of the 1,4-Dioxane-Degrading Pseudonocardia dioxanivoransStrain CB1190

Cited by 56 publications

References 18 publications

Identification of Biomarker Genes To Predict Biodegradation of 1,4-Dioxane

Identification of Biomarker Genes To Predict Biodegradation of 1,4-Dioxane

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011

Practical Perspectives of 1,4‐Dioxane Investigation and Remediation

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