Genome Sequences of Alicycliphilus denitrificans Strains BC and K601
            <sup>T</sup>

Oosterkamp, Margreet J.; Veuskens, Teun; Plugge, Caroline M.; Langenhoff, Alette; Gerritse, Jan; Berkel, Willem J.H. van; Pieper, Dietmar H.; Junca, Howard; Goodwin, Lynne; Daligault, Hajnalka E.; Bruce, David; Detter, John C.; Tapia, Roxanne; Han, Cliff; Land, Miriam; Hauser, Loren; Smidt, Hauke; Stams, A.J.M.

doi:10.1128/jb.00365-11

Cited by 33 publications

(31 citation statements)

References 8 publications

(9 reference statements)

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“…The denitrifying bacteria group was also observed in the present study, exemplified by the Azoarcus / Thauera group use the aromatic compounds as m -xylene, phenol, toluene, ethylbenzene and others as carbon sources in anaerobic conditions [36]. Some strains of the genus Alicycliphilus , such as A. denitrificans BC and A. denitrificans K601, have been shown to degrade cyclic hydrocarbons [37]. Another denitrifying bacterium found in this work was Aromatoleum aromaticum EbN1, which is able to use a wide range of aromatic and nonaromatic compounds besides toluene, phenol, acetone and alcohols under anoxic and oxic conditions [38].…”

Section: Resultssupporting

confidence: 69%

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

et al. 2013

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Two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. The library screening based on PCR and biological activity assays revealed more than 400 positive clones for phenol degradation. From these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of phenol and aromatic compound degradation. The sequence analysis of selected clones yielded 129,635 reads at an estimated 17-fold coverage. The phylogenetic analysis showed Burkholderiales and Rhodocyclales as the most abundant orders among the selected fosmid clones. The MG-RAST analysis revealed a broad metabolic profile with important functions for wastewater treatment, including metabolism of aromatic compounds, nitrogen, sulphur and phosphorus. The predicted 2,276 proteins included phenol hydroxylases and cathecol 2,3- dioxygenases, involved in the catabolism of aromatic compounds, such as phenol, byphenol, benzoate and phenylpropanoid. The sequencing of one fosmid insert of 33 kb unraveled the gene that permitted the host, Escherichia coli EPI300, to grow in the presence of aromatic compounds. Additionally, the comparison of the whole fosmid sequence against bacterial genomes deposited in GenBank showed that about 90% of sequence showed no identity to known sequences of Proteobacteria deposited in the NCBI database. This study surveyed the functional potential of fosmid clones for aromatic compound degradation and contributed to our knowledge of the biodegradative capacity and pathways of microbial assemblages present in refinery wastewater treatment system.

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Section: Resultssupporting

confidence: 69%

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

et al. 2013

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“…Alicycliphilus denitrificans BC was isolated as a benzene-degrading chlorate reducer and has been genome sequenced (31). Genes for chlorate reduction are located on a 119,718-bp plasmid, pALIDE01 (GenBank accession no.…”

Section: Resultsmentioning

confidence: 99%

Structure and Evolution of Chlorate Reduction Composite Transposons

Clark

Melnyk

Engelbrektson

et al. 2013

mBio

114

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The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration.

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“…The genomes of A. denitrificans strains BC and K601 T have been annotated [38]. Based on 16S rRNA gene sequence analysis A. denitrificans clusters in the family Comamonadaceae of the Betaproteobacteria [3].…”

Section: Resultsmentioning

confidence: 99%

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

et al. 2013

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The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.

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Genome Sequences of Alicycliphilus denitrificans Strains BC and K601 ^T

Cited by 33 publications

References 8 publications

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

Structure and Evolution of Chlorate Reduction Composite Transposons

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

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Genome Sequences of Alicycliphilus denitrificans Strains BC and K601 T

Cited by 33 publications

References 8 publications

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

Structure and Evolution of Chlorate Reduction Composite Transposons

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

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Genome Sequences of Alicycliphilus denitrificans Strains BC and K601 ^T