Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer

Ikuma, Kaoru; Gunsch, Claudia K.

doi:10.1007/s00253-012-3949-8

Cited by 22 publications

(28 citation statements)

References 52 publications

(49 reference statements)

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“…A wild isolate with its ability to transfer catabolic genes through natural processes (HGT) such as conjugation, may provide a better solution to contain and remediate these compounds [55], [56]. Pseudomonas putida IncP-9 TOL plasmid pWW0, has been studied for genetic bioaugmentation of soil, wastewater and aerobic microbial granules [57]. In another example, dissemination of plasmid pGKT2 harboring catabolic genes for hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) degradation was studied by means of conjugation between the Gordonia sp.…”

Section: Resultsmentioning

confidence: 99%

Pseudomonas putida CSV86: A Candidate Genome for Genetic Bioaugmentation

et al. 2014

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Pseudomonas putida CSV86, a plasmid-free strain possessing capability to transfer the naphthalene degradation property, has been explored for its metabolic diversity through genome sequencing. The analysis of draft genome sequence of CSV86 (6.4 Mb) revealed the presence of genes involved in the degradation of naphthalene, salicylate, benzoate, benzylalcohol, p-hydroxybenzoate, phenylacetate and p-hydroxyphenylacetate on the chromosome thus ensuring the stability of the catabolic potential. Moreover, genes involved in the metabolism of phenylpropanoid and homogentisate, as well as heavy metal resistance, were additionally identified. Ability to grow on vanillin, veratraldehyde and ferulic acid, detection of inducible homogentisate dioxygenase and growth on aromatic compounds in the presence of heavy metals like copper, cadmium, cobalt and arsenic confirm in silico observations reflecting the metabolic versatility. In silico analysis revealed the arrangement of genes in the order: tRNAGly, integrase followed by nah operon, supporting earlier hypothesis of existence of a genomic island (GI) for naphthalene degradation. Deciphering the genomic architecture of CSV86 for aromatic degradation pathways and identification of elements responsible for horizontal gene transfer (HGT) suggests that genetic bioaugmentation strategies could be planned using CSV86 for effective bioremediation.

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Section: Resultsmentioning

confidence: 99%

Pseudomonas putida CSV86: A Candidate Genome for Genetic Bioaugmentation

et al. 2014

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“…In addition to the introduction of the genes for the transposon delivery, however, consideration must be given to the ability of the strain to express the transposase and the selectable marker. The GϩC content of the recipient genome has been shown to play an important role in expression of foreign DNA (29). As such, it may be necessary to tailor the type of transposon or antibiotic resistance marker and codon usage to accommodate the strain being analyzed by TnLE-seq.…”

Section: Resultsmentioning

confidence: 99%

Rapid Transposon Liquid Enrichment Sequencing (TnLE-seq) for Gene Fitness Evaluation in Underdeveloped Bacterial Systems

Fels

Zane

Blake

et al. 2013

Appl Environ Microbiol

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cWhole-genome fitness analysis in microbes that uses saturating transposon mutagenesis combined with massively parallel sequencing (Tn-seq) is providing a measure of the contribution of each gene to a given growth condition. With this technique, gene fitness profiles and essential genes are discovered by simultaneous analyses of whether the absence of each gene product alters the growth kinetics of the bacterium. Here we modify the standard Tn-seq procedure to simplify and shorten the process by including delivery of the transposon through conjugation and liquid culture enrichment of the mutant pool, creating transposon liquid enrichment sequencing (TnLE-seq). To illustrate the success of these modifications and the robustness of the procedure, analyses of gene fitness of two cultures of the strictly anaerobic bacterium Desulfovibrio vulgaris Hildenborough were performed, with growth on lactate as the electron donor and sulfate as the electron acceptor. These data demonstrate reproducibility and provide a base condition for analysis of fitness changes in deletion mutants and in various growth conditions. The procedural modifications will facilitate the application of this powerful genetic analysis to microbes lacking a facile genetic system. Pilot studies produced 2.5 ؋ 10 5 and 3.4 ؋ 10 5 unique insertion mutants in the anaerobe Desulfovibrio vulgaris Hildenborough grown under typical laboratory conditions in rich medium. These analyses provided two similar high-resolution maps of gene fitness across the genome, and the method was also applied to growth in minimal medium. These results were also compared to the coverage obtained with a ca. 13,000-member cataloged transposon library constructed by sequencing transposon insertion sites in individual mutants.

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“…We showed that the toluene degradation rates of transconjugant strains in the absence of additional carbon sources were dependent on genomic G + C content, although lacking a clear correlation function. 16 However, the limited toluene degradation rates of the tested strains were significantly enhanced by the simultaneous presence of an easily biodegradable carbon source. 16 Our results in Figure 2 further imply that the enhancement effects of glucose and LB broth may be larger in transconjugant strains with larger deviation in genomic G + C content from the TOL plasmid average of 59%.…”

Section: G Enetic Bioaugmentation Is An In Situ Bioremediation Methodmentioning

confidence: 99%

“…16 However, the limited toluene degradation rates of the tested strains were significantly enhanced by the simultaneous presence of an easily biodegradable carbon source. 16 Our results in Figure 2 further imply that the enhancement effects of glucose and LB broth may be larger in transconjugant strains with larger deviation in genomic G + C content from the TOL plasmid average of 59%. On the other hand, the fold changes by glucose or LB broth addition had no correlation with the phylogenetic distance of the transconjugants from the donor strains (data not shown).…”

Section: G Enetic Bioaugmentation Is An In Situ Bioremediation Methodmentioning

confidence: 99%

“…G + C contents in the presence of toluene alone, 16 the enhancement by carbon source addition may only directly relieve the phenotypic limitations brought upon by G + C content differences. Furthermore, glucose appeared to have a larger effect on transconjugants with lower genomic G + C contents compared with LB broth, suggesting that glucose would be a more favorable carbon source to add to stimulate genetic bioaugmentation of the TOL plasmid in microbial communities that have lower G + C contents.…”

Section: G Enetic Bioaugmentation Is An In Situ Bioremediation Methodmentioning

confidence: 99%

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