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Ecotoxicology and Environmental Safety Feb 2016A series of toxicity bioassays was conducted to monitor the ecotoxicity of soils in the different phases of bioremediation. Artificially oil-contaminated soil was...
A series of toxicity bioassays was conducted to monitor the ecotoxicity of soils in the different phases of bioremediation. Artificially oil-contaminated soil was inoculated with a petroleum hydrocarbon-degrading bacterial consortium containing Burkholderia cepacia GS3C, Sphingomonas GY2B and Pandoraea pnomenusa GP3B strains adapted to crude oil. Soil ecotoxicity in different phases of bioremediation was examined by monitoring total petroleum hydrocarbons, soil enzyme activities, phytotoxicity (inhibition of seed germination and plant growth), malonaldehyde content, superoxide dismutase activity and bacterial luminescence. Although the total petroleum hydrocarbon (TPH) concentration in soil was reduced by 64.4%, forty days after bioremediation, the phytotoxicity and Photobacterium phosphoreum ecotoxicity test results indicated an initial increase in ecotoxicity, suggesting the formation of intermediate metabolites characterized by high toxicity and low bioavailability during bioremediation. The ecotoxicity values are a more valid indicator for evaluating the effectiveness of bioremediation techniques compared with only using the total petroleum hydrocarbon concentrations. Among all of the potential indicators that could be used to evaluate the effectiveness of bioremediation techniques, soil enzyme activities, phytotoxicity (inhibition of plant height, shoot weight and root fresh weight), malonaldehyde content, superoxide dismutase activity and luminescence of P. phosphoreum were the most sensitive.
Topics: Bacteria; Biodegradation, Environmental; Germination; Hydrocarbons; Magnoliopsida; Malondialdehyde; Petroleum; Plant Development; Plant Roots; Seeds; Soil Microbiology; Soil Pollutants; Superoxide Dismutase
PubMed: 26491984
DOI: 10.1016/j.ecoenv.2015.10.005 -
Journal of Biotechnology Nov 2015Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate...
Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens.
Topics: Burkholderiaceae; DNA, Bacterial; Environmental Microbiology; Genome, Bacterial; Solid Waste; Waste Disposal Facilities
PubMed: 26393955
DOI: 10.1016/j.jbiotec.2015.09.018 -
PeerJ 2015In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair...
In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.
PubMed: 26336650
DOI: 10.7717/peerj.1225 -
Applied and Environmental Microbiology Jul 2015In this work, we examined the profile of metabolites produced from the doubly para-substituted biphenyl analogs 4,4'-dihydroxybiphenyl, 4-hydroxy-4'-chlorobiphenyl,...
In this work, we examined the profile of metabolites produced from the doubly para-substituted biphenyl analogs 4,4'-dihydroxybiphenyl, 4-hydroxy-4'-chlorobiphenyl, 3-hydroxy-4,4'-dichlorobiphenyl, and 3,3'-dihydroxy-4,4'-chlorobiphenyl by biphenyl-induced Pandoraea pnomenusa B356 and by its biphenyl dioxygenase (BPDO). 4-Hydroxy-4'-chlorobiphenyl was hydroxylated principally through a 2,3-dioxygenation of the hydroxylated ring to generate 2,3-dihydro-2,3,4-trihydroxy-4'-chlorobiphenyl and 3,4-dihydroxy-4'-chlorobiphenyl after the removal of water. The former was further oxidized by the biphenyl dioxygenase to produce ultimately 3,4,5-trihydroxy-4'-chlorobiphenyl, a dead-end metabolite. 3-Hydroxy-4,4'-dichlorobiphenyl was oxygenated on both rings. Hydroxylation of the nonhydroxylated ring generated 2,3,3'-trihydroxy-4'-chlorobiphenyl with concomitant dechlorination, and 2,3,3'-trihydroxy-4'-chlorobiphenyl was ultimately metabolized to 2-hydroxy-4-chlorobenzoate, but hydroxylation of the hydroxylated ring generated dead-end metabolites. 3,3'-Dihydroxy-4,4'-dichlorobiphenyl was principally metabolized through a 2,3-dioxygenation to generate 2,3-dihydro-2,3,3'-trihydroxy-4,4'-dichlorobiphenyl, which was ultimately converted to 3-hydroxy-4-chlorobenzoate. Similar metabolites were produced when the biphenyl dioxygenase of Burkholderia xenovorans LB400 was used to catalyze the reactions, except that for the three substrates used, the BPDO of LB400 was less efficient than that of B356, and unlike that of B356, it was unable to further oxidize the initial reaction products. Together the data show that BPDO oxidation of doubly para-substituted hydroxychlorobiphenyls may generate nonnegligible amounts of dead-end metabolites. Therefore, biphenyl dioxygenase could produce metabolites other than those expected, corresponding to dihydrodihydroxy metabolites from initial doubly para-substituted substrates. This finding shows that a clear picture of the fate of polychlorinated biphenyls in contaminated sites will require more insights into the bacterial metabolism of hydroxychlorobiphenyls and the chemistry of the dihydrodihydroxylated metabolites derived from them.
Topics: Bacterial Proteins; Biocatalysis; Biodegradation, Environmental; Burkholderia; Burkholderiaceae; Dioxygenases; Molecular Structure; Oxidation-Reduction; Polychlorinated Biphenyls; Substrate Specificity
PubMed: 25956777
DOI: 10.1128/AEM.00786-15 -
Genome Announcements Feb 2015Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in people with cystic fibrosis (CF), but the clinical significance of this...
Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in people with cystic fibrosis (CF), but the clinical significance of this infection is ambiguous. We have sequenced and annotated the genomes of two multidrug-resistant Pandoraea pnomenusa isolates recovered 11 months apart from the same CF patient.
PubMed: 25657265
DOI: 10.1128/genomeA.01389-14 -
Journal of Molecular Modeling Dec 2014In recent years, techniques involving the use of organisms to remove or neutralize pollutants from contaminated sites have attracted great attention. The aim of...
In recent years, techniques involving the use of organisms to remove or neutralize pollutants from contaminated sites have attracted great attention. The aim of bioremediation is to use naturally occurring organisms to degrade dangerous substances to less toxic or non toxic molecules. The gram-negative bacterium Pandoraea pnomenusa strain B-356 (Pp) has been found to be able to transform a persistent class of organic pollutant compounds, namely the biphenyl and polychlorinated biphenyls (PCBs). A key enzyme in the PCB catabolic pathway is NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB), for which the crystal structure from Pp has been crystallized in apo-, NAD-bound and biphenyldiol-/NAD-bound forms. The substrate binding loop structure has not been completely resolved to date in the former two bound states. Here we report the results of the first extensive molecular dynamics simulations on the three different states of PpBphB. This allowed an in depth characterization of the mechanism of ligand uptake and binding, including unraveling of the gating mechanism. Our simulations give a deep insight into several dynamic features of the enzyme that were not captured by crystal structures.
Topics: Bacterial Proteins; Binding Sites; Biodegradation, Environmental; Biphenyl Compounds; Crystallization; Crystallography, X-Ray; Gram-Negative Bacteria; Kinetics; Ligands; Molecular Dynamics Simulation; Molecular Structure; Oxidoreductases; Polychlorinated Biphenyls; Protein Binding; Protein Conformation; Structure-Activity Relationship; Substrate Specificity
PubMed: 25433599
DOI: 10.1007/s00894-014-2531-y -
Journal of Environmental Sciences... May 2014A strain Pandoraea pnomenusa LX-1 that uses dichloromethane (DCM) as sole carbon and energy source has been isolated and identified in our laboratory. The optimum...
A strain Pandoraea pnomenusa LX-1 that uses dichloromethane (DCM) as sole carbon and energy source has been isolated and identified in our laboratory. The optimum aerobic biodegradation of DCM in batch culture was evaluated by response surface methodology. Maximum biodegradation (5.35 mg/(L·hr)) was achieved under cultivation at 32.8°C, pH 7.3, and 0.66% NaCl. The growth and biodegradation processes were well fitted by Haldane's kinetic model, yielding maximum specific growth and degradation rates of 0.133 hr(-1) and 0.856 hr(-1), respectively. The microorganism efficiently degraded a mixture of DCM and coexisting components (benzene, toluene and chlorobenzene). The carbon recovery (52.80%-94.59%) indicated that the targets were predominantly mineralized and incorporated into cell materials. Electron acceptors increased the DCM biodegradation rate in the following order: mixed > oxygen > iron > sulfate > nitrate. The highest dechlorination rate was 0.365 mg Cl(-)/(hr·mg biomass), obtained in the presence of mixed electron acceptors. Removal was achieved in a continuous biotrickling filter at 56%-85% efficiency, with a mineralization rate of 75.2%. Molecular biology techniques revealed the predominant strain as P. pnomenusa LX-1. These results clearly demonstrated the effectiveness of strain LX-1 in treating DCM-containing industrial effluents. As such, the strain is a strong candidate for remediation of DCM coexisting with other organic compounds.
Topics: Biodegradation, Environmental; Burkholderiaceae; Filtration; Methylene Chloride; Time Factors; Waste Disposal, Fluid; Water Pollutants, Chemical
PubMed: 25079641
DOI: 10.1016/S1001-0742(13)60538-0 -
Sensors (Basel, Switzerland) Jun 2014Strain RB38 was recovered from a former dumping area in Malaysia. MALDI-TOF mass spectrometry and genomic analysis identified strain RB-38 as Pandoraea pnomenusa....
Strain RB38 was recovered from a former dumping area in Malaysia. MALDI-TOF mass spectrometry and genomic analysis identified strain RB-38 as Pandoraea pnomenusa. Various biosensors confirmed its quorum sensing properties. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis was subsequently used to characterize the N-acyl homoserine lactone production profile of P. pnomenusa strain RB38, which validated that this isolate produced N-octanoyl homoserine lactone as a quorum sensing molecule. This is the first report of the production of N-octanoyl homoserine lactone by P. pnomenusa strain RB38.
Topics: Burkholderiaceae; Chromatography, Liquid; Homoserine; Lactones; Quorum Sensing; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 24919016
DOI: 10.3390/s140610177 -
Genome Announcements May 2014Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from soil. Here, we report the complete genome sequence of P. pnomenusa strain...
Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from soil. Here, we report the complete genome sequence of P. pnomenusa strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS SMRT) sequencer high-resolution technology.
PubMed: 24812228
DOI: 10.1128/genomeA.00427-14 -
Journal of Bacteriology Aug 2013In this work, we have compared the ability of Pandoraea pnomenusa B356 and of Burkholderia xenovorans LB400 to metabolize diphenylmethane and benzophenone, two biphenyl...
In this work, we have compared the ability of Pandoraea pnomenusa B356 and of Burkholderia xenovorans LB400 to metabolize diphenylmethane and benzophenone, two biphenyl analogs in which the phenyl rings are bonded to a single carbon. Both chemicals are of environmental concern. P. pnomenusa B356 grew well on diphenylmethane. On the basis of growth kinetics analyses, diphenylmethane and biphenyl were shown to induce the same catabolic pathway. The profile of metabolites produced during growth of strain B356 on diphenylmethane was the same as the one produced by isolated enzymes of the biphenyl catabolic pathway acting individually or in coupled reactions. The biphenyl dioxygenase oxidizes diphenylmethane to 3-benzylcyclohexa-3,5-diene-1,2-diol very efficiently, and ultimately this metabolite is transformed to phenylacetic acid, which is further metabolized by a lower pathway. Strain B356 was also able to cometabolize benzophenone through its biphenyl pathway, although in this case, this substrate was unable to induce the biphenyl catabolic pathway and the degradation was incomplete, with accumulation of 2-hydroxy-6,7-dioxo-7-phenylheptanoic acid. Unlike strain B356, B. xenovorans LB400 did not grow on diphenylmethane. Its biphenyl pathway enzymes metabolized diphenylmethane, but they poorly metabolize benzophenone. The fact that the biphenyl catabolic pathway of strain B356 metabolized diphenylmethane and benzophenone more efficiently than that of strain LB400 brings us to postulate that in strain B356, this pathway evolved divergently to serve other functions not related to biphenyl degradation.
Topics: Bacteriological Techniques; Benzhydryl Compounds; Benzophenones; Biphenyl Compounds; Burkholderiaceae; Gene Expression Regulation, Bacterial; Models, Molecular; Molecular Structure
PubMed: 23749969
DOI: 10.1128/JB.00161-13