[show abstract][hide abstract] ABSTRACT: The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon and with an element composition similar to the strain was generated. The optimal pH and temperature for strain growth were determined using shaker flasks and verified in bioreactors. Glucose, fructose, and glycerol were suitable carbon sources for MSH1 (μ = 0.1 h(-1)); slower growth was observed on succinate and acetic acid (μ = 0.01 h(-1)). Standard conditions for growth of the MSH1 strain were defined at pH 7 and 25 °C, with glucose as the carbon source. In bioreactors (1 and 5 L), the specific growth rate of MSH1 increased from μ = 0.1 h(-1) on traditional mineral salt medium to μ = 0.18 h(-1) on the optimized mineral salt medium. The biomass yield under standard conditions was 0.47 g dry weight biomass/g glucose consumed. An investigation of the catabolic capacity of MSH1 cells harvested in exponential and stationary growth phases showed a degradation activity per cell of about 3 × 10(-9) μg BAM h(-1). Thus, fast, efficient, large-scale production of herbicide-degrading Aminobacter was possible, bringing the use of this bacterium in bioaugmentation field remediation closer to reality.
Applied Microbiology and Biotechnology 03/2014; 98(5):2335-44. · 3.69 Impact Factor
[show abstract][hide abstract] ABSTRACT: The herbicide dichlobenil was banned in the European Union after its metabolite, BAM (2,6-dichlorobenzamide), was encountered in groundwater. Due to structural similarities, bromoxynil and ioxynil might be converted to persistent metabolites in a similar manner. To examine this, we used an indigenous soil bacterium Aminobacter sp. MSH1, capable of mineralizing dichlobenil via BAM and 2,6-DCBA (2,6-dichlorobenzoic acid).
Strain MSH1 converted bromoxynil and ioxynil to the corresponding aromatic metabolites, BrAC (3,5-dibromo-4-hydroxybenzoic acid) and IAC (3,5-diiodo-4-hydroxybenzoic acid) following Michaelis-Menten kinetics (adjusted R(2) between 0.907 and 0.999). However, in contrast to 2,6-DCBA, degradation of these metabolites was not detected in the pure culture studies, suggesting that they could pose an environmental risk, if similar partial degradation should occur in soil. Contrarily, experiments with natural soils indicated 20-30% mineralization of ioxynil and bromoxynil within the first week.
The degradation pathway of the three benzonitriles is initially driven by similar enzymes, where-after more specific enzymes are responsible for further degradation. Ioxynil and bromoxynil mineralization in soil is not dependent on previous benzonitrile exposure. Accumulation of dead-end metabolites, as seen for dichlobenil, is not a major problem.
Pest Management Science 12/2013; · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads.
PLoS ONE 01/2013; 8(12):e83346. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg L(-1)) or high (25 mg L(-1)) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different community compositions and major shifts in community structure following exposure to different MCPA concentrations were observed using both 16S rRNA gene denaturing gradient gel electrophoresis fingerprinting and pyrosequencing. The communities also differed in their MCPA-mineralizing activity. The enrichments selected on low concentrations mineralized MCPA with shorter lag phases than those selected on high concentrations. Flow cytometry measurements revealed that mineralization led to cell growth. The presence of low nucleic acid (LNA)-content bacteria was correlated with mineralization activity in cultures selected on low herbicide concentration. This suggests that LNA bacteria may play a role in degradation of low herbicide concentrations in aquifers impacted by agriculture. This study shows that subpopulations of herbicide-degrading bacteria that are adapted to different pesticide concentrations can coexist in the same environment and that using low herbicide concentration enables enrichment of apparently oligotrophic subpopulations.
Applied and environmental microbiology 11/2012; · 3.69 Impact Factor
[show abstract][hide abstract] ABSTRACT: The Greenland ice sheet (GrIS) receives organic carbon (OC) of anthropogenic origin, including pesticides, from the atmosphere and/or local sources, and the fate of these compounds in the ice is currently unknown. The ability of supraglacial heterotrophic microbes to mineralize different types of OC is likely a significant factor determining the fate of anthropogenic OC on the ice sheet. Here we determine the potential of the microbial community from the surface of the GrIS to mineralize the widely used herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). Surface ice cores were collected and incubated for up to 529 days in microcosms simulating in situ conditions. Mineralization of side chain- and ring-labeled [(14)C]2,4-D was measured in the samples, and quantitative PCR targeting the tfdA genes in total DNA extracted from the ice after the experiment was performed. We show that the supraglacial microbial community on the GrIS contains microbes that are capable of degrading 2,4-D and that they are likely present in very low numbers. They can mineralize 2,4-D at a rate of up to 1 nmol per m(2) per day, equivalent to ∼26 ng C m(-2) day(-1). Thus, the GrIS should not be considered a mere reservoir of all atmospheric contaminants, as it is likely that some deposited compounds will be removed from the system via biodegradation processes before their potential release due to the accelerated melting of the ice sheet.
Applied and environmental microbiology 05/2012; 78(15):5070-6. · 3.69 Impact Factor
[show abstract][hide abstract] ABSTRACT: Centimetre-scale vertical distribution of mineralization potential was determined for 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA) and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) by 96-well microplate radiorespirometric analysis in aquifer sediment sampled just below the groundwater table. Mineralization of 2,4-D and MCPA was fastest in sediment samples taken close to the groundwater table, whereas only minor mineralization of MCPP was seen. Considerable variability was exhibited at increasing aquifer depth, more so with 2,4-D than with MCPA. This suggests that the abundance of MCPA degraders was greater than that of 2,4-D degraders, possibly due to the fact that the overlying agricultural soil had long been treated with MCPA. Mineralization of 2,4-D and MCPA was followed by increased abundance of tfdA class I and class III catabolic genes, which are known to be involved in the metabolism of phenoxy acid herbicides. tfdA class III gene copy number was approximately 100-fold greater in samples able to mineralize MCPA than in samples able to mineralize 2,4-D, suggesting that tfdA class III gene plays a greater role in the metabolism of MCPA than of 2,4-D. Degradation rate was found to correlate positively with tfdA gene copy number, as well as with the total organic carbon content of the sediment.
[show abstract][hide abstract] ABSTRACT: 2,6-Dichlorobenzamide (BAM) is a metabolite of the herbicide 2,6-dichlorobenzonitrile (dichlobenil), and a prominent groundwater contaminant. Observable compound-specific isotope fractionation during BAM formation-through transformation of dichlobenil by Rhodococcus erythropolis DSM 9685-was small. In contrast, isotope fractionation during BAM degradation-with Aminobacter sp. MSH1 and ASI1, the only known bacterial strains capable of mineralizing BAM-was large, with pronounced carbon (ε(C) = -7.5‰ to -7.8‰) and nitrogen (ε(N) = -10.7‰ to -13.5‰) isotopic enrichment factors. BAM isotope values in natural samples are therefore expected to be dominated by the effects of its degradation rather than formation. Dual isotope slopes Δ (=Δδ(15)N/Δδ(13)C ≈ ε(N)/ε(C)) showed only small differences for MSH1 (1.75 ± 0.03) and ASI1 (1.45 ± 0.03) suggesting similar transformation mechanisms of BAM hydrolysis. Observations are in agreement with either a tetrahedral intermediate promoted by OH(-) or H(3)O(+) catalysis, or a concerted reaction mechanism. Therefore, owing to consistent carbon isotopic fractionation, isotope shifts of BAM can be linked to BAM biodegradation, and may even be used to quantify degradation of this persistent metabolite. In contrast, nitrogen isotope values may be rather indicative of different sources. Our results delineate a new approach to assessing the fate of BAM in the environment.
[show abstract][hide abstract] ABSTRACT: The soil bacterial isolate Variovorax sp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatechol ortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ∼55 kDa with a K(m) and a V(max) for linuron of 5.8 μM and 0.16 nmol min⁻¹, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues of libA are present in all other tested linuron-degrading Variovorax strains with the exception of Variovorax strains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in different Variovorax strains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria.
Applied and environmental microbiology 12/2011; 77(24):8754-64. · 3.69 Impact Factor
[show abstract][hide abstract] ABSTRACT: Degradation and mineralisation of the groundwater contaminant 2,6-dichloro-benzamide (BAM) was investigated in two Aminobacter strains focussing on the induction of BAM degradation and mineralisation and occurrence of intermediate metabolites. The BAM degradation rate was independent of whether the cells were pre-grown in the absence or presence of BAM, thus indicating that the first step in the degradation pathway was constitutively expressed. In contrast, (14)CO(2) production was stimulated when cells were pre-grown in the presence of BAM, suggesting that one or more of the subsequent steps in the degradation pathway were inducible. Accumulation of 2,6-dichlorobenzoate (DCBA) during degradation of BAM demonstrated that the first step involved amidase activity. Mass balance calculations and thin-layer chromatography coupled with autoradiographic detection indicated that degradation of DCBA and at least one unknown metabolite may comprise a bottleneck for BAM mineralisation by Aminobacter spp. The study thus provides novel information about the BAM degradation pathway and points to the involvement of unknown intermediate metabolites in degradation of this important groundwater contaminant.
Applied Microbiology and Biotechnology 10/2011; 94(1):237-45. · 3.69 Impact Factor
[show abstract][hide abstract] ABSTRACT: The degradation of pesticides in deeper soil layers and groundwater is
of growing interest, because they have repeatedly been found in drinking
water supply wells and may pose a risk to future water resources.
Current assessment schemes face a common problem, however: natural
degradation often cannot be reliably assessed by concentration
measurements alone, since mass balances are difficult to establish and
transformation cannot be distinguished from sorption or dilution. Even
detection of metabolites may only give an incomplete picture. When
several transformation pathways occur, some metabolites may be degraded
or form bound residues so that the associated pathways may be missed.
Our research shows that dual isotope plots derived from compound
specific isotope analysis offer a novel approach to give additional,
complementary insight into the natural degradation of pesticides.
Detection of metabolites is not required, since the isotope
fractionation can be fully observed in the pesticide itself.
Specifically, different initial biotransformation reactions of the
phenylurea herbicide isoproturon
(3-(4-isopropylphenyl)-1,1-dimethylurea) in pure culture experiments
with bacterial and fungal strains showed strongly pathway-dependent
isotope fractionation. When analyzing isotopic changes in different
parts of the isoproturon molecule, hydroxylation of the isopropyl group
by fungi was found to be associated with C and H isotope fractionation.
In contrast, hydrolysis by Arthrobacter globiformis D47 caused strong C
and N isotope fractionation, albeit in a different manner than abiotic
hydrolysis so that isotope measurements can distinguish between both
modes of transformation. Likewise, we observed highly
pathway-dependent C and N isotope fractionation of atrazine
of atrazine by Rhodococcus sp. strain NI86/21 resulted in enrichment of
both 13-C and 15-N in atrazine, whereas hydrolysis to hydroxyatrazine by
Chelatobacter heintzii, Pseudomonas sp. ADP and Arthrobacter aurescens
TC1 gave enrichment of 13-C, but depletion of 15-N. Comparison with
abiotic reference experiments provided novel insight into the underlying
enzymatic transformation mechanisms. Our investigations show how
characteristic isotope patterns may significantly add to the present
understanding of the environmental fate of pesticides.
[show abstract][hide abstract] ABSTRACT: Fuel-contaminated soils from Station Nord (St. Nord) in Greenland were sampled with the aim of assessing the intrinsic attenuation potential by quantifying the presence and activity of degradative microbial populations using phenanthrene as a model compound. Mineralization of [(14)C]phenanthrene to (14)CO(2) was measured in contaminated soils at temperatures down to 0 degrees C and sizable naphthalene-, undecane-, biphenyl- and phenanthrene-degrading populations were measured by microplate-based most-probable-number analysis. Cloning and 16S rRNA gene sequencing, focused on the dominant phenanthrene-degrading bacteria, revealed strains related to bacteria previously found in cold and contaminated environments. Overall, we provide evidence for the presence and potential activity of phenanthrene-degrading bacteria in polluted St. Nord soils and this study is the first to indicate an intrinsic bioremediation potential in hydrocarbon-contaminated soils from the Greenland High Arctic.
[show abstract][hide abstract] ABSTRACT: The fate of pesticides in the subsurface is of great interest to the public, industry, and regulatory authorities. Compound-specific isotope analysis (CSIA) is a promising tool complementary to existing methods for elucidating pesticide degradation reactions. Here, we address three different initial biotransformation reactions of the phenylurea herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) in pure culture experiments with bacterial and fungal strains. When analyzing isotopic changes in different parts of the isoproturon molecule, hydroxylation of the isopropyl group by fungi was found to be associated with C and H isotope fractionation. In contrast, hydrolysis by Arthrobacter globiformis D47 caused strong C and N isotope fractionation, albeit in a different manner than abiotic hydrolysis so that isotope measurements can distinguish between both modes of transformation. No significant isotope fractionation was observed during N-demethylation by Sphingomonas sp. SRS2. The observed isotope fractionation patterns were in agreement with the type of reactions and elements involved. Moreover, their substantially different nature suggests that isotope changes in natural samples may be uniquely attributed to either pathway, allowing even to distinguish the abiotic versus biotic nature of hydrolysis. Our investigations show how characteristic isotope patterns may significantly add to the present understanding of the environmental fate of pesticides.
Environmental Science and Technology 02/2010; 44(7):2372-8. · 5.26 Impact Factor
[show abstract][hide abstract] ABSTRACT: Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and diversity of tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT50) was approximately 12 days in soil sampled from <30 cm depth, and increased progressively with soil depth, reaching over 84 days at 70–80 cm. In sub-soil there was a lag period of between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in top-soil samples prior to the onset of degradation. The maximum degradation rate was the same in top-soil and sub-soil samples. Although diverse tfdAα and tfdA genes were present prior to mecoprop-p degradation, real time PCR revealed that degradation was associated with proliferation of tfdA genes. The number of tfdA genes and the most probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p addition were below the limit of quantification and detection respectively. Melting curves from the real time PCR analysis showed that prior to mecoprop-p degradation both class I and class III tfdA genes were present in top- and sub-soil samples. However at all soil depths only tfdA class III genes proliferated during degradation. Denaturing gradient gel electrophoresis confirmed that class III tfdA genes were associated with mecoprop-p degradation. Degradation was not associated with the induction of novel tfdA genes in top- or sub-soil samples, and there were no apparent differences in tfdA gene diversity with soil depth prior to or following degradation.
[show abstract][hide abstract] ABSTRACT: The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized by a bacterial culture isolated from an agricultural soil regularly exposed to IPU. Molecular analysis of the bacterial culture by DNA fingerprinting, cloning and sequencing of the 16S rRNA genes revealed that it consisted of six different members among whom the dominant was related to Sphingomonas sp. Six bacterial strains belonging to genera Ancylobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Variovorax and Agrobacterium were isolated from the IPU-degrading culture. None of these were able to degrade IPU in pure culture and only the intact culture sustained the ability to mineralize IPU. The composition of the culture appeared stable suggesting that yet unknown interactions are involved in the IPU mineralization. IPU degradation involved the transitory accumulation of three known IPU metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, and 4-isopropylaniline and their further degradation. Thus, it indicates a metabolic pathway initiated by two successive N-demethylations, followed by cleavage of the urea side chain. This culture did not degrade other structurally related phenylurea herbicides. The degrading activity of the bacterial culture was deeply influenced by the pH, being completely inhibited at pH 5.5 and optimal at pH 7.5.
[show abstract][hide abstract] ABSTRACT: The mineralization of the herbicide linuron at concentrations of microg and mg L(-1) was studied in liquid batch experiments with Variovorax sp. strain SRS16. The strain was highly efficient at mineralizing a range of linuron concentrations (0.002-10 mg L(-1)) with 20-60% of the added (14)C-ring-labeled linuron metabolized to (14)CO(2) within hours to days depending on the initial linuron concentration and incubation period. At mg L(-1) linuron concentrations the mineralization activity by SRS16 was inducible and a shift to constitutive mineralization activity was apparent with a reduction in the linuron concentration to microg L(-1) levels. This study revealed that strain SRS16 is a promising candidate for bioaugmentation of water or soil resources contaminated with low linuron concentrations.
[show abstract][hide abstract] ABSTRACT: The benzonitriles dichlobenil, bromoxynil and ioxynil are important broad-spectrum or selective herbicides used in agriculture, orchards and public areas worldwide. The dichlobenil metabolite 2,6-dichlorobenzamide is the most frequently encountered groundwater contaminant in Denmark, which suggests that the environmental fate of these three structurally related benzonitrile herbicides should be addressed in detail. This review summarises the current knowledge on microbial degradation of dichlobenil, bromoxynil and ioxynil with particular focus on common features of degradation rates and pathways, accumulation of persistent metabolites and diversity of the involved degrader organisms.
[show abstract][hide abstract] ABSTRACT: The phenylurea herbicide diuron [N-(3,4-dichlorophenyl)-N,N-dimethylurea] is widely used in a broad range of herbicide formulations, and consequently, it is frequently detected as a major water contaminant in areas where there is extensive use. We constructed a linuron [N-(3,4-dichlorophenyl)-N-methoxy-N-methylurea]- and diuron-mineralizing two-member consortium by combining the cooperative degradation capacities of the diuron-degrading organism Arthrobacter globiformis strain D47 and the linuron-mineralizing organism Variovorax sp. strain SRS16. Neither of the strains mineralized diuron alone in a mineral medium, but combined, the two strains mineralized 31 to 62% of the added [ring-U-(14)C]diuron to (14)CO(2), depending on the initial diuron concentration and the cultivation conditions. The constructed consortium was used to initiate the degradation and mineralization of diuron in soil without natural attenuation potential. This approach led to the unexpected finding that Variovorax sp. strain SRS16 was able to mineralize diuron in a pure culture when it was supplemented with appropriate growth substrates, making this strain the first known bacterium capable of mineralizing diuron and representatives of both the N,N-dimethyl- and N-methoxy-N-methyl-substituted phenylurea herbicides. The ability of the coculture to mineralize microgram-per-liter levels of diuron was compared to the ability of strain SRS16 alone, which revealed the greater extent of mineralization by the two-member consortium (31 to 33% of the added [ring-U-(14)C]diuron was mineralized to (14)CO(2) when 15.5 to 38.9 mug liter(-1) diuron was used). These results suggest that the consortium consisting of strains SRS16 and D47 could be a promising candidate for remediation of soil and water contaminated with diuron and linuron and their shared metabolite 3,4-dichloroaniline.
Applied and environmental microbiology 05/2008; 74(8):2332-40. · 3.69 Impact Factor