Mineralisation of the herbicide linuron by Variovorax sp strain RA8 isolated from Japanese river sediment using an ecosystem model (microcosm)

Article · August 2010with13 Reads
DOI: 10.1002/ps.1951 · Source: PubMed
Abstract
Linuron is a globally used phenylurea herbicide, and a large number of studies have been made on the microbial degradation of the herbicide. However, to date, the few bacteria able individually to mineralise linuron have been isolated only from European agricultural soils. An attempt was made to isolate linuron-mineralising bacteria from Japanese river sediment using a uniquely designed river ecosystem model (microcosm) treated with (14)C-ring-labelled linuron (approximately 1 mg L(-1)). A linuron-mineralising bacterium that inhabits river sediment was successfully isolated. The isolate belongs to the genera Variovorax and was designated as strain RA8. Strain RA8 gradually used linuron in basal salt medium (5.2 mg L(-1)) with slight growth. In 15 days, approximately 25% of (14)C-linuron was mineralised to (14)CO(2), with 3,4-dichloroaniline as an intermediate. Conversely, in 100-fold diluted R2A broth, strain RA8 rapidly mineralised (14)C-linuron (5.5 mg L(-1)) and more than 70% of the applied radioactivity was released as (14)CO(2) within 3 days, and a trace amount of 3,4-dichloroaniline was detected. Additionally, the isolate also degraded monolinuron, metobromuron and chlorobromuron, but not diuron, monuron or isoproturon. Although strain RA8 can grow on linuron, some elements in the R2A broth seemed significantly to stimulate its growth and ability to degrade. The isolate strictly recognised the structural difference between N-methoxy-N-methyl and N,N-dimethyl substitution of various phenylurea herbicides.
    • PBL-H6 Belgium Linuron [147] Variovorax sp. RA8 Japan Linuron [148] Chlorotoluron Metobromuron converted into 4-isopropylcatechol (4-IPC) by the aniline dioxygenase system AdoQTA1A2BR followed by the catechol meta-cleavage pathway (AdoXEGKLIJC) and the TCA cycle (Fig. 8A) [132,133]. Regarding the second pathway, the phenylurea hydrolase-encoding genes puhA, puhB, libA and hylA were identified in strains D47 [126], JK1 [134], SRS16 [141] and WDL1 [146], respectively.
    [Show abstract] [Hide abstract] ABSTRACT: Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.
    Full-text · Article · Nov 2016
    • This is in contrast to our study where the genus specificity of the catabolic function was retained, that is, the enrichment in both soil and in suspension resulted in the growth of Variovorax bacteria. In contrast to biodegradation of naphthalene, a function that is widespread between various microbial guilds, degradation of pesticides is often associated with a specific microbial group as in the case of linuron degradation (Engelhardt et al., 1971; El-Fantroussi, 2000; Dejonghe et al., 2003; Sorensen et al., 2005; Breugelmans et al., 2007; Satsuma, 2010). Also, studies that used a DNA/RNA SIP approach to identify organisms related with a specific catabolic function pointed towards the occurrence of such biases but none of those studies actually compared SIP data with the outcome of an enrichment procedure for the same environmental sample (Jones et al., 2008).
    [Show abstract] [Hide abstract] ABSTRACT: To assess the involvement of the genus Variovorax and the linuron hydrolase gene libA in in situ linuron degradation in agricultural fields, changes in Variovorax community size and composition, in libA abundance and in linuron mineralization capacity were monitored in field soil plots either treated or not with a linuron-containing herbicide mixture. Changes in Variovorax community composition, due to the proliferation of a hereto unknown Variovorax phylotype D, and increases in libA numbers occurred concomitant to increases in linuron mineralization capacity in the plot treated with the herbicide mixture. The observations suggest that Variovorax and libA proliferated as a response to linuron and hence their contribution to in situ linuron degradation. The involvement of Variovorax phylotype D and libA in linuron degradation in the examined soil was supported by laboratory soil microcosm experiments. Attempts to enrich in suspended cultures and isolate the organism corresponding to phylotype D from the soil were unsuccessful as the enrichment resulted in replacement of Variovorax phylotype D by other Variovorax phylotypes. This illustrates that linuron-degrading strains isolated by liquid enrichment cultures are not always representatives of those responsive to linuron in the field, although the genus specificity of linuron degradation was retained. This article is protected by copyright. All rights reserved.
    Article · Apr 2013
  • [Show abstract] [Hide abstract] ABSTRACT: Herbicides have become an important tool as a plant protection agent for boosting food production. Herbicides can be defined as crop protecting chemicals used to kill weedy plants or interrupt normal plant growth. Herbicides provide a convenient, economical, and effective way to help manage weeds. Also, herbicides allow fields to be planted with less tillage and allow earlier planting dates. However, herbicide use also carries risks that include environmental, ecological, and human health effects. Additionally there are a number of factors that influence the inactivation, breakdown, and disappearance of herbicides. Amongst these factors are: microbial and chemical degradation, runoff, adsorption, volatilization, photodecomposition, and leaching. Some of these factors lead to environmental hazards. The state of art review of herbicide usage and properties, herbicide degradation studies and environmental implications is reported.
    Article · Feb 2011 · Journal of Agricultural and Food Chemistry
  • [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 Km and a Vmax 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.
    Full-text · Article · Dec 2011
  • [Show abstract] [Hide abstract] ABSTRACT: libA, a gene encoding a novel type of linuron hydrolase, was recently identified in the linuron-mineralizing Variovorax sp. strain SRS16. In order to assess the contribution of libA to linuron degradation in environmental settings, libA abundance was monitored in response to the application of linuron and to environmental perturbations in agricultural soil microcosms and microcosms simulating the matrix of on-farm biopurification systems. libA numbers were measured by real-time PCR and linked to reported data of Variovorax community composition and linuron mineralization capacity. In the soil microcosms and one biopurification system setup, libA numbers responded to the application of linuron and environmental changes in congruency with the modulation of linuron mineralization capacity and the occurrence of a particular Variovorax phylotype (phylotype A). However, in another biopurification system setup, no such correlations were found. Our data suggest that in the simulated environmental settings, the occurrence of libA can be linked to the linuron mineralization capacity and that libA is primarily hosted by Variovorax phylotype A strains. However, the results also suggest that, apart from libA, other, as-yet-unknown isofunctional genes play an important role in linuron mineralization in the environment.
    Article · Feb 2012
  • [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 soil and water contaminant in areas where there is extensive use. Diuron has the unfortunate combination of being strongly adsorbed by soil organic matter particles and, hence, slowly degraded in the environment due to its reduced bioavailability. N-Phenylurea herbicides seem to be biodegraded in soil, but it must be kept in mind that this biotic or abiotic degradation could lead to accumulation of very toxic derived compounds, such as 3,4-dichloroaniline. Research was conducted to find procedures that might result in an increase in the bioavailability of diuron in contaminated soils, through solubility enhancement. For this purpose a double system composed of hydroxypropyl-β-cyclodextrin (HPBCD), which is capable of forming inclusion complexes in solution, and a two-member bacterial consortium formed by the diuron-degrading Arthrobacter sulfonivorans (Arthrobacter sp. N2) and the linuron-degrading Variovorax soli (Variovorax sp. SRS16) was used. This consortium can achieve a complete biodegradation of diuron to CO(2) with regard to that observed in the absence of the CD solution, where only a 45% biodegradation was observed. The cyclodextrin-based bioremediation technology here described shows for the first time an almost complete mineralization of diuron in a soil system, in contrast to previous incomplete mineralization based on single or consortium bacterial degradation.
    Article · Sep 2012
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