Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation.

IS1071, an insertion element that primarily flanks organic xenobiotic degradation genes in cultured isolates, is suggested to play a key role in the formation and distribution of bacterial catabolic pathway gene clusters. However, in environmental settings, the identity of the IS1071 genetic cargo and its correspondence to the local selective conditions remain unknown. To respond, we developed a long-range PCR approach amplifying accessory genes between two IS1071 copies from community DNA followed by amplicon sequencing.

Application of biodegradation in mitigating and remediating pesticide contamination of freshwater resources: state of the art and challenges for optimization.

In recent years, the application of pesticide biodegradation in remediation of pesticide-contaminated matrices moved from remediating bulk soil to remediating and mitigating pesticide pollution of groundwater and surface water bodies. Specialized pesticide-degrading microbial populations are used, which can be endogenous to the ecosystem of interest or introduced by means of bioaugmentation. It involves (semi-)natural ecosystems like agricultural fields, vegetated filter strips, and riparian wetlands and man-made ecosystems like on-farm biopurification systems, groundwater treatment systems, and dedicated modules in drinking water treatment.

Functional Redundancy of Linuron Degradation in Microbial Communities in Agricultural Soil and Biopurification Systems.

Unlabelled: The abundance of libA, encoding a hydrolase that initiates linuron degradation in the linuron-metabolizing Variovorax sp. strain SRS16, was previously found to correlate well with linuron mineralization, but not in all tested environments. Recently, an alternative linuron hydrolase, HylA, was identified in Variovorax sp.

Genetic and metabolic analysis of the carbofuran catabolic pathway in Novosphingobium sp. KN65.2.

The widespread agricultural application of carbofuran and concomitant contamination of surface and ground waters has raised health concerns due to the reported toxic effects of this insecticide and its degradation products. Most bacteria that degrade carbofuran only perform partial degradation involving carbamate hydrolysis without breakdown of the resulting phenolic metabolite. The capacity to mineralize carbofuran beyond the benzofuran ring has been reported for some bacterial strains, especially sphingomonads, and some common metabolites, including carbofuran phenol, were identified.

Heat-transfer resistance measurement method (HTM)-based cell detection at trace levels using a progressive enrichment approach with highly selective cell-binding surface imprints.

Surface-imprinted polymers allow for specific cell detection based on simultaneous recognition of the cell shape, cell size, and cell membrane functionalities by macromolecular cell imprints. In this study, the specificity of detection and the detection sensitivity for target cells within a pool of non-target cells were analyzed for a cell-specific surface-imprinted polymer combined with a heat-transfer-based read-out technique (HTM). A modified Chinese hamster ovarian cell line (CHO-ldlD) was used as a model system on which the transmembrane protein mucin-1 (MUC1) could be excessively expressed and for which the occurrence of MUC1 glycosylation could be controlled.

Optimizing the thermal read-out technique for MIP-based biomimetic sensors: towards nanomolar detection limits.

In previous work, the novel heat-transfer method (HTM) for the detection of small molecules with Molecularly Imprinted Polymers (MIP)-type receptors was presented. In this study we focus on optimization of this sensor performance, with as final aim to lower the detection limit by reducing the noise level. It was determined that the noise originates foremost from the power supply, which can be controlled by varying the PID parameters.

High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments.

Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS1071, two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil.

In situ response of the linuron degradation potential to linuron application in an agricultural field.

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.

Minimal pesticide-primed soil inoculum density to secure maximum pesticide degradation efficiency in on-farm biopurification systems.

Addition of pesticide-primed soil containing adapted pesticide degrading bacteria to the biofilter matrix of on farm biopurification systems (BPS) which treat pesticide contaminated wastewater, has been recommended, in order to ensure rapid establishment of a pesticide degrading microbial community in BPS. However, uncertainties exist about the minimal soil inoculum density needed for successful bioaugmentation of BPS. Therefore, in this study, BPS microcosm experiments were initiated with different linuron primed soil inoculum densities ranging from 0.

Dynamics of the linuron hydrolase libA gene pool size in response to linuron application and environmental perturbations in agricultural soil and on-farm biopurification systems.

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.

A novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by Variovorax sp. strain SRS16.

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.

Robust linuron degradation in on-farm biopurification systems exposed to sequential environmental changes.

On-farm biopurification systems (BPS) treat pesticide-contaminated wastewater of farms through biodegradation. Adding pesticide-primed soil has been shown to be beneficial for the establishment of pesticide-degrading populations in BPS. However, no data exist on the response of pesticide-degrading microbiota, either endogenous or introduced with pesticide-primed soil, when BPS are exposed to expected less favorable environmental conditions like cold periods, drought periods, and periods without a pesticide supply.

Improvement of pesticide mineralization in on-farm biopurification systems by bioaugmentation with pesticide-primed soil.

Microcosms were used to examine whether pesticide-primed soils could be preferentially used over nonprimed soils for bioaugmentation of on-farm biopurification systems (BPS) to improve pesticide mineralization. Microcosms containing a mixture of peat, straw and either linuron-primed soil or nonprimed soil were irrigated with clean or linuron-contaminated water. The lag time of linuron mineralization, recorded for microcosm samples, was indicative of the dynamics of the linuron-mineralizing biomass in the system.

A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron.

Real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE) approaches that specifically target the Variovorax 16S rRNA gene were developed to estimate the number and diversity of Variovorax in environmental ecosystems. PCR primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. PCR specificity was maximized by combining PCR with a targeted endonuclease treatment of template DNA to eliminate 16S rRNA genes of the closely related Acidovorax.

Proteomic study of linuron and 3,4-dichloroaniline degradation by Variovorax sp. WDL1: evidence for the involvement of an aniline dioxygenase-related multicomponent protein.

A proteomic approach was used to explore the metabolism of the phenylurea herbicide linuron and 3,4-dichloroaniline (3,4-DCA) in Variovorax sp. WDL1. This bacterium grows on linuron as sole source of carbon, nitrogen and energy, while it transiently accumulates 3,4-DCA as a metabolite.