Dynamics of the Linuron Hydrolase<i>libA</i>Gene Pool Size in Response to Linuron Application and Environmental Perturbations in Agricultural Soil and On-Farm Biopurification Systems

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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. strain WDL1, a strain that initiates linuron degradation in a linuron-mineralizing commensal bacterial consortium. The discovery of alternative linuron hydrolases poses questions about the respective contribution and competitive character of hylA-and libA-carrying bacteria as well as the role of linuron-mineralizing consortia versus single strains in linuron-exposed settings. Therefore, dynamics of hylA as well as dcaQ as a marker for downstream catabolic functions involved in linuron mineralization, in response to linuron treatment in agricultural soil and on-farm biopurification systems (BPS), were compared with previously reported libA dynamics. The results suggest that (i) organisms containing either libA or hylA contribute simultaneously to linuron biodegradation in the same environment, albeit to various extents, (ii) environmental linuron mineralization depends on multispecies bacterial food webs, and (iii) initiation of linuron mineralization can be governed by currently unidentified enzymes. IMPORTANCEA limited set of different isofunctional catabolic gene functions is known for the bacterial degradation of the phenylurea herbicide linuron, but the role of this redundancy in linuron degradation in environmental settings is not known. In this study, the simultaneous involvement of bacteria carrying one of two isofunctional linuron hydrolysis genes in the degradation of linuron was shown in agricultural soil and on-farm biopurification systems, as was the involvement of other bacterial populations that mineralize the downstream metabolites of linuron hydrolysis. This study illustrates the importance of the synergistic metabolism of pesticides in environmental settings.

Section: Discussionmentioning

confidence: 53%

Section: Methodsmentioning

confidence: 99%

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

Horemans

Bers

Romero

et al. 2016

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“…BPS act like biofilters in which the filter matrix (biomix) is composed of a mixture of different adsorbing materials, such as peat, straw, and topsoil (2), and contain microorganisms carrying mobile genetic elements (MGEs) that harbor genes involved in biodegradation of xenobiotic compounds (3,37). Although it is well known that biodegradation is the main process in the removal of xenobiotic compounds from the environment (3), abiotic factors such as temperature and concentration of pesticides can substantially influence their degradation (4).…”

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confidence: 99%

Shifts in Abundance and Diversity of Mobile Genetic Elements after the Introduction of Diverse Pesticides into an On-Farm Biopurification System over the Course of a Year

Dealtry

Holmsgaard

Dunon

et al. 2014

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f Biopurification systems (BPS) are used on farms to control pollution by treating pesticide-contaminated water. It is assumed that mobile genetic elements (MGEs) carrying genes coding for enzymes involved in degradation might contribute to the degradation of pesticides. Therefore, the composition and shifts of MGEs, in particular, of IncP-1 plasmids carried by BPS bacterial communities exposed to various pesticides, were monitored over the course of an agricultural season. PCR amplification of total community DNA using primers targeting genes specific to different plasmid groups combined with Southern blot hybridization indicated a high abundance of plasmids belonging to IncP-1, IncP-7, IncP-9, IncQ, and IncW, while IncU and IncN plasmids were less abundant or not detected. Furthermore, the integrase genes of class 1 and 2 integrons (intI1, intI2) and genes encoding resistance to sulfonamides (sul1, sul2) and streptomycin (aadA) were detected and seasonality was revealed. Amplicon pyrosequencing of the IncP-1 trfA gene coding for the replication initiation protein revealed high IncP-1 plasmid diversity and an increase in the abundance of IncP-1␤ and a decrease in the abundance of IncP-1 over time. The data of the chemical analysis showed increasing concentrations of various pesticides over the course of the agricultural season. As an increase in the relative abundances of bacteria carrying IncP-1␤ plasmids also occurred, this might point to a role of these plasmids in the degradation of many different pesticides.

“…In the past, ecological studies showed that the dynamics of linuron-degrading activity in the environment as a response to linuron application (i.e., in linuron-treated agricultural soil and on-farm biopurification systems), is not always explained by the abundance of libA (26). We are currently investigating whether hylA provides an alternative explanation in those case studies, whether organisms containing hylA or libA coexist or compete in linuron-treated and -contaminated environments, and whether still other linuron hydrolysis gene functions exist.…”

Section: Discussionmentioning

confidence: 99%

HylA, an Alternative Hydrolase for Initiation of Catabolism of the Phenylurea Herbicide Linuron in Variovorax sp. Strains

Bers

Batisson

Proost

et al. 2013

f Variovorax sp. strain WDL1, which mineralizes the phenylurea herbicide linuron, expresses a novel linuron-hydrolyzing enzyme, HylA, that converts linuron to 3,4-dichloroaniline (DCA). The enzyme is distinct from the linuron hydrolase LibA enzyme recently identified in other linuron-mineralizing Variovorax strains and from phenylurea-hydrolyzing enzymes (PuhA, PuhB) found in Gram-positive bacteria. The dimeric enzyme belongs to a separate family of hydrolases and differs in K m , temperature optimum, and phenylurea herbicide substrate range. Within the metal-dependent amidohydrolase superfamily, HylA and PuhA/PuhB belong to two distinct protein families, while LibA is a member of the unrelated amidase signature family. The hylA gene was identified in a draft genome sequence of strain WDL1. The involvement of hylA in linuron degradation by strain WDL1 is inferred from its absence in spontaneous WDL1 mutants defective in linuron hydrolysis and its presence in linuron-degrading Variovorax strains that lack libA. In strain WDL1, the hylA gene is combined with catabolic gene modules encoding the downstream pathways for DCA degradation, which are very similar to those present in Variovorax sp. SRS16, which contains libA. Our results show that the expansion of a DCA catabolic pathway toward linuron degradation in Variovorax can involve different but isofunctional linuron hydrolysis genes encoding proteins that belong to evolutionary unrelated hydrolase families. This may be explained by divergent evolution and the independent acquisition of the corresponding genetic modules.is a phenylurea herbicide widely used in agriculture to control germinating and newly emerging grasses and broad-leafed weeds. Biodegradation contributes largely to the dissipation of linuron in the environment. Several single bacterial strains (1, 2) and consortia (3, 4) that degrade (3, 5) or even mineralize and use linuron as the sole source of carbon, nitrogen, and energy have been reported (1-4). Bacterial degradation of linuron is initiated by amide hydrolysis of linuron to 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine (N,O-DMHA). In the case of linuron mineralization, DCA is further converted to water and carbon dioxide (Fig. 1). Bacteria belonging to the genus Variovorax appear to play a crucial role in linuron biodegradation. In linuron-degrading consortia, they are almost always responsible for at least the initial hydrolysis step in linuron degradation, and most linuron-mineralizing single-strain isolates are of the genus Variovorax (1, 2). The genetic basis of linuron degradation in the linuron-mineralizing Variovorax sp. strain SRS16 was recently elucidated (6) and involves three major catabolic gene modules. In strain SRS16, conversion of linuron to DCA is catalyzed by the hydrolase LibA, encoded by the libA gene. Further mineralization of DCA involves a multicomponent dioxygenase complex encoded by dcaQTA 1 A 2 BR, which degrades DCA to a chlorocatechol intermediate. The latter is further degraded by a modified ortho-cleava...