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

Romero

et al. 2016

Self Cite

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: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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

Horemans

Romero

et al. 2016

Self Cite

“…Variovorax population was based on real-time PCR amplification of targeted 16S rRNA gene fragments as described by Bers et al (2). Averages of the 16S rRNA gene copy numbers of triplicate BM samples and significant differences between samples were analyzed by analysis of variance (ANOVA) (P Ͻ 0.05).…”

Section: Vol 77 2011 Pesticide Degradation In On-farm Purification mentioning

confidence: 99%

Robust Linuron Degradation in On-Farm Biopurification Systems Exposed to Sequential Environmental Changes

Sniegowski

Ryckeboer

et al. 2011

Self Cite

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 pesticidedegrading 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. Therefore, the response of microbiota mineralizing the herbicide linuron in BPS microcosm setups inoculated either with a linuron-primed soil or a nonprimed soil to a sequence of such less favorable conditions was examined. A period without linuron supply or a drought period reduced the size of the linuron-mineralizing community in both setups. The most severe effect was recorded for the setup containing nonprimed soil, in which stopping the linuron supply decreased the linuron degradation capacity to nondetectable levels. In both systems, linuron mineralization rapidly reestablished after conventional operation conditions were restored. A cold period and feeding with a pesticide mixture did not affect linuron mineralization. The changes in the linuron-mineralizing capacity in microcosms containing primed soil were associated with the dynamics of a particular Variovorax phylotype that previously had been associated with linuron mineralization. This study suggests that the pesticide-mineralizing community in BPS is robust in stress situations imposed by changes in environmental conditions expected to occur on farms. Moreover, it suggests that, in cases where effects do occur, recovery is rapid after restoring conventional operation conditions.The treatment of pesticide-contaminated wastewater in onfarm biopurification systems (BPS) is a low-cost and effortless solution for farmers to minimize the direct losses of pesticides to surface water (6). On-farm BPS operate as biofilters in which the pesticides are removed from the wastewater by biodegradation and sorption processes occurring in the biofilter matrix. The matrix in a BPS, designated a biomix, is composed of a mixture of soil, peat, and straw or other organic waste materials (6, 9). The addition of pesticide-primed soil to BPS has been proposed as an alternative for bioaugmentation with axenic cultures of specialized pesticide-degrading bacteria to accelerate pesticide degradation and avoid the production of toxic metabolites (7, 18). Sniegowski et al. (18) showed that bioaugmentation with a linuron-primed soil containing linuron-mineralizing microorganisms immediately resulted in the establishment of a linuron mineralization capacity in BPS microcosms. The size of the linuron-mineralizing populations in the system further increased when the microcosms were fed linuron. BPS microcosms inoculated with nonprimed soils also developed a linuron mineralization capacity but only after a much longer period of linuron supply. In the BPS microcosms contain...

“…Studies using molecular techniques to monitor the dynamics of the Variovorax community composition in response to linuron addition in agricultural soil microcosms (SMs) (5) and in biofilter microcosms (BMs) that simulate the matrix of on-farm biopurification systems used to treat agricultural wastewater (21) only partially support this hypothesis. A coinciding increase in linuron mineralization capacity and the proliferation of a specific Variovorax phylotype (phylotype A) upon linuron application was observed in SMs (5) and in BMs containing a linuron-primed soil (21). Moreover, in the latter, an additional congruency existed between linuron mineralization capacity and Variovorax community composition in response to several environmental perturbations (20).…”

mentioning

confidence: 99%

“…Therefore, a libAspecific real-time PCR was developed and used to monitor the libA gene abundance in the above-mentioned SM and BM setups in response to linuron application and/or controlled environmental perturbations. The dynamics in libA abundance were compared to the previously reported dynamics of the linuron mineralization capacity and Variovorax community composition (5,21). The present study is the first to use catabolic gene markers to assess phenylurea herbicide degradation in environmental settings.…”

mentioning

confidence: 99%

Dynamics of the Linuron HydrolaselibAGene Pool Size in Response to Linuron Application and Environmental Perturbations in Agricultural Soil and On-Farm Biopurification Systems

Sniegowski

Mot

et al. 2012

Self Cite

ABSTRACTlibA, a gene encoding a novel type of linuron hydrolase, was recently identified in the linuron-mineralizingVariovoraxsp. strain SRS16. In order to assess the contribution oflibAto linuron degradation in environmental settings,libAabundance 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.libAnumbers were measured by real-time PCR and linked to reported data ofVariovoraxcommunity composition and linuron mineralization capacity. In the soil microcosms and one biopurification system setup,libAnumbers responded to the application of linuron and environmental changes in congruency with the modulation of linuron mineralization capacity and the occurrence of a particularVariovoraxphylotype (phylotype A). However, in another biopurification system setup, no such correlations were found. Our data suggest that in the simulated environmental settings, the occurrence oflibAcan be linked to the linuron mineralization capacity and thatlibAis primarily hosted byVariovoraxphylotype A strains. However, the results also suggest that, apart fromlibA, other, as-yet-unknown isofunctional genes play an important role in linuron mineralization in the environment.