Degradation and mineralization of nanomolar concentrations of the herbicide dichlobenil and its persistent metabolite 2,6-dichlorobenzamide by Aminobacter spp. isolated from dichlobenil-treated soils

The gompertz function can coherently describe microbial mineralization of growth-sustaining pesticides

Mineralization of (14)C-labeled tracers is a common way of studying the environmental fate of xenobiotics, but it can be difficult to extract relevant kinetic parameters from such experiments since complex kinetic functions or several kinetic functions may be needed to adequately describe large data sets. In this study, we suggest using a two-parameter, sigmoid Gompertz function for parametrizing mineralization curves. The function was applied to a data set of 252 normalized mineralization curves that represented the potential for degradation of the herbicide MCPA in three horizons of an agricultural soil. The Gompertz function fitted most of the normalized curves, and trends in the data set could be visualized by a scatter plot of the two Gompertz parameters (rate constant and time delay). For agricultural topsoil, we also tested the effect of the MCPA concentration on the mineralization kinetics. Reduced initial concentrations lead to shortened lag-phases, probably due to reduced need for bacterial growth. The effect of substrate concentration could be predicted by simply changing the time delay of the Gompertz curves. This delay could to some extent also simulate concentration effects for 2,4-D mineralization in agricultural soil and aquifer sediment and 2,6-dichlorobenzamide mineralization in single-species, mineral medium.

Using 2,6-dichlorobenzamide (BAM) degrading Aminobacter sp. MSH1 in flow through biofilters--initial adhesion and BAM degradation potentials

Micropollutants in groundwater are given significant attention by water companies and authorities due to an increasing awareness that they might be present even above the legal threshold values. As part of our investigations of the possibility to remove the common groundwater pollutant 2,6-dichlorobenzamide (BAM) by introducing the efficient BAM degrader Aminobacter sp. MSH1 into biologically active sand filters, we investigated if the strain adheres to filters containing various filter materials and if the initial adherence and subsequent degradation of BAM could be optimized. We found that most of the inoculated MSH1 cells adhered fast and that parameters like pH and ionic strength had only a minor influence on the adhesion despite huge influence on cell surface hydrophobicity. At the given growth protocol, the MSH1 strain apparently developed a subpopulation that had lost its ability to adhere to the filter materials, which was supported by attempted reinoculation of non-adhered cells. Analysis by quantitative PCR showed that most cells adhered in the top of the filters and that some of these were lost from the filters during initial operation, while insignificant losses occurred after 1 day of operation. The inoculated filters were found to degrade 2.7 μg/L BAM to below 0.1 μg/L at a 1.1-h residence time with insignificant formation of known degradation products. In conclusion, most filter materials and water types should be feasible for inoculation with the MSH1 strain, while more research into degradation at low concentrations and temperatures is needed before this technology is ready for use at actual waterworks.

Biotransformation of benzonitrile herbicides via the nitrile hydratase-amidase pathway in rhodococci

The aim of this work was to determine the ability of rhodococci to transform 3,5-dichloro-4-hydroxybenzonitrile (chloroxynil), 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil), 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and 2,6-dichlorobenzonitrile (dichlobenil); to identify the products and determine their acute toxicities. Rhodococcus erythropolis A4 and Rhodococcus rhodochrous PA-34 converted benzonitrile herbicides into amides, but only the former strain was able to hydrolyze 2,6-dichlorobenzamide into 2,6-dichlorobenzoic acid, and produced also more of the carboxylic acids from the other herbicides compared to strain PA-34. Transformation of nitriles into amides decreased acute toxicities for chloroxynil and dichlobenil, but increased them for bromoxynil and ioxynil. The amides inhibited root growth in Lactuca sativa less than the nitriles but more than the acids. The conversion of the nitrile group may be the first step in the mineralization of benzonitrile herbicides but cannot be itself considered to be a detoxification.

Comparing metabolic functionalities, community structures, and dynamics of herbicide-degrading communities cultivated with different substrate concentrations

Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter(-1)) or high (25 mg liter(-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 activities. 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-content bacteria (LNA bacteria) was correlated with mineralization activity in cultures selected on low herbicide concentrations. 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 a low herbicide concentration enables enrichment of apparently oligotrophic subpopulations.

C and N isotope fractionation during biodegradation of the pesticide metabolite 2,6-dichlorobenzamide (BAM): potential for environmental assessments

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.

Biodegradation of chlorobenzoic acids by ligninolytic fungi

We investigated the abilities of several perspective ligninolytic fungal strains to degrade 12 mono-, di- and trichloro representatives of chlorobenzoic acids (CBAs) under model liquid conditions and in contaminated soil. Attention was also paid to toxicity changes during the degradation, estimated using two luminescent assay variations with Vibrio fischeri. The results show that almost all the fungi were able to efficiently degrade CBAs in liquid media, where Irpex lacteus, Pycnoporus cinnabarinus and Dichomitus squalens appeared to be the most effective in the main factors: degradation and toxicity removal. Analysis of the degradation products revealed that methoxy and hydroxy derivatives were produced together with reduced forms of the original acids. The findings suggest that probably more than one mechanism is involved in the process. Generally, the tested fungal strains were able to degrade CBAs in soil in the 85-99% range within 60 days. Analysis of ergosterol showed that active colonization is an important factor for degradation of CBAs by fungi. The most efficient strains in terms of degradation were I. lacteus, Pleurotus ostreatus, Bjerkandera adusta in soil, which were also able to actively colonize the soil. However, in contrast to P. ostreatus and I. lacteus, B. adusta was not able to significantly reduce the measured toxicity.

Inherent mineralization of 2,6-dichlorobenzamide (BAM) in unsaturated zone and aquifers--effect of initial concentrations and adaptation

The dichlobenil metabolite BAM (2,6-dichlorobenzamide) is frequently detected in aquifers e.g. in Denmark despite the mother compound dichlobenil was banned here since 1997. BAM mineralization was investigated at environmentally relevant concentrations in sediment samples. Undisturbed sediment cores with known dichlobenil application were collected from topsoil to 8.5 m below surface resulting in 57 samples hereof 4 aquifer samples. Mineralization was only substantial (>10%) in the uppermost meter of the unsaturated zone. Microbial adaptation, observed as faster mineralization in pre-exposed than in pristine sediments from the same location, was only evident in sandy sediment where dichlobenil was still present, but not in clayey sediments. Higher initial concentrations (1-5000 μg/kg) did not stimulate mineralization in pristine clayey or sandy sediments, or in pre-exposed sand. However, in pre-exposed clay mineralization was stimulated at high concentrations. Furthermore BAM was for the first time mineralized in aerobic aquifer sediments from different BAM-contaminated groundwater locations.

2,6-Dichlorobenzamide (BAM) herbicide mineralisation by Aminobacter sp. MSH1 during starvation depends on a subpopulation of intact cells maintaining vital membrane functions

Mineralisation capability was studied in the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 under growth-arrested conditions. Cells were starved in mineral salts (MS) solution or groundwater before (14)C-labelled BAM (0.1mM) was added. Cell physiology was monitored with a panel of vitality stains combined with flow cytometry to differentiate intact, depolarised and dead cells. Cells starved for up to 3 weeks in MS solution showed immediate growth-linked mineralisation after BAM amendment while a lag-phase was seen after 8 weeks of starvation. In contrast, cells amended with BAM in natural groundwater showed BAM mineralisation but no growth. The cell-specific mineralisation rate was always comparable (10(-16)molCintact cell(-1)day(-1)) independent of media, growth, or starvation period after BAM amendment; lower rates were only observed as BAM concentration decreased. MSH1 seems useful for bioremediation and should be optimised to maintain an intact cell subpopulation as this seems to be the key parameter for successful mineralisation.

Enhancement of aerobic degradation of benzoate and 2-chlorobenzoate by adapted activated sludge

Activated sludge from the Stickney Water Reclamation Plant of the Metropolitan Water Reclamation District of Greater Chicago was adapted in the laboratory to either benzoate or 2-chlorobenzoate as the sole carbon source in sequencing batch reactors with a 48-h feed-aerate-settle-draw cycle and a mean cell residence time (MCRT) of 10 days. Benzoate degradation increased by more than 80-fold after 7 MCRTs compared to unadapted activated sludge. A greater than 15-fold increase in 2-chlorobenzoate metabolism occurred after adaptation for about 5-7 MCRTs. For each substrate the maximum rate measured for adapted cultures was near or above the highest previously reported in the literature. For both adapted and unadapted sludges, benzoate metabolism was considerably faster than that of 2-chlorobenzoate, and for both substrates the rate of metabolism increased incrementally with time of adaptation. As expected, addition of the benzoate-adapted sludge to unadapted sludge enhanced the latter's ability to degrade benzoate.

Degrader density determines spatial variability of 2,6-dichlorobenzamide mineralisation in soil

The metabolite 2,6-dichlorobenzamide (BAM) is a frequent groundwater pollutant produced during degradation of the herbicide 2,6-dichlorobenzonitrile (dichlobenile). Spatial variability of BAM mineralisation is uncharacterized in surface soil, however, and factors controlling the heterogeneity remain unknown. We addressed these issues by sample-to-sample comparisons of BAM mineralisation rates and a range of soil characteristics at spatial scales ranging from meters to centimetres. For mineralisation assays nano-molar concentrations of labelled BAM were added to determine mineralisation rates under realistic conditions. We found a significant variability of BAM mineralisation which increased with decreasing spatial scale. BAM mineralisation rates were correlated to the density of BAM-degrading bacteria but not to water content, TOC, NH(4)(+), NO(3)(-), or pH. The genus Aminobacter, which contains the only BAM degraders known, was detected in MPN samples of BAM degraders by a specific PCR assay targeting the 16S rRNA gene, confirming a role of Aminobacter in BAM mineralisation.

Biodegradation potential of the genus Rhodococcus

A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.

Microbial degradation of the benzonitrile herbicides dichlobenil, bromoxynil and ioxynil in soil and subsurface environments--insights into degradation pathways, persistent metabolites and involved degrader organisms

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.

Rapid mineralization of the phenylurea herbicide diuron by Variovorax sp. strain SRS16 in pure culture and within a two-member consortium

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.