Assessing the effects of ß-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches.

4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of ß-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that ß-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of ß-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three ß-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of ß-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.

Optimal pharmacotherapy pathway in adults with diabetic peripheral neuropathic pain: the OPTION-DM RCT.

BACKGROUND: The mainstay of treatment for diabetic peripheral neuropathic pain is pharmacotherapy, but the current National Institute for Health and Care Excellence guideline is not based on robust evidence, as the treatments and their combinations have not been directly compared. OBJECTIVES: To determine the most clinically beneficial, cost-effective and tolerated treatment pathway for diabetic peripheral neuropathic pain. DESIGN: A randomised crossover trial with health economic analysis. SETTING: Twenty-one secondary care centres in the UK. PARTICIPANTS: Adults with diabetic peripheral neuropathic pain with a 7-day average self-rated pain score of ≥ 4 points (Numeric Rating Scale 0-10). INTERVENTIONS: Participants were randomised to three commonly used treatment pathways: (1) amitriptyline supplemented with pregabalin, (2) duloxetine supplemented with pregabalin and (3) pregabalin supplemented with amitriptyline. Participants and research teams were blinded to treatment allocation, using over-encapsulated capsules and matching placebos. Site pharmacists were unblinded. OUTCOMES: The primary outcome was the difference in 7-day average 24-hour Numeric Rating Scale score between pathways, measured during the final week of each pathway. Secondary end points included 7-day average daily Numeric Rating Scale pain score at week 6 between monotherapies, quality of life (Short Form questionnaire-36 items), Hospital Anxiety and Depression Scale score, the proportion of patients achieving 30% and 50% pain reduction, Brief Pain Inventory - Modified Short Form items scores, Insomnia Severity Index score, Neuropathic Pain Symptom Inventory score, tolerability (scale 0-10), Patient Global Impression of Change score at week 16 and patients' preferred treatment pathway at week 50. Adverse events and serious adverse events were recorded. A within-trial cost-utility analysis was carried out to compare treatment pathways using incremental costs per quality-adjusted life-years from an NHS and social care perspective. RESULTS: A total of 140 participants were randomised from 13 UK centres, 130 of whom were included in the analyses. Pain score at week 16 was similar between the arms, with a mean difference of -0.1 points (98.3% confidence interval -0.5 to 0.3 points) for duloxetine supplemented with pregabalin compared with amitriptyline supplemented with pregabalin, a mean difference of -0.1 points (98.3% confidence interval -0.5 to 0.3 points) for pregabalin supplemented with amitriptyline compared with amitriptyline supplemented with pregabalin and a mean difference of 0.0 points (98.3% confidence interval -0.4 to 0.4 points) for pregabalin supplemented with amitriptyline compared with duloxetine supplemented with pregabalin. Results for tolerability, discontinuation and quality of life were similar. The adverse events were predictable for each drug. Combination therapy (weeks 6-16) was associated with a further reduction in Numeric Rating Scale pain score (mean 1.0 points, 98.3% confidence interval 0.6 to 1.3 points) compared with those who remained on monotherapy (mean 0.2 points, 98.3% confidence interval -0.1 to 0.5 points). The pregabalin supplemented with amitriptyline pathway had the fewest monotherapy discontinuations due to treatment-emergent adverse events and was most commonly preferred (most commonly preferred by participants: amitriptyline supplemented with pregabalin, 24%; duloxetine supplemented with pregabalin, 33%; pregabalin supplemented with amitriptyline, 43%; p = 0.26). No single pathway was superior in cost-effectiveness. The incremental gains in quality-adjusted life-years were small for each pathway comparison [amitriptyline supplemented with pregabalin compared with duloxetine supplemented with pregabalin -0.002 (95% confidence interval -0.011 to 0.007) quality-adjusted life-years, amitriptyline supplemented with pregabalin compared with pregabalin supplemented with amitriptyline -0.006 (95% confidence interval -0.002 to 0.014) quality-adjusted life-years and duloxetine supplemented with pregabalin compared with pregabalin supplemented with amitriptyline 0.007 (95% confidence interval 0.0002 to 0.015) quality-adjusted life-years] and incremental costs over 16 weeks were similar [amitriptyline supplemented with pregabalin compared with duloxetine supplemented with pregabalin -£113 (95% confidence interval -£381 to £90), amitriptyline supplemented with pregabalin compared with pregabalin supplemented with amitriptyline £155 (95% confidence interval -£37 to £625) and duloxetine supplemented with pregabalin compared with pregabalin supplemented with amitriptyline £141 (95% confidence interval -£13 to £398)]. LIMITATIONS: Although there was no placebo arm, there is strong evidence for the use of each study medication from randomised placebo-controlled trials. The addition of a placebo arm would have increased the duration of this already long and demanding trial and it was not felt to be ethically justifiable. FUTURE WORK: Future research should explore (1) variations in diabetic peripheral neuropathic pain management at the practice level, (2) how OPTION-DM (Optimal Pathway for TreatIng neurOpathic paiN in Diabetes Mellitus) trial findings can be best implemented, (3) why some patients respond to a particular drug and others do not and (4) what options there are for further treatments for those patients on combination treatment with inadequate pain relief. CONCLUSIONS: The three treatment pathways appear to give comparable patient outcomes at similar costs, suggesting that the optimal treatment may depend on patients' preference in terms of side effects. TRIAL REGISTRATION: The trial is registered as ISRCTN17545443 and EudraCT 2016-003146-89. FUNDING: This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme, and will be published in full in Health Technology Assessment; Vol. 26, No. 39. See the NIHR Journals Library website for further project information.

The number of people with diabetes is growing rapidly in the UK and is predicted to rise to over 5 million by 2025. Diabetes causes nerve damage that can lead to severe painful symptoms in the feet, legs and hands. One-quarter of all people with diabetes experience these symptoms, known as 'painful diabetic neuropathy'. Current individual medications provide only partial benefit, and in only around half of patients. The individual drugs, and their combinations, have not been compared directly against each other to see which is best. We conducted a study to see which treatment pathway would be best for patients with painful diabetic neuropathy. The study included three treatment pathways using combinations of amitriptyline, duloxetine and pregabalin. Patients received all three treatment pathways (i.e. amitriptyline treatment for 6 weeks and pregabalin added if needed for a further 10 weeks, duloxetine treatment for 6 weeks and pregabalin added if needed for a further 10 weeks and pregabalin treatment for 6 weeks and amitriptyline added if needed for a further 10 weeks); however, the order of the treatment pathways was decided at random. We compared the level of pain that participants experienced in each treatment pathway to see which worked best. On average, people said that their pain was similar after each of the three treatments and their combinations. However, two treatments in combination helped some patients with additional pain relief if they only partially responded to one. People also reported improved quality of life and sleep with the treatments, but these were similar for all the treatments. In the health economic analysis, the value for money and quality of life were similar for each pathway, and this resulted in uncertainty in the cost-effectiveness conclusions, with no one pathway being more cost-effective than the others. The treatments had different side effects, however; pregabalin appeared to make more people feel dizzy, duloxetine made more people nauseous and amitriptyline resulted in more people having a dry mouth. The pregabalin supplemented by amitriptyline pathway had the smallest number of treatment discontinuations due to side effects and may be the safest for patients.

Comparison of amitriptyline supplemented with pregabalin, pregabalin supplemented with amitriptyline, and duloxetine supplemented with pregabalin for the treatment of diabetic peripheral neuropathic pain (OPTION-DM): a multicentre, double-blind, randomised crossover trial.

BACKGROUND: Diabetic peripheral neuropathic pain (DPNP) is common and often distressing. Most guidelines recommend amitriptyline, duloxetine, pregabalin, or gabapentin as initial analgesic treatment for DPNP, but there is little comparative evidence on which one is best or whether they should be combined. We aimed to assess the efficacy and tolerability of different combinations of first-line drugs for treatment of DPNP. METHODS: OPTION-DM was a multicentre, randomised, double-blind, crossover trial in patients with DPNP with mean daily pain numerical rating scale (NRS) of 4 or higher (scale is 0-10) from 13 UK centres. Participants were randomly assigned (1:1:1:1:1:1), with a predetermined randomisation schedule stratified by site using permuted blocks of size six or 12, to receive one of six ordered sequences of the three treatment pathways: amitriptyline supplemented with pregabalin (A-P), pregabalin supplemented with amitriptyline (P-A), and duloxetine supplemented with pregabalin (D-P), each pathway lasting 16 weeks. Monotherapy was given for 6 weeks and was supplemented with the combination medication if there was suboptimal pain relief (NRS >3), reflecting current clinical practice. Both treatments were titrated towards maximum tolerated dose (75 mg per day for amitriptyline, 120 mg per day for duloxetine, and 600 mg per day for pregabalin). The primary outcome was the difference in 7-day average daily pain during the final week of each pathway. This trial is registered with ISRCTN, ISRCTN17545443. FINDINGS: Between Nov 14, 2017, and July 29, 2019, 252 patients were screened, 140 patients were randomly assigned, and 130 started a treatment pathway (with 84 completing at least two pathways) and were analysed for the primary outcome. The 7-day average NRS scores at week 16 decreased from a mean 6·6 (SD 1·5) at baseline to 3·3 (1·8) at week 16 in all three pathways. The mean difference was -0·1 (98·3% CI -0·5 to 0·3) for D-P versus A-P, -0·1 (-0·5 to 0·3) for P-A versus A-P, and 0·0 (-0·4 to 0·4) for P-A versus D-P, and thus not significant. Mean NRS reduction in patients on combination therapy was greater than in those who remained on monotherapy (1·0 [SD 1·3] vs 0·2 [1·5]). Adverse events were predictable for the monotherapies: we observed a significant increase in dizziness in the P-A pathway, nausea in the D-P pathway, and dry mouth in the A-P pathway. INTERPRETATION: To our knowledge, this was the largest and longest ever, head-to-head, crossover neuropathic pain trial. We showed that all three treatment pathways and monotherapies had similar analgesic efficacy. Combination treatment was well tolerated and led to improved pain relief in patients with suboptimal pain control with a monotherapy. FUNDING: National Institute for Health Research (NIHR) Health Technology Assessment programme.

Evidence for enhanced dissipation of chlorpyrifos in an agricultural soil inoculated with Serratia rubidaea strain ABS 10.

The insecticide 14C-chlorpyrifos was found mineralized in a Tunisian soil with repeated exposure to it. From this soil, a bacterial strain was isolated that was able to grow in a minimal salt medium (MSM) supplemented with 25 mg L-1 of chlorpyrifos. It was characterized as Serratia rubidaea strain ABS 10 using morphological and biochemical analyses, as well as 16S rRNA sequencing. In a liquid culture, the S. rubidaea strain ABS 10 was able to dissipate chlorpyrifos almost entirely within 48 h of incubation. Although the S. rubidaea strain ABS 10 was able to grow in an MSM supplemented with chlorpyrifos and dissipate it in a liquid culture, it was not able to mineralize 14C-chlorpyrifos. Therefore, it can be concluded that the dissipation capability of this bacteria might be attributed to its capacity to adsorb CHL. It can also be ascribed to other reasons such as the formation of biogenic non-extractable residues. In both non-sterile and sterile soil inoculated with S. rubidaea strain ABS 10, chlorpyrifos was more rapidly dissipated than in controls with DT50 of 1.38 and 1.05 days, respectively.

Environmental Concentrations of Sulfonamides Can Alter Bacterial Structure and Induce Diatom Deformities in Freshwater Biofilm Communities.

Since the early 1920s, the intensive use of antibiotics has led to the contamination of the aquatic environment through diffuse sources and wastewater effluents. The antibiotics commonly found in surface waters include sulfamethoxazole (SMX) and sulfamethazine (SMZ), which belong to the class of sulfonamides, the oldest antibiotic class still in use. These antibiotics have been detected in all European surface waters with median concentrations of around 50 ng L-1 and peak concentrations of up to 4-6 µg L-1. Sulfonamides are known to inhibit bacterial growth by altering microbial production of folic acid, but sub-lethal doses may trigger antimicrobial resistance, with unknown consequences for exposed microbial communities. We investigated the effects of two environmentally relevant concentrations (500 and 5,000 ng L-1) of SMZ and SMX on microbial activity and structure of periphytic biofilms in stream mesocosms for 28 days. Measurement of sulfonamides in the mesocosms revealed contamination levels of about half the nominal concentrations. Exposure to sulfonamides led to slight, transitory effects on heterotrophic functions, but persistent effects were observed on the bacterial structure. After 4 weeks of exposure, sulfonamides also altered the autotrophs in periphyton and particularly the diversity, viability and cell integrity of the diatom community. The higher concentration of SMX tested decreased both diversity (Shannon index) and evenness of the diatom community. Exposure to SMZ reduced diatom species richness and diversity. The mortality of diatoms in biofilms exposed to sulfonamides was twice that in non-exposed biofilms. SMZ also induced an increase in diatom teratologies from 1.1% in non-exposed biofilms up to 3% in biofilms exposed to SMZ. To our knowledge, this is the first report on the teratological effects of sulfonamides on diatoms within periphyton. The increase of both diatom growth rate and mortality suggests a high renewal of diatoms under sulfonamide exposure. In conclusion, our study shows that sulfonamides can alter microbial community structures and diversity at concentrations currently present in the environment, with unknown consequences for the ecosystem. The experimental set-up presented here emphasizes the interest of using natural communities to increase the ecological realism of ecotoxicological studies and to detect potential toxic effects on non-target species.

Potential of preventive bioremediation to reduce environmental contamination by pesticides in an agricultural context: A case study with the herbicide 2,4-D.

One of the major problems with pesticides is linked to the non-negligible proportion of the sprayed active ingredient that does not reach its intended target and contaminates environmental compartments. Here, we have implemented and provided new insights to the preventive bioremediation process based on the simultaneous application of the pesticide with pesticide-degrading microorganisms to reduce the risk of leaching into the environment. This study pioneers such a practice, in an actual farming context. The 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) and one of its bacterial mineralizing-strains (Cupriavidus necator JMP134) were used as models. The 2,4-D biodegradation was studied in soil microcosms planted with sensitive (mustard) and insensitive (wheat) plants. Simultaneous application of a 2,4-D commercial formulation (DAM®) at agricultural recommended doses with 105 cells.g-1 dw of soil of the JMP134 strain considerably accelerated mineralization of the herbicide since its persistence was reduced threefold for soil supplemented with the mineralizing bacterium without reducing the herbicide efficiency. Furthermore, the inoculation of the Cupriavidus necator strain did not significantly affect the α- and ß-diversity of the bacterial community. By tackling the contamination immediately at source, the preventive bioremediation process proves to be an effective and promising way to reduce environmental contamination by agricultural pesticides.

Labour sharing promotes coexistence in atrazine degrading bacterial communities.

Microbial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called 'helpers' provide publicly common goods obtained from the costly degradation of a compound, while others called 'beneficiaries' take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

Diabetic foot infection: Antibiotic therapy and good practice recommendations.

BACKGROUND: Healthcare events related to diabetic foot disease carry a burden of morbidity, mortality and economic cost. Prompt identification of clinical infection with appropriate tissue sampling limits use of broad spectrum empirical antibiotics and improves antibiotic stewardship. Staphylococcus aureus remains the commonest infecting organism and high-dose flucloxacillin remains the empirical antibiotic of choice for antibiotic naïve patients. Barriers to microbe-specific treatment include: adequate tissue sampling, delays in culture results, drug allergies and the emergence of multidrug-resistant organisms which can complicate the choice of targeted antibiotics. Even appropriate antibiotic treatment carries a risk of adverse events including the selection of resistant organisms. AIMS: Multidisciplinary clinical assessment of a diabetic foot infection is supported by the use of appropriate imaging modalities and deep tissue sampling, both of which are encouraged to enhance sampling accuracy. Narrow-spectrum, high dose, short duration antimicrobial therapy is ideal. Further clarity in these areas would be of benefit to clinicians involved in management of diabetic foot infections. METHODS: A combination of literature review with expert discussion was used to generate consensus on management of diabetic foot infection, with a specific focus on empirical antimicrobial therapy. RESULTS: Gram positive organisms represent the commonest pathogens in diabetic foot infection. However there are developing challenges in antimicrobial resistance and antibiotic availability. DISCUSSION: Recommendations for empirical therapy, including the choice of alternative oral agents and use of outpatient antibiotics would be of benefit to those involved in diabetic foot care. CONCLUSION: This paper provides advice on empirical antibiotic therapy that may be used as a framework for local guideline development to support clinicians in the management of diabetic foot infection.

Influence of age on the prevalence and components of the metabolic syndrome and the association with cardiovascular disease.

OBJECTIVE: The significance of the metabolic syndrome (MS) is debated. We investigated whether MS component (by ATPIII and IDF definitions) clustering and any association between MS and prevalent cardiovascular disease (CVD) varied with age. RESEARCH DESIGN AND METHODS: In all, 1429 adults (≥25 years) from randomly selected households in rural Victoria, Australia, were assessed for components of MS and prevalent CVD. The expected prevalence of MS was calculated following a simple probabilistic model using the prevalence of each MS component. RESULTS: The observed prevalence of MS was greater than expected: 27.0% vs 21.2% (ATPIII) and 36.0% vs 30.1% (IDF; p<0.0001), based on the prevalence of individual components. There was significant clustering of 4 and 5 MS components in participants <65 years (p<0.0001). CVD was more prevalent in MS participants, 13.5% (IDF), 14.5% (ATPIII) versus 5.3% (no MS) p<0.0001. The OR for CVD in MS participants was greatest in those <45 years OR (95% CI): IDF 17.5 (1.8 to 172); ATPIII 24.3(2.4 to 241), p<0.001 for both, and was not significant in those >65 years. The prevalence of MS (ATPIII) with normal waist circumference (WC) was less than expected (4.8% vs 7.9%, p<0.002). Low levels of high-density lipoprotein and high triglyceride were less common in older MS participants. CONCLUSIONS: ATPIII MS is rare among those with a normal WC. MS components cluster most markedly among those aged <65 years, who also experience substantially greater rates of CVD. Younger patients with MS may warrant more aggressive CVD preventative treatment than suggested by the summation of their individual risk factors.

Evaluation of the ecotoxicological impact of the organochlorine chlordecone on soil microbial community structure, abundance, and function.

The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (ß-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil microcosms of sandy loam soil exposed to chlordecone as compared to the control (D0). These data show that chlordecone exposure induced changes in microbial community taxonomic composition and function in one of the two soils, suggesting microbial toxicity of this organochlorine.

Evidence for the importance of litter as a co-substrate for MCPA dissipation in an agricultural soil.

Environmental controls of 2-methyl-4-chlorophenoxyacetic acid (MCPA) degradation are poorly understood. We investigated whether microbial MCPA degraders are stimulated by (maize) litter and whether this process depends on concentrations of MCPA and litter. In a microcosm experiment, different amounts of litter (0, 10 and 20 g kg(-1)) were added to soils exposed to three levels of the herbicide (0, 5 and 30 mg kg(-1)). The treated soils were incubated at 20 °C for 6 weeks, and samples were taken after 1, 3 and 6 weeks of incubation. In soils with 5 mg kg(-1) MCPA, about 50 % of the MCPA was dissipated within 1 week of the incubation. Almost complete dissipation of the herbicide had occurred by the end of the incubation with no differences between the three litter amendments. At the higher concentration (30 mg kg(-1)), MCPA endured longer in the soil, with only 31 % of the initial amount being removed at the end of the experiment in the absence of litter. Litter addition greatly increased the dissipation rate with 70 and 80 % of the herbicide being dissipated in the 10 and 20 g kg(-1) litter treatments, respectively. Signs of toxic effects of MCPA on soil bacteria were observed from related phospholipid fatty acid (PLFA) analyses, while fungi showed higher tolerance to the increased MCPA levels. The abundance of bacterial tfdA genes in soil increased with the co-occurrence of litter and high MCPA concentration, indicating the importance of substrate availability in fostering MCPA-degrading bacteria and thereby improving the potential for removal of MCPA in the environment.

Characterization of chlordecone-tolerant fungal populations isolated from long-term polluted tropical volcanic soil in the French West Indies.

The insecticide chlordecone is a contaminant found in most of the banana plantations in the French West Indies. This study aims to search for fungal populations able to grow on it. An Andosol heavily contaminated with chlordecone, perfused for 1 year in a soil-charcoal system, was used to conduct enrichment cultures. A total of 103 fungal strains able to grow on chlordecone-mineral salt medium were isolated, purified, and deposited in the MIAE collection (Microorganismes d'Intérêt Agro-Environnemental, UMR Agroécologie, Institut National de la Recherche Agronomique, Dijon, France). Internal transcribed spacer sequencing revealed that all isolated strains belonged to the Ascomycota phylum and gathered in 11 genera: Metacordyceps, Cordyceps, Pochonia, Acremonium, Fusarium, Paecilomyces, Ophiocordyceps, Purpureocillium, Bionectria, Penicillium, and Aspergillus. Among predominant species, only one isolate, Fusarium oxysporum MIAE01197, was able to grow in a liquid culture medium that contained chlordecone as sole carbon source. Chlordecone increased F. oxysporum MIAE01197 growth rate, attesting for its tolerance to this organochlorine. Moreover, F. oxysporum MIAE01197 exhibited a higher EC50 value than the reference strain F. oxysporum MIAE00047. This further suggests its adaptation to chlordecone tolerance up to 29.2 mg l(-1). Gas chromatography-mass spectrometry (GC-MS) analysis revealed that 40 % of chlordecone was dissipated in F. oxysporum MIAE01197 suspension culture. No chlordecone metabolite was detected by GC-MS. However, weak amount of (14)CO2 evolved from (14)C10-chlordecone and (14)C10-metabolites were observed. Sorption of (14)C10-chlordecone onto fungal biomass followed a linear relationship (r (2) = 0.99) suggesting that it may also account for chlordecone dissipation in F. oxysporum MIAE01197 culture.

Diuron mineralisation in a Mediterranean vineyard soil: impact of moisture content and temperature.

BACKGROUND: The diuron-mineralising ability of the microbiota of a Mediterranean vineyard soil exposed each year to this herbicide was measured. The impact of soil moisture and temperature on this microbial activity was assessed. RESULTS: The soil microbiota was shown to mineralise diuron. This mineralising activity was positively correlated with soil moisture content, being negligible at 5% and more than 30% at 20% soil moisture content. According to a double Gaussian model applied to fit the dataset, the optimum temperature/soil moisture conditions were 27.9 degrees C/19.3% for maximum mineralisation rate and 21.9 degrees C/18.3% for maximum percentage mineralisation. The impact of temperature and soil moisture content variations on diuron mineralisation was estimated. A simulated drought period had a suppressive effect on subsequent diuron mineralisation. This drought effect was more marked when higher temperatures were used to dry (40 degrees C versus 28 degrees C) or incubate (28 degrees C versus 20 degrees C) the soil. The diuron kinetic parameters measured after drought conditions were no longer in accordance with those estimated by the Gaussian model. CONCLUSION: Although soil microbiota can adapt to diuron mineralisation, its activity is strongly dependent on climatic conditions. It suggests that diuron is not rapidly degraded under Mediterranean climate, and that arable Mediterranean soils are likely to accumulate diuron residues.

Evidence for 2,4-D mineralisation in Mediterranean soils: impact of moisture content and temperature.

BACKGROUND: The 2,4-D degradation ability of the microbiota of three arable Mediterranean soils was estimated. The impact of soil moisture and temperature on 2,4-D degradation was investigated. RESULTS: The microbiota of the three soils regularly exposed to 2,4-D were able rapidly to mineralise this herbicide. The half-life of 2,4-D ranged from 8 to 30 days, and maximum mineralisation of (14)C-2,4-D ranged from 57 to 71%. Extractable (14)C-2,4-D and (14)C-bound residues accounted for less than 1 and 15% respectively of the (14)C-2,4-D initially added. The highest amounts of (14)C-2,4-D bound residues were recorded in the soil with the lowest 2,4-D-mineralising ability. Although all three soils were able to mineralise 2,4-D, multivariate analysis revealed that performance of this degrading microbial activity was dependent on clay content and magnesium oxide. Soil temperature affected the global structure of soil microbial community, but it had only a moderate effect on 2,4-D-mineralising ability. 2,4-D-mineralising ability was positively correlated with soil moisture content. Negligible 2,4-D mineralisation occurred in all three soils when incubated at 10 or 15% soil moisture content, i.e. within the range naturally occurring under the Mediterranean climate of Algeria. CONCLUSION: This study shows that, although soil microbiota can adapt to rapid mineralisation of 2,4-D, this microbial activity is strongly dependent on climatic parameters. It suggests that only limited pesticide biodegradation occurs under Mediterranean climate, and that arable Mediterranean soils are therefore fragile and likely to accumulate pesticide residues.

Fitness drift of an atrazine-degrading population under atrazine selection pressure.

Pseudomonas sp. ADP harbouring the atrazine catabolic plasmid ADP1 was subcultured in liquid medium containing atrazine as sole source of nitrogen. After approximately 320 generations, a new population evolved which replaced the initial population. This newly evolved population grew faster and degraded atrazine more rapidly than the initial population. Plasmid profiles and Southern blot analyses revealed that the evolved strain, unlike the ancestral strain, presented a tandem duplication of the atzB gene encoding the second enzyme of the atrazine catabolic pathway responsible for the transformation of hydroxyatrazine to N-isopropylammelide. This duplication resulted from a homologous recombination that occurred between two direct repeats of 6.2 kb flanking the atzB gene and constituted by the insertion sequences IS1071, ISPps1 and a pdhL homologous sequence. This study highlights the IS-mediated plasticity of atrazine-degrading potential and demonstrates that insertion sequences not only help to disperse the atrazine-degrading gene but also improve the fitness of the atrazine-degrading population.

Detection and organization of atrazine-degrading genetic potential of seventeen bacterial isolates belonging to divergent taxa indicate a recent common origin of their catabolic functions.

A collection of 17 atrazine-degrading bacteria isolated from soils was studied to determine the composition of the atrazine-degrading genetic potential (i.e. trzN, trzD and atz) and the presence of IS1071. The characterization of seven new atrazine-degrading bacteria revealed for the first time the trzN-atzBC gene composition in Gram-negative bacteria such as Sinorhizobium sp. or Polaromonas sp. Three main atrazine-degrading gene combinations (i) trzN-atzBC, (ii) atzABC-trzD and (iii) atzABCDEF were observed. The atz and trz genes were often located on plasmids, suggesting that plasmid conjugation could play an important role in their dispersion. In addition, the observation of these genes (i) on the chromosome, (ii) on the same DNA fragment but on different plasmids and (iii) on DNA fragments also hybridizing with IS1071 suggests that transposition may also contribute to disperse the atrazine-degrading genes.

Genetic rearrangement of the atzAB atrazine-degrading gene cassette from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2.

We report the characterization of the rearrangement phenomena responsible for the movement of the atrazine-degrading atzA and B genes from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2. Long PCRs and Southern blot analyses revealed that the two genes forming a gene cassette moved in a unique rearrangement event. It also revealed that the boundaries of the plasmid sequence inserted in the chromosome correspond to IS1071or to sequences close to IS1071. It suggests that this genetic rearrangement could result from the transposition of the composite transposon delimited by IS1071 insertion sequences and containing atzA and atzB genes. In addition, for MD1 and MD2 strains the sequencing of the remaining sequence on pADP1::Tn5 indicated that the deletion of the atzA and B genes from the plasmid might be the result of a recombination event that occurred between the IS1071 insertion sequences surrounding the atzAB gene cassette.

Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1::Tn5 to bacteria of maize-cultivated soil.

The plasmid pADP1::Tn5 derived from pADP1[Atr+] carrying a Tn5 transposon conferring kanamycin and streptomycin resistances was constructed and introduced in Agrobacterium tumefaciens St96-4. This genetically modified strain was inoculated (approximately 10(8) cfu g(-1)) in potted soils planted with maize and treated or not with atrazine (1.5 mg kg(-1)). Bulk and maize rhizosphere soils were sampled 39 days after planting to look for soil indigenous bacteria that had acquired pADP1::Tn5. Four transconjugants were isolated from four different soil samples. The estimated transfer frequency of pADP1::Tn5 was 10(-4) per donor. Maize rhizosphere and atrazine treatment had no obvious effect on pADP1::Tn5 transfer frequency. The sequencing of the 16S rDNA sequences of the transconjugants revealed that they were almost identical and highly similar to that of Variovorax spp (97%). In addition, their characterization suggested that the atzA and atzB genes had been transferred from pADP1::Tn5 to the bacterial chromosome in two of the four transconjugants. These data suggest that the atz degrading genes are horizontally transferred in soil and possibly subjected to gene rearrangement.

Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil.

The level of expression of highly conserved, plasmid-borne, and widely dispersed atrazine catabolic genes (atz) was studied by RT-qPCR in two telluric atrazine-degrading microbes. RT-qPCR assays, based on the use of real-time PCR, were developed in order to quantify atzABCDEF mRNAs in Pseudomonas sp. ADP and atzABC mRNAs in Chelatobacter heintzii. atz gene expression was expressed as mRNA copy number per 10(6) 16S rRNA. In Pseudomonas sp. ADP, atz genes were basally expressed. It confirmed atrazine-degrading kinetics indicating that catabolic activity starts immediately after adding the herbicide. atz gene expression increased transitorily in response to atrazine treatment. This increase was only observed while low amount of atrazine remained in the medium. In C. heintzii, only atzA was basally expressed. atzA and atzB expression levels were similarly and significantly increased in response to atrazine treatment. atzC was not expressed even in the presence of high amounts of atrazine. This study showed that atz genes are basally expressed and up-regulated in response to atrazine treatment. atz gene expression patterns are different in Pseudomonas ADP and C. heintzii suggesting that the host may influence the expression of plasmid-borne atrazine-catabolic potential.