Isolation and characterization of diuron-degrading bacteria from lotic surface water

Changes in soil microbial community and activity caused by application of dimethachlor and linuron

Soil microorganisms and their activities are essential for maintaining soil health and fertility. Microorganisms can be negatively affected by application of herbicides. Although effects of herbicides on microorganisms are widely studied, there is a lack of information for chloroacetamide herbicide dimethachlor. Thus, dimethachlor and well known linuron were applied to silty-loam luvisol and their effects on microorganisms were evaluated during112 days long laboratory assay. Dimethachlor and linuron were applied in doses 1.0 kg ha-1 and 0.8 kg ha-1 corresponding to 3.33 mg kg-1 and 2.66 mg kg-1 respectively. Also 100-fold doses were used for magnification of impacts. Linuron in 100-fold dose caused minor increase of respiration, temporal increase of soil microbial biomass, decrease of soil dehydrogenase activity, and altered microbial community. Dimethachlor in 100-fold dose significantly increased respiration; microbial biomass and decreased soil enzymatic activities. Microbial composition changed significantly, Proteobacteria abundance, particularly Pseudomonas and Achromobacter genera increased from 7 to 28th day. In-silico prediction of microbial gene expression by PICRUSt2 software revealed increased expression of genes related to xenobiotic degradation pathways. Evaluated characteristics of microbial community and activity were not affected by herbicides in recommended doses and the responsible use of both herbicides will not harm soil microbial community.

Influence of plant beneficial Stenotrophomonas rhizophila strain CASB3 on the degradation of diuron-contaminated saline soil and improvement of Lactuca sativa growth

Diuron is one of the major hazardous pollutants which posses severe risk to the environment and human healthiness. On the other hand, salinity is the most severe environmental stressor that limits crop productivity. Therefore, it is required to address this co-existing abiotic stresses in agricultural soil. Plant growth-promoting rhizobacteria have gained an engaging role in the degradation of pesticides in agricultural soil. However, their role against the restoration of diuron-contaminated saline soil is still not known. Thus, in this study, diuron-degrading, salinity-tolerant Stenotrophomonas rhizophila strain CASB3 was isolated and characterized. Strain CASB3 showed important PGP traits under normal and diuron or salt stresses. Complete degradation of 10-50 mg L-1 diuron in the aqueous medium under normal and salinity stress conditions was achieved within 48-120 h and 48-192 h, respectively. A unique pathway for diuron biodegradation was proposed based on GC-MS analysis. In a greenhouse study, CASB3 inoculated into diuron-contaminated saline soil efficiently degraded diuron (50 mg kg-1) by 94% in 42 days and simultaneously resulted in an enhancement of root-shoot length (47.22-63.41%), fresh-dry biomass (136.36-156.66%), and photosynthetic pigments (36.93-92.28%) in Lactuca sativa plants. These results suggest the strain CASB3 could be used as a bioresource for the reclamation of diuron-contaminated saline soils.

Degradation of Phenylurea Herbicides by a Novel Bacterial Consortium Containing Synergistically Catabolic Species and Functionally Complementary Hydrolases

Phenylurea herbicides (PHs) are frequently detected as major water contaminants in areas where there is extensive use. In this study, Diaphorobacter sp. strain LR2014-1, which initially hydrolyzes linuron to 3,4-dichloroanaline, and Achromobacter sp. strain ANB-1, which further mineralizes the produced aniline derivatives, were isolated from a linuron-mineralizing consortium despite being present at low abundance in the community. The synergistic catabolism of linuron by the consortium containing these two strains resulted in more efficient catabolism of linuron and growth of both strains. Strain LR2014-1 harbors two evolutionary divergent hydrolases from the amidohydrolase superfamily Phh and the amidase superfamily TccA2, which functioned complementarily in the hydrolysis of various types of PHs, including linuron ( N-methoxy- N-methyl-substituted), diuron, chlorotoluron, fluomethuron ( N, N-dimethyl-substituted), and siduron. These findings show that a bacterial consortium can contain catabolically synergistic species for PH mineralization, and one strain could harbor functionally complementary hydrolases for a broadened substrate range.

Isolation, characterization, and identification of potential Diuron-degrading bacteria from surface sediments of Port Klang, Malaysia

Diuron is an alternative biocide suggested to replace organotin in formulating antifouling paints to be applied on water-going vessels hull. However, it is potentially harmful to various non-targeted marine organisms due to its toxic properties. Present study aimed to isolate, screen and identify the potential of Diuron-degrading bacteria collected from the marine sediments of Port Klang, Malaysia. Preliminary screening was conducted by exposing isolated bacteria to 430ng/L (background level), followed by 600ng/L and 1000ng/L of Diuron concentrations. Nine bacteria colonies survived the exposure of the above concentrations. However, only two strains can tolerate to survive up to 1000μg/L, which were then characterised and identified using phenotypic tests and the standard 16S rRNA molecular identification. The strains were identified as Comamonas jiangduensis SZZ 10 and Bacillus aerius SZZ 19 (GenBank accession numbers: KU942479 and KU942480, respectively). Both strains have the potential of Diuron biodegradation for future use.

Diuron degradation by bacteria from soil of sugarcane crops

The isolation of microorganisms from soil impacted by xenobiotic chemicals and exposing them in the laboratory to the contaminant can provide important information about their response to the contaminants. The purpose of this study was to isolate bacteria from soil with historical application of herbicides and to evaluate their potential to degrade diuron. The isolation media contained either glucose or diuron as carbon source. A total of 400 bacteria were isolated, with 68% being Gram-positive and 32% Gram-negative. Most isolates showed potential to degrade between 10 and 30% diuron after five days of cultivation; however Stenotrophomonas acidophila TD4.7 and Bacillus cereus TD4.31 were able to degrade 87% and 68%, respectively. The degradation of diuron resulted in the formation of the metabolites DCPMU, DCPU, DCA, 3,4-CAC, 4-CA, 4-CAC and aniline. Based on these results it was proposed that Pseudomonas aeruginosa TD2.3, Stenotrophomonas acidaminiphila TD4.7, B. cereus TD4.31 and Alcaligenes faecalis TG 4.48, act on 3,4-DCA and 4-CA by alkylation and dealkylation while Micrococcus luteus and Achromobacter sp follow dehalogenation directly to aniline. Growth on aniline as sole carbon source demonstrates the capacity of strains to open the aromatic ring. In conclusion, the results show that the role of microorganisms in the degradation of xenobiotics in the environment depends on their own metabolism and also on their synergistic interactions.

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes

Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.

Biodegradation of diuron by an endophytic fungus Neurospora intermedia DP8-1 isolated from sugarcane and its potential for remediating diuron-contaminated soils

A diuron-degrading endophyte DP8-1 was isolated from sugarcane root grown in diuron-treated soil in the present study. The endophyte was identified as Neurospora intermedia based on the morphological characteristics and sequence analysis. The fermentation parameters including temperature, pH, inoculation size, carbon source, and initial diuron concentration were also investigated for the optimization of degradation efficiency. The results indicated that strain DP8-1 was capable of degrading up to 99% diuron within 3 days under the optimal degrading condition. The study of degradation spectrum indicated that strain DP8-1 could also degrade and utilize fenuron, monuron, metobromuron, isoproturon, chlorbromuron, linuron, and chlortoluron as substrate for strain growth. On basis of liquid chromatography-mass spectrometry analysis for the products of the degradation of diuron, strain DP8-1 metabolized diuron to produce N-(3,4-dichlorophenyl)-urea and N-(3,4-dichlorophenyl)-N-methylurea through sequential N-dealkylations. In a soil bioaugmentation experiment, the inoculation of strain DP8-1 into diuron-treated soil effectively enhanced the disappearance rate of diuron.

Perspectives of using fungi as bioresource for bioremediation of pesticides in the environment: a critical review

Pesticides are used for controlling the development of various pests in agricultural crops worldwide. Despite their agricultural benefits, pesticides are often considered a serious threat to the environment because of their persistent nature and the anomalies they create. Hence removal of such pesticides from the environment is a topic of interest for the researchers nowadays. During the recent years, use of biological resources to degrade or remove pesticides has emerged as a powerful tool for their in situ degradation and remediation. Fungi are among such bioresources that have been widely characterized and applied for biodegradation and bioremediation of pesticides. This review article presents the perspectives of using fungi for biodegradation and bioremediation of pesticides in liquid and soil media. This review clearly indicates that fungal isolates are an effective bioresource to degrade different pesticides including lindane, methamidophos, endosulfan, chlorpyrifos, atrazine, cypermethrin, dieldrin, methyl parathion, heptachlor, etc. However, rate of fungal degradation of pesticides depends on soil moisture content, nutrient availability, pH, temperature, oxygen level, etc. Fungal strains were found to harbor different processes including hydroxylation, demethylation, dechlorination, dioxygenation, esterification, dehydrochlorination, oxidation, etc during the biodegradation of different pesticides having varying functional groups. Moreover, the biodegradation of different pesticides was found to be mediated by involvement of different enzymes including laccase, hydrolase, peroxidase, esterase, dehydrogenase, manganese peroxidase, lignin peroxidase, etc. The recent advances in understanding the fungal biodegradation of pesticides focusing on the processes, pathways, genes/enzymes and factors affecting the biodegradation have also been presented in this review article.

Effect of transportation on fecal bacterial communities and fermentative activities in horses: impact of Saccharomyces cerevisiae CNCM I-1077 supplementation

This study evaluated the effect of transportation on fecal bacterial communities and activities in horses with or without supplementation of live yeast and attempted to link those effects with changes in blood stress markers. Four mature horses were assigned to a crossover design and fed a basal diet (60:40 forage to concentrate; 1.45% BW on a DM basis), with or without supplementation, of 2 × 10(10) cfu/d of Saccharomyces cerevisiae CNCM I-1077. After a 14-d adaptation to dietary treatments, the 5-d experiment started 1 d before transportation (d -1). At d 0, horses were simultaneously transported in a truck for 2 h. Feces were sampled 4 h after the morning meal of concentrate at d -1, 0 (immediately after transportation), and 3 for enumeration of the main functional bacterial groups and determination of fermentative variables. Within each dietary treatment, feces were pooled before DNA extraction and molecular analysis of the bacterial communities, using temporal temperature gradient electrophoreses (TTGE). Blood samples were collected at the same time for determination of white blood cells (WBC) counts and glucose and total protein concentrations. Regardless of dietary treatment, the neutrophil to lymphocyte ratio increased during transportation (P < 0.01), indicating that horses were stressed. In both treatments, TTGE profiles were clearly different before and 3 d after transportation, and the percentage of similarity between profiles at d -1 and 3 was greater in supplemented horses compared with the controls. From d 0 to 3, the molar percentage of propionate increased and total concentration of VFA and the acetate + butyrate to propionate ratio decreased, regardless of dietary treatment (P < 0.01, P = 0.02, and P < 0.01, respectively), whereas pH decreased only in control horses (P = 0.03). Regardless of day of sampling, fecal concentrations of lactate-utilizing bacteria and cellulolytic bacteria were greater in supplemented horses than in control horses (P = 0.04 and 0.08, respectively). Our results indicate that transportation for 2 h disturbed the fecal bacterial ecosystem in horses that could increase the risk of triggering microbial dysbiosis on a longer term in the equine large intestine. Supplementing Saccharomyces cerevisiae CNCM I-1077 could help reduce the negative impact of transportation on the fecal bacterial ecosystem.

Enhanced mineralization of diuron using a cyclodextrin-based bioremediation technology

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 soil and water contaminant in areas where there is extensive use. Diuron has the unfortunate combination of being strongly adsorbed by soil organic matter particles and, hence, slowly degraded in the environment due to its reduced bioavailability. N-Phenylurea herbicides seem to be biodegraded in soil, but it must be kept in mind that this biotic or abiotic degradation could lead to accumulation of very toxic derived compounds, such as 3,4-dichloroaniline. Research was conducted to find procedures that might result in an increase in the bioavailability of diuron in contaminated soils, through solubility enhancement. For this purpose a double system composed of hydroxypropyl-β-cyclodextrin (HPBCD), which is capable of forming inclusion complexes in solution, and a two-member bacterial consortium formed by the diuron-degrading Arthrobacter sulfonivorans (Arthrobacter sp. N2) and the linuron-degrading Variovorax soli (Variovorax sp. SRS16) was used. This consortium can achieve a complete biodegradation of diuron to CO2 with regard to that observed in the absence of the CD solution, where only a 45% biodegradation was observed. The cyclodextrin-based bioremediation technology here described shows for the first time an almost complete mineralization of diuron in a soil system, in contrast to previous incomplete mineralization based on single or consortium bacterial degradation.

Stratification of Archaea in the deep sediments of a freshwater meromictic lake: vertical shift from methanogenic to uncultured archaeal lineages

As for lineages of known methanogens, several lineages of uncultured archaea were recurrently retrieved in freshwater sediments. However, knowledge is missing about how these lineages might be affected and structured according to depth. In the present study, the vertical changes of archaeal communities were characterized in the deep sediment of the freshwater meromictic Lake Pavin. For that purpose, an integrated molecular approach was performed to gain information on the structure, composition, abundance and vertical stratification of archaeal communities thriving in anoxic freshwater sediments along a gradient of sediments encompassing 130 years of sedimentation. Huge changes occurred in the structure and composition of archaeal assemblages along the sediment core. Methanogenic taxa (i.e. Methanosaeta and Methanomicrobiales) were progressively replaced by uncultured archaeal lineages (i.e. Marine Benthic Group-D (MBG-D) and Miscellaneous Crenarchaeal Group (MCG)) which are suspected to be involved in the methane cycle.

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0-10 cm) could be discriminated from those of the intermediate (11-27 cm) and deep (28-40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.

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.

Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France)

The vertical distribution of OP11, OD1 and SR1 divisions in the oxycline and in the anoxic water column of Lake Pavin, a freshwater permanently stratified mountain lake in France, was determined by temporal temperature gel gradient electrophoresis and 16S rRNA clone libraries. Gradual changes in the community structure were noted in relation to environmental variables along the oxidized/reduced environment. In addition, a separate effort to identify members of these lineages in the oxic mixolimnion identified sequences affiliated to SR1 and OP11 divisions, indicating that they are more widespread than previously expected.

Potential for microbial diuron mineralisation in a small wine-growing watershed: from treated plots to lotic receiver hydrosystem

BACKGROUND

Since biological degradation processes are known to be a major driver of the natural attenuation of pesticide residues in the environment, microbial communities adapted to pesticide biodegradation are likely to play a key environmental role in reducing pesticide exposure in contaminated ecosystems. The aim of this study was to assess the diuron-mineralising potential of microbial communities at a small-scale watershed level, including a diuron-treated vineyard (pollution source), its associated grass buffer strip (as a river protection area against pesticide runoff) and the lotic receiver hydrosystem (sediments and epilithon), by using radiorespirometry.

RESULTS

Comparison of results obtained at different sampling sites (in both soil and aquatic systems) revealed the importance of diuron exposure in the adaptation of microbial communities to rapid diuron mineralisation in the vineyard but also in the contaminated grass strip and in downstream epilithic biofilms and sediments.

CONCLUSION

This study provides strong suggestive evidence for high diuron biodegradation potential throughout its course, from the pollution source to the final receiving hydrosystem, and suggests that, after microbial adaptation, grass strips may represent an effective environmental tool for mineralisation and attenuation of intercepted pesticides.

Isolation and characterization of mesotrione-degrading Bacillus sp. from soil

Dissipation kinetics of mesotrione, a new triketone herbicide, sprayed on soil from Limagne (Puy-de-Dôme, France) showed that the soil microflora were able to biotransform it. Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods. Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it.

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.