Metabolism of nitrodiphenyl ether herbicides by dioxin-degrading bacterium Sphingomonas wittichii RW1

A Review of Remediation Strategies for Diphenyl Ether Herbicide Contamination

In agriculture, diphenyl ether herbicides are a broad-spectrum family of pesticides mainly used to control annual weeds in agriculture. Although diphenyl ether herbicides have a long-lasting effect in weed control, they can also be harmful to succeeding crops, as well as to the water and soil environment. Residual herbicides can also harm a large number of non-target organisms, leading to the death of pest predators and other beneficial organisms. Therefore, it is of great significance to control and remediate the contamination caused by diphenyl ether herbicide residues for the sake of environmental, nutritional, and biological safety. This review provides an overview of the techniques used for remediating diphenyl ether herbicide contamination, including biological, physical, and chemical remediation. Among these techniques, bioremediation, particularly microbial biodegradation technology, is extensively employed. The mechanisms and influencing factors of different remediation techniques in eliminating diphenyl ether herbicide contamination are discussed, together with a prospect for future development directions. This review serves as a scientific reference for the efficient remediation of residual contamination from diphenyl ether herbicides.

Fate, behaviour and microbial response of diluted bitumen and conventional crude spills in a simulated warm freshwater environment

Diluted bitumen (DB), one of the most transported unconventional crude oils in Canada's pipelines, raises public concerns due to its potential spillage into freshwater environments. This study aimed to compare the fate and behaviour of DB versus conventional crude (CC) in a simulated warm freshwater environment. An equivalent of 10 L of either DB or CC was spilled into 1200 L of North Saskatchewan River (NSR) water containing natural NSR sediment (2.4 kg) in a mesoscale spill tank and its fate and behaviour at air/water temperatures of 18 °C/24 °C were monitored for 56 days. Oil mass distribution analysis showed that 42.3 wt % of CC and 63.6 wt% of DB resided in the oil slicks at the end of 56-day tests, consisting mainly high molecular weight (HMW) compounds (i.e., resins and asphaltenes). The lost oil contained mainly low molecular weight (LMW) compounds (i.e., light saturates and some aromatics) into the atmosphere, water column, and sediment through collective weathering processes. Notably, weathered CC emulsified with water and remained floating until the end, while the weathered DB mat started to lose its buoyancy after 24 days under quiescent conditions and resurfaced once waves were applied. Analysis of the microbial communities of water pre- and post-spills revealed the replacement of indigenous microbial communities with hydrocarbon-degrading species. Exposure to CC reduced the microbial diversity by 12%, while exposure to DB increased the diversity by 10%. During the early stages of the spill (up to Day 21), most dominant species were positively correlated with the benzene, toluene, ethylbenzene, and xylenes (BTEX) content or polycyclic aromatic hydrocarbon (PAH) content of the water column, while the dominant species at the later stages (Days 21-56) of the spill were negatively correlated with BTEX or PAH content and positively correlated with the total organic carbon (TOC) content in waters.

Design and Synthesis of Novel Diphenyl Ether Carboxamide Derivatives To Control the Phytopathogenic Fungus Sclerotinia sclerotiorum

Sclerotinia stem rot (SSR) caused by the phytopathogenic fungus Sclerotinia sclerotiorum has led to serious losses in the yields of oilseed rape and other crops every year. Here, we designed and synthesized a series of carboxamide derivatives containing a diphenyl ether skeleton by adopting the scaffold splicing strategy. From the results of the mycelium growth inhibition experiment, inhibition rates of compounds 4j and 4i showed more than 80% to control S. sclerotiorum at a dose of 50 μg/mL, which is close to that of the positive control (flubeneteram, 95%). Then, the results of a structure-activity relationship study showed that the benzyl scaffold was very important for antifungal activity and that introducing a halogen atom on the benzyl ring would improve antifungal activity. Furthermore, the results of an in vitro activity test suggested that these novel compounds can inhibit the activity of succinate dehydrogenase (SDH), and the binding mode of 4j with SDH was basically similar to that of the flutolanil derivative. Morphological observation of mycelium revealed that compound 4j could cause a damage on the mycelial morphology and cell structure of S. sclerotiorum, resulting in inhibition of the growth of mycelia. Furthermore, in vivo antifungal activity assessment of 4j displayed a good control of S. sclerotiorum (>97%) with a result similar to that of the positive control at a concentration of 200 mg/L. Thus, the diphenyl ether carboxamide skeleton is a new starting point for the discovery of new SDH inhibitors and is worthy of further development.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Endophyte Community Changes in the Seeds of Eight Plant Species following Inoculation with a Multi-Endophytic Bacterial Consortium and an Individual Sphingomonas wittichii Strain Obtained from Noccaea caerulescens

Noccaea caerulescens, a hyperaccumulator plant species known for its metal tolerance and accumulation abilities, harbours a microbiome of interest within its seed. These seed-associated bacteria, often referred to as seed endophytes, play a unique role in seed germination and plant growth and health. This work aimed to address how inoculating seeds of eight different plant species-Medicago sativa (alfalfa), Zea mays (corn), Raphanus sativus (radish), Helianthus annus (sunflower), Cucurbita pepo subsp. pepo (squash), Beta vulgaris subsp. cicla (rainbow chard), Arabidopsis thaliana (thale cress), and Noccaea caerulescens (penny cress)-with a bacterial consortium made from the seed endophytes of N. caerulescens would affect the seed microbiome of each test plant species, as well as inoculation with a strain of the bacterium Sphingomonas wittichii, which was previously isolated from seeds of N. caerulescens. Additionally, we aimed to offer preliminary plant tests in order to determine the best seed treatment plan for future research. The results showed that inoculation with the bacterial consortium held the most potential for increasing plant size (p < 0.001) and increasing germination rate (p < 0.05). The plant that responded best to inoculation was N. caerulescens (penny cress), likely because the microbes being introduced into the seed were not foreign. This paper also offers the first insight into the seed endophytes of Beta vulgaris subsp. cicla, highlighting an abundance of Proteobacteria, Firmicutes, and Actinobacteriota.

Community Profiling of Seed Endophytes from the Pb-Zn Hyperaccumulator Noccaea caerulescens and Their Plant Growth Promotion Potential

Endophytes within plants are known to be crucial for plant fitness, and while their presence and functions in many compartments have been studied in depth, the research on seed endophytes is still limited. This work aimed to characterize the seed endophytic and rhizospheric bacterial community of two Noccaea caerulescens Pb-Zn hyperaccumulator populations, growing on two heavy-metal-polluted sites in Belgium. Cultured representatives were evaluated for their potential to enhance seed germination and root length of the model species Arabidopsis thaliana. The results indicated that the community structure within the seed is conserved between the two locations, comprising mainly of Proteobacteria (seeds), and Actinobacteria in the bulk soil. Root length of A. thaliana was significantly increased when inoculated with Sphingomonas vulcanisoli. The results of this paper offer insights into the importance of the selection of the core seed endophytic microbiome and highlight the precarious symbiotic relationship they have with the plant and seed.

Insights into the recent advances in nano-bioremediation of pesticides from the contaminated soil

In the present scenario, the uncontrolled and irrational use of pesticides is affecting the environment, agriculture and livelihood worldwide. The excessive application of pesticides for better production of crops and to maintain sufficient food production is leading to cause many serious environmental issues such as soil pollution, water pollution and also affecting the food chain. The efficient management of pesticide use and remediation of pesticide-contaminated soil is one of the most significant challenges to overcome. The efficiency of the current methods of biodegradation of pesticides using different microbes and enzymes depends on the various physical and chemical conditions of the soil and they have certain limitations. Hence, a novel strategy is the need of the hour to safeguard the ecosystem from the serious environmental hazard. In recent years, the application of nanomaterials has drawn attention in many areas due to their unique properties of small size and increased surface area. Nanotechnology is considered to be a promising and effective technology in various bioremediation processes and provides many significant benefits for improving the environmental technologies using nanomaterials with efficient performance. The present article focuses on and discusses the role, application and importance of nano-bioremediation of pesticides and toxic pollutants to explore the potential of nanomaterials in the bioremediation of hazardous compounds from the environment.

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

Heavy metal and pesticide pollution have become an inevitable part of the modern industrialized environment that find their way into all ecosystems. Because of their persistent nature, recalcitrance, high toxicity and biological enrichment, metal and pesticide pollution has threatened the stability of the environment as well as the health of living beings. Due to the environmental persistence of heavy metals and pesticides, they get accumulated in the environs and consequently lead to food chain contamination. Therefore, remediation of heavy metals and pesticide contaminations needs to be addressed as a high priority. Various physico-chemical approaches have been employed for this purpose, but they have significant drawbacks such as high expenses, high labor, alteration in soil properties, disruption of native soil microflora and generation of toxic by-products. Researchers worldwide are focusing on bioremediation strategies to overcome this multifaceted problem, i.e., the removal, immobilization and detoxification of pesticides and heavy metals, in the most efficient and cost-effective ways. For a period of millions of evolutionary years, microorganisms have become resistant to intoxicants and have developed the capability to remediate heavy metal ions and pesticides, and as a result, they have helped in the restoration of the natural state of degraded environs with long term environmental benefits. Keeping in view the environmental and health concerns imposed by heavy metals and pesticides in our society, we aimed to present a generalized picture of the bioremediation capacity of microorganisms. We explore the use of bacteria, fungi, algae and genetically engineered microbes for the remediation of both metals and pesticides. This review summarizes the major detoxification pathways and bioremediation technologies; in addition to that, a brief account is given of molecular approaches such as systemic biology, gene editing and omics that have enhanced the bioremediation process and widened its microbiological techniques toward the remediation of heavy metals and pesticides.

Atlas of the microbial degradation of fluorinated pesticides

Fluorine-based agrochemicals have been benchmarked as the golden standard in pesticide development, prompting their widespread use in agriculture. As a result, fluorinated pesticides can now be found in the environment, entailing serious ecological implications due to their harmfulness and persistence. Microbial degradation might be an option to mitigate these impacts, though environmental microorganisms are not expected to easily cope with these fluoroaromatics due to their recalcitrance. Here, we provide an outlook on the microbial metabolism of fluorinated pesticides by analyzing the degradation pathways and biochemical processes involved, while also highlighting the central role of enzymatic defluorination in their productive metabolism. Finally, the potential contribution of these microbial processes for the dissipation of fluorinated pesticides from the environment is also discussed.

Degradation Potential of the Nonylphenol Monooxygenase of Sphingomonas sp. NP5 for Bisphenols and Their Structural Analogs

The nonylphenol-degrading bacterium Sphingomonas sp. strain NP5 has a very unique monooxygenase that can attack a wide range of 4-alkylphenols with a branched side chain. Due to the structural similarity, it can also attack bisphenolic compounds, which are very important materials for the synthesis of plastics and resins, but many of them are known to or suspected to have endocrine disrupting effects to fish and animals. In this study, to clarify the substrate specificity of the enzyme (NmoA) for bisphenolic compounds, degradation tests using the cell suspension of Pseudomonas putida harboring the nonylphenol monooxygenase gene (nmoA) were conducted. The cell suspension degraded several bisphenols including bisphenol F, bisphenol S, 4,4′-dihydroxybenzophenone, 4,4′-dihydroxydiphenylether, and 4,4′-thiodiphenol, indicating that this monooxygenase has a broad substrate specificity for compounds with a bisphenolic structure.

Removal of oxyfluorfen from polluted effluents by combined bio-electro processes

In this work, the combination of biological and electrochemical processes to mineralize oxyfluorfen has been studied. First, an acclimatized mixed-culture biological treatment was used to degrade the biodegradable fraction of the pesticide, reaching up to 90% removal. After that, the non-biodegraded fraction was oxidised by electrolysis using boron-doped diamond as the anode. The results showed that the electrochemical technique was able to completely mineralize the residual pollutants. The study of the influence of the supporting electrolyte on the electrochemical process showed that the trace mineral solution used in the biological treatment was enough to completely mineralize the oxyfluorfen, resulting in total organic carbon removal rates that were well-fitted by a first-order model with a kinetic constant of 0.91 h^-1. However, the first-order degradation rate increased approximately 20% when Na₂SO₄ was added as supporting electrolyte, reaching a degradation rate of 1.16 h^-1 with a power consumption that was approximately 70% lower.

Rapid sonochemical synthesis of silver nano-leaves encapsulated on iron pyrite nanocomposite: An excellent catalytic application in the electrochemical detection of herbicide (Acifluorfen)

Herein, we developed a silver nanoparticles decorated iron pyrite flowers (FeS₂@Ag NL) based nanocomposite was prepared by a sonochemical method. The formation of FeS₂@Ag NL nanocomposite was confirmed by XRD, XPS, HR-TEM and analytical techniques. The FeS₂@Ag NL/SPCE was potentially applied towards electrochemical detection of toxic herbicide (acifluorfen-AFF). This provided an efficient sensor platform anchoring FeS₂@Ag NL on its surface. Under optimized conditions of differential pulse voltammetric transduction, a linear relationship between the current and the concentration was obtained in the range of 0.05-1126.45 µM for Acifluorfen. The detection limit was observed to be 0.0025 µM. the modified sensor exhibits excellent electrochemical performance, including good linear range, nanomolar detection limit, high sensitivity, and desirable stability. Particularly, the practical applicability was revealed by quantifying the AFF concentration in biological samples.

Toxicological impact of oxyfluorfen 24% herbicide on the reproductive system, antioxidant enzymes, and endocrine disruption of Biomphalaria alexandrina (Ehrenberg, 1831) snails

Oxyfluorfen (Goal 24%EC) herbicide is widely used in agriculture for weed control. Biomphalaria alexandrina snails can be used as bioindicator of the chemical pollution in the aquatic environment. The objective of this study was to evaluate the molluscicidal activity of this herbicide on Biomphalaria alexandrina snails and how it affected its biological system. The present study revealed a molluscicidal effect of oxyfluorfen 24%EC on these snails at LC₅₀ 5.9 mg/l. After exposure of snails to the sub-lethal concentrations (LC₀, LC₁₀, or LC₂₅) of this herbicide, the survival rates, reproductive rate (R₀), and fecundity (M_x) of adult B. alexandrina snails were significantly decreased in comparison with the control group. Also, levels of testosterone and estradiol were decreased significantly. It caused alterations in the antioxidant system, where exposure to sub-lethal concentration of this herbicide caused significant increases in levels of lipid peroxide malondialdehyde (MDA), catalase (CAT), and superoxide dismutase (SOD), while it significantly decreased glutathione transferase (GST). Histopathological changes in the digestive gland included severe damage in the digestive cells, where, they lost their tips and some were degenerated, while the secretory cells increased in number. Regarding the hermaphrodite gland, there were losses of the connective tissues, irregular sperms, and the eggs degenerated. These findings concluded that B. alexandrina snails can be used as a bioindicator for pollution with pesticide in the aquatic environment.

Soil Particles and Phenanthrene Interact in Defining the Metabolic Profile of Pseudomonas putida G7: A Vibrational Spectroscopy Approach

In soil, organic matter and mineral particles (soil particles; SPs) strongly influence the bio-available fraction of organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), and the metabolic activity of bacteria. However, the effect of SPs as well as comparative approaches to discriminate the metabolic responses to PAHs from those to simple carbon sources are seldom considered in mineralization experiments, limiting our knowledge concerning the dynamics of contaminants in soil. In this study, the metabolic profile of a model PAH-degrading bacterium, Pseudomonas putida G7, grown in the absence and presence of different SPs (i.e., sand, clays and humic acids), using either phenanthrene or glucose as the sole carbon and energy source, was characterized using vibrational spectroscopy (i.e., FT-Raman and FT-IR spectroscopy) and multivariate classification analysis (i.e., PLS-DA). The different type of SPs specifically altered the metabolic profile of P. putida, especially in combination with phenanthrene. In comparison to the cells grown in the absence of SPs, sand induced no remarkable change in the metabolic profile of the cells, whereas clays and humic acids affected it the most, as revealed by the higher discriminative accuracy (R², RMSEP and sensitivity) of the PLS-DA for those conditions. With respect to the carbon-source (phenanthrene vs. glucose), no effect on the metabolic profile was evident in the absence of SPs or in the presence of sand. On the other hand, with clays and humic acids, more pronounced spectral clusters between cells grown on glucose or on phenanthrene were evident, suggesting that these SPs modify the way cells access and metabolize PAHs. The macromolecular changes regarded mainly protein secondary structures (a shift from α-helices to β-sheets), amino acid levels, nucleic acid conformation and cell wall carbohydrates. Our results provide new interesting evidences that SPs specifically interact with PAHs in defining bacteria metabolic profiles and further emphasize the importance of studying the interaction of bacteria with their surrounding matrix to deeply understand PAHs degradation in soils.

Microbial degradation of fomesafen and detoxification of fomesafen-contaminated soil by the newly isolated strain Bacillus sp. FE-1 via a proposed biochemical degradation pathway

Fomesafen is a long residual herbicide and poses a potential risk to environmental safety, leading to an increasing need to find eco-friendly and cost-effective techniques to remediate fomesafen-contaminated soils. In this article, a novel strain of Bacillus sp., FE-1 was isolated from paddy field soil. This strain was found to degrade fomesafen both in liquid medium and in soil. >82.9% of fomesafen, at concentrations of 0.5, 1 and 10mgL^-1, was degraded by Bacillus sp. FE-1 in liquid medium within 14h. The optimal pH and temperature for degradation were 7.0 and 35°C, respectively. Soil samples inoculated with strain FE-1 showed significantly increased rates of fomesafen degradation. Two metabolites of fomesafen degradation were detected and identified as amino-fomesafen and 5-[2-chloro-4-(trifluoromethyl) phenoxy]-2-amino-benzoic acid. This is the first report of a novel fomesafen biodegradation pathway involving the reduction of a nitro group followed by the hydrolysis of an amide bond. The excellent remediation capability of the isolate FE-1 to detoxify fomesafen-contaminated soil was shown by bioassay of the sensitive aftercrop corn. The results indicate that Bacillus sp. FE-1 has potential for use in the bioremediation of fomesafen-contaminated soil.

Detoxification of diphenyl ether herbicide lactofen by Bacillus sp. Za and enantioselective characteristics of an esterase gene lacE

A bacterial strain Za capable of degrading diphenyl ether herbicide lactofen was isolated and identified as Bacillus sp. This strain could degrade 94.8% of 50mgL^-1 lactofen after 4days of inoculation in flasks. It was revealed that lactofen was initially hydrolyzed to desethyl lactofen, which was further transformed to acifluorfen, followed by the reduction of the nitro group to yield aminoacifluorfen. The phytotoxicity of the transformed product aminoacifluorfen to maize was decreased significantly compared with the lactofen. A gene lacE, encoding an esterase responsible for lactofen hydrolysis to desethyl lactofen and acifluorfen continuously, was cloned from Bacillus sp. Za. The deduced amino acid belonging to the esterase family VII contained a typical Ser-His-Asp/Glu catalytic triad and the conserved motifs GXSXG. The purified recombinant protein LacE displayed maximal esterase activity at 40°C and pH 7.0. Additionally, LacE had broad substrate specificity and was capable of hydrolyzing p-nitrophenyl esters. The enantioselectivity of LacE during lactofen degradation was further studied, and the results indicated that the (S)-(+)-lactofen was degraded faster than the (R)-(-)-lactofen, which could illustrate the reported phenomenon that (S)-(+)-lactofen was preferentially degraded in soil and sediment.

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.

An aldo-keto reductase is responsible for Fusarium toxin-degrading activity in a soil Sphingomonas strain

Degradation of toxins by microorganisms is a promising approach for detoxification of agricultural products. Here, a bacterial strain, Sphingomonas S3-4, that has the ability to degrade the mycotoxin deoxynivalenol (DON) was isolated from wheat fields. Incubation of Fusarium-infected wheat grains with S3-4 completely eliminated DON. In S3-4 DON is catabolized into compounds with no detectable phytotoxicity, 3-oxo-DON and 3-epi-DON, via two sequential reactions. Comparative analysis of genome sequences from two DON-degrading strains, S3-4 and Devosia D17, and one non-DON-degrading strain, Sphingobium S26, combined with functional screening of a S3-4 genomic BAC library led to the discovery that a novel aldo/keto reductase superfamily member, AKR18A1, is responsible for oxidation of DON into 3-oxo-DON. DON-degrading activity is completely abolished in a mutant S3-4 strain where the AKR18A1 gene is disrupted. Recombinant AKR18A1 protein expressed in Escherichia coli catalyzed the reversible oxidation/reduction of DON at a wide range of pH values (7.5 to 11) and temperatures (10 to 50 °C). The S3-4 strain and recombinant AKR18A1 also catabolized zearalenone and the aldehydes glyoxal and methyglyoxal. The S3-4 strain and the AKR18A1 gene are promising agents for the control of Fusarium pathogens and detoxification of mycotoxins in plants and in food/feed products.

Enhancing pesticide degradation using indigenous microorganisms isolated under high pesticide load in bioremediation systems with vermicomposts

In biobed bioremediation systems (BBSs) with vermicomposts exposed to a high load of pesticides, 6 bacteria and 4 fungus strains were isolated, identified, and investigated to enhance the removal of pesticides. Three different mixtures of BBSs composed of vermicomposts made from greenhouse (GM), olive-mill (OM) and winery (WM) wastes were contaminated, inoculated, and incubated for one month (GMI, OMI and WMI). The inoculums maintenance was evaluated by DGGE and Q-PCR. Pesticides were monitored by HPLC-DAD. The highest bacterial and fungal abundance was observed in WMI and OMI respectively. In WMI, the consortia improved the removal of tebuconazole, metalaxyl, and oxyfluorfen by 1.6-, 3.8-, and 7.7-fold, respectively. The dissipation of oxyfluorfen was also accelerated in OMI, with less than 30% remaining after 30d. One metabolite for metalaxyl and 4 for oxyfluorfen were identified by GC-MS. The isolates could be suitable to improve the efficiency of bioremediation systems.

Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery

The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.

Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1

Sphingomonas wittichii RW1 has no reported denitrifying activity yet encodes nitrite and nitric oxide reductases. The aims of this study were to determine conditions under which S. wittichii RW1 consumes nitrite (NO(-) 2) and produces nitrous oxide (N2O), examine expression of putative genes for N-oxide metabolism, and determine the functionality of chromosomal (ch) and plasmid (p) encoded quinol-dependent nitric oxide reductases (NorZ). Batch cultures of wildtype (WT) and a norZ ch mutant of S. wittichii RW1 consumed NO(-) 2 and produced N2O during stationary phase. The norZ ch mutant produced N2O, although at significantly lower levels (c.a. 66-87%) relative to the WT. Rates of N2O production were 2-3 times higher in cultures initiated at low relative to atmospheric O2 per unit biomass, although rates of NO(-) 2 consumption were elevated in cultures initiated with atmospheric O2 and 1 mM NaNO2. Levels of mRNA encoding nitrite reductase (nirK), plasmid-encoded nitric oxide dioxygenase (hmp p) and plasmid-encoded nitric oxide reductase (norZ p) were significantly higher in the norZ ch mutant over a growth curve relative to WT. The presence of NO(-) 2 further increased levels of nirK and hmp p mRNA in both the WT and norZ ch mutant; levels of norZ p mRNA compensated for the loss of norZ ch expression in the norZ ch mutant. Together, the results suggest that S. wittichii RW1 denitrifies NO(-) 2 to N2O and expresses gene products predicted to detoxify N-oxides. So far, only S. wittichii strains within four closely related taxa have been observed to encode both nirK and norZ genes, indicating a species-specific lateral gene transfer that may be relevant to the niche preference of S. wittichii.

Microbial degradation of fomesafen by a newly isolated strain Pseudomonas zeshuii BY-1 and the biochemical degradation pathway

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. Although the degradation of fomesafen in soils was thought to occur primarily by microbial activity, little was known about the kinetic and metabolic behaviors of this herbicide. This paper reported the capability of the newly isolated strain Pseudomonas zeshuii BY-1 to use fomesafen as the sole source of carbon in pure culture for its growth. Up to 88.7% of 50 mg of L(-1) fomesafen was degraded by this bacterium in mineral medium within 3 days. Strain BY-1 could also degrade other diphenyl ethers, including lactofen, acifluorfen, and fluoroglycofen. During the fomesafen degradation, five metabolites were detected and identified by liquid chromatography-mass spectrometry and tandem mass spectrometry. The primary degradation pathway of fomesafen might be the reduction of the nitro group to an amino group, followed by the acetylation of the amino derivative, dechlorination, and cleavage of the S-N bond. The addition of the BY-1 stain into soils treated with fomesafen resulted in a higher degradation rate than that observed in uninoculated soils, and the bacteria community in contaminated soil recovered after inoculation of the BY-1 stain. On the basis of these results, strain P. zeshuii BY-1 has the potential to be used in the bioremediation of fomesafen-contaminated soils.

Triclosan susceptibility and co-metabolism--a comparison for three aerobic pollutant-degrading bacteria

The antimicrobial agent triclosan is an emerging and persistent environmental pollutant. This study evaluated the susceptibility and biodegradation potential of triclosan by three bacterial strains (Sphingomonas wittichii RW1, Burkholderia xenovorans LB400 and Sphingomonas sp. PH-07) that are able to degrade aromatic pollutants (dibenzofuran, biphenyl and diphenyl ether, respectively) with structural similarities to triclosan. These strains showed less susceptibility to triclosan when grown in complex and mineral salts media. Biodegradation experiments revealed that only strain PH-07 was able to catabolize triclosan to intermediates that included hydroxylated compounds (monohydroxy-triclosan, and dihydroxy-triclosan) and the ether bond cleavage products (4-chlorophenol and 2,4-dichlorophenol), indicating that the initial dihydroxylation occurred on both aromatic rings of triclosan. Additional growth inhibition tests demonstrated that the main intermediate, 2,4-dichlorophenol, was less toxic to strain PH-07 than was triclosan. Our results indicate that ether bond cleavage might be the primary mechanism of avoiding triclosan toxicity by this strain.

Biotransformation of the diphenyl ether herbicide lactofen and purification of a lactofen esterase from Brevundimonas sp. LY-2

The diphenyl ether herbicide lactofen is commonly used to control broadleaf weeds. Once released into the environment, this herbicide is subject to microbial reactions. This study describes the biotransformation of lactofen by Brevundimonas sp. LY-2 isolated from enrichment cultures inoculated with soil sample. This strain degraded about 80% of 50 mg L(-1) lactofen in 5 days of incubation in flasks. The metabolic behaviors of the herbicide in the media are described. The results show a transformation pathway of lactofen by the bacterium leading to the formation of 1-(carboxy)ethyl-5-(2-chloro-4-(trifluoromethyl)phenoxy)-2-nitrobenzoate and ethanol. An esterase, which could cleave the right ester bond of the alkanoic side chain of lactofen, was purified 113.3-fold to homogeneity with 6.83% recovery. The current results suggested that Brevundimonas sp. LY-2 degraded lactofen via the ester bond cleavage catalyzed by esterase.

Biodegradation of fomesafen by strain Lysinibacillus sp. ZB-1 isolated from soil

The fomesafen degrading bacterium ZB-1 was isolated from contaminated agricultural soil, and identified as Lysinibacillus sp. based on the comparative analysis of 16S rRNA gene. The strain could utilize fomesafen as the sole carbon source for growth, and the total degradation rate was 81.32% after 7 d of inoculation in mineral salts medium. Strain ZB-1 could also degrade other diphenyl ethers including lactofen and fluoroglycofen. The optimum temperature for fomesafen degradation by strain ZB-1 was 30 degrees C. The effect of fomesafen concentration on degradation was also examined. Cell-free extract of strain ZB-1 was able to degrade fomesafen and other diphenyl ethers. Metabolism of fomesafen was accompanied by a transient accumulation of a metabolite identified as [N-[4-{4-(trifluoromethyl)phenoxy}-2-methanamidephenyl]acetamide] using liquid chromatography-mass spectrometry, thus indicating a metabolic pathway involving reduction, acetylation of nitro groups and dechlorination. The inoculation of strain ZB-1 to soil treated with fomesafen resulted in a higher degradation rate than in noninoculated soil regardless of the soil sterilized or nonsterilized.