Microbial metabolism of sulfur- and phosphorus-containing xenobiotics

Glyphosate (Roundup) as phosphorus nutrient enhances carbon and nitrogen accumulation and up-regulates phosphorus metabolisms in the haptophyte Isochrysis galbana

Inorganic phosphate limitation for phytoplankton may be intensified with water stratification by global warming, and with the increasing nitrogen: phosphorus (N:P) ratio in coastal zones resulting from continuous anthropogenic N overloading. Under these circumstances, phytoplankton's ability to use dissolved organic phosphorus (DOP) will give species a competitive advantage. In our previous study, we have shown that the haptophyte Isochrysis galbana can use glyphosate (Roundup) as a P nutrient source to support growth, but the mechanism of how remains unexplored. Here, we show that three genes encoding PhnC (IgPhnCs), which exhibit up-regulated expression in glyphosate-grown cultures, are probably responsible for glyphosate uptake, while homologs of PhnK and PhnL (IgPhnK and IgPhnL) probably provide auxiliary support for the intracellular degradation of glyphosate. Meanwhile, we found the use efficiency of glyphosate was low compared with phosphate, probably because glyphosate uptake and hydrolysis cost energy and because glyphosate induces oxidative stress in I. galbana. Meanwhile, genes encoding 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the target of the herbicide, were up-regulated in glyphosate cultures. Furthermore, our data showed the up-regulation of P metabolisms (transcription) in glyphosate-grown cultures, which further induced the up-regulation of nitrate/nitrite transport and biosynthesis of some amino acids. Meanwhile, glyphosate-grown cells accumulated more C and N, resulting in remarkably high C:N:P ratio, and this, along with the up-regulated P metabolisms, was under transcriptional and epigenetic regulation. This study sheds lights on the mechanism of glyphosate utilization as a source of P nutrient by I. galbana, and these findings have biogeochemical implications.

The Microbial Degradation of Natural and Anthropogenic Phosphonates

Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.

Understanding Reactive Sulfur Species through P/S Synergy

We investigated the differential oxidative and nucleophilic chemistry of reactive sulfur and oxygen anions (SSNO-, SNO-, NO2-, S42-, and HS-) using the simple reducing electrophile PPh2Cl. In the case of SSNO- reacting with PPh2Cl, a complex mixture of mono and diphosphorus products is formed exclusively in the P(V) oxidation state. We found that the phosphine stoichiometry dictates selectivity for oxidation to P=S/P=O products or transformation to P2 species. Interestingly, only chalcogen atoms are incorporated into the phosphorus products and, instead, nitrogen is released in the form of NO gas. Finally, we demonstrate that more reducing anions (S42- and HS-) also react with PPh2Cl with P=S bond formation as a key reaction driving force.

Amazonian soil fungi are efficient degraders of glyphosate herbicide; novel isolates of Penicillium, Aspergillus, and Trichoderma

Pesticide residues that contaminate the environment circulate within the hydrological cycle can accumulate within the food chain and cause problems to both environmental and human health. Microbes, however, are well known for their metabolic versatility and the ability to degrade chemically stable substances, including recalcitrant xenobiotics. The current study focused on bio-prospecting within Amazonian rainforest soils to find novel strains fungi capable of efficiently degrading the agriculturally and environmentally ubiquitous herbicide, glyphosate. Of 50 fungal strains isolated (using culture media supplemented with glyphosate as the sole carbon-substrate), the majority were Penicillium strains (60%) and the others were Aspergillus and Trichoderma strains (26 and 8%, respectively). All 50 fungal isolates could use glyphosate as a phosphorous source. Eight of these isolates grew better on glyphosate-supplemented media than on regular Czapek Dox medium. LC-MS revealed that glyphosate degradation by Penicillium 4A21 resulted in sarcosine and aminomethylphosphonic acid.

Comparison of gut bacterial communities and their associations with host diets in four fruit borers

BACKGROUND

Microbiota that live in the gut of insects have a wide range of effects on host nutrition, physiology, and behavior. They may shape the adaptation of their hosts to different habitats and lifestyles. To characterize the gut microbiota of fruit borers comprehensively, we compared bacterial communities among Grapholita molesta, Conogethes punctiferalis, Carposina sasakii, and Cydia pomonella, which are serious lepidopteran pests. We selected G. molesta as a representative pest to more explicitly test the influence of host dietary niche on the insect gut microbiome, and compared the bacterial microbial communities of G. molesta fed different diets (peach shoots and apple) using Illumina high-throughput sequencing technology.

RESULTS

The results show that Proteobacteria and Firmicutes are dominant in their gut microbiota. The C. sasakii had the highest richness values and G. molesta (shoot-feeding) had the highest diversity, whereas C. pomonella and G. molesta (fruit-feeding) had the lowest bacterial richness and diversity, respectively. The ANOSIM analysis revealed significant differences in the structure of gut microbiota among different insects. In addition, G. molesta with a different feeding diet had significant differences in gut microbiota composition. PICRUSt analysis indicated that most functional prediction categories were related to metabolism.

CONCLUSION

Our results show that gut microbiota composition is affected significantly not only by host species but also host diets. An enhanced understanding of these herbivore-associated microbial symbionts is essential for understanding the biology and ecology of the host insect, and may offer new possibilities to improve integrated pest-management strategies for efficient control of fruit borers. © 2019 Society of Chemical Industry.

Antigerminative comparison between naturally occurring naphthoquinones and commercial pesticides. Soil dehydrogenase activity used as bioindicator to test soil toxicity

As important secondary plant metabolites, naphthoquinones exhibit a wide range of biological activities, and one of their roles in the competition among plants is a well-known process called allelopathy. Their potential as a sustainable alternatives to herbicides has been investigated. In this study, we aim to take advantage of these naturally occurring substances to control the germination of spontaneous flora. In this work, the sensitivity of the germination of different plant species (horticultural, grasses and spontaneous flora) was tested. The results indicate that most of the plants are sensitive to juglone. The comparison between naphthoquinones and commercial pesticides did not provide enough evidence to use naphthoquinones to control spontaneous flora. Assessing the toxicity of pesticides is crucial because the sustainability of the ecosystem could be endangered by their use. In this study, the toxicity of certain pesticides (metam Na, oxyfluorfen, glyphosate, metribuzin and diuron) was evaluated based on dehydrogenase activity (DHA). DHA has become a good bioindicator for assessing the toxicity of xenobiotics. A toxicity index was proposed to compare the different degrees of toxicity among the tested substances. Finally, a toxicity threshold was constructed using the slopes of the fitted lines of the data, assuming that the maximum toxicity (10) represented the slope of the biocide HgCl₂ and that the minimum toxicity (1) was attributed to the DHA obtained from soil without pesticides.

A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity

The haloacid dehalogenase (HAD) superfamily is one of the largest known groups of enzymes and the majority of its members catalyze the hydrolysis of phosphoric acid monoesters into a phosphate ion and an alcohol. Despite the fact that sequence similarity between HAD phosphatases is generally very low, the members of the family possess some characteristic features, such as a Rossmann-like fold, HAD signature motifs or the requirement for Mg²⁺ ion as an obligatory cofactor. This study focuses on a new hypothetical HAD phosphatase from Thermococcus thioreducens. The protein crystallized in space group P2₁2₁2, with unit-cell parameters a = 66.3, b = 117.0, c = 33.8 Å, and the crystals contained one molecule in the asymmetric unit. The protein structure was determined by X-ray crystallography and was refined to 1.75 Å resolution. The structure revealed a putative active site common to all HAD members. Computational docking into the crystal structure was used to propose substrates of the enzyme. The activity of this thermophilic enzyme towards several of the selected substrates was confirmed at temperatures of 37°C as well as 60°C.

Production and characterization of extracellular polymeric substances (EPS) generated by a carbofuran degrading strain Cupriavidus sp. ISTL7

The present study demonstrates EPS production by Cupriavidus sp. ISTL7 along with its capability to remediate a toxic carbamate pesticide, carbofuran. The strain ISTL7 efficiently degraded approximately 98% of carbofuran (400 ppm) within 96 h. GC-MS analysis showed catabolic metabolites of degradation which included carbofuran-7-phenol, methylamine, 2-hydroxy-3-(3-methylpropan-2-ol)benzene-N-methyl-carbamate etc. EPS production from the mineral medium supplemented with carbofuran was observed to be 3.112 ± 0.3682 g L^-1. FTIR confirmed its carbohydrate composition and the monomeric sugars: glucose, xylose, sorbitol and fructose were identified by GC-MS analysis. The toxic potential of degradation experiment and the produced EPS was evaluated on HepG2 (mammalian liver cell line). The cytotoxicity of carbofuran was reduced upon bacterial degradation and the formed EPS was found to be non-toxic as inferred from percentage cell viability. The present research can possibly influence the development strategies of biological remediation.

Biochemical responses of the golden mussel Limnoperna fortunei under dietary glyphosate exposure

The aim of this study was to analyze the biochemical alterations in the golden mussel Limnoperna fortunei under dietary glyphosate exposure. Mussels were fed during 4 weeks with the green algae Scenedesmus vacuolatus previously exposed to a commercial formulation of glyphosate (6 mg L-1 active principle) with the addition of alkyl aryl polyglycol ether surfactant. After 1, 7, 14, 21 and 28 days of dietary exposure, glutathione-S-transferase (GST), catalase (CAT), superoxide dismutase (SOD), acetylcholinesterase (AChE), carboxylesterases (CES) and alkaline phosphatase (ALP) activities, glutathione (GSH) content and damage to lipids and proteins levels were analyzed. A significant increase (72%) in the GST activity and a significant decrease (26%) in the CES activity in the mussels fed on glyphosate exposed algae for 28 days were observed. The ALP activity was significantly increased at 21 and 28 days of dietary exposure (48% and 72%, respectively). GSH content and CAT, SOD and AchE activities did not show any differences between the exposed and non exposed bivalves. No oxidative damage to lipids and proteins, measured as TBARS and carbonyl content respectively, was observed in response to glyphosate dietary exposure. The decrease in the CES activity and the increases in GST and ALP activities observed in L. fortunei indicate that dietary exposure to glyphosate provokes metabolic alterations, related with detoxification mechanisms.

Pathway and rate-limiting step of glyphosate degradation by Aspergillus oryzae A-F02

Aspergillus oryzae A-F02, a glyphosate-degrading fungus, was isolated from an aeration tank in a pesticide factory. The pathway and rate-limiting step of glyphosate (GP) degradation were investigated through metabolite analysis. GP, aminomethylphosphonic acid (AMPA), and methylamine were detected in the fermentation liquid of A. oryzae A-F02, whereas sarcosine and glycine were not. The pathway of GP degradation in A. oryzae A-F02 was revealed: GP was first degraded into AMPA, which was then degraded into methylamine. Finally, methylamine was further degraded into other products. Investigating the effects of the exogenous addition of substrates and metabolites showed that the degradation of GP to AMPA is the rate-limiting step of GP degradation by A. oryzae A-F02. In addition, the accumulation of AMPA and methylamine did not cause feedback inhibition in GP degradation. Results showed that degrading GP to AMPA was a crucial step in the degradation of GP, which determines the degradation rate of GP by A. oryzae A-F02.

Isolation and Molecular Characterization of Novel Chlorpyrifos and 3,5,6-trichloro-2-pyridinol-degrading Bacteria from Sugarcane Farm Soils

Chlorpyrifos (CP) is one of the most widely used organophosphate pesticides in agriculture worldwide, but its extensive use has led to the contamination of various soil and water systems. Microbial bioremediation is considered to be one of the most viable options for the removal of CP from the environment; however, little is known about the soil bacterial diversity that degrade CP. Sequential soil and liquid culture enrichments enabled the isolation of bacterial CP degraders with sequence homologies to Xanthomonas sp., Pseudomonas sp., and Rhizobium sp. The efficacy of the three isolated strains: Xanthomonas sp. 4R3-M1, Pseudomonas sp. 4H1-M3, and Rhizobium sp. 4H1-M1 was further investigated for biodegradation of CP and its primary metabolic product, 3,5,6-trichloro-2-pyridinol (TCP). The results indicate that all three bacterial strains almost completely metabolized CP (10 mg/L) and TCP, occurring as a metabolic degradation product, in mineral salt media as a sole source of carbon and nitrogen. The isolated bacterial strains Xanthomonas sp. 4R3-M1 and Pseudomonas sp. 4H1-M3 could also degrade TCP (10 mg/L) as a sole carbon and nitrogen source, when provided externally. Thus, these bacterial strains may be effective in practical application of bioremediation of both CP and TCP.

Detoxifying symbionts in agriculturally important pest insects

Pest insects lead to excessive agricultural and therefore economical losses on crops worldwide. These insects have to withstand toxic molecules that are inherent to plant defences, as well as those that are produced and introduced by humans in the form of insecticides. In recent years, research on insect–microbe symbioses has recognized that microbial symbionts may play a role protecting against these toxins, leading to a form of defensive symbiosis between the pest insect and different types of microorganisms that we term detoxifying symbioses. In this minireview, we will highlight well‐characterized and emerging insect model systems of detoxifying symbioses and assess how the microorganisms influence the host's success.

The role of bacteria and mycorrhiza in plant sulfur supply

Plant growth is highly dependent on bacteria, saprophytic, and mycorrhizal fungi which facilitate the cycling and mobilization of nutrients. Over 95% of the sulfur (S) in soil is present in an organic form. Sulfate-esters and sulfonates, the major forms of organo-S in soils, arise through deposition of biological material and are transformed through subsequent humification. Fungi and bacteria release S from sulfate-esters using sulfatases, however, release of S from sulfonates is catalyzed by a bacterial multi-component mono-oxygenase system. The asfA gene is used as a key marker in this desulfonation process to study sulfonatase activity in soil bacteria identified as Variovorax, Polaromonas, Acidovorax, and Rhodococcus. The rhizosphere is regarded as a hot spot for microbial activity and recent studies indicate that this is also the case for the mycorrhizosphere where bacteria may attach to the fungal hyphae capable of mobilizing organo-S. While current evidence is not showing sulfatase and sulfonatase activity in arbuscular mycorrhiza, their effect on the expression of plant host sulfate transporters is documented. A revision of the role of bacteria, fungi and the interactions between soil bacteria and mycorrhiza in plant S supply was conducted.

Inter and intra plant variability of enzyme profiles including various phosphoesterases and sulfatase of six wastewater treatment plants

Biodegradation of organic wastewater constituents by activated sludge microorganisms is based on enzymatic processes. It is supposed that wastewater treatment plants (WWTP) differ in their enzymatic fingerprints. To determine such fingerprints, activated sludges from nine aerated tanks of six WWTPs were repeatedly sampled and analyzed for the activities of l-alanine aminopeptidase, esterase, α- and β-glucosidase, alkaline phosphatase, phosphodiesterase, phosphotriesterase, and sulfatase. In one WWTP the enzymatic activities and their variations within 1 week were assayed in various process stages. Mostly the enzymatic profiles were dominated by l-alanine aminopeptidase, followed by alkaline phosphatase. They differed in variable contributions of esterase, phosphodiesterase, α- and β-glucosidase. The sulfatase activity was generally low. For the first time phosphotriesterase activity was detected in various samples, but with limited analytical validity. Particle mass-related activities of individual enzymes varied between plants by factors 2-4 and up to 11, when related to suspension volumes.

Similar connotation in chronic hepatitis B and nonalcoholic Fatty liver patients with dampness-heat syndrome

The phenomenon that the same syndrome turns up in different diseases appears in the sight of people around the world, which raises the thought for possibility of “Same Treatment for Different Diseases.” Actually, treatment based on ZHENG classification in Traditional Chinese Medicine could bring revelation for the former finding. The dampness-heat syndrome in chronic hepatitis B and nonalcoholic fatty liver is regarded as the breakthrough point. We discussed the molecular mechanism of similar connotation that exists in chronic hepatitis B and nonalcoholic fatty liver by metabonomics to give the modern understanding of dampness-heat syndrome. Both urine and serum metabolic profiling revealed that obvious differences existed between dampness-heat syndrome and non-dampness-heat syndrome but the commonality was proved to appear in chronic hepatitis B and nonalcoholic fatty liver patients with dampness-heat syndrome. Furthermore, disorder of body fluid metabolism, decline in digestive capacity, and imbalance of intestinal flora were found to be the new guiding for treatment, with the hope to provide the basis for Chinese personalized medicine.

Isolation of Arthrobacter species from the phyllosphere and demonstration of their epiphytic fitness

Bacteria of the genus Arthrobacter are common inhabitants of the soil environment, but can also be recovered from leaf surfaces (the phyllosphere). Using enrichment cultures on 4-chlorophenol, we succeeded in specifically isolating Arthrobacter bacteria from ground cover vegetation in an apple orchard. Based on 16S rRNA gene sequencing, the isolates were found to belong to at least three different species of Arthrobacter. Compared to the model bacterial epiphyte Pantoea agglomerans, the Arthrobacter isolates performed as well or even better in a standardized laboratory test of phyllosphere fitness. A similar performance was observed with the well-characterized soil isolate Arthrobacter chlorophenolicus A6. These findings suggest that the frequently reported presence of Arthrobacter strains on plant foliage can be explained by the capacity to multiply and persist in the phyllosphere environment. As bacteria from the genus Arthrobacter are known for their ability to degrade a wide variety of organic pollutants, their high phyllosphere competency marks them as a promising group for future studies on phyllosphere-based bioremediation, for example, as foliar bioaugmentation on ground cover or buffer-zone vegetation to prevent pesticides from reaching soil, surface-, or groundwater.

Soil bacterial consortia and previous exposure enhance the biodegradation of sulfonamides from pig manure

Persistence or degradation of synthetic antibiotics in soil is crucial in assessing their environmental risks. Microbial catabolic activity in a sandy loamy soil with pig manure using 12C- and 14C-labelled sulfamethazine (SMZ) respirometry showed that SMZ was not readily degradable. But after 100 days, degradation in sulfadiazine-exposed manure was 9.2%, far greater than soil and organic manure (0.5% and 0.11%, respectively, p < 0.05). Abiotic degradation was not detected suggesting microbial catabolism as main degradation mechanism. Terminal restriction fragment length polymorphism showed biodiversity increases within 1 day of SMZ spiking and especially after 200 days, although some species plummeted. A clone library from the treatment with highest degradation showed that most bacteria belonged to α, β and γ classes of Proteobacteria, Firmicutes, Bacteroidetes and Acidobacteria. Proteobacteria (α, β and γ), Firmicutes and Bacteroidetes which were the most abundant classes on day 1 also decreased most following prolonged exposure. From the matrix showing the highest degradation rate, 17 SMZ-resistant isolates biodegraded low levels of 14C-labelled SMZ when each species was incubated separately (0.2-1.5%) but biodegradation was enhanced when the four isolates with the highest biodegradation were incubated in a consortium (Bacillus licheniformis, Pseudomonas putida, Alcaligenes sp. and Aquamicrobium defluvium as per 16S rRNA gene sequencing), removing up to 7.8% of SMZ after 20 days. One of these species (B. licheniformis) was a known livestock and occasional human pathogen. Despite an environmental role of these species in sulfonamide bioremediation, the possibility of horizontal transfer of pathogenicity and resistance genes should caution against an indiscriminate use of these species as sulfonamide degraders.

Agricultural impacts of glyphosate-resistant soybean cultivation in South America

In the 2009/2010 growing season, Brazil was the second largest world soybean producer, followed by Argentina. Glyphosate-resistant soybeans (GRS) are being cultivated in most of the soybean area in South America. Overall, the GRS system is beneficial to the environment when compared to conventional soybean. GRS resulted in a significant shift toward no-tillage practices in Brazil and Argentina, but weed resistance may reduce this trend. Probably the highest agricultural risk in adopting GRS in Brazil and South America is related to weed resistance due to use of glyphosate. Weed species in GRS fields have shifted in Brazil to those that can more successfully withstand glyphosate or to those that avoid the time of its application. Five weed species, in order of importance, Conyza bonariensis (L.) Cronquist, Conyza canadensis (L.) Cronquist, Lolium multiflorum Lam., Digitaria insularis (L.) Mez ex Ekman, and Euphorbia heterophylla L., have evolved resistance to glyphosate in GRS in Brazil. Conyza spp. are the most difficult to control. A glyphosate-resistant biotype of Sorghum halepense L. has evolved in GRS in Argentina and one of D. insularis in Paraguay. The following actions are proposed to minimize weed resistance problem: (a) rotation of GRS with conventional soybeans in order to rotate herbicide modes of action; (b) avoidance of lower than recommended glyphosate rates; (c) keeping soil covered with a crop or legume at intercrop intervals; (d) keeping machinery free of weed seeds; and (d) use of a preplant nonselective herbicide plus residuals to eliminate early weed interference with the crop and to minimize escapes from later applications of glyphosate due to natural resistance of older weeds and/or incomplete glyphosate coverage.

Organophosphorus hydrolase (OpdB) of Lactobacillus brevis WCP902 from kimchi is able to degrade organophosphorus pesticides

Lactobacillus brevis WCP902 that is capable of biodegrading chlorpyrifos was isolated from kimchi. The opdB gene cloned from this strain revealed 825 bp, encoding 274 aa, and an enzyme molecular weight of about 27 kDa. OpdB contains the same Gly-X-Ser-X-Gly motif found in most bacterial and eukaryotic esterase, lipase, and serine hydrolases, yet it is a novel member of the GDSVG family of esterolytic enzymes. Its conserved serine residue, Ser82, is significantly involved with enzyme activity that may have application for removing some pesticides. Optimum organophosphorus hydrolase (OpdB) activity appeared at pH 6.0 and 35 degrees C and during degradation of chlorpyrifos, coumaphos, diazinon, methylparathion, and parathion.

Adsorption of 5-sodiosulfoisophthalic acids from aqueous solution onto poly(2-vinylpyridine) resin

In the present study, the performance, behavior and mechanism of synthetic poly(2-vinylpyridine) resin (WH-225) adsorbing 5-sodiosulfoisophthalic acids (SIPA) from the aqueous solution were investigated, and two commercial adsorbents, namely, hypercrosslinked adsorbent NDA-100 and macroporous adsorbent XAD-4 were employed as reference. Compared to NDA-100 and XAD-4, WH-225 has the highest capacity for adsorbing SIPA from the aqueous solution, which is verified by the related adsorption experiments. The investigation indicated that electrostatic interaction is an important factor in affecting the adsorption behavior of WH-225. The Freundlich isotherm equation was successfully applied to describe the adsorption isotherms. The negative values of the adsorptive enthalpy changes indicate an exothermic process for WH-225, and the absolute values (<43 kJ mol(-1)) further manifest a physical adsorption process. The column adsorption and desorption tests further proved WH-225 is a promising adsorbent for field applications to remove and recover aromatic acids (e.g. SIPA) from aqueous solution.

Oxidative degradation of 1,5-naphthalenedisulfonic acid in aqueous solutions by UV-photolysis in the absence and presence of H2O2

Sulfonated aromatic pollutants such as 1,5-naphthalenedisulfonic acid (NDS or Armstrong's acid) are persistent compounds and thus resist environmental breakdown and microbial treatment. This study investigated the photo-oxidative degradation of such a persistent polar pollutant in the absence and presence of H2O2. The degradation of aqueous NDS solutions by photolysis was found to be efficient only in the presence of H2O2. The combination of UV irradiation and H2O2 leads to progressive degradation of NDS, which is converted into new, more biodegradable and non-toxic species.

Effects of repeated glyphosate applications on soil microbial community composition and the mineralization of glyphosate

BACKGROUND

Repeated applications may have a greater impact on the soil microbial community than a single application of glyphosate. Experiments were conducted to study the effect of one, two, three, four or five applications of glyphosate on soil microbial community composition and glyphosate mineralization and distribution of (14)C residues in soil.

RESULTS

Fatty acid methyl esters (FAMEs) common to gram-negative bacteria were present in higher concentrations following five applications relative to one, two, three or four applications both 7 and 14 days after application (DAA). Additionally, sequencing of 16S rRNA bacterial genes indicated that the abundance of the gram-negative Burkholderia spp. was increased following the application of glyphosate. The cumulative percentage (14)C mineralized 14 DAA was reduced when glyphosate was applied 4 or 5 times relative to the amount of (14)C mineralized following one, two or three applications. Incorporation of (14)C residues into soil microbial biomass was greater following five glyphosate applications than following the first application 3 and 7 DAA.

CONCLUSION

These studies suggest that the changes in the dissipation or distribution of glyphosate following repeated applications of glyphosate may be related to shifts in the soil microbial community composition.

Characterisation of Campylobacter jejuni genes potentially involved in phosphonate degradation

Potential biological roles of the Campylobacter jejuni genes cj0641, cj0774c and cj1663 were investigated. The proteins encoded by these genes showed sequence similarities to the phosphonate utilisation PhnH, K and L gene products of Escherichia coli. The genes cj0641, cj0774c and cj1663 were amplified from the pathogenic C. jejuni strain 81116, sequenced, and cloned into pGEM-T Easy vectors. Recombinant plasmids were used to disrupt each one of the genes by inserting a kanamycin resistance (Km^R) cassette employing site-directed mutagenesis or inverse PCR. Campylobacter jejuni 81116 isogenic mutants were generated by integration of the mutated genes into the genome of the wild-type strain. The C. jejuni mutants grew on primary isolation plates, but they could not be purified by subsequent passages owing to cell death. The mutant C. jejuni strains survived and proliferated in co-cultures with wild-type bacteria or in media in which wild-type C. jejuni had been previously grown. PCR analyses of mixed wild-type/mutant cultures served to verify the presence of the mutated gene in the genome of a fraction of the total bacterial population. The data suggested that each mutation inactivated a gene essential for survival. Rates of phosphonate catabolism in lysates of E. coli strain DH5α were determined using proton nuclear magnetic resonance spectroscopy. Whole-cell lysates of the wild-type degraded phosphonoacetate, phenylphosphonate and aminomethylphosphonate. Significant differences in the rates of phosphonate degradation were observed between lysates of wild-type E. coli, and of bacteria transformed with each one of the vectors carrying one of the C. jejuni genes, suggesting that these genes were involved in phosphonate catabolism.

Biodegradation of p-nitrophenol by Rhodococcus sp. CN6 with high cell surface hydrophobicity

Rhodococcus sp. CN6, isolated from a pesticide industry's effluent-sediment, was able to completely degrade and utilize 100mg/L p-nitrophenol (PNP) as the sole carbon, nitrogen and energy sources for growth in the minimal salt media (MSM) within 12h. To study the applicability of the strain for bioremediation of PNP, its degradation potential was examined in the presence of different supplemented carbon and nitrogen sources in MSM with 100mg/L PNP. Dextrin was experienced as the best supplemented carbon source used by the strain CN6 during degrading PNP. Addition of ammonium nitrate could also increase the PNP degradation rate. Preliminary studies on the surface characters of Rhodococcus sp. CN6 were undertaken for the sake of exploring its high efficiency on the degradation of PNP. Microbial adherence to hydrocarbons (MATH) assays illuminated that the strain CN6 was of higher hydrophobicity while grown on higher concentration of PNP. The results suggested that the strain CN6 could be used as a potential and efficient PNP degrader for the bioremediation of contaminated sites.

Isolation and characterization of a phorate degrading bacterium

AIMS

To study the degradation of phorate by a bacterium isolated from phorate-contaminated sites.

METHODS AND RESULTS

Ralstonia eutropha strain AAJ1 isolated from soil was found to degrade phorate (supplied as sole carbon source) upto 85% in 10 days in liquid medium. Half-life (t((1/2))) of phorate in the liquid medium in control (uninoculated) and in experimental (inoculated with R. eutropha, strain AAJ1) samples was recorded as 36.49 and 6.29 days, respectively. Kinetics revealed that phorate degradation depends on time and the reaction follows the first order kinetics. Diethyl dithiophosphate was one of the degradation products, which is markedly less toxic than the parent compound; other degradation products included phorate sulfoxide and phorate sulfone. Release of inorganic phosphates and sulfates indicated the potential of the isolate to further degrade the above-mentioned metabolites to simpler forms. The strain was also found to poses phosphomonoesterase and phosphodiesterase enzymatic activity, which are involved in biodegradation of organophosphorus compounds.

CONCLUSIONS

Ralstonia eutropha AAJ1 could degrade and detoxify phorate upto 85% in 10 days in laboratory conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

The isolate has the potential to be utilized for remediation of phorate-contaminated water and soil.

Biodegradation of chlorpyrifos by lactic acid bacteria during kimchi fermentation

We examined the role of microorganisms in the degradation of the organophosphorus (OP) insecticide chlorpyrifos (CP) during kimchi fermentation. During the fermentation of kimchi, 30 mg L(-1) of CP was added and its stability assayed during fermentation. CP was degraded rapidly until day 3 (83.3%) and degraded completely by day 9. Four CP-degrading lactic acid bacteria (LAB) were isolated from kimchi fermentation in the presence of 200 mg L(-1) CP and were identified as Leuconostoc mesenteroides WCP907, Lactobacillus brevis WCP902, Lactobacillus plantarum WCP931, and Lactobacillus sakei WCP904. CP could be utilized by these four strains as the sole source of carbon and phosphorus. Coumaphos (CM), diazinon (DZ), parathion (PT), and methylparathion (MPT) were also degraded by WCP907, WCP902, WCP931, and WCP904 when provided as sole sources of carbon and phosphorus.

Oxidative degradation of 1,5-naphthalenedisulfonic acid in aqueous solutions by microwave irradiation in the presence of H2O2

Sulfonated aromatic pollutants such as Armstrong's acid, or 1,5-naphthalenedisulfonic acid (NDS), are recalcitrant to environmental breakdown and microbial treatment. This study investigated the effects of H(2)O(2) concentration, pH, microwave (MW) power and irradiation time on the oxidative degradation of NDS in aqueous solutions. The formation of hydroxyl radicals as the active oxidant was confirmed by electron paramagnetic resonance spin trapping. A combination of both H(2)O(2) and MW heating proved essential for NDS degradation. Degradation factors of f70% were obtained after about 20min of irradiation at [H(2)O(2)]:[NDS] ratios=10. Acidic conditions were found to be more favorable to the degradation of NDS, and the process follows pseudo-first-order kinetics. Attempts to scale-up the process using a conventional MW reactor provided less striking results.

Review of potential environmental impacts of transgenic glyphosate-resistant soybean in Brazil

Transgenic glyphosate-resistant soybeans (GRS) have been commercialized and grown extensively in the Western Hemisphere, including Brazil. Worldwide, several studies have shown that previous and potential effects of glyphosate on contamination of soil, water, and air are minimal, compared to those caused by the herbicides that they replace when GRS are adopted. In the USA and Argentina, the advent of glyphosate-resistant soybeans resulted in a significant shift to reduced- and no-tillage practices, thereby significantly reducing environmental degradation by agriculture. Similar shifts in tillage practiced with GRS might be expected in Brazil. Transgenes encoding glyphosate resistance in soybeans are highly unlikely to be a risk to wild plant species in Brazil. Soybean is almost completely self-pollinated and is a non-native species in Brazil, without wild relatives, making introgression of transgenes from GRS virtually impossible. Probably the highest agricultural risk in adopting GRS in Brazil is related to weed resistance. Weed species in GRS fields have shifted in Brazil to those that can more successfully withstand glyphosate or to those that avoid the time of its application. These include Chamaesyce hirta (erva-de-Santa-Luzia), Commelina benghalensis (trapoeraba), Spermacoce latifolia (erva-quente), Richardia brasiliensis (poaia-branca), and Ipomoea spp. (corda-de-viola). Four weed species, Conyza bonariensis, Conyza Canadensis (buva), Lolium multiflorum (azevem), and Euphorbia heterophylla (amendoim bravo), have evolved resistance to glyphosate in GRS in Brazil and have great potential to become problems.

Biochemical interpretation of quantitative structure-activity relationships (QSAR) for biodegradation of N-heterocycles: a complementary approach to predict biodegradability

Prediction of the biodegradability of organic compounds is an ecologically desirable and economically feasible tool for estimating the environmental fate of chemicals. We combined quantitative structure-activity relationships (QSAR) with the systematic collection of biochemical knowledge to establish rules for the prediction of aerobic biodegradation of N-heterocycles. Validated biodegradation data of 194 N-heterocyclic compounds were analyzed using the MULTICASE-method which delivered two QSAR models based on 17 activating (OSAR 1) and on 16 inactivating molecular fragments (GSAR 2), which were statistically significantly linked to efficient or poor biodegradability, respectively. The percentages of correct classifications were over 99% for both models, and cross-validation resulted in 67.9% (GSAR 1) and 70.4% (OSAR 2) correct predictions. Biochemical interpretation of the activating and inactivating characteristics of the molecular fragments delivered plausible mechanistic interpretations and enabled us to establish the following biodegradation rules: (1) Target sites for amidohydrolases and for cytochrome P450 monooxygenases enhance biodegradation of nonaromatic N-heterocycles. (2) Target sites for molybdenum hydroxylases enhance biodegradation of aromatic N-heterocycles. (3) Target sites for hydratation by an urocanase-like mechanism enhance biodegradation of imidazoles. Our complementary approach represents a feasible strategy for generating concrete rules for the prediction of biodegradability of organic compounds.

Microbial degradation of organophosphorus xenobiotics: metabolic pathways and molecular basis

Organophosphorus (OP) xenobiotics are used worldwide as pesticides and petroleum additives. OP compounds share the major portion of the pesticide market globally. Owing to large-scale use of OP compounds, contaminations of soil and water systems have been reported from all parts of the world. OP compounds possess very high mammalian toxicity and therefore early detection and subsequent decontamination and detoxification of the polluted environment is essential. Additionally, about 200,000 tons of extremely toxic OP chemical warfare agents are required to be destroyed by 2007 under Chemical Warfare Convention (1993). Chemical and physical methods of decontamination are not only expensive and time-consuming, but also in most cases they do not provide a complete solution. These approaches convert compounds from toxic into less toxic states, which in some cases can accumulate in the environment and still be toxic to a range of organisms. Bioremediation provides a suitable way to remove contaminants from the environment as, in most of the cases, OP compounds are totally mineralized by the microorganisms. Most OP compounds are degraded by microorganisms in the environment as a source of phosphorus or carbon or both. Several soil bacteria have been isolated and characterized, which can degrade OP compounds in laboratory cultures and in the field. The biochemical and genetic basis of microbial degradation has received considerable attention. Several genes/enzymes, which provide microorganisms with the ability to degrade OP compounds, have been identified and characterized. Some of these genes and enzymes have been engineered for better efficacy. Bacteria capable of complete mineralization are constructed by transferring the complete degradation pathway for specific compounds to one bacterium. In the present article, we review microbial degradation and metabolic pathways for some OP compounds. The biochemical and molecular basis of OP degradation by microbes and the evolution and distribution of genes/enzymes are also reviewed. This article also examines applications and future use of OP-degrading microbes and enzymes for bioremediation, treatment of OP poisoning, and as biosensors.

Soil microbial activity is affected by Roundup WeatherMax and pesticides applied to cotton (Gossypium hirsutum)

Adoption of glyphosate-based weed control systems has led to increased use of the herbicide with continued use of additional pesticides. Combinations of pesticides may affect soil microbial activity differently than pesticides applied alone. Research was conducted to evaluate the influence of glyphosate-based cotton pest management systems on soil microbial activity. Soil was treated with commercial formulations of trifluralin, aldicarb, and mefenoxam + pentachloronitrobenzene (PCNB) with or without glyphosate (applied as Roundup WeatherMax). The soil microbial activity was measured by quantifying C and N mineralization. Soil microbial biomass was determined using the chloroform fumigation-incubation method. Soils treated with glyphosate alone exhibited greater cumulative C mineralization 30 days after treatment than all other treatments, which were similar to the untreated control. The addition of Roundup WeatherMax reduced C mineralization in soils treated with fluometuron, aldicarb, or mefenoxam + PCNB formulations. These results indicate that glyphosate-based herbicides alter the soil microbial response to other pesticides.

Sorption, desorption and mineralisation of the herbicides glyphosate and MCPA in samples from two Danish soil and subsurface profiles

The vertical distribution of the sorption, desorption and mineralisation of glyphosate and MCPA was examined in samples from two contrasting soil and subsurface profiles, obtained from a sandy agricultural site and a non-agricultural clay rich site. The highest mineralisation of [14C-methylen]glyphosate, with 9.3-14.7% degraded to 14CO2 within 3 months was found in the deepest sample from the clay site. In the deeper parts of the sandy profile high sorption and low desorption of glyphosate coincided with no or minor mineralisation indicating a limited glyphosate bioavailability. MCPA was readily mineralised except in the deepest samples from both sites. The highest MCPA mineralisation was detected just below the surface layers with 72% or 44% degraded to 14CO2 at the sandy or the clay sites, respectively. MCPA sorped to a minor extent in all samples and no indications of sorption-controlled mineralisation was revealed. None of the herbicides were mineralised under anoxic conditions.

Microbial degradation of organophosphorus compounds

Synthetic organophosphorus compounds are used as pesticides, plasticizers, air fuel ingredients and chemical warfare agents. Organophosphorus compounds are the most widely used insecticides, accounting for an estimated 34% of world-wide insecticide sales. Contamination of soil from pesticides as a result of their bulk handling at the farmyard or following application in the field or accidental release may lead occasionally to contamination of surface and ground water. Several reports suggest that a wide range of water and terrestrial ecosystems may be contaminated with organophosphorus compounds. These compounds possess high mammalian toxicity and it is therefore essential to remove them from the environments. In addition, about 200,000 metric tons of nerve (chemical warfare) agents have to be destroyed world-wide under Chemical Weapons Convention (1993). Bioremediation can offer an efficient and cheap option for decontamination of polluted ecosystems and destruction of nerve agents. The first micro-organism that could degrade organophosphorus compounds was isolated in 1973 and identified as Flavobacterium sp. Since then several bacterial and a few fungal species have been isolated which can degrade a wide range of organophosphorus compounds in liquid cultures and soil systems. The biochemistry of organophosphorus compound degradation by most of the bacteria seems to be identical, in which a structurally similar enzyme called organophosphate hydrolase or phosphotriesterase catalyzes the first step of the degradation. organophosphate hydrolase encoding gene opd (organophosphate degrading) gene has been isolated from geographically different regions and taxonomically different species. This gene has been sequenced, cloned in different organisms, and altered for better activity and stability. Recently, genes with similar function but different sequences have also been isolated and characterized. Engineered microorganisms have been tested for their ability to degrade different organophosphorus pollutants, including nerve agents. In this article, we review and propose pathways for degradation of some organophosphorus compounds by microorganisms. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are discussed. The major achievements and technological advancements towards bioremediation of organophosphorus compounds, limitations of available technologies and future challenge are also discussed.

Fate and biodegradability of sulfonated aromatic amines

Ten sulfonated aromatic amines were tested for their aerobic and anaerobic biodegradability and toxicity potential in a variety of environmental inocula. Of all the compounds tested, only two aminobenzenesulfonic acid (ABS) isomers, 2- and 4-ABS, were degraded. The observed degradation occurred only under aerobic conditions with inocula sources that were historically polluted with sulfonated aromatic amines. Bioreactor experiments, with non-sterile synthetic wastewater, confirmed the results from the aerobic batch degradation experiments. Both ABS isomers were degraded in long-term continuous experiment by a bioaugmented enrichment culture. The maximum degradation rate in the aerobic bioreactor was 1.6-1.8 g 1(-1) d(-1) for 2-ABS and a somewhat lower value for 4-ABS at hydraulic retention times (HRT) of 2.8-3.3 h. Evidence for extensive mineralization of 2- and 4-ABS was based on oxygen uptake and carbon dioxide production during the batch experiments and the high levels of chemical oxygen demand (COD) removal in the bioreactor. Furthermore, mineralization of the sulfonate group was demonstrated by high recovery of sulfate. The sulfonated aromatic amines did not show any toxic effects on the aerobic and anaerobic bacterial populations tested. The poor biodegradability of sulfonated aromatic amines indicated under the laboratory conditions of this study suggests that these compounds may not be adequately removed during biological wastewater treatment.

Biodegradation of naphthalene-2-sulfonic acid present in tannery wastewater by bacterial isolates Arthrobacter sp. 2AC and Comamonas sp. 4BC

Two bacterial strains, 2AC and 4BC, both capable of utilizing naphthalene-2-sulfonic acid (2-NSA) as a sole source of carbon, were isolated from activated sludges previously exposed to tannery wastewater. Enrichments were carried out in mineral salt medium (MSM) with 2-NSA as the sole carbon source. 16S rDNA sequencing analysis indicated that 2AC is an Arthrobacter sp. and 4BC is a Comamonas sp. Within 33 h, both isolates degraded 100% of 2-NSA in MSM and also 2-NSA in non-sterile tannery wastewater. The yield coefficient was 0.33 g biomass dry weight per gram of 2-NSA. A conceptual model, which describes the aerobic transformation of organic matter, was used for interpreting the biodegradation kinetics of 2-NSA. The half-lives for 2-NSA, at initial concentrations of 100 and 500 mg/l in MSM, ranged from 20 h (2AC) to 26 h (4BC) with lag-phases of 8 h (2AC) and 12 h (4BC). The carbon balance indicates that 75-90% of the initial TOC (total organic carbon) was mineralized, 5-20% remained as DOC (dissolved organic carbon) and 3-10% was biomass carbon. The principal metabolite of 2-NSA biodegradation (in both MSM and tannery wastewater) produced by Comamonas sp. 4BC had a MW of 174 and accounted for the residual DOC (7.0-19.0% of the initial TOC and 66% of the remaining TOC). Three to ten percent of the initial TOC (33% of the remaining TOC) was associated with biomass. The metabolite was not detected when Arthrobacter sp. 2AC was used, and a lower residual DOC and biomass carbon were recorded. This suggests that the two strains may use different catabolic pathways for 2-NSA degradation. The rapid biodegradation of 2-NSA (100 mg/l) added to non-sterile tannery wastewater (total 2-NSA, 105 mg/l) when inoculated with either Arthrobacter 2AC or Comamonas 4BC showed that both strains were able to compete with the indigenous microorganisms and degrade 2-NSA even in the presence of alternate carbon sources (DOC in tannery wastewater = 91 mg/l). The results provide information useful for the rational design of bioreactors for tannery wastewater treatment.

Biodegradation of chlorpyrifos by enterobacter strain B-14 and its use in bioremediation of contaminated soils

Six chlorpyrifos-degrading bacteria were isolated from an Australian soil and compared by biochemical and molecular methods. The isolates were indistinguishable, and one (strain B-14) was selected for further analysis. This strain showed greatest similarity to members of the order Enterobacteriales and was closest to members of the Enterobacter asburiae group. The ability of the strain to mineralize chlorpyrifos was investigated under different culture conditions, and the strain utilized chlorpyrifos as the sole source of carbon and phosphorus. Studies with ring or uniformly labeled [(14)C]chlorpyrifos in liquid culture demonstrated that the isolate hydrolyzed chlorpyrifos to diethylthiophospshate (DETP) and 3, 5, 6-trichloro-2-pyridinol, and utilized DETP for growth and energy. The isolate was found to possess mono- and diphosphatase activities along with a phosphotriesterase activity. Addition of other sources of carbon (glucose and succinate) resulted in slowing down of the initial rate of degradation of chlorpyrifos. The isolate degraded the DETP-containing organophosphates parathion, diazinon, coumaphos, and isazofos when provided as the sole source of carbon and phosphorus, but not fenamiphos, fonofos, ethoprop, and cadusafos, which have different side chains. Studies of the molecular basis of degradation suggested that the degrading ability could be polygenic and chromosome based. Further studies revealed that the strain possessed a novel phosphotriesterase enzyme system, as the gene coding for this enzyme had a different sequence from the widely studied organophosphate-degrading gene (opd). The addition of strain B-14 (10(6) cells g(-1)) to soil with a low indigenous population of chlorpyrifos-degrading bacteria treated with 35 mg of chlorpyrifos kg(-1) resulted in a higher degradation rate than was observed in noninoculated soils. These results highlight the potential of this bacterium to be used in the cleanup of contaminated pesticide waste in the environment.

First example of the chemical, oxidative cleavage of the C–P bond in aminophosphonate chemistry. The oxidation of 1-amino-1-(3,4-dihydroxyphenyl)methylphosphonic acid by NaIO4

Oxidative, chemical cleavage of the C-P bond in 1-amino-1-(3,4-dihydroxyphenyl)methylphosphonic acid upon the action of NaIO(4) have been the subject of the NMR, EPR and UV-Vis investigations in acidic and basic conditions.

Probabilistic assessment of biodegradability based on metabolic pathways: catabol system

A novel mechanistic modeling approach has been developed that assesses chemical biodegradability in a quantitative manner. It is an expert system predicting biotransformation pathway working together with a probabilistic model that calculates probabilities of the individual transformations. The expert system contains a library of hierarchically ordered individual transformations and matching substructure engine. The hierarchy in the expert system was set according to the descending order of the individual transformation probabilities. The integrated principal catabolic steps are derived from set of metabolic pathways predicted for each chemical from the training set and encompass more than one real biodegradation step to improve the speed of predictions. In the current work, we modeled O2 yield during OECD 302 C (MITI I) test. MITI-I database of 532 chemicals was used as a training set. To make biodegradability predictions, the model only needs structure of a chemical. The output is given as percentage of theoretical biological oxygen demand (BOD). The model allows for identifying potentially persistent catabolic intermediates and their molar amounts. The data in the training set agreed well with the calculated BODs (r2 = 0.90) in the entire range i.e. a good fit was observed for readily, intermediate and difficult to degrade chemicals. After introducing 60% ThOD as a cut off value the model predicted correctly 98% ready biodegradable structures and 96% not ready biodegradable structures. Crossvalidation by four times leaving 25% of data resulted in Q2 = 0.88 between observed and predicted values. Presented approach and obtained results were used to develop computer software for biodegradability prediction CATABOL.

Sulphonated aromatic pollutants. Limits of microbial degradability and potential of phytoremediation

Many synthetic sulphonated aromatic compounds are used as starting material to produce dyes and pigments, or are released as by-products in the effluents of the textile and dye industry. A large number of these chemicals are poorly biodegradable and cannot be eliminated by classical wastewater treatment plants. To limit the impact of these pollutants on the environment, new processes, based on the use of higher plants (constructed wetlands or hydroponic systems), are under development. Detergents and surfactants are essential for both industrial and domestic applications, the most important family being the alkylbenzene sulphonates. Originally, the alkyl side chains were branched and thus recalcitrant to biodegradation. Therefore, they have been replaced by linear alkylbenzene sulphonates. Although more acceptable, present formulations still have adverse environmental and toxic effects. In this context, phytoremediation appears to be a promising approach to remove these compounds from contaminated soils and waters.

Analysis of sulfophthalimide and some of its derivatives by liquid chromatography-electrospray ionization tandem mass spectrometry

A system was developed for the separation of sulfophthalimide (SPI), sulfophthalamide (SPAM), sulfophthalamic acid (SPAA) and sulfophthalic acid (SPA) by ion-pair liquid chromatography and their detection by electrospray ionization tandem mass spectrometry (ESI-MS-MS). Except for SPAM, the 3- and 4-sulfo-isomers of the analytes were separated by HPLC using volatile tributylamine as ion-pairing agent. Initial fragmentations of the analytes in the negative mode involve losses of CO2 or HNCO or condensation via H2O or NH3 elimination. ortho-Effects of the sulfonate group were recognized in the fragmentation of the respective 3-sulfo-isomers and allowed us to assign the order of elution of the SPAA isomers. Quantitative analysis of these sulfonated aromatic compounds with MRM detection was elaborated and resulted in detection limits ranging from 1 pg for SPA to 13 pg for SPAA isomers and in limits of quantification of 2-10 microg/L for 5 microL volumes of injected tap water, municipal wastewater or industrial effluents up to salt contents of 0.5-1 g/L. The method was applied to study the isomer-specific chemical and microbial transformations of SPI, which was previously shown to be formed by white-rot fungi from sulfophthalocyanine textile dyes.