Cloning and sequencing of the genes involved in glyphosate utilization by Pseudomonas pseudomallei

Wild mushrooms as potential reservoirs of plant pathogenic bacteria: a case study on Burkholderia gladioli

Fruit bodies (sporocarps) of wild mushrooms growing in natural environments play a substantial role in the preservation of microbial communities, for example, clinical and food-poisoning bacteria. However, the role of wild mushrooms as natural reservoirs of plant pathogenic bacteria remains almost entirely unknown. Furthermore, bacterial transmission from a mushroom species to agricultural plants has rarely been recorded in the literature. In September 2021, a creamy-white Gram-negative bacterial strain was isolated from the sporocarp of Suillus luteus (slippery jack) growing in Bermuda grass (Cynodon dactylon) lawn in Southern Iran. A similar strain was isolated from the same fungus in the same area in September 2022. Both strains were identified as Burkholderia gladioli based on phenotypic features as well as phylogeny of 16S rRNA and three housekeeping genes. The strains were not only pathogenic on white button mushrooms (Agaricus bisporus) but also induced hypersensitive reaction (HR) on tobacco and common bean leaves and caused soft rot on a set of diverse plant species, that is, chili pepper, common bean pod, cucumber, eggplant, garlic, gladiolus, narcissus, onion, potato, spring onion, okra, kohlrabi, mango, and watermelon. Isolation of plant pathogenic B. gladioli strains from sporocarp of S. luteus in two consecutive years in the same area could be indicative of the role of this fungus in the preservation of the bacterium in the natural environment. B. gladioli associated with naturally growing S. luteus could potentially invade neighboring agricultural crops, for example, vegetables and ornamentals. The potential role of wild mushrooms as natural reservoirs of phytopathogenic bacteria is further discussed.IMPORTANCEThe bacterial genus Burkholderia contains biologically heterogeneous strains that can be isolated from diverse habitats, that is, soil, water, diseased plant material, and clinical specimens. In this study, two Gram-negative pectinolytic bacterial strains were isolated from the sporocarps of Suillus luteus in September 2021 and 2022. Molecular phylogenetic analyses revealed that both strains belonged to the complex species Burkholderia gladioli, while the pathovar status of the strains remained undetermined. Biological investigations accomplished with pathogenicity and host range assays showed that B. gladioli strains isolated from S. luteus in two consecutive years were pathogenic on a set of diverse plant species ranging from ornamentals to both monocotyledonous and dicotyledonous vegetables. Thus, B. gladioli could be considered an infectious pathogen capable of being transmitted from wild mushrooms to annual crops. Our results raise a hypothesis that wild mushrooms could be considered as potential reservoirs for phytopathogenic B. gladioli.

The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates

Glyphosate (GS) inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that is required for aromatic amino acid, folate and quinone biosynthesis in Bacillus subtilis and Escherichia coli. The inhibition of the EPSP synthase by GS depletes the cell of these metabolites, resulting in cell death. Here, we show that like the laboratory B. subtilis strains also environmental and undomesticated isolates adapt to GS by reducing herbicide uptake. Although B. subtilis possesses a GS-insensitive EPSP synthase, the enzyme is strongly inhibited by GS in the native environment. Moreover, the B. subtilis EPSP synthase mutant was only viable in rich medium containing menaquinone, indicating that the bacteria require a catalytically efficient EPSP synthase under nutrient-poor conditions. The dependency of B. subtilis on the EPSP synthase probably limits its evolvability. In contrast, E. coli rapidly acquires GS resistance by target modification. However, the evolution of a GS-resistant EPSP synthase under non-selective growth conditions indicates that GS resistance causes fitness costs. Therefore, in both model organisms, the proper function of the EPSP synthase is critical for the cellular viability. This study also revealed that the uptake systems for folate precursors, phenylalanine and tyrosine need to be identified and characterized in B. subtilis.

Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism

Glyphosate (GS) specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that converts phosphoenolpyruvate (PEP) and shikimate-3-phosphate to EPSP in the shikimate pathway of bacteria and other organisms. The inhibition of the EPSP synthase depletes the cell of the EPSP-derived aromatic amino acids as well as of folate and quinones. A variety of mechanisms (e.g., EPSP synthase modification) has been described that confer GS resistance to bacteria. Here, we show that the Burkholderia anthina strain DSM 16086 quickly evolves GS resistance by the acquisition of mutations in the ppsR gene. ppsR codes for the pyruvate/ortho-Pi dikinase PpsR that physically interacts and regulates the activity of the PEP synthetase PpsA. The mutational inactivation of ppsR causes an increase in the cellular PEP concentration, thereby abolishing the inhibition of the EPSP synthase by GS that competes with PEP for binding to the enzyme. Since the overexpression of the Escherichia coli ppsA gene in Bacillus subtilis and E. coli did not increase GS resistance in these organisms, the mutational inactivation of the ppsR gene resulting in PpsA overactivity is a GS resistance mechanism that is probably unique to B. anthina.

Glyphosate in the environment: interactions and fate in complex soil and water settings, and (phyto) remediation strategies

Glyphosate (Gly) and its formulations are broad-spectrum herbicides globally used for pre- and post-emergent weed control. Glyphosate has been applied to terrestrial and aquatic ecosystems. Critics have claimed that Gly-treated plants have altered mineral nutrition and increased susceptibility to plant pathogens because of Gly ability to chelate divalent metal cations. Still, the complete resistance of Gly indicates that chelation of metal cations does not play a role in herbicidal efficacy or have a substantial impact on mineral nutrition. Due to its extensive and inadequate use, this herbicide has been frequently detected in soil (2 mg kg-1, European Union) and in stream water (328 µg L-1, USA), mostly in surface (7.6 µg L-1, USA) and groundwater (2.5 µg L-1, Denmark). International Agency for Research on Cancer (IARC) already classified Gly as a category 2 A carcinogen in 2016. Therefore, it is necessary to find the best degradation techniques to remediate soil and aquatic environments polluted with Gly. This review elucidates the effects of Gly on humans, soil microbiota, plants, algae, and water. This review develops deeper insight toward the advances in Gly biodegradation using microbial communities. This review provides a thorough understanding of Gly interaction with mineral elements and its limitations by interfering with the plants biochemical and morphological attributes.

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.

Insights into the microbial degradation and resistance mechanisms of glyphosate

Glyphosate, as one of the broad-spectrum herbicides for controlling annual and perennial weeds, is widely distributed in various environments and seriously threatens the safety of human beings and ecology. Glyphosate is currently degraded by abiotic and biotic methods, such as adsorption, photolysis, ozone oxidation, and microbial degradation. Of these, microbial degradation has become the most promising method to treat glyphosate because of its high efficiency and environmental protection. Microorganisms are capable of using glyphosate as a phosphorus, nitrogen, or carbon source and subsequently degrade glyphosate into harmless products by cleaving C-N and C-P bonds, in which enzymes and functional genes related to glyphosate degradation play an indispensable role. There have been many studies on the abiotic and biotic treatment technologies, microbial degradation pathways and intermediate products of glyphosate, but the related enzymes and functional genes involved in the glyphosate degradation pathways have not been further discussed. There is little information on the resistance mechanisms of bacteria and fungi to glyphosate, and previous investigations of resistance mechanisms have mainly focused on how bacteria resist glyphosate damage. Therefore, this review explores the microorganisms, enzymes and functional genes related to the microbial degradation of glyphosate and discusses the pathways of microbial degradation and the resistance mechanisms of microorganisms to glyphosate. This review is expected to provide reference for the application and improvement of the microbial degradation of glyphosate in microbial remediation.

Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil

Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.

Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution

Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia.

Role of glyphosate in the emergence of antimicrobial resistance in bacteria?

There is a discrepancy between antibiotic use in medicine and agriculture in the intertropical zone and frequency of antibiotic resistance in clinical bacteria in these countries. We provide evidence that glyphosate (a herbicide but also an antibiotic drug) could be a possible driver of antibiotic resistance in countries where this herbicide is widely used because of modification of the microbial environment. Emergence of resistance in bacteria and fungi is correlated with glyphosate use in the world over the last 40 years.

Molecular mechanisms underlying glyphosate resistance in bacteria

Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.

Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies

Widespread application of glyphosate poses a threat to living organisms. Microbial strains are able to degrade glyphosate via contrasting metabolic pathways with the help of enzymes. Glyphosate oxidoreductase (GOX) and C-P lyase are the key enzymes for the biodegradation of glyphosate and its intermediate metabolite aminomethylphosphonic acid (AMPA) in microbes. The microbial degradation of glyphosate has been reported, but the underlying molecular mechanism is still unclear. Therefore, in this study, the interaction mechanism of GOX and C-P lyase with glyphosate and AMPA were investigated by using molecular docking and molecular dynamics (MD) simulations. The results indicate that glyphosate contacts with the active site of GOX and C-P lyase by hydrogen bonds as well as hydrophobic and van der Waals interactions in aqueous solution to maintain its stability. The presence of glyphosate and AMPA in the active site significantly changes the conformation of GOX and C-P lyase. The results of the MD simulations confirm that GOX and C-P lyase complexes are stable during the catalytic reaction. This study offers a molecular level of understanding of the expression and function of GOX and C-P lyase for the bioremediation of glyphosate.

Treatment technologies and degradation pathways of glyphosate: A critical review

Glyphosate is one of the most widely used post-emergence broad-spectrum herbicides in the world. This molecule has been frequently detected in aqueous environment and can cause adverse effects to plants, animals, microorganisms, and humans. This review offers a comparative assessment of current treatment methods (physical, biological, and advanced oxidation process) for glyphosate wastewaters, considering their advantages and drawbacks. As for other molecules, adsorption does not destroy glyphosate. It can be used before other processes, if glyphosate concentrations are very high, or after, to decrease the final concentration of glyphosate and its by-products. Most of biological and oxidation processes can destroy glyphosate molecules, leading to by-products (the main ones being AMAP and sarcosine) that can be or not affected by these processes. This point is of major importance to control process efficiency. That is the reason why a specific focus on glyphosate degradation pathways by biological treatment or different advanced oxidation processes is proposed. However, one process is usually not efficient enough to reach the required standards. Therefore, the combination of processes (for instance biological and oxidation ones) seems to be high-performance technologies for the treatment of glyphosate-containing wastewater, due to their potential to overcome some drawbacks of each individual process. Finally, this review provides indications for future work for different treatment processes to increase their performances and gives some insights into the treatment of glyphosate or other organic contaminants in wastewater.

Herbicide Glyphosate: Toxicity and Microbial Degradation

Glyphosate is a non-specific organophosphate pesticide, which finds widespread application in shielding crops against the weeds. Its high solubility in hydrophilic solvents, especially water and high mobility allows the rapid leaching of the glyphosate into the soil leading to contamination of groundwater and accumulation into the plant tissues, therefore intricating the elimination of the herbicides. Despite the widespread application, only a few percentages of the total applied glyphosate serve the actual purpose, dispensing the rest in the environment, thus resulting in reduced crop yields, low quality agricultural products, deteriorating soil fertility, contributing to water pollution, and consequently threatening human and animal life. This review gives an insight into the toxicological effects of the herbicide glyphosate and current approaches to track and identify trace amounts of this agrochemical along with its biodegradability and possible remediating strategies. Efforts have also been made to summarize the biodegradation mechanisms and catabolic enzymes involved in glyphosate metabolism.

Bacillus aryabhattai FACU: A promising bacterial strain capable of manipulate the glyphosate herbicide residues

Glyphosate is a commonly used organophosphate herbicide that has an adverse impact on humans, mammals and soil microbial ecosystems. The redundant utilize of glyphosate to control weed growth cause the pollution of the soil environment by this chemical. The discharge of glyphosate in the agricultural drainage can also cause serious environmental damage and water pollution problems. Therefore, it is important to develop methods for enhancing glyphosate degradation in the soil through bioremediation. In this study, thirty bacterial isolates were selected from an agro-industrial zone located in Sadat City of Monufia Governorate, Egypt. The isolates were able to grow in LB medium supplemented with 7.2 mg/ml glyphosate. Ten isolates only had the ability to grow in a medium containing different concentrations of glyphosate (50, 100, 150, 200 and 250 mg/ml). The FACU3 bacterial isolate showed the highest CFU in the different concentrations of glyphosate. The FACU3 isolate was Gram-positive, spore-forming and rod-shape bacteria. Based on API 50 CHB/E medium kit, biochemical properties and 16S rRNA gene sequencing, the FACU3 isolate was identified as Bacillus aryabhattai. Different bioinformatics tools, including multiple sequence alignment (MSA), basic local alignment search tool (BLAST) and primer alignment, were used to design specific primers for goxB gene amplification and isolation. The goxB gene encodes FAD-dependent glyphosate oxidase enzyme that responsible for biodegradation process. The selected primers were successfully used to amplify the goxB gene from Bacillus aryabhattai FACU3. The results indicated that the Bacillus aryabhattai FACU3 can be utilized in glyphosate-contaminated environments for bioremediation. According to our knowledge, this is the first time to isolate of FAD-dependent glyphosate oxidase (goxB) gene from Bacillus aryabhattai.

Comparison of three Agrobacterium-mediated co-transformation methods for generating marker-free transgenic Brassica napus plants

BACKGROUND

Generation of marker-free transgenic plants is very important to the regulatory permission and commercial release of transgenic crops. Co-transformation methods that enable the removal of selectable marker genes have been extensively used because they are simple and clean. Few comparisons are currently available between different strain/plasmid co-transformation systems, and also data are related to variation in co-transformation frequencies caused by other details of the vector design.

RESULTS

In this study, we constructed three vector systems for the co-transformation of allotetraploid Brassica napus (B. napus) mediated by Agrobacterium tumefaciens and compared these co-transformation methods. We tested a mixed-strain system, in which a single T-DNA is harbored in two plasmids, as well as two "double T-DNA" vector systems, in which two independent T-DNAs are harbored in one plasmid in a tandem orientation or in an inverted orientation. As confirmed by the use of PCR analysis, test strips, and Southern blot, the average co-transformation frequencies from these systems ranged from 24 to 81% in T₀ plants, with the highest frequency of 81% for 1:1 treatment of the mixed-strain system. These vector systems are valuable for generating marker-free transgenic B. napus plants, and marker-free plants were successfully obtained in the T₁ generation from 50 to 77% of T₀ transgenic lines using these systems, with the highest frequency of 77% for "double T-DNA" vector systems of pBID RT Enhanced. We further found that marker-free B. napus plants were more frequently encountered in the progeny of transgenic lines which has only one or two marker gene copies in the T₀ generation. Two types of herbicide resistant transgenic B. napus plants, Bar ⁺ with phosphinothricin resistance and Bar ⁺ EPSPS ⁺ GOX ⁺ with phosphinothricin and glyphosate resistance, were obtained.

CONCLUSION

We were successful in removing selectable marker genes in transgenic B. napus plants using all three co-transformation systems developed in this study. It was proved that if a appropriate mole ratio was designed for the specific length ratio of the twin T-DNAs for the mixed-strain method, high unlinked co-insertion frequency and overall success frequency could be achieved. Our study provides useful information for the construction of efficient co-transformation system for marker-free transgenic crop production and developed transgenic B. napus with various types of herbicide resistance.

Carbon-Phosphorus Lyase-the State of the Art

Organophosphonates are molecules that contain a very chemically stable carbon-phosphorus (C-P) bond. Microorganisms can utilize phosphonates as potential source of crucial elements for their growth, as developed several pathways to metabolize these compounds. One among these pathways is catalyzed by C-P lyase complex, which has a broad substrate specifity; therefore, it has a wide application in degradation of herbicides deposited in the environment, such as glyphosate. This multi-enzyme system accurately recognized in Escherichia coli and genetic studies have demonstrated that it is encoded by phn operon containing 14 genes (phnC-phnP). The phn operon is a member of the Pho regulon induced by phosphate starvation. Ability to degradation of phosphonates is also found in other microorganisms, especially soil and marine bacteria, that have homologous genes to those in E. coli. Despite the existence of differences in structure and composition of phn gene cluster, each of these strains contains phnGHIJKLM genes necessary in the C-P bond cleavage mechanism. The review provides a detailed description and summary of achievements on the C-P lyase enzymatic pathway over the last 50 years.

Mitigation of environmental pollution by genetically engineered bacteria - Current challenges and future perspectives

Industries are the paramount driving force for the economic and technological development of society. However, the flourishing industrialization and unimpeded growth of current production unit's result in widespread environmental pollution due to increased discharge of wastes loaded with baleful, hazardous, and carcinogenic contaminants. Physicochemical-based remediation means are costly, create a secondary disposal problem and remain inadequate for pollution mitigating because of the continuous emergence of new recalcitrant pollutants. Due to eco-friendly, social acceptance, and lesser health hazards, microbial bioremediation has received considerable global attention for pollution abatement. Moreover, with the recent advancement in biotechnology and microbiology, genetically engineered bacteria with high ability to remove environmental pollutants are widely used in the fields of environmental restoration, resulting in the bioremediation in a more viable and eco-friendly way. This review summarized the advantages of genetically engineered bacteria and their application in the treatment of a wide variety of environmental contaminants such as synthetic dyestuff, heavy metal, petroleum hydrocarbons, polychlorinated biphenyls, phenazines and agricultural chemicals which will include herbicides, pesticides, and fertilizers. Considering the risk of genetic material exchange by using genetically engineered bacteria, the challenges and limitations associated with the application of recombinant bacteria on contaminated sites are also discussed. An integrated microbiological, biological and ecological acquaintance accompanied by field engineering designs are the desired features for effective in situ bioremediation of hazardous waste polluted sites by recombinant bacteria.

Identification of the first glyphosate transporter by genomic adaptation

The soil bacterium Bacillus subtilis can get into contact with growth-inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high-affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.

Recent advances in glyphosate biodegradation

Glyphosate has emerged as the most widespread herbicide to control annual and perennial weeds. Massive use of glyphosate for decades has resulted in its ubiquitous presence in the environment, and poses a threat to humans and ecosystem. Different approaches such as adsorption, photocatalytic degradation, and microbial degradation have been studied to break down glyphosate in the environment. Among these, microbial degradation is the most effective and eco-friendly method. During its degradation, various microorganisms can use glyphosate as a sole source of phosphorus, carbon, and nitrogen. Major glyphosate degradation pathways and its metabolites have been frequently investigated, but the related enzymes and genes have been rarely studied. There are many reviews about the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid. However, there is lack of reviews on biodegradation and bioremediation of glyphosate. The aims of this review are to summarize the microbial degradation of glyphosate and discuss the potential of glyphosate-degrading microorganisms to bioremediate glyphosate-contaminated environments. This review will provide an instructive direction to apply glyphosate-degrading microorganisms in the environment for bioremediation.

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.

Organophosphonates utilization by soil strains of Ochrobactrum anthropi and Achromobacter sp

Four bacterial strains from glyphosate- or alkylphosphonates-contaminated soils were tested for ability to utilize different organophosphonates. All studied strains readily utilized methylphosphonic acid and a number of other phosphonates, but differed in their ability to degrade glyphosate. Only strains Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16 utilized this compound after isolation from enrichment cultures with glyphosate. Achromobacter sp. MPK 7 from the same enrichment culture, similar to Achromobacter sp. MPS 12 from methylphosphonate-polluted source, required adaptation to growth on GP. Studied strains varied significantly in their growth parameters, efficiency of phosphonates degradation and characteristic products of this process, as well as in their energy metabolism. These differences give grounds to propose a possible model of interaction between these strains in microbial consortium in phosphonate-contaminated soils.

Bioremediation potential of glyphosate-degrading Pseudomonas spp. strains isolated from contaminated soil

Bacterial strains capable of utilizing glyphosate as the sole carbon source were isolated from contaminated soil by the enrichment culture method and identified based on partial 16S rRNA gene sequence analysis. Pseudomonas spp. strains GA07, GA09 and GC04 demonstrated the best degradation capabilities towards glyphosate and were used for the laboratory experiments of glyphosate bioremediation. Inoculating glyphosate-treated soil samples with these three strains resulted in a 2-3 times higher rate of glyphosate removal than that in non-inoculated soil. The degradation kinetics was found to follow a first-order model with regression values greater than 0.96. Cell numbers of the introduced bacteria decreased from 4.4 × 10(6) CFU/g to 3.4-6.7 × 10(5) CFU/g dry soil within 18 days of inoculation. Due to the intense degradation of glyphosate, the total dehydrogenase activity of the soil microbial community increased by 21.2-25.6%. Analysis of glyphosate degradation products in cell-free extracts showed that glyphosate breakdown in strain GA09 was catalyzed both by C-P lyase and glyphosate oxidoreductase. Strains GA07 and GC04 degraded glyphosate only via glyphosate oxidoreductase, but no further metabolite was detected. These results highlight the potential of the isolated bacteria to be used in the bioremediation of GP-contaminated soils.

Influence of glyphosate in planktonic and biofilm growth of Pseudomonas aeruginosa

This study evaluated the impact of different concentrations of glyphosate (Rondup(®)) on planktonic and biofilm growth of P. aeruginosa. Aerobic and anaerobic cultures of P. aeruginosa ATCC(®)15442 inoculated in MHB + glyphosate (0.845 ppm, 1.690 ppm, 8.45 ppm, 16.90 ppm, 84.50 ppm, 169 ppm, 845 ppm, and 1690 ppm) and cultured in normoxia and anoxia, following their OD(560nm) every hour for 24 h. Biofilms of adapted cells were formed in the presence of glyphosate (0.845 to 1690 ppm) in normoxia and anoxia for 36 h. Glyphosate at concentrations higher than 84.5 ppm reduces the cell density of planktonic aerobic cultures (p < 0.05). However, these same concentrations favor the planktonic anaerobic growth (p < 0.05). On the other hand, the herbicide favors a slight growth of biofilms in a concentration-dependent manner up to 84.5 ppm (p > 0.05), and more pronounced over 169 ppm. Anaerobic biofilms have their growth more readily favored (p < 0.05), regardless of concentration. In a concentration-dependent manner, glyphosate interferes with the growth ability of P. aeruginosa ATCC(®)15442.

Microbial degradation of herbicides

Herbicides remain the most effective, efficient and economical way to control weeds; and its market continues to grow even with the plethora of generic products. With the development of herbicide-tolerant crops, use of herbicides is increasing around the world that has resulted in severe contamination of the environment. The strategies are now being developed to clean these substances in an economical and eco-friendly manner. In this review, an attempt has been made to pool all the available literature on the biodegradation of key herbicides, clodinafop propargyl, 2,4-dichlorophenoxyacetic acid, atrazine, metolachlor, diuron, glyphosate, imazapyr, pendimethalin and paraquat under the following objectives: (1) to highlight the general characteristic and mode of action, (2) to enlist toxicity in animals, (3) to pool microorganisms capable of degrading herbicides, (4) to discuss the assessment of herbicides degradation by efficient microbes, (5) to highlight biodegradation pathways, (6) to discuss the molecular basis of degradation, (7) to enlist the products of herbicides under degradation process, (8) to highlight the factors effecting biodegradation of herbicides and (9) to discuss the future aspects of herbicides degradation. This review may be useful in developing safer and economic microbiological methods for cleanup of soil and water contaminated with such compounds.

Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase

After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses.

Identification of regulated genes conferring resistance to high concentrations of glyphosate in a new strain of Enterobacter

Glyphosate is a widely used herbicide that inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity. Most plants and microbes are sensitive to glyphosate. However, transgenic-resistant crops that contain a modified epsps obtained from the resistant microbes have been commercially successful and therefore, new resistance genes and their adaptive regulatory mechanisms are of great interest. In this study, a soil-borne, glyphosate-resistant bacterium was selected and identified as Enterobacter. The EPSPS in this strain was found to have been altered to a resistant one. A total of 42 differentially expressed genes (DEGs) in the glyphosate were screened using microarray techniques. Under treatment, argF, sdhA, ivbL, rrfA-H were downregulated, whereas the transcripts of speA, osmY, pflB, ahpC, fusA, deoA, uxaC, rpoD and a few ribosomal protein genes were upregulated. Data were verified by quantitative real-time PCR on selected genes. All transcriptional changes appeared to protect the bacteria from glyphosate and associated osmotic, acidic and oxidative stresses. Many DEGs may have the potential to confer resistance to glyphosate alone, and some may be closely related to the shikimate pathway, reflecting the complex gene interaction network for glyphosate resistance.

Isolation, identification and characterization of a glyphosate-degrading bacterium, Bacillus cereus CB4, from soil

A bacterial strain named CB4, with highly effective glyphosate degradation capability, was isolated from soil after enrichment. On the basis of the Biolog omniLog identification system (Biolog) and 16S ribosomal RNA (rRNA) gene sequencing methods, strain CB4 was identified as Bacillus cereus. Further experiments were carried out to optimize the growth of strain CB4 and the glyphosate degradation activity by high performance liquid chromatography (HPLC). The optimal conditions were found as follows: initial pH 6.0, incubation temperature 35°C, glyphosate concentration 6 g L(-1), inoculation amount 5% and incubation time 5 days. Under the optimal conditions, stain CB4 utilized 94.47% of glyphosate. This is the first report on B. cereus with a capacity to utilize herbicide glyphosate, and it can degrade glyphosate concentrations up to 12 g L(-1). Metabolization of glyphosate by strain B. cereus CB4 was studied. Results indicated that two concurrent pathways were capable of degrading glyphosate to AMPA, glyoxylate, sarcosine, glycine and formaldehyde as products. Glyphosate breakdown in B. cereus CB4 was achieved by the C-P lyase activity and the glyphosate oxidoreductase activity.

Glyphosate resistance as a novel select-agent-compliant, non-antibiotic-selectable marker in chromosomal mutagenesis of the essential genes asd and dapB of Burkholderia pseudomallei

Genetic manipulation of the category B select agents Burkholderia pseudomallei and Burkholderia mallei has been stifled due to the lack of compliant selectable markers. Hence, there is a need for additional select-agent-compliant selectable markers. We engineered a selectable marker based on the gat gene (encoding glyphosate acetyltransferase), which confers resistance to the common herbicide glyphosate (GS). To show the ability of GS to inhibit bacterial growth, we determined the effective concentrations of GS against Escherichia coli and several Burkholderia species. Plasmids based on gat, flanked by unique flip recombination target (FRT) sequences, were constructed for allelic-replacement. Both allelic-replacement approaches, one using the counterselectable marker pheS and the gat-FRT cassette and one using the DNA incubation method with the gat-FRT cassette, were successfully utilized to create deletions in the asd and dapB genes of wild-type B. pseudomallei strains. The asd and dapB genes encode an aspartate-semialdehyde dehydrogenase (BPSS1704, chromosome 2) and dihydrodipicolinate reductase (BPSL2941, chromosome 1), respectively. Mutants unable to grow on media without diaminopimelate (DAP) and other amino acids of this pathway were PCR verified. These mutants displayed cellular morphologies consistent with the inability to cross-link peptidoglycan in the absence of DAP. The B. pseudomallei 1026b Deltaasd::gat-FRT mutant was complemented with the B. pseudomallei asd gene on a site-specific transposon, mini-Tn7-bar, by selecting for the bar gene (encoding bialaphos/PPT resistance) with PPT. We conclude that the gat gene is one of very few appropriate, effective, and beneficial compliant markers available for Burkholderia select-agent species. Together with the bar gene, the gat cassette will facilitate various genetic manipulations of Burkholderia select-agent species.

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.

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.

Identification and specific detection of a novel pseudomonadaceae cluster associated with soils from winter wheat plots of a long-term agricultural field experiment

The genus Pseudomonas (sensu stricto) represents a group of microorganisms directly involved in functions conferring plant health. We performed a study in the DOK long-term agricultural field experiment on the basis of previously published Pseudomonas-selective PCR primers in order to investigate the community structure of the microbial groups defined by the target range of these primers. Three different agricultural management systems, i.e., conventional, biodynamic, and bio-organic, along with mineral and unfertilized controls were investigated, with each system planted with either winter wheat or a grass-clover ley. Amplified small-subunit rRNA gene fragments were analyzed using the genetic profiling techniques restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE), revealing distinct differences between soils planted with winter wheat and grass clover but only minor differences between the management systems. Phylogenetic analyses of 59 clone sequences retrieved from bio-organic and unfertilized systems identified sequences related to Pseudomonas fluorescens and a novel cluster termed Cellvibrio-related Pseudomonadaceae (CRP). The CRP clones were exclusively isolated from winter wheat soil samples and were responsible for the crop-specific differences observed in RFLP and DGGE profiles. New primers were designed for the amplification of CRP targets directly from soil DNA, yielding strong signals exclusively for winter wheat soils. We concluded that crop-associated CRP exist in agricultural soils and that genetic profiling followed by specific probe design represents a valuable approach for identification as well as sensitive and rapid monitoring of novel microbial groups in the environment.

Molecular ecotoxicology of plants

Plant molecular exotoxicology investigates ecological implications of genetic and molecular responses to toxins, herbicides, pollutants and natural stress factors. Plant fitness is analysed by examining the relationships between plant genotype and ecological phenotype, enabling regulatory networks formed by second messenger molecules and transcriptional as well as post-transcriptional events to be elucidated. This general approach is illustrated here by specific case studies: detoxification by glucosyl transfer or binding to cell wall macromolecules; roles of the multifunctional formaldehyde dehydrogenase; and abiotic induction of plant immunity through reactive oxygen species. As a practical application of molecular ecotoxicology, the interaction of commercialized transgenic crop plants with potential environmental selection factors is discussed.

The effect of quicklime (calcium oxide) as an inhibitor of Burkholderia pseudomallei

Measurement of in vitro activity of quicklime against Burkholderia pseudomallei revealed that quicklime at concentrations of 10% or more was bactericidal for up to 35 d. The effect of quicklime as an inhibitor of B. pseudomallei in soil from a rice field was studied in a laboratory setting. The soil, collected from a rice field in north-eastern Thailand, was mixed with B. pseudomallei. In experiment 1, quicklime was mixed with the soil in different amounts. In experiment 2, quicklime was spread over the soil surface. In experiment 3, quicklime solution was poured onto the soil. It was found that the pH of the soil in experiment 1 was much higher than that in experiments 2 and 3. Only quicklime mixed with soil at a concentration of 40% or more (weight/weight) was effective in inhibiting the growth of B. pseudomallei for up to six weeks.

Ecology of Burkholderia pseudomallei and the interactions between environmental Burkholderia spp. and human-animal hosts

Early workers thought that melioidosis was a zoonosis with a reservoir in rodents, but we now know that Burkholderia pseudomallei is a widely distributed environmental saprophyte. In northeast Thailand, two thirds of paddy fields yield the organism, and 80% of children have antibodies by the time they are 4 years old. However, interpretation of these results has been complicated by the recent recognition of avirulent, antigenically cross-reacting environmental organisms for which the name B. thailandensis has been proposed. We still know very little about the climatic, physical, chemical and biological factors which control the proliferation and survival of Burkholderia spp. in the environment, although epidemiological studies show space-time clustering of melioidosis. It is assumed that most human and animal melioidosis arises through exposure to contaminated soil or muddy water, although only 6% of human cases have a clear history of inoculation, and a further 0.5% of cases follow near-drowning. Laboratory animals have also been infected by ingestion, inhalation and insect bites, but evidence of infection acquired naturally by these routes remains anecdotal. Sporadic cases have resulted from iatrogenic inoculation, laboratory accidents, and person-to-person or animal-to-person spread. Whether exposure to B. pseudomallei will result in disease probably depends on the balance between the virulence of the strain, the immune status of the host (e.g. diabetes mellitus) and the size of the inoculum.

Multiple replicons constitute the 6.5-megabase genome of Burkholderia pseudomallei

Burkholderia pseudomallei is a causative agent of melioidosis, a fatal tropical infectious disease endemic in Southeast Asia and Northern Australia. In order to determine the size and characteristics of the bacterial genome, the B. pseudomallei genome and genes were analyzed by pulsed field gel electrophoresis of the undigested, intact megabase DNA, and by computational analysis of nucleotide sequences of B. pseudomallei genes which have been sequenced by several investigators and already deposited in a public database. The results showed that the B. pseudomallei genome consists of two large replicons, and that both contain ribosomal RNA gene sequences, indicating the presence of two chromosomes. The classical arabinose-negative B. pseudomallei isolate K96243 has chromosomes of approximately 3563 +/- 73 and 2974 +/- 40 kilobase-pairs in size, giving a total genome size of about 6.5 million base-pairs. The arabinose-positive nonvirulent biotype of B. pseudomallei also has two replicons which are smaller than those of the arabinose-negative biotype. Analysis of the publicly-available nucleotide sequences showed that the average B. pseudomallei gene is approximately 1031 base-pairs in size, with an average G + C content of 65.7%. The genome is gene-rich and about 89% of the coding capacity is used as coding sequences. It can therefore be estimated that the entire B. pseudomallei genome encodes about 5600 genes.

Melioidosis as an emerging global problem

There is remarkably little known about the incidence of melioidosis outside a few countries (Thailand, Australia, Singapore and Malaysia). Presumably it is widespread in tropical south east Asia. Elsewhere there are tantalising glimpses of the tip of what may be a large iceberg. Since a specific diagnosis of melioidosis requires awareness on the part of clinicians, and the existence of a laboratory capable of isolating and identifying Burkholderia pseudomallei, a luxury not available in most rural tropical areas, the size of this iceberg is likely to remain unknown for the foreseeable future. There is mounting evidence that the disease is endemic in the Indian sub-continent and the Caribbean, and there have been unsubstantiated reports of recent cases in South Africa and the Middle East. It is unclear whether melioidosis has really spread to such areas relatively recently, or has been there but unrecognised for a long time. Almost all cases diagnosed in temperate climates have been imported from the tropics, with the exception of a unique outbreak which occurred in France in the mid-1970s. With increasing world wide travel of both humans and other animals, the potential exists for melioidosis to spread to new and fertile pastures.

Aminoglycoside-modifying enzymes

Bacterial resistance to the aminoglycoside antibiotics is most frequently associated with the expression of modifying enzymes that can phosphorylate, adenylate or acetylate these compounds. The recent availability of representative crystal structures for all three classes of modifying enzymes has greatly expanded our knowledge of enzyme function, and has revealed unexpected and exciting connections to other families of enzymes. Furthermore, the complete genome sequences for several bacteria have revealed many potential aminoglycoside-resistance elements.