Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity

Unleashing potential of Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 for chlorpyrifos biodegradation by genome analysis and kinetic studies

Chlorpyrifos (CP) is an extensively used organophosphate (OP) pesticide that inhibits the biogeochemical cycle with subsequent loss of soil fertility. In this view, indigenous soil bacteria with significant CP degradation capacity were identified as Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 through 16 S rRNA. The optimum values of independent variables for CP degradation were found to be 30 ℃, pH 7, 100 mgL-1 of CP, and 1 OD600 cell culture. RNC3 and RNC7 showed 82.5 mgL-1 and 77.1 mgL-1 CP degradation within 5 days. A Michaelis-Menten kinetic model estimated the degradation rate (Vmax) and substrate binding affinity (Ks) for RNC3 were 1.23 mgL-1h-1 and 123 mgL-1 whereas for RNC7 as 1.19 mgL-1h -1 and 124.3 mgL-1, respectively. The major metabolites 3,5,6-trichloro-2-pyridinol (TCP) and 2-hydroxy pyridine were identified during CP degradation by RNC3 whereas, only TCP by RNC7 using GC-MS. Key enzymes encoded by opd and opch2 genes were annotated in the genomes of RNC3 and RNC7 along with the set of putative degradation genes (tcp, yieH, pho, prp). Protein-ligand docking between OPCH2 and CP found - 7.9 kcal mol -1 as a high binding affinity with the conserved catalytic triad (Ser155-Asp251-His281) in the active site. The study suggests that RNC3 can completely mineralize CP, whereas both strains have shown robust degradation ability of OP group of pesticides. The potential of rapid acclimatization to natural soil environment and non-virulent nature of the selected strains are beneficial for in situ application. Thus, selected indigenous strains can be applied for the bioremediation of OP-contaminated soil.

Pesticide-tolerant microbial consortia: Potential candidates for remediation/clean-up of pesticide-contaminated agricultural soil

Reclamation of pesticide-polluted lands has long been a difficult endeavour. The use of synthetic pesticides could not be restricted due to rising agricultural demand. Pesticide toxicity has become a pressing agronomic problem due to its adverse impact on agroecosystems, agricultural output, and consequently food security and safety. Among different techniques used for the reclamation of pesticide-polluted sites, microbial bioremediation is an eco-friendly approach, which focuses on the application of resilient plant growth promoting rhizobacteria (PGPR) that may transform or degrade chemical pesticides to innocuous forms. Such pesticide-resilient PGPR has demonstrated favourable effects on soil-plant systems, even in pesticide-contaminated environments, by degrading pesticides, providing macro-and micronutrients, and secreting active but variable secondary metabolites like-phytohormones, siderophores, ACC deaminase, etc. This review critically aims to advance mechanistic understanding related to the reduction of phytotoxicity of pesticides via the use of microbe-mediated remediation techniques leading to crop optimization in pesticide-stressed soils. The literature surveyed and data presented herein are extremely useful, offering agronomists-and crop protectionists microbes-assisted remedial strategies for affordably enhancing crop productivity in pesticide-stressed soils.

Functional Characterization and Structural Modeling of a Novel Glycine Oxidase from Variovorax paradoxus Iso1

The N-acyl-d-amino acid amidohydrolase (N-d-AAase) of Variovorax paradoxus Iso1 can enantioselectively catalyze the zinc-assisted deacetylation of N-acyl-d-amino acids to yield consistent d-amino acids. A putative FAD-binding glycine/d-amino acid oxidase was located immediately upstream of the N-d-AAase gene. The gene encoding this protein was cloned into Escherichia coli BL21 (DE3)pLysS and overexpressed at 25°C for 6 h with 0.5 mM isopropyl β-d-1-thiogalactopyranoside induction. After purification, the tag-free recombinant protein was obtained. The enzyme could metabolize glycine, sarcosine, and d-alanine, but not l-amino acids or bulky d-amino acids. Protein modeling further supported these results, demonstrating that glycine, sarcosine, and d-alanine could fit into the pocket of the enzyme's activation site, while l-alanine and d-threonine were out of position. Therefore, this protein was proposed as a glycine oxidase, and we designated it VpGO. Interestingly, VpGO showed low sequence similarity to other well-characterized glycine oxidases. We found that VpGO and N-d-AAase were expressed on the same mRNA and could be transcriptionally induced by various N-acetyl-d-amino acids. Western blotting and zymography showed that both proteins had similar expression patterns in response to different types of inducers. Thus, we have identified a novel glycine oxidase that is co-regulated with N-d-AAase in an operon, and metabolizes N-acyl-d-amino acids in the metabolically versatile V. paradoxus Iso1. IMPORTANCE The Gram-negative bacterium Variovorax paradoxus has numerous metabolic capabilities, including the association with important catabolic processes and the promotion of plant growth. We had previously identified and characterized an N-acyl-d-amino-acid amidohydrolase (N-d-AAase) gene from the strain of V. paradoxus Iso1. The aim of this study was to isolate and characterize (both in vitro and in vivo) another potential gene found in the promoter region of this N-d-AAase gene. The protein was identified as a glycine oxidase, and the gene existed in an operon with N-d-AAase. The structural basis for its FAD-binding potential and substrate stereo-specificity were also elucidated. This study first reported a novel glycine oxidase from V. paradoxus. We believe that our study makes a significant contribution to the literature, because this enzyme has great potential for use as an industrial catalysis, as a biosensor, and in agricultural biotechnology.

Isolation and characterization of cyromazine degrading Acinetobacter sp. ZX01 from a Chinese ginger cultivated soil

Cyromazine, a symmetrical triazine insecticide, is used to control dipteran larvae in chicken manure by feeding to the poultry, flies on animals, and leafminers in vegetables. Its extensive use has resulted in the widespread contamination in the environment. In the current study, a cyromazine degrading bacterium (designated strain ZX01) was isolated and characterized from a Chinese ginger cultivated soil by selective enrichment culture method. On the basis of morphological, biochemical characteristics, and 16S rRNA gene sequence, this bacterium showed strong similarity to the Pseudomonadales members and was closely related to the Acinetobacter baumannii group. Spectrophotometric and HPLC analyses revealed that strain ZX01 degraded cyromazine and utilized it as the sole carbon source for its growth. This process hydrolyzes cyromazine to melamine. Strain ZX01 degraded most of the cyromazine in 60 h. Besides, its substrate specificity against four symmetrical triazine herbicides, one triazinone herbicide, as well as 10 insecticides and its antibiotic sensitivity towards eight commercial antibiotics were also tested. At the concentration of 100 µg/mL for 60 h, it could effectively degrade a variety of different pesticides, including atrazine, prometon, simazine, prometryn, enitrothion, diazinon, cypermethrin, and acetamiprid, and the degradation was in the range of 71-87%. In particular, melamine, the main degradation product of cyromazine, was degraded by 47.3%. This microorganism was sensitive to chloramphenicol and tetracycline and intermediate to amoxicillin and trimethoprim. These results highlight that strain ZX01 can be used as a potential biological agent for the remediation of soil, water, or crop contaminated with cyromazine and other symmetrical triazine insecticides.

Microbiomes and glyphosate biodegradation in edaphic and aquatic environments: recent issues and trends

Glyphosate (N-(phosphonomethyl)glycine) has emerged as the top-selling herbicide worldwide because of its versatility in controlling annual and perennial weeds and the extensive use of glyphosate-resistant crops. Concerns related to the widespread use of glyphosate and its ubiquitous presence in the environment has led to a large number of studies and reviews, which examined the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid (AMPA) in the environment. Because the biological breakdown of glyphosate is most likely the main elimination process, the biodegradation of glyphosate has also been the object of abundant experimental work. Importantly, glyphosate biodegradation in aquatic and soil ecosystems is affected not only by the composition and the activity of microbial communities, but also by the physical environment. However, the interplay between microbiomes and glyphosate biodegradation in edaphic and aquatic environments has rarely been considered before. The proposed minireview aims at filling this gap. We summarize the most recent work exploring glyphosate biodegradation in natural aquatic biofilms, the biological, chemical and physical factors and processes playing on the adsorption, transport and biodegradation of glyphosate at different levels of soil organization and under different agricultural managements, and its impact on soil microbial communities.

An Enzyme-Based Biosensor for the Detection of Organophosphate Compounds Using Mutant Phosphotriesterase Immobilized onto Reduced Graphene Oxide

Enzymatic detection of organophosphate (OP) compounds can be tailored using highly sensitive and selective enzymes in the development of biosensors. Previously, mutant (YT) phosphotriesterase (PTE) was reported to efficiently hydrolyze Sp and Rp enantiomers of phosphotriester. This study reports the use of phosphotriesterase mutant YT (YT-PTE) immobilized onto reduced graphene oxide (rGO) and fabricated onto a screen-printed carbon electrode (SPCE) for electrochemical detection of OP compounds. Immobilization of YT-PTE onto rGO was secured using N-hydroxysuccinimide (NHS) and N-(3-dimethylaminopropyl)-N’-ethylcarbodiimide (EDC) cross-linker, and the resulting immobilized enzyme was able to retain up to 90% of its activity. Electrochemical analysis of the SPCE/rGO/YT-PTE showed detection of paraoxon in a linear range of 1 mM–0.005 μM with its limit of detection as low as 0.11 μM. SPCE/rGO/YT-PTE exhibited high selectivity towards paraoxon and parathion and have good reproducibility. Furthermore, detection of paraoxon was also possible in a real water sample with only minor interferences.

Bacterial isolates from Argentine Pampas and their ability to degrade glyphosate

Glyphosate is a synthetic phosphonate compound characterized by a carbon‑phosphorus bond. Glyphosate based herbicides (GBH) are widely distributed in most of the economically productive lands in which crop production is mainly based on glyphosate-resistant genetically modified plants. Naturally, glyphosate is remediated by soil microorganisms, which accelerate its degradation. Technology based on microorganisms is considered highly efficient, low-cost and eco-friendly to remediate contaminated environments, denoting the importance of characterizing new bacterial strains able to degrade glyphosate to perform its bioremediation. In this work, 13 different bacterial strains able to grow in GBH as only phosphorous source were isolated from different environmental samples from the Argentine vastly productive glyphosate-resistant soybean crop area. These strains were identified and they belong to the genera Acinetobacter, Achromobacter, Agrobacterium, Ochrobactrum, Pantoea and Pseudomonas. Their ability to grow and consume GBH, glyphosate or the aminomethylphosphonic acid (AMPA), another phosphonate derived from glyphosate degradation, was evaluated. The best degradation performance was observed for bacteria from the genera Achromobacter, Agrobacterium and Ochrobactrum. The genome of the highly efficient GBH degrader Agrobacterium tumefaciens CHLDO was sequenced revealing the presence of a phn cluster, responsible for phosphonate metabolization. Expression analysis of A. tumefaciens CHLDO phn genes in the presence of 1.5 mM GBH compared to inorganic phosphorous showed that most of them are highly expressed during growth in the presence of the herbicide, suggesting a strong participation of phn cluster in GBH degradation. The importance of discovering new bacterial strains and the value of deciphering molecular determinants of GBH degradation give promising tools for bioremediation techniques to be used in glyphosate-contaminated environments is discussed.

Glyphosate Biodegradation Potential in Soil Based on Glycine Oxidase Gene (thiO) from Bradyrhizobium

Despite the intensive use of glyphosate (GP) and its ubiquitous presence in the environment, studies addressing the presence of microbial genes involved in glyphosate degradation in natural conditions are scarce. Based on the agronomical importance of Bradyrhizobium genus and its metabolic versatility, we tested the hypothesis that species or genotypes of Bradyrhizobium could be a proxy for GP degrader potential in soil. A quantitative PCR assay was designed to target a specific region of the glycine oxidase gene (thiO), involved in the oxidation of glyphosate to AMPA, from known sequences of Bradyrhizobium species. The abundance of the thiO gene was determined in response to herbicide application in soils with different GP exposure history both under field and microcosm conditions. The gene coding for RNA polymerase subunitB (rpoB) was used as a reference for the abundance of total Bradyrhizobia. The assay using the designed primers was linear over a very large concentration range of the target and showed high efficiency and specificity. In a field experiment, there was a differential response related to the history of glyphosate use and the native Bradyrhizobium genotypes. In a soil without previous exposure to herbicides, thiO gene increased over time after glyphosate application with most genotypes belonging to the B. jicamae and B. elkanni supergroups. Conversely, in an agricultural soil with more than 10 years of continuous glyphosate application, the abundance of thiO gene decreased and most genotypes belonged to B. japonicum supergroup. In a microcosm assay, the amount of herbicide degraded after a single application was positively correlated to the number of thiO copies in different agricultural soils from the Pampean Region. Our results suggest that Bradyrhizobium species are differently involved in glyphosate degradation, denoting the existence of metabolically versatile microorganisms which can be explored for sustainable agriculture practices. The relationship between the abundance of thiO gene and the GP degraded in soil point to the use of thiO gene as a proxy for GP degradation in soil.