Cloning and expression of ophB gene encoding organophosphorus hydrolase from endophytic Pseudomonas sp. BF1-3 degrades organophosphorus pesticide chlorpyrifos

Enhancement of novel Endo-polygalacturonase expression in Rhodotorula mucilaginosa PY18: insights from mutagenesis and molecular docking

Pectinase is a particular type of enzyme that can break down pectin compounds and is extensively utilised in the agricultural field. In this study, twenty yeast isolates were isolated and assayed for pectinase activity. Molecular identification by PCR amplification and sequencing of internal transcribed spacer (ITS) regions of isolate no. 18 had the highest pectinase activity of 46.35 U/mg, was identified as Rhodotorula mucilaginosa PY18, and was submitted under accession no. (OM275426) in NCBI. Rhodotorula mucilaginosa PY18 was further enhanced through sequential mutagenesis, resulting in a mutant designated as Rhodotorula mucilaginosa E54 with a specific activity of 114.2 U/mg. Using Response Surface Methodology (RSM), the best culture conditions for the pectinase-producing yeast mutant Rhodotorula mucilaginosa E54 were pH 5, 72-h incubation, 2.5% xylose, and 2.5% malt extract, with a pectinase-specific activity of 156.55 U/mg. Then, the obtained sequences of the endo-polygalacturonase PGI gene from Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were isolated for the first time, sequenced, and submitted to NCBI accession numbers OQ283005 and OQ283006, respectively. The modelled 3D structure of the endo-PGI enzyme (485 residues) was validated using Ramachandran's plot, which showed 87.71, 85.56, and 91.57% in the most favourable region for template Rhodotorula mucilaginosa KR, strain Rhodotorula mucilaginosa PY18, and mutant Rhodotorula mucilaginosa E54, respectively. In molecular docking studies, the results of template Rhodotorula mucilaginosa KR endo-PG1 showed an interaction with an affinity score of - 6.0, - 5.9, and - 5.6 kcal/mol for active sites 1, 2, and 3, respectively. Rhodotorula mucilaginosa PY18 endo-PG1 showed an interaction affinity with a score of - 5.8, - 6.0, and - 5.0 kcal/mol for active sites 1, 2, and 3, respectively. Mutant Rhodotorula mucilaginosa E54 endo-PG1 showed an interaction affinity of - 5.6, - 5.5, - 5.5 and - 5.4 kcal/mol for active sites 1, 2, and 3, respectively. The endo-PGI genes of both the yeast strain Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were successfully cloned and expressed in E. coli DH5α, showing significantly higher endo-PG1 activity, which recorded 94.57 and 153.10 U/mg for recombinant Rhodotorula mucilaginosa pGEM-PGI-PY18 and recombinant mutant Rhotorula pGEM-PGI-E54, respectively.

Structure prediction, docking studies and molecular cloning of novel Pichia kudriavzevii YK46 metalloprotease (MetPr) for improvement of feather waste biodegradation

This study addresses the environmental risks associated with the accumulation of keratin waste from poultry, which is resistant to conventional protein degradation methods. To tackle this issue, microbial keratinases have emerged as promising tools for transforming resilient keratin materials into valuable products. We focus on the Metalloprotease (MetPr) gene isolated from novel Pichia kudriavzevii YK46, sequenced, and deposited in the NCBI GenBank database with the accession number OQ511281. The MetPr gene encodes a protein consisting of 557 amino acids and demonstrates a keratinase activity of 164.04 U/ml. The 3D structure of the protein was validated using Ramachandran's plot, revealing that 93% and 97.26% of the 557 residues were situated within the most favoured region for the MetPr proteins of template Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Computational analyses were employed to determine the binding affinities between the deduced protein and beta keratin. Molecular docking studies elucidated the optimal binding affinities between the metalloprotease (MetPr) and beta-keratin, yielding values of - 260.75 kcal/mol and - 257.02 kcal/mol for the template strains Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Subsequent molecular cloning and expression of the MetPr gene in E. coli DH5α led to a significantly higher keratinase activity of 281 ± 12.34 U/ml. These findings provide valuable insights into the potential of the MetPr gene and its encoded protein for keratin waste biotransformation, with implications for addressing environmental concerns related to keratinous waste accumulation.

Postbiotics as Potential Detoxification Tools for Mitigation of Pesticides

Pesticides possess a pivotal role in the realm of agriculture and food manufacturing, as they effectively manage the proliferation of weeds, insects, plant pathogens, and microbial contaminations. They are valuable in some ways, but if misused, they can cause health issues like cancer, reproductive toxicity, neurological illnesses, and endocrine system disturbances. In this regard, practical methods for reducing pesticide residue in food should be used. For reducing pesticide residue in food processing, some strategies have been suggested. Recent research has been done on detoxification processes, including microorganisms like probiotics and their metabolites. The term "postbiotics" describes soluble substances, such as peptides, enzymes, teichoic acids, muropeptides generated from peptidoglycans, polysaccharides, proteins, and organic acids that are secreted by living bacteria or released after bacterial lysis. Due to their distinct chemical makeup, safe dosage guidelines, lengthy shelf lives, and presence of various signaling molecules that may have antioxidant, anti-inflammatory, anti-obesogenic, immunomodulatory, anti-hypertensive, and immunomodulatory effects, these postbiotics have attracted interest. They also can detoxify heavy metals, mycotoxins, and pesticides. Hydrolytic enzymes have been proposed as a potential mechanism for pesticide degradation. Postbiotics can also reduce reactive oxygen species production, enhance gastrointestinal barrier function, reduce inflammation, and modulate host xenobiotic metabolism. This review highlights pesticide residues in food products, definitions and safety aspect of postbiotics, as well as their biological role in detoxification of pesticides and the protective role of these compounds against the adverse effects of pesticides.

Cultivating antimicrobial resistance: how intensive agriculture ploughs the way for antibiotic resistance

Antimicrobial resistance (AMR) is a growing threat to public health, global food security and animal welfare. Despite efforts in antibiotic stewardship, AMR continues to rise worldwide. Anthropogenic activities, particularly intensive agriculture, play an integral role in the dissemination of AMR genes within natural microbial communities - which current antibiotic stewardship typically overlooks. In this review, we examine the impact of anthropogenically induced temperature fluctuations, increased soil salinity, soil fertility loss, and contaminants such as metals and pesticides on the de novo evolution and dissemination of AMR in the environment. These stressors can select for AMR - even in the absence of antibiotics - via mechanisms such as cross-resistance, co-resistance and co-regulation. Moreover, anthropogenic stressors can prime bacterial physiology against stress, potentially widening the window of opportunity for the de novo evolution of AMR. However, research to date is typically limited to the study of single isolated bacterial species - we lack data on how intensive agricultural practices drive AMR over evolutionary timescales in more complex microbial communities. Furthermore, a multidisciplinary approach to fighting AMR is urgently needed, as it is clear that the drivers of AMR extend far beyond the clinical environment.

Multiple Metabolism Pathways of Bentazone Potentially Regulated by Metabolic Enzymes in Rice

Bentazone (BNTZ) is a selective and efficient herbicide used in crop production worldwide. However, the persistence of BNTZ residues in the environment has led to their increasing accumulation in farmland and crops, posing a high risk to human health. To evaluate its impact on crop growth and environmental safety, a comprehensive study was conducted on BNTZ toxicity, metabolic mechanism, and resultant pathways in rice. The rice growth was compromised to the treatment with BNTZ at 0.2-0.8 mg/L (529.95-1060.05 g a.i./ha), while the activities of enzymes including SOD, POD, CAT, GST, GT, and CYP450 were elevated under BNTZ stress. A genome-wide RNA-sequencing (RNA-Seq) was performed to dissect the variation of transcriptomes and metabolic mechanisms in rice exposed to BNTZ. The degradative pathways of BNTZ in rice are involved in glycosylation, hydrolysis, acetylation, and conjugation processes catalyzed by the enzymes. Our data provided evidence that helps understand the BNTZ metabolic and detoxic mechanisms.

The Probiotic Lactobacillus sakei Subsp. Sakei and Hawthorn Extract Supplements Improved Growth Performance, Digestive Enzymes, Immunity, and Resistance to the Pesticide Acetamiprid in Common Carp (Cyprinus carpio)

This study evaluated the impacts of the probiotic, Lactobacillus sakei (L. sakei), and the extract of hawthorn, Crataegus elbursensis, on growth and immunity of the common carp exposed to acetamiprid. Fish (mean ± SE: 11.48 ± 0.1 g) feeding was done with formulated diets (T ₁ (control): no supplementation, T ₂: 1 × 10⁶ CFU/g LS (Lactobacillus sakei), T3: 1 × 10⁸ CFU/g LS, T ₄: 0.5% hawthorn extract (HWE), and T ₅: 1% HWE) for 60 days and then exposed to acetamiprid for 14 days. The growth performance improved in the fish fed LS at dietary level of 1 × 10⁸ CFU/g, even after exposure to acetamiprid (P < 0.05). Intestinal Lactobacillus sakei (CFU/g) load increased (P < 0.05), following supplementation with the probiotic-enriched diet. The LS-treated fish had increases in the activity of digestive enzymes (P < 0.05). Both LS and HWE stimulated antioxidant enzymes and immune system components in serum and mucus (alkaline phosphatase (ALP), protease, total Ig, and lysozyme) (P < 0.05). However, the changes were different depending on the kind of the supplement. The malondialdehyde (MDA) levels decreased in HWE-treated fish after acetamiprid exposure (P < 0.05). Both LS and HWE reduced the liver metabolic enzymes (LDH, ALP, AST, ALT, and LDH) in serum both before and after exposure to the pesticide (P < 0.05). However, each enzyme exhibited a different change trend depending on the type of the supplement. HWE showed a stress-ameliorating effect, as glucose and cortisol levels declined in the HWE-treated fish (P < 0.05). This study indicated the immunomodulatory impacts of LS (1 × 10⁸ CFU/g) and HWE (at dietary levels of 0.5-1%). The probiotic showed more performance compared to HWE. However, the HWE mitigated oxidative stress more efficiently than the probiotic.

A systematic review on the implementation of advanced and evolutionary biotechnological tools for efficient bioremediation of organophosphorus pesticides

Ever since the concept of bioremediation was introduced, microorganisms, microbial enzymes and plants have been used as principal elements for Organophosphate pesticide (OPP) bioremediation. The enzyme systems and genetic profile of these microbes have been studied deeply in past years. Plant growth promoting rhizobacteria (PGPR) are considered as one of the potential candidates for OPP bioremediation and has been widely used to stimulate the phytoremediation potential of plants. Constructed wetlands (CWs) in OPP biodegradation have brought new prospects to microcosm and mesocosm based remediation strategies. Application of synthetic biology has provided a new dimension to the field of OPP bioremediation by introducing concepts like, gene manipulation andediting, expression and regulation of catabolic enzymes, implementation of whole-cell based and enzyme based biosensor systems for the detection and monitoring of OPP pollution in both terrestrial and aquatic environment. System biology and bioinformatics tools have rendered significant knowledge regarding the genetic, enzymatic and biochemical aspects of microbes and plants thereby, helping researchers to analyze the mechanism of OPP biodegradation. Structural biology has provided significant conceptual information regarding OPP biodegradation pathways, structural and functional characterization of metabolites and enzymes, enzyme-pollutant interactions, etc. Therefore, this review discussed the prospects and challenges of most advanced and high throughput strategies implemented for OPP biodegradation. The review also established a comparative analysis of various bioremediation techniques and highlighted the interdependency among them. The review highly suggested the simultaneous implementation of more than one remediation strategy or a combinational approach creating an advantageous hybrid technique for OPP bioremediation.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Enhancement of MBBR reactor efficiency using effective microorganism for treatment of wastewater containing diazinon by engineered Pseudomonas putida KT2440 with manganese peroxidase 2 gene

Pesticides not only are harmful to humans but they are noxious for water reservoirs, soil, and air quality as well. In this research, diazinon was removed from aqueous solutions by Moving Bed Biofilm Reactor (MBBR). The MBBR was spiked with transgenic Pseudomonas putida KT2440 with Pleurotus ostreatus fungus manganese peroxidase 2 gene to enhance the capabilities of Pseudomonas putida KT2440 in the degradation of diazinon. Although the amount of diazinon and COD and diazinon removal in the reactor including transgenic P. putida KT2440 was 95.46% and 97.47% and they were greater than the control and wild type (non-modified) P. putida KT2440 reactors, the surprising result was related to the adaptation pace of transgenic P. putida KT2440. The produced metabolites and the quantity of diazinon were assessed by HPLC and LC/MS. The metabolite hydroxyisopropyl diazinon was not found in the transgenic P. putida KT2440 reactor. Furthermore, a new sequence of cloned manganese peroxidase 2 gene has been recorded in GenBank with the accession number MT185558. According to bacterial identification of provided sludge the most frequent genus belonged to Aeromonas. Therefore, it seems that the MBBR in the presence of transgenic P. putida KT2440 with manganese peroxidase 2 gene can effectively remove the diazinon.

Indigenous functional microbial degradation of the chiral fungicide mandipropamid in repeatedly treated soils: Preferential changes in the R-enantiomer

This study investigated the indigenous functional microbial communities associated with the degradation of chiral fungicide mandipropamid enantiomers in soils repeatedly treated with a single enantiomer. The R-enantiomer degraded faster than the S-enantiomer, with degradation half-lives ranging from 10.2 d to 79.2 d for the R-enantiomer and 10.4 d to 130.5 d for the S-enantiomer. Six bacterial genera, (Burkholderia, Paraburkholderia, Hyphomicrobium, Methylobacterium, Caballeronia, and Ralstonia) with R-enantiomer substrate preference and three bacterial genera (Haliangium, Sorangium, and Sandaracinus) with S-enantiomer substate preference were responsible for the preferential degradation of the R-enantiomer and S-enantiomer, respectively. KEGG analysis indicated that Burkholderia, Paraburkholderia, Hyphomicrobium, and Methylobacterium were the dominant contributors to soil microbial metabolic functions. Notably, six microbial metabolic pathways and twelve functional enzyme genes were associated with the preferential degradation of the R-enantiomer, whose relative abundances in the R-enantiomer treatment were higher than those in the S-enantiomer treatment. A constructed biodegradation gene (BDG) protein database analysis further confirmed that Burkholderia, Paraburkholderia, Hyphomicrobium, Methylobacterium, and Ralstonia were the potential hosts of five dominant BDGs, bphA1, benA, bph, p450, and ppah. We concluded that bacterial genera Burkholderia, Paraburkholderia, Hyphomicrobium, and Methylobacterium may play pivotal roles in the preferential degradation of mandipropamid R-enantiomer in repeatedly treated soils.

Toxicological effect of sumithion pesticide on the hematological parameters and its recovery pattern using probiotic in Barbonymus gonionotus

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Sumithion induced hematoxicity and their recovery pattern in Barbonymus gonionotus was measured.

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Sumithion induces severe formation and prevalence of micronuclei and significantly (p< 0.05) increased white blood cells.

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Blood glucose, red blood cell, hematocrit, and hemoglobin were found to be decreased after the exposure of sumithion.

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In recovery experiment, the recovery rate was significantly higher in probiotic treated groups than other treatments.

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Fish micronucleus and hematology is an effective biomarker for toxicity test of an organophosphate.

The experiment was conducted to clarify sumithion induced hematoxicity in silver barb (Barbonymus gonionotus) through in vivo exposures (25 % and 50 % of LC₅₀ of sumithion) and subsequent recovery patterns using normal and probiotic treated feed were also assessed. Three treatments each incorporating three replications were used in the experiment for different days (1, 7, 14, 21, and 28). Treatment T₁ was control (0 mg/L), and two concentrations, such as 2.61 mg/L (25 % of 96 h LC₅₀), 5.21 mg/L (50 % of 96 h LC₅₀) were used as Treatment T₂ and T₃, respectively. After 28 days of exposure to pesticide half of the fishes of T₂ and T₃ were reared in sumithion free water with normal (T₂N, T₃N) and probiotic treated feed (T₂P, T₃P). The median lethal concentration (50 %) for 96 h was 10.42 mg/L. In pesticide-treated groups, values of each hematological parameter (blood glucose, red blood cell, hematocrit, and hemoglobin) decreased but prevalence and severity of micronucleus and white blood cells increased significantly (p< 0.05) with concentration and time duration. Other blood indices including mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) and mean corpuscular hemoglobin concentration (MCHC) were correspondingly changed in comparison to the control. In the recovery experiment, the silver barb recovered spontaneously, but the recovery rate was significantly higher in probiotic treated groups than normally treated groups in time and duration reliant fashion. In conclusion, persistent sublethal dosages of sumithion caused hematological abnormalities in silver barb. Probiotic supplement can recover the damage but only 28 days of recovery is not enough to recover the total alterations.

Growth, respiratory activity and chlorpyrifos biodegradation in cultures of Azotobacter vinelandii ATCC 12837

This study aimed to evaluate the growth, respiratory activity, and biodegradation of chlorpyrifos in cultures of Azotobacter vinelandii ATCC 12837. A strategy based on the modification of culture media and aeration conditions was carried out to increase the cell concentration of A. vinelandii, in order to favor and determine its tolerance to chlorpyrifos and its degradation ability. The culture in shaken flasks, using sucrose as a carbon source, significantly improved the growth compared to media with mannitol. When the strain was cultivated under oxygen-limited (5.5, 11.25 mmol L⁻¹ h⁻¹) and no-oxygen-limited conditions (22 mmol L⁻¹ h⁻¹), the growth parameters were not affected. In cultures in a liquid medium with chlorpyrifos, the bacteria tolerated a high pesticide concentration (500 ppm) and the growth parameters were improved even under conditions with a reduced carbon source (sucrose 2 g L⁻¹). The strain degraded 99.6% of chlorpyrifos at 60 h of cultivation, in co-metabolism with sucrose; notably, A. vinelandii ATCC 12837 reduced by 50% the initial pesticide concentration in only 6 h (DT₅₀).

A review on the microbial degradation of chlorpyrifos and its metabolite TCP

Chlorpyrifos (CPF) falls under the category of organophosphorus pesticides which are in huge demand in the agricultural sector. Overuse of this pesticide has led to the degradation of the quality of terrestrial and aquatic life. The chemical is moderately persistent in the environment but its primary metabolite 3,5,6-trichloro-2-pyridinol (TCP) is comparatively highly persistent. Thus, it is important to degrade the chemical and there are many proposed techniques of degradation. Out of which bioremediation is considered to be highly cost-effective and efficient. Many previous studies have attempted to isolate appropriate microbial strains to degrade CPF which established the fact that chlorine atoms released while mineralising TCP inhibits further proliferation of microorganisms. Thus, it has been increasingly important to experiment with strains that can simultaneously degrade both CPF and TCP. In this review paper, the need for degrading CPF specifically the problems related to it has been discussed elaborately. Alongside these, the metabolism pathways undertaken by different kinds of microorganisms have been included. This paper also gives a detailed insight into the potential strains of microorganisms which has been confirmed through experiments conducted previously. It can be concluded that a wide range of microorganisms has to be studied to understand the possibility of applying bioremediation in wastewater treatment to remove pesticide residues. In addition to this, in the case of recalcitrant pesticides, options of treating it with hybrid techniques like bioremediation clubbed with photocatalytic biodegradation can be attempted.

Overview of a bioremediation tool: organophosphorus hydrolase and its significant application in the food, environmental, and therapy fields

In the past decades, the organophosphorus compounds had been widely used in the environment and food industries as pesticides. Owing to the life-threatening and long-lasting problems of organophosphorus insecticide (OPs), an effective detection and removal of OPs have garnered growing attention both in the scientific and practical fields in recent years. Bacterial organophosphorus hydrolases (OPHs) have been extensively studied due to their high specific activity against OPs. OPH could efficiently hydrolyze a broad range of substrates both including the OP pesticides and some nerve agents, suggesting a great potential for the remediation of OPs. In this review, the microbial identification, molecular modification, and practical application of OPHs were comprehensively discussed.Key points• Microbial OPH is a significant bioremediation tool against OPs.• Identification and molecular modification of OPH was discussed in detail.• The applications of OPH in food, environmental, and therapy fields are presented.

Chlorpyrifos in environment and food: a critical review of detection methods and degradation pathways

Chlorpyrifos (CP) is a class of organophosphorus (OP) pesticides, which find extensive applications as acaricide, insecticide and termiticide. The use of CP has been indicated in environmental contamination and disturbance in the biogeochemical cycles. CP has been reported to be neurotoxic and has a detrimental effect on immunological and psychological health. Therefore, it is necessary to design and develop effective degradation methods for the removal of CP from the environment. In the past few years, physicochemical (advanced oxidation process) and biological treatment approaches have been widely employed for the pesticide removal. However, the byproducts of this process are more toxic than the parent compound and along with an incomplete degradation of CP. This review focuses on the toxicity of CP, the sources of contamination, degradation pathways, physicochemical, biological, and nano-technology based methods employed for the degradation of CP. In addition, consolidated information on various detection methods and materials used for the detection have been provided in this review.

Selection of Endophytic Strains for Enhanced Bacteria-Assisted Phytoremediation of Organic Pollutants Posing a Public Health Hazard

Anthropogenic activities generate a high quantity of organic pollutants, which have an impact on human health and cause adverse environmental effects. Monitoring of many hazardous contaminations is subject to legal regulations, but some substances such as therapeutic agents, personal care products, hormones, and derivatives of common organic compounds are currently not included in these regulations. Classical methods of removal of organic pollutants involve economically challenging processes. In this regard, remediation with biological agents can be an alternative. For in situ decontamination, the plant-based approach called phytoremediation can be used. However, the main disadvantages of this method are the limited accumulation capacity of plants, sensitivity to the action of high concentrations of hazardous pollutants, and no possibility of using pollutants for growth. To overcome these drawbacks and additionally increase the efficiency of the process, an integrated technology of bacteria-assisted phytoremediation is being used recently. For the system to work, it is necessary to properly select partners, especially endophytes for specific plants, based on the knowledge of their metabolic abilities and plant colonization capacity. The best approach that allows broad recognition of all relationships occurring in a complex community of endophytic bacteria and its variability under the influence of various factors can be obtained using culture-independent techniques. However, for practical application, culture-based techniques have priority.

Re-vitalizing of endophytic microbes for soil health management and plant protection

Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.

Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges

The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.

Biological approaches practised using genetically engineered microbes for a sustainable environment: A review

Conventional methods used to remediate toxic substances from the environment have failed drastically, and thereby, advancement in newer remediation techniques can be one of the ways to improve the quality of bioremediation. The increased environmental pollution led to the exploration of microorganisms and construction of genetically engineered microbes (GEMs) for pollution abatement through bioremediation. The present review deals with the successful bioremediation techniques and approaches practised using genetically modified or engineered microbes. In the present scenario, physical and chemical strategies have been practised for the remediation of domestic and industrial wastes but these techniques are expensive and toxic to the environment. Involving engineered microbes can provide a much safer and cost effective strategy in comparison with the other techniques. With the aid of biotechnology and genetic engineering, GEMs are designed by transforming microbes with a more potent protein to overexpress the desired character. GEMs such as bacteria, fungi and algae have been used to degrade oil spills, camphor, hexane, naphthalene, toluene, octane, xylene, halobenzoates, trichloroethylene etc. These engineered microbes are more potent than the natural strains and have higher degradative capacities with quick adaptation for various pollutants as substrates or cometabolize. The road ahead for the implementation of genetic engineering to produce such organisms for the welfare of the environment and finally, public health is indeed long and worthwhile.

Insights into the microbial degradation and catalytic mechanisms of chlorpyrifos

Chlorpyrifos is extensively used worldwide as an insecticide to control various insect pests. Long-term and irregular applications of chlorpyrifos have resulted in large-scale soil, groundwater, sediment, and air pollution. Numerous studies have shown that chlorpyrifos and its major intermediate metabolite 3,5,6-trichloropyridinol (TCP) accumulate in non-target organisms through biomagnification and have a strong toxic effect on non-target organisms, including human beings. Bioremediation based on microbial metabolism is considered an eco-friendly and efficient strategy to remove chlorpyrifos residues. To date, a variety of bacterial and fungal species have been isolated and characterized for the biodegradation of chlorpyrifos and TCP. The metabolites and degradation pathways of chlorpyrifos have been investigated. In addition, the chlorpyrifos-degrading enzymes and functional genes in microbes have been reported. Hydrolases can catalyze the first step in ester-bond hydrolysis, and this initial regulatory metabolic reaction plays a key role in the degradation of chlorpyrifos. Previous studies have shown that the active site of hydrolase contains serine residues, which can initiate a catalytic reaction by nucleophilic attack on the P-atom of chlorpyrifos. However, few reviews have focused on the microbial degradation and catalytic mechanisms of chlorpyrifos. Therefore, this review discusses the deep understanding of chlorpyrifos degradation mechanisms with microbial strains, metabolic pathways, catalytic mechanisms, and their genetic basis in bioremediation.

Can probiotics win the battle against environmental endocrine disruptors?

Compounds that have negative effects on the endocrine system are called endocrine disrupting compounds (EDCs). There are several different types of compounds, with several different usage areas in the environment, which can be classified as EDCs. These chemicals have a wide range of negative health effects in organisms, depending on their target hormone system. EDCs are among the most popular topics of scientific research, as they are widely used and organisms are frequently exposed to these chemicals. There are various exposure routes for EDCs, such as oral, inhalation and dermal exposure. Parabens, phenolic compounds, phthalates, and pesticides are the most common EDCs. Nowadays, intestinal microorganism distribution, probiotics, and food supplements that regulate these microorganisms and their protective effects against various harmful chemicals attract attention. For this reason, many studies have been carried out in this field and certain diet schemes have been created according to the results of these studies. In fact, probiotics are preferred in order to reduce and eliminate the negative effects of harmful chemicals and to ensure that the organism reacts strongly in these conditions. In this review, we will focus on EDCs, their health effects and positive effects of probiotics on EDCs exposure conditions.

A treatise on Organophosphate pesticide pollution: Current strategies and advancements in their environmental degradation and elimination

Pesticides have been used in the field of agriculture ever since their role in protection of crops from pests which include four different categories namely insects, mites, rodents and animals has been identified. Organophosphate pesticides are one of the most extensively applied insecticides in the field of agriculture such that around 40% of all the pesticides that are produced and used commercially belong to this category. The main toxicological effect of these pesticides when exposed to a living being encompasses the irremediable inhibition of the acetylcholinesterase (AChE) enzyme which is involved in the neurotransmission of signals and hence its inhibition causes impairment of the respiratory tract and neuromuscular transmission. Apart from being used as a pesticide, organophosphates have also been applied as herbicides to some extent. The residues of these highly toxic chemicals have found route into the underground water system by seeping into the ground, in rivers where the agricultural run off water is disposed, and in the air when sprayed on the crops hence posing a threat to all the living strata exposed to these chemicals in various ways which are discussed further. Many significant studies have been carried out in order to evaluate the health risks associated with these pesticides which commonly include acute neurological disorders. This review emphasizes on the toxicological effects of organophosphate pesticides and the recent methods of detection that are used to identify trace amounts of organophosphate pesticides along with strategies which are used for their degradation.

Simultaneous degradation of triazophos, methamidophos and carbofuran pesticides in wastewater using an Enterobacter bacterial bioreactor and analysis of toxicity and biosafety

Triazophos (TAP), methamidophos (MAP) and carbofuran (CF) pesticides are highly toxic, soluble and absorbable. Efficient co-degradation of multi-pesticides is rare reported. The objectives of this study were to investigate TAP, MAP and CF co-degradative ability of Enterobacter sp. Z1 and study the degradation mechanisms. Strain Z1 was shown to efficiently co-degrade TAP, MAP and CF when they were used as primary carbon sources. The degradation occurred over a wide range of temperatures, pH values and pesticide concentrations and followed first-order kinetics. Under the optimum conditions (37 °C, pH 7 and 100 mg/L of each pesticide), the degradation efficiencies were 100%, 100%, and 95.3% for TAP, MAP and CF, respectively. In addition, strain Z1 could simultaneously degrade TAP, MAP, CF and total nitrogen in wastewater in a batch bioreactor, with high removal efficiencies of 98.3%, 100%, 98.7% and 100%, respectively. Genomics, proteomics, qRT-PCR and gene overexpression analyses revealed that the degradation mechanisms involved the activities of multiple proteins, among which, organophosphorus hydrolase (Oph) and 3-hydroxyacyl-CoA dehydrogenase (PaaC) are primarily responsible for TAP and MAP degradation, while carbofuran hydrolase (Mcd) and amidohydrolase (RamA) primarily degrade CF. Among these enzymes, PaaC and RamA are newly identified pesticide-degrading enzymes. Toxicity assays of strain Z1 using reporter recombinase gene (recA) and zebrafish showed that there was no accumulation of toxic metabolites during the degradation process. Biosafety test using zebrafish showed that the strain was nontoxic toward zebrafish. Strain Z1 provides a good purification effect for pesticides-containing wastewater and novel microbial pesticide-degrading mechanisms were discovered.

Exploration of Root-associated Bacteria from the Medicinal Plant Platycodon grandiflorum

The present study was performed to investigate root-associated bacteria from Platycodon grandiflorum, a medicinal plant commonly grown in East Asia. Isolates were obtained from the rhizosphere or root interior with various culture media, and phylogenetic analyses were performed based on their 16S rDNA sequences. In consideration of practical applications, traits related to plant growth promotion and niche adaptation were assessed in several endophytic strains with fewer biosafety concerns. The effects of a bacterial inoculation on seedling and mature plant growth were evaluated. Seventeen genera that encompassed more than 30 bacterial lineages were successfully retrieved from the roots, the majority of which have not been reported as P. grandiflorum-associated bacteria, particularly for non-negligible Proteobacteria. Although nitrogen-fixing or phosphate-solubilizing and indole acetic acid-producing activities were recorded in all of the strains selected, these strains were beneficial or detrimental to plant growth as evidenced by their influence on the length of seedlings and biomass of mature plants. Among the 4 endophytic Rhizobium species tested in the present study, the potentially novel Rhizobium sp. BF-E16, which was more compatible with the non-leguminous medicinal plant P. grandiflorum, was identified. Other than plant growth-promoting traits, characteristics such as plant constituent-hydrolyzing activities need to be taken into consideration and their roles clarified when investigating plant growth-promoting rhizobacteria.

Microbial degradation of organophosphorus pesticides: novel degraders, kinetics, functional genes, and genotoxicity assessment

Farmland soil sprayed with organophosphorus pesticides (OPs) annually was investigated for the identification and characterization of OP-degrading microorganisms. Six bacterial strains were identified, including Brevundimonas faecalis MA-B12 and Alcaligenes faecalis subsp. parafaecalis MA-B13 for methamidophos degradation, Citrobacter freundii TF-B21 and Ochrobactrum intermedium TF-B23 for trichlorfon degradation, Ochrobactrum intermedium DV-B31 for dichlorvos degradation, and Bacillus cereus for dimethoate degradation. The optimal biodegradation conditions for OPs were obtained at pH 7.0 and incubation temperature ranging from 28 to 37 °C. In an 8-day batch test, biodegradation of the four OPs all followed first-order kinetics, with biodegradation rates ranging from 58.08 to 96.42%. Functional genes responsible for OPs degradation were obtained, including ophB, ampA, opdE, opd, opdA, and mpd. As these strains were indigenous strains isolated from farmland soils, they can be potentially used as bacterial consortium for the bioremediation of mixed OP-contaminated soils. A time-course genotoxicity assessment of the degradation products was done by a bacterial whole-cell bioreporter, revealing that biodegradation of trichlorfon, dichlorvos, and dimethoate resulted a decreased genotoxicity within 5 days, which, however, significantly increased on day 8. The result demonstrated that more toxic products may be produced during the biodegradation processes of OPs, and more attention should be put not only on the pesticides themselves, but also on the toxic effects of their degradation products. To the best of our knowledge, this is for the first time that the genotoxicity of OP degradation products was evaluated by the bioreporter assay, broadening our understanding on the genotoxic risks of OPs during biodegradation process. Graphical Abstract.

Degradation of chlorpyrifos by an endophytic bacterium of the Sphingomonas genus (strain HJY) isolated from Chinese chives (Allium tuberosum)

The degradation of chlorpyrifos (CP) by an endophytic bacterial strain (HJY) isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng) was investigated. Strain HJY was identified as Sphingomonas sp. based on morphological, physiological, and biochemical tests and a 16S rDNA sequence analysis. Approximately 96% of 20 mg L^-1 CP was degraded by strain HJY over 15 days in liquid minimal salts medium (MSM). The CP degradation rate could also be increased by glucose supplementation. The optimal conditions for the removal of 20 mg L^-1 CP by strain HJY in MSM were 2% inoculum density, pH 6.0, and 30-35°C. The CP degradation rate constant and half-life were 0.2136 ± 0.0063 d^-1 and 3.2451 ± 0.0975 d, respectively, under these conditions, but were raised to 0.7961 ± 0.1925 d^-1 and 0.8707 ± 0.3079 d with 1% glucose supplementation. The detection of metabolic products and screening for degrading genes indicated that O,O-diethyl O-3,5,6-trichloropyridinol was the major degradation product from CP, while it was likely that some functional genes were undetected and the mechanism responsible for CP degradation by strain HJY remained unknown. Strain HJY is potentially useful for the reduction of CP residues in Chinese chives and may be used for the in situ phytoremediation of CP.

Binding affinity and adhesion force of organophosphate hydrolase enzyme with soil particles related to the isoelectric point of the enzyme

The binding affinity of organophosphate hydrolase enzyme (OphB) with soil particles in relation to the isoelectric point (pI) was studied. Immobilization of OphB with soil particles was observed by confocal microscopy, Fourier transform infrared spectroscopy (FT-IR), and Atomic force microscopy (AFM). The calculated pI of OphB enzyme was increased from 8.69 to 8.89, 9.04 and 9.16 by the single, double and triple mutant of OphB enzyme, respectively through the replacement of negatively charged aspartate with positively charged histidine. Practically, the binding affinity was increased to 5.30%, 11.50%, and 16.80% for single, double and triple mutants, respectively. In contrast, enzyme activity of OphB did not change by the mutation of the enzyme. On the other hand, adhesion forces were gradually increased for wild type OphB enzyme (90 pN) to 96, 100 and 104 pN for single, double and triple mutants of OphB enzyme, respectively. There was an increasing trend of binding affinity and adhesion force by the increase of isoelectric point (pI) of OphB enzyme.

Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships

Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.

Diazinon degradation by a novel strain Ralstonia sp. DI-3 and X-ray crystal structure determination of the metabolite of diazinon

Diazinon is a widely used organophosphorus insecticide often detected in the environment. A highly effective diazinon-degrading Ralstonia sp. strain DI-3 was isolated from agricultural soil. Strain DI-3 can utilize dimethoate as its sole carbon source for growth and degrade an initial concentration of 100 mg L-1 diazinon to non-detectable levels within 60 h in liquid culture. A small amount of second carbon source as co-substrate could slightly enhance the biodegradation of diazinon. In addition, a less toxic metabolic intermediate formed during the degradation of diazinon mediated by strain DI-3 was purified using thin-layer chromatography (TLC) and identified based on single-crystal Xray diffraction analysis, allowing a degradation pathway for diazinon by pure culture to be proposed. Finally, this is the first providing authentic evidence to describe the metabolite.

Probiotic lactobacilli: a potential prophylactic treatment for reducing pesticide absorption in humans and wildlife

Numerous pesticides are used in agriculture, gardening, and wildlife-control. Despite their intended toxicity to pests, these compounds can also cause harm to wildlife and humans due to their ability to potentially bioaccumulate, leach into soils, and persist in the environment. Humans and animals are commonly exposed to these compounds through agricultural practices and consumption of contaminated foods and water. Pesticides can cause a range of adverse effects in humans ranging from minor irritation, to endocrine or nervous system disruption, cancer, or even death. A convenient and cost-effective method to reduce unavoidable pesticide absorption in humans and wildlife could be the use of probiotic lactobacilli. Lactobacillus is a genus of Gram-positive gut commensal bacteria used in the production of functional foods, such as yoghurt, cheese, sauerkraut and pickles, as well as silage for animal feed. Preliminary in vitro experiments suggested that lactobacilli are able to degrade some pesticides. Probiotic Lactobacillus rhamnosus GR-1-supplemented yoghurt reduced the bioaccumulation of mercury and arsenic in pregnant women and children. A similar study is warranted to test if this approach can reduce pesticide absorption in vivo, given that the lactobacilli can also attenuate reactive oxygen production, enhance gastrointestinal barrier function, reduce inflammation, and modulate host xenobiotic metabolism.