Biotechnological basis of microbial consortia for the removal of pesticides from the environment

Enhanced bioremediation of soils contaminated with nicosulfuron using the bacterial complex A12

AIMS

To construct an efficient bacterial complex to degrade nicosulfuron and clarify its degradative characteristics, promote the growth of maize (Zea mays), and provide a theoretical foundation for the efficient remediation of soil contaminated with nicosulfuron.

METHODS AND RESULTS

Biocompatibility was determined by the filter paper sheet method by mixing Serratia marcescens A1 and Bacillus cereus A2 in a 1:1 ratio, yielding A12. The optimum culture conditions for the bacterial composite were obtained based on a three-factor, three-level analysis using response surface methodology, with 29.25 g l-1 for maltodextrin, 10.04 g l-1 for yeast extract, and 19.93 g l-1 for NaCl, which resulted in 92.42% degradation at 4 d. The degradation characteristics of A12 were clarified as follows: temperature 30°C, pH 7, initial concentration of nicosulfuron 20 mg l-1, and 4% inoculum. The ability to promote growth was determined by measuring the ratio of the lysosphere diameter (D) to the colony diameter (d), and the ability of the complex A12 to promote growth was higher than that of the two single strains.

CONCLUSIONS

Nicosulfuron degradation in sterilized and unsterilized soils reached 85.4% and 91.2% within 28 d, respectively. The ability of the strains to colonize the soil was determined by extraction of total soil DNA, primer design, and gel electrophoresis. The bioremediation effect of A12 was confirmed by the maximum recovery of fresh weight (124.35%) of nicosulfuron-sensitive crop plants and the significant recovery of soil enzyme activities, as measured by the physiological indices in the sensitive plants.

Isolation of Monocrotophos degrading bacterial consortium from agricultural soil for in vivo analysis of pesticide degradation

Extensive Monocrotophos (MCP) application in agricultural soils has led to its ubiquitous accumulation in the environment. Human health can be adversely affected by chronic exposure to produce and water from such areas, causing endocrine dysfunction, birth defects, blood and nervous disorders. This study investigated the possibility of detecting Monocrotophos-degrading bacteria in soil samples taken from a cotton cultivation field in a local area. We isolated a consortium that could tolerate and neutralize Monocrotophos upto a concentration of 2000 ppm. The consortium on 16 S rRNA sequencing were identified as Micrococcus luteus SBR2, Rhodococcus SBR5, Bacillus aryabhattai SBR8, Ochrobactrum intermedium SBK2. Significant tolerance of individual strains in the range of 500-5000 ppm was observed when incubating them in vitro with Monocrotophos in minimal salt medium. An analysis of the degrading genes opdA, mpd, and opd revealed plasmid borne opdA and mpd in the O.intermedium strain and B.aryabhattai strain. All the strains indicated genomic opdA and mpd whereas opd was not detected in plasmid or genomic DNA. The HPLC showed no peak at 2.5 min, when individual strains were incubated with Monocrotophos. The HPLC analysis of soil samples incubated with the consortium for two weeks showed complete degradation of Monocrotophos. GC-MS analysis confirmed that Monocrotophos and its solvent cyclohexamide were degraded into non-toxic compounds such as cyclotrisiloxane compounds, acetic acid, and others. This study indicates that the expression of organophosphate hydrolyzing enzymes in the consortium can greatly contribute to the neutralization of organophosphorus compounds and also serve as a bioremediation method for agricultural soils.

Bioremediation strategies against pesticides: An overview of current knowledge and innovations

Pesticides pose significant risks to both human health, such as cancer, neurological disorders, and endocrine disruption, and ecosystems, through the destruction of beneficial insects, contamination of soil and water, and impact on non-target species. In the face of escalating pesticide pollution, there is an urgent need for multifaceted approaches to address the issue. Bioremediation emerges as a potent tool in the environmental pollution mitigation arsenal. Ideally aiming for the complete decomposition of pesticides into harmless molecules, bioremediation encompasses diverse approaches - from bioabsorption, bioadsorption, and biotransformation using enzymes and nanoenzymes to comprehensive degradation facilitated by microorganisms such as bacteria, fungi, macro- and microalgae, or phytoremediation. Exploring nature's biodiversity offers a promising avenue to find solutions to this pressing human-induced problem. The acceleration of biodegradation necessitates identifying and developing efficient organisms, achieved through bioprospection and targeted modifications. Specific strategies to enhance process efficiency and throughput include optimizing biomass production, strategic inoculation in diverse environments, and employing bioreactor systems for processing heavily contaminated waters or soils. This comprehensive review presents various bioremediation approaches, emphasizing the importance of microorganisms' exploration and new technologies development, including current innovations and patents to effectively combat pesticide pollution. Furthermore, challenges regarding the effective implementation of these technologies are also addressed.

Microorganism-Driven 2,4-D Biodegradation: Current Status and Emerging Opportunities

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used around the world in both agricultural and non-agricultural fields due to its high activity. However, the heavy use of 2,4-D has resulted in serious environmental contamination, posing a significant risk to non-target organisms, including human beings. This has raised substantial concerns regarding its impact. In addition to agricultural use, accidental spills of 2,4-D can pose serious threats to human health and the ecosystem, emphasizing the importance of prompt pollution remediation. A variety of technologies have been developed to remove 2,4-D residues from the environment, such as incineration, adsorption, ozonation, photodegradation, the photo-Fenton process, and microbial degradation. Compared with traditional physical and chemical remediation methods, microorganisms are the most effective way to remediate 2,4-D pollution because of their rich species, wide distribution, and diverse metabolic pathways. Numerous studies demonstrate that the degradation of 2,4-D in the environment is primarily driven by enzymatic processes carried out by soil microorganisms. To date, a number of bacterial and fungal strains associated with 2,4-D biodegradation have been isolated, such as Sphingomonas, Pseudomonas, Cupriavidus, Achromobacter, Ochrobactrum, Mortierella, and Umbelopsis. Moreover, several key enzymes and genes responsible for 2,4-D biodegradation are also being identified. However, further in-depth research based on multi-omics is needed to elaborate their role in the evolution of novel catabolic pathways and the microbial degradation of 2,4-D. Here, this review provides a comprehensive analysis of recent progress on elucidating the degradation mechanisms of the herbicide 2,4-D, including the microbial strains responsible for its degradation, the enzymes participating in its degradation, and the associated genetic components. Furthermore, it explores the complex biochemical pathways and molecular mechanisms involved in the biodegradation of 2,4-D. In addition, molecular docking techniques are employed to identify crucial amino acids within an alpha-ketoglutarate-dependent 2,4-D dioxygenase that interacts with 2,4-D, thereby offering valuable insights that can inform the development of effective strategies for the biological remediation of this herbicide.

PGPR-Enabled bioremediation of pesticide and heavy metal-contaminated soil: A review of recent advances and emerging challenges

The excessive usage of agrochemicals, including pesticides, along with various reckless human actions, has ensued discriminating prevalence of pesticides and heavy metals (HMs) in crop plants and the environment. The enhanced exposure to these chemicals is a menace to living organisms. The pesticides may get bioaccumulated in the food chain, thereby leading to several deteriorative changes in the ecosystem health and a rise in the cases of some serious human ailments including cancer. Further, both HMs and pesticides cause some major metabolic disturbances in plants, which include oxidative burst, osmotic alterations and reduced levels of photosynthesis, leading to a decline in plant productivity. Moreover, the synergistic interaction between pesticides and HMs has a more serious impact on human and ecosystem health. Various attempts have been made to explore eco-friendly and environmentally sustainable methods of improving plant health under HMs and/or pesticide stress. Among these methods, the employment of PGPR can be a suitable and effective strategy for managing these contaminants and providing a long-term remedy. Although, the application of PGPR alone can alleviate HM-induced phytotoxicities; however, several recent reports advocate using PGPR with other micro- and macro-organisms, biochar, chelating agents, organic acids, plant growth regulators, etc., to further improve their stress ameliorative potential. Further, some PGPR are also capable of assisting in the degradation of pesticides or their sequestration, reducing their harmful effects on plants and the environment. This present review attempts to present the current status of our understanding of PGPR's potential in the remediation of pesticides and HMs-contaminated soil for the researchers working in the area.

Insect-microbe interactions and their influence on organisms and ecosystems

Microorganisms are important associates of insect and arthropod species. Insect-associated microbes, including bacteria, fungi, and viruses, can drastically impact host physiology, ecology, and fitness, while many microbes still have no known role. Over the past decade, we have increased our knowledge of the taxonomic composition and functional roles of insect-associated microbiomes and viromes. There has been a more recent shift toward examining the complexity of microbial communities, including how they vary in response to different factors (e.g., host genome, microbial strain, environment, and time), and the consequences of this variation for the host and the wider ecological community. We provide an overview of insect-microbe interactions, the variety of associated microbial functions, and the evolutionary ecology of these relationships. We explore the influence of the environment and the interactive effects of insects and their microbiomes across trophic levels. Additionally, we discuss the potential for subsequent synergistic and reciprocal impacts on the associated microbiomes, ecological interactions, and communities. Lastly, we discuss some potential avenues for the future of insect-microbe interactions that include the modification of existing microbial symbionts as well as the construction of synthetic microbial communities.

Bioremediation and bioscavenging for elimination of organophosphorus threats: An approach using enzymatic advancements

Organophosphorus compounds (OP) are highly toxic pesticides and nerve agents widely used in agriculture and chemical warfare. The extensive use of these chemicals has severe environmental implications, such as contamination of soil, water bodies, and food chains, thus endangering ecosystems and biodiversity. Plants absorb pesticide residues, which then enter the food chain and accumulate in the body fat of both humans and animals. Numerous human cases of OP poisoning have been linked to both acute and long-term exposure to these toxic OP compounds. These compounds inhibit the action of the acetylcholinesterase enzyme (AChE) by phosphorylation, which prevents the breakdown of acetylcholine (ACh) neurotransmitter into choline and acetate. Thus, it becomes vital to cleanse the environment from these chemicals utilizing various physical, chemical, and biological methods. Biological methods encompassing bioremediation using immobilized microbes and enzymes have emerged as environment-friendly and cost-effective approaches for pesticide removal. Cell/enzyme immobilized systems offer higher stability, reusability, and ease of product recovery, making them ideal tools for OP bioremediation. Interestingly, enzymatic bioscavengers (stoichiometric, pseudo-catalytic, and catalytic) play a vital role in detoxifying pesticides from the human body. Catalytic bioscavenging enzymes such as Organophosphate Hydrolase, Organophosphorus acid anhydrolase, and Paraoxonase 1 show high degradation efficiency within the animal body as well as in the environment. Moreover, these enzymes can also be employed to decontaminate pesticides from food, ensuring food safety and thus minimizing human exposure. This review aims to provide insights to potential collaborators in research organizations, government bodies, and industries to bring advancements in the field of bioremediation and bioscavenging technologies for the mitigation of OP-induced health hazards.

The role and mechanisms of microbes in dichlorodiphenyltrichloroethane (DDT) and its residues bioremediation

Environmental contamination with dichlorodiphenyltrichloroethane (DDT) has sever effects on the ecosystem worldwide. DDT is a recalcitrant synthetic chemical with high toxicity and lipophilicity. It is also bioaccumulated in the food chain and causes genotoxic, estrogenic, carcinogenic, and mutagenic effects on aquatic organisms and humans. Microbial remediation mechanism and its enzymes are very important for removing DDT from environment. DDT and its main residues dichlorodiphenyldichloroethylene (DDE) and dichlorodiphenyldichloroethane (DDD) can biodegrade slowly in soil and water. To enhance this process, a number of strategies are proposed, such as bio-attenuation, biostimulation, bioaugmentation and the manipulation of environmental conditions to enhance the activity of microbial enzymes. The addition of organic matter and flooding of the soil enhance DDT degradation. Microbial candidates for DDT remediation include micro-algae, fungi and bacteria. This review provide brief information and recommendation on microbial DDT remediation and its mechanisms.

Microbial degradation of the benzimidazole fungicide carbendazim by Bacillus velezensis HY-3479

Carbendazim (methyl benzimidazol-2-ylcarbamate: MBC) is a fungicide of the benzimidazole group that is widely used in the cultivation of pepper, ginseng, and many other crops. To remove the remnant carbendazim, many rhizobacteria are used as biodegradation agents. A bacterial strain of soil-isolated Bacillus velezensis HY-3479 was found to be capable of degrading MBC in M9 minimal medium supplemented with 250 mg/L carbendazim. The strain had a significantly higher degradation efficiency compared to the control strain Bacillus subtilis KACC 15590 in high-performance liquid chromatography (HPLC) analysis, and HY-3479 had the best degradation efficiency of 76.99% at 48 h. In gene expression analysis, upregulation of carbendazim-degrading genes (mheI, hdx) was observed in the strain. HY-3479 was able to use MBC as the sole source of carbon and nitrogen, but the addition of 12.5 mM NH4NO3 significantly increased the degradation efficiency. HPLC analysis showed that the degradation efficiency increased to 87.19% when NH4NO3 was added. Relative gene expression of mheI and hdx also increased for samples with NH4NO3 supplementation. The enzyme activity of the carbendazim-degrading enzyme and the 2-aminobenzimidazole-degrading enzyme was found to be highly present in the HY-3479 strain. It is the first reported B. velezensis strain to biodegrade carbendazim (MBC). The biodegradation activity of strain HY-3479 may be developed as a useful means for bioremediation and used as a potential microbial agent in sustainable agriculture.

Efficacy of novel bacterial consortia in degrading fipronil and thiobencarb in paddy soil: a survey for community structure and metabolic pathways

Introduction

Fipronil (FIP) and thiobencarb (THIO) represent widely utilized pesticides in paddy fields, presenting environmental challenges that necessitate effective remediation approaches. Despite the recognized need, exploring bacterial consortia efficiently degrading FIP and THIO remains limited.

Methods

This study isolated three unique bacterial consortia-FD, TD, and MD-demonstrating the capability to degrade FIP, THIO, and an FIP + THIO mixture within a 10-day timeframe. Furthermore, the bioaugmentation abilities of the selected consortia were evaluated in paddy soils under various conditions.

Results

Sequencing results shed light on the consortia's composition, revealing a diverse bacterial population prominently featuring Azospirillum, Ochrobactrum, Sphingobium, and Sphingomonas genera. All consortia efficiently degraded pesticides at 800 µg/mL concentrations, primarily through oxidative and hydrolytic processes. This metabolic activity yields more hydrophilic metabolites, including 4-(Trifluoromethyl)-phenol and 1,4-Benzenediol, 2-methyl-, for FIP, and carbamothioic acid, diethyl-, S-ethyl ester, and Benzenecarbothioic acid, S-methyl ester for THIO. Soil bioaugmentation tests highlight the consortia's effectiveness, showcasing accelerated degradation of FIP and THIO-individually or in a mixture-by 1.3 to 13-fold. These assessments encompass diverse soil moisture levels (20 and 100% v/v), pesticide concentrations (15 and 150 µg/g), and sterile conditions (sterile and non-sterile soils).

Discussion

This study offers an understanding of bacterial communities adept at degrading FIP and THIO, introducing FD, TD, and MD consortia as promising contenders for bioremediation endeavors.

Chlorpyrifos enrichment enhances tolerance of Anabaena sp. PCC 7119 to dimethoate

Organophosphorus (OP) insecticides are widely used for on-field pest control, constituting about 38% of global pesticide consumption. Insecticide tolerance has been recorded in microorganisms isolated from the contaminated soil. However, the cross-tolerance of laboratory-enriched cultures remains poorly understood. A chlorpyrifos tolerant (T) strain of Anabaena sp. PCC 7119 was developed through continuous enrichment of the wild strain (W). The cross-tolerance of the T strain to the OP insecticide dimethoate was assessed by measuring photosynthetic performance, key enzyme activities and degradation potential. The presence of dimethoate led to a significant reduction in the growth and pigment content of the W strain. In contrast, the T strain demonstrated improved growth and metabolic performance. Chl a and carotenoids were degraded faster than phycobiliproteins in both strains. The T strain exhibited superior photosynthetic performance, metabolic efficiency and photosystem functions, than of W strain, at both the tested dimethoate concentrations (100 and 200 μM). The treated T strain had more or less a normal OJIP fluorescence transient and bioenergetic functions, while the W strain showed a greater fluorescence rise at ≤ 300 μs indicating the inhibition of electron donation to PS II, and at 2 ms due to reduced electron release beyond QA. The T strain had significantly higher levels of esterase and phosphatases, further enhanced by insecticide treatment. Dimethoate degradation efficiency of the T strain was significantly higher than of the W strain. T strain also removed chlorpyrifos more efficiently than W strain at both the tested concentrations. The BCFs of both chlorpyrifos and dimethoate were lower in the T strain compared to the W strain. These findings suggest that the enriched strain exhibits promising results in withstanding dimethoate toxicity and could be explored for its potential as a bioremediating organism for OP degradation.

Biofilm formation in xenobiotic-degrading microorganisms

The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.

The pesticide thiamethoxam induced toxicity in Brassica juncea and its detoxification by Pseudomonas putida through biochemical and molecular modifications

Insecticides are extensively exploited by humans to destroy the pests one such compound thiamethoxam is widely used over crops to offer control over wide-array of sucking insect pests. The present study unravels the detoxification potential of Pseudomonas putida in thiamethoxam exposed B. juncea seedlings. The thiamethoxam application curtailed the fresh weight, dry weight and seedling length by 106.22%, 80.29% and 116.78% while P. putida revived these growth parameters in thiamethoxam exposed B. juncea seedlings by 59.65%, 72.99% and 164.56% respectively. The exogenous supplementation of P. putida resuscitated the photosynthetic efficiency of B. juncea seedlings exposed to thiamethoxam as total chlorophyll, chlorophyll a, chlorophyll b, carotenoid, flavonoid and anthocyanin contents were enhanced by 169.42%, 62.90%, 72.89%, 78.53%, 47.36% and 515.15% respectively in contrast to TMX exposed seedlings. Further, P. putida pre-treatment reinvigorated the osmoprotectant content in B. juncea seedlings grown in thiamethoxam as trehalose, glycine betaine and proline contents were thrusted by 21.20%, 58.98% and 34.26% respectively. The thiamethoxam exposure exorbitated the superoxide anion, hydrogen peroxide and MDA levels by 223.03%, 130.18% and 74.63% while P. putida supplementation slackened these oxidative burst levels by 41.75%, 3.79% and 29.09% respectively in thiamethoxam treated seedlings. Notably, P. putida inoculation in thiamethoxam exposed seedlings upregulated the enzymatic antioxidant and non-enzymatic antioxidant activities as SOD, CAT and glutathione were enhanced by 163.76%, 99.29% and 114.91% respectively in contrast to thiamethoxam treated seedlings. The gene expression analysis exhibited the negative impact of thiamethoxam on B. juncea seedlings as conferred by upregulation of chlorophyllase by 443.86 folds whereas P. putida application in thiamethoxam exposed seedlings downregulated the chlorophyllase expression by 248.73 folds and upregulated CXE, GST, NADH and POD genes by 0.44, 4.07, 1.43 and 0.98 folds respectively suggesting the molecular-level thiamethoxam detoxification efficiency of P. putida.

Pseudomonas aeruginosa based concurrent degradation of beta-cypermethrin and metabolite 3-phenoxybenzaldehyde, and its bioremediation efficacy in contaminated soils

Beta-cypermethrin is one of the widely used pyrethroid insecticides, and problems associated with the accumulation of its residues have aroused public attention. Thus, there is an urgent need to effectively remove the beta-cypermethrin that is present in the environment. Biodegradation is considered a cost-effective and environmentally friendly method for removing pesticide residues. However, the beta-cypermethrin-degrading microbes that are currently available are not optimal. In this study, Pseudomonas aeruginosa PAO1 was capable of efficiently degrading beta-cypermethrin and its major metabolite 3-phenoxybenzaldehyde in water/soil environments. Strain PAO1 could remove 91.4% of beta-cypermethrin (50 mg/L) in mineral salt medium within 120 h. At the same time, it also possesses a significant ability to metabolize 3-phenoxybenzaldehyde-a toxic intermediate of beta-cypermethrin. The Andrews equation showed that the maximum substrate utilization concentrations of beta-cypermethrin and 3-phenoxybenzaldehyde by PAO1 were 65.3558 and 49.6808 mg/L, respectively. Box-Behnken design-based response surface methodology revealed optimum conditions for the PAO1 strain-based degradation of beta-cypermethrin as temperature 30.6 °C, pH 7.7, and 0.2 g/L inoculum size. The results of soil remediation experiments showed that indigenous micro-organisms helped to promote the biodegradation of beta-cypermethrin in soil, and beta-cypermethrin half-life in non-sterilized soil was 6.84 days. The bacterium transformed beta-cypermethrin to produce five possible metabolites, including 3-phenoxybenzyl alcohol, methyl 2-(4-hydroxyphenoxy)benzoate, diisobutyl phthalate, 3,5-dimethoxyphenol, and 2,2-dimethyl-1-(4-phenoxyphenyl)propanone. Among them, methyl 2-(4-hydroxyphenoxy)benzoate and 3,5-dimethoxyphenol were first identified as the intermediate products during the beta-cypermethrin degradation. In addition, we propose a degradation pathway for beta-cypermethrin that is metabolized by strain PAO1. Beta-cypermethrin could be biotransformed firstly by hydrolysis of its carboxylester linkage, followed by cleavage of the diaryl bond and subsequent metabolism. Based on the above results, P. aeruginosa PAO1 could be a potent candidate for the beta-cypermethrin-contaminated environmental bioremediation.

Deciphering the kinetics and pathway of lindane biodegradation by novel soil ascomycete fungi for its implication in bioremediation

Lindane, an organochlorine pesticide, negatively affects living beings and the ecosystem. In this study, the potential of 9 Ascomycetes fungi, isolated from an hexachlorocyclohexane dumpsite soil, was tested for biodegradation of lindane. The strain Pleurostoma richardsiae (FN5) showed lindane biodegradation rate constant (K value) of 0.144 d-1 and a half-life of 4.8d. The formation of intermediate metabolites upon lindane degradation including γ-pentachlorocyclohexene, 2,4-dichlorophenol, phenol, benzene, 1,3- cyclohexadiene, and benzoic acid detected by GC-MS and the potential pathway adopted by the novel fungal strain FN5 for lindane biodegradation has been elucidated. The study of gene profiles with reference to linA and linB in strain FN5 confirmed the same protein family with the reported heterologs from other fungal strains in the NCBI database. This study for the first time provides a thorough understanding of lindane biodegradation by a novel soil-borne Ascomycota fungal strain for its possible application in field-scale bioremediation.

Synthetic biology tools for environmental protection

Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.

New roles for Bacillus thuringiensis in the removal of environmental pollutants

For a long time, the well-known Gram-positive bacterium Bacillus thuringiensis (Bt) has been extensively studied and developed as a biological insecticide for Lepidoptera and Coleoptera pests due to its ability to secrete a large number of specific insecticidal proteins. In recent years, studies have found that Bt strains can also potentially biodegrade residual pollutants in the environment. Many researchers have isolated Bt strains from multiple sites polluted by exogenous compounds and characterized and identified their xenobiotic-degrading potential. Furthermore, its pathway for degradation was also investigated at molecular level, and a number of major genes/enzymes responsible for degradation have been explored. At present, a variety of xenobiotics involved in degradation in Bt have been reported, including inorganic pollutants (used in the field of heavy metal biosorption and recovery and precious metal recovery and regeneration), pesticides (chlorpyrifos, cypermethrin, 2,2-dichloropropionic acid, etc.), organic tin, petroleum and polycyclic aromatic hydrocarbons, reactive dyes (congo red, methyl orange, methyl blue, etc.), and ibuprofen, among others. In this paper, the biodegrading ability of Bt is reviewed according to the categories of related pollutants, so as to emphasize that Bt is a powerful agent for removing environmental pollutants.

Microbial degradation as a powerful weapon in the removal of sulfonylurea herbicides

Sulfonylurea herbicides have been widely used worldwide and play a significant role in modern agricultural production. However, these herbicides have adverse biological effects that can damage the ecosystems and harm human health. As such, rapid and effective techniques that remove sulfonylurea residues from the environment are urgently required. Attempts have been made to remove sulfonylurea residues from environment using various techniques such as incineration, adsorption, photolysis, ozonation, and microbial degradation. Among them, biodegradation is regarded as a practical and environmentally responsible way to eliminate pesticide residues. Microbial strains such as Talaromyces flavus LZM1, Methylopila sp. SD-1, Ochrobactrum sp. ZWS16, Staphylococcus cohnii ZWS13, Enterobacter ludwigii sp. CE-1, Phlebia sp. 606, and Bacillus subtilis LXL-7 can almost completely degrade sulfonylureas. The degradation mechanism of the strains is such that sulfonylureas can be catalyzed by bridge hydrolysis to produce sulfonamides and heterocyclic compounds, which deactivate sulfonylureas. The molecular mechanisms associated with microbial degradation of sulfonylureas are relatively poorly studied, with hydrolase, oxidase, dehydrogenase and esterase currently known to play a pivotal role in the catabolic pathways of sulfonylureas. Till date, there are no reports specifically on the microbial degrading species and biochemical mechanisms of sulfonylureas. Hence, in this article, the degradation strains, metabolic pathways, and biochemical mechanisms of sulfonylurea biodegradation, along with its toxic effects on aquatic and terrestrial animals, are discussed in depth in order to provide new ideas for remediation of soil and sediments polluted by sulfonylurea herbicides.

Insights into the metabolic pathways and biodegradation mechanisms of chloroacetamide herbicides

Chloroacetamide herbicides are widely used around the world due to their high efficiency, resulting in increasing levels of their residues in the environment. Residual chloroacetamides and their metabolites have been frequently detected in soil, water and organisms and shown to have toxic effects on non-target organisms, posing a serious threat to the ecosystem. As such, rapid and efficient techniques that eliminate chloroacetamide residues from the ecosystem are urgently needed. Degradation of these herbicides in the environment mainly occurs through microbial metabolism. Microbial strains such as Acinetobacter baumannii DT, Bacillus altitudinis A16, Pseudomonas aeruginosa JD115, Sphingobium baderi DE-13, Catellibacterium caeni DCA-1, Stenotrophomonas acidaminiphila JS-1, Klebsiella variicola B2, and Paecilomyces marquandii can effectively degrade chloroacetamide herbicides. The degradation pathway of chloroacetamide herbicides in aerobic bacteria is mainly initiated by an N/C-dealkylation reaction, followed by aromatic ring hydroxylation and cleavage processes, whereas dechlorination is the initial reaction in anaerobic bacteria. The molecular mechanisms associated with bacterial degradation of chloroacetamide herbicides have been explored, with amidase, hydrolase, reductase, ferredoxin and cytochrome P450 oxygenase currently known to play a pivotal role in the catabolic pathways of chloroacetamides. The fungal pathway for the degradation of these herbicides is more complex with more diversified products, and the degradation enzymes and genes involved remain to be discovered. However, there are few reviews specifically summarizing the microbial degrading species and biochemical mechanisms of chloroacetamide herbicides. Here, we briefly summarize the latest progress resulting from research on microbial strain resources and enzymes involved in degradation of these herbicides and their corresponding genes. Furthermore, we explore the biochemical pathways and molecular mechanisms for biodegradation of chloroacetamide herbicides in depth, thereby providing a reference for further research on the bioremediation of such herbicides.

Combination of slurry-bioreactors and actinobacteria consortia as strategy to bioremediate chlordane-contaminated soils

Soil contamination caused by pesticides poses a significant environmental challenge, and addressing it requires effective solutions. Bioremediation, combining the utilization of slurry-bioreactors and microbial consortia, emerges as an appropiated strategy to tackle this issue. Therefore, this research evaluated the chlordane (CLD) removal efficiency by a Streptomyces consortium through bioaugmentation of polluted soils, and slurry-bioreactors. For that, a Streptomyces defined consortium with CLD removal abilities was inoculated in soil microcosms and soil-slurry bioreactors (SB), with (SB-TSB) and without stimulation (SB-water). In soil, CLD presence has no negative effect on consortium growth. This was supported by comparing its duplication time (7.48 ± 0.14 h) with the obtained in the biotic control (7.45 ± 0.04 h). Furthermore, 17% of pesticide removal by microbial action was detected in the treated microcosms. In SB, the microbial development was not affected by the pesticide presence. In SB-TSB, the microbial growth was higher than in SB-water. This was supported by its lesser duplication time (7.27 ± 0.17 h) with respect to the non-stimulated systems (10.88 ± 0.29 h). However, SB-water showed the highest CLD removal ability (34.8%), with a concomitant increase in the chloride ion release. In the phytotoxicity test, the vigor index showed that the bioremediation in SB-water did not exert adverse effects greater than those generated by the CLD. Indeed, the root length increased after the treatment. These findings demonstrate the versatility of the Streptomyces consortium to remediate solid and semi-solid matrices impacted with pesticides, and the advantage of using bioaugmented SB to enhance the pollutants removal and accelerating the clean-up time required.

High-efficiency degradation of methomyl by the novel bacterial consortium MF0904: Performance, structural analysis, metabolic pathways, and environmental bioremediation

Methomyl is a widely used carbamate pesticide, which has adverse biological effects and poses a serious threat to ecological environments and human health. Several bacterial isolates have been investigated for removing methomyl from environment. However, low degradation efficiency and poor environmental adaptability of pure cultures severely limits their potential for bioremediation of methomyl-contaminated environment. Here, a novel microbial consortium, MF0904, can degrade 100% of 25 mg/L methomyl within 96 h, an efficiency higher than that of any other consortia or pure microbes reported so far. The sequencing analysis revealed that Pandoraea, Stenotrophomonas and Paracoccus were the predominant members of MF0904 in the degradation process, suggesting that these genera might play pivotal roles in methomyl biodegradation. Moreover, five new metabolites including ethanamine, 1,2-dimethyldisulfane, 2-hydroxyacetonitrile, N-hydroxyacetamide, and acetaldehyde were identified using gas chromatography-mass spectrometry, indicating that methomyl could be degraded firstly by hydrolysis of its ester bond, followed by cleavage of the C-S ring and subsequent metabolism. Furthermore, MF0904 can successfully colonize and substantially enhance methomyl degradation in different soils, with complete degradation of 25 mg/L methomyl within 96 and 72 h in sterile and nonsterile soil, respectively. Together, the discovery of microbial consortium MF0904 fills a gap in the synergistic metabolism of methomyl at the community level and provides a potential candidate for bioremediation applications.

Esterase and ALDH dehydrogenase-based pesticide degradation by Bacillus brevis 1B from a contaminated environment

The isolated bacterial strain (Bacillus brevis strain 1 B) showed a maximum tolerated level of 450 mg L^-1 of the selected pesticides namely: imidacloprid, fipronil, cypermethrin, and sulfosulfuron. Within 15 days of the experiment, strain 1 B was able to reduce up to 95% of a pesticide mixture (20 mg L^-1) in a carbon-deficient medium (minimal medium). The optimal conditions obtained using Response Surface Methodology (RSM) were: inoculums; 2.0 × 10⁷ CFU mL^-1, shaking speed; 120 rpm, and pesticide concentration; 80 mg L^-1. After 15 days of soil-based bioremediation using strain 1 B, the degradation pattern for imidacloprid, fipronil, cypermethrin, sulfosulfuron, and control was 99, 98.5, 94, 91.67, and 7%, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis was used to determine the intermediate metabolites of cypermethrin with bacterial 1 B as 2-cyclopenten-1-one, 2-methylpyrrolidine, 2-oxonanone, 2-pentenoic acid, 2-penten-1-ol, hexadecanoic acid or palmitic acid, pentadecanoic acid, 3-cyclopentylpropionic acid, and 2-dimethyl. Furthermore, genes encoding aldehyde dehydrogenase (ALDH) and esterase were expressed under stress conditions and connected to pesticide bioremediation. Hence the efficacy of Bacillus brevis (1 B) could be employed for the bioremediation of pesticide mixtures and other toxic substances (dye, polyaromatic hydrocarbon, etc.) from contaminated sites.

Review on Performance of Aspergillus and Penicillium Species in Biodegradation of Organochlorine and Organophosphorus Pesticides

The use of pesticides in agricultural practices raises concerns considering the toxic effects they generate in the environment; thus, their sustainable application in crop production remains a challenge. One of the frequently addressed issues regarding their application includes the development of a sustainable and ecofriendly approach for their degradation. Since the filamentous fungi can bioremediate various xenobiotics owing to their efficient and versatile enzymatic machinery, this review has addressed their performance in the biodegradation of organochlorine and organophosphorus pesticides. It is focused particularly on fungal strains belonging to the genera Aspergillus and Penicillium, since both are ubiquitous in the environment, and often abundant in soils contaminated with xenobiotics. Most of the recent reviews on microbial biodegradation of pesticides focus primarily on bacteria, and the soil filamentous fungi are mentioned only marginally there. Therefore, in this review, we have attempted to demonstrate and highlight the exceptional potential of aspergilli and penicillia in degrading the organochlorine and organophosphorus pesticides (e.g., endosulfan, lindane, chlorpyrifos, and methyl parathion). These biologically active xenobiotics have been degraded by fungi into various metabolites efficaciously, or these are completely mineralized within a few days. Since they have demonstrated high rates of degradation activity, as well as high tolerance to pesticides, most of the Aspergillus and Penicillium species strains listed in this review are excellent candidates for the remediation of pesticide-contaminated soils.

Current insights into the microbial degradation of nicosulfuron: Strains, metabolic pathways, and molecular mechanisms

Nicosulfuron is among the sulfonylurea herbicides that are widely used to control annual and perennial grass weeds in cornfields. However, nicosulfuron residues in the environment are likely to cause long-lasting harmful environmental and biological effects. Nicosulfuron degrades via photo-degradation, chemical hydrolysis, and microbial degradation. The latter is crucial for pesticide degradation and has become an essential strategy to remove nicosulfuron residues from the environment. Most previous studies have focused on the screening, degradation characteristics, and degradation pathways of biodegrader microorganisms. The isolated nicosulfuron-degrading strains include Bacillus, Pseudomonas, Klebsiella, Alcaligenes, Rhodopseudomonas, Ochrobactrum, Micrococcus, Serratia, Penicillium, Aspergillus, among others, all of which have good degradation efficiency. Two main intermediates, 2-amino-4,6-dimethoxypyrimidine (ADMP) and 2-aminosulfonyl-N,N-dimethylnicotinamide (ASDM), are produced during microbial degradation and are derived from the C-N, C-S, and S-N bond breaks on the sulfonylurea bridge, covering almost every bacterial degradation pathway. In addition, enzymes related to the degradation of nicosulfuron have been identified successively, including the manganese ABC transporter (hydrolase), Flavin-containing monooxygenase (oxidase), and E3 (esterase). Further in-depth studies based on molecular biology and genetics are needed to elaborate on their role in the evolution of novel catabolic pathways and the microbial degradation of nicosulfuron. To date, few reviews have focused on the microbial degradation and degradation mechanisms of nicosulfuron. This review summarizes recent advances in nicosulfuron degradation and comprehensively discusses the potential of nicosulfuron-degrading microorganisms for bioremediating contaminated environments, providing a reference for further research development on nicosulfuron biodegradation in the future.

Detoxification of typical nitrogenous heterocyclic compound from pharmaceutical wastewater by mixed microbial consortia

Microbial consortia HY3 and JY3 with high degradation efficiency of 2-Diethylamino-4-hydroxy-6-methylpyrimidine (DHMP) were isolated from aerobic and parthenogenic ponds of DHMP-containing pharmaceutical wastewater, respectively. Both consortia were enriched and reached stable degradation performance with a DHMP concentration of 1500 mg L^-1. The DHMP degradation efficiencies of HY3 and JY3 were 95.66% ± 0.24% and 92.16% ± 2.34% under the condition of shaking at 180 r·min^-1 and the temperature of 30 °C for 72 h. And the removal efficiencies of chemical oxygen demand were 89.14% ± 4.78% and 80.30% ± 11.74%, respectively. High-throughput sequencing results indicated that three bacterial phyla of Proteobacteria, Bacteroidetes, and Actinobacteria were dominant in both HY3 and JY3, but their dominances varied. At the genus level, the richness of Unclassified Comamonadaceae (34.23%), Paracoccus (14.75%), and Brevundimonas (13.94%) ranked top three in HY3 whereas Unclassified Comamonadaceae (40.80%), Unclassified Burkholderiales (13.81%) and Delftia (13.11%) were dominant in JY3. The metabolites of DHMP degradation by HY3 and JY3 were analyzed in detail. Two pathways for cleavage of the nitrogenous heterocyclic ring were speculated, one of which was identified for the first time in this study.

Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia

Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.

Cellular Response and Molecular Mechanism of Glyphosate Degradation by Chryseobacterium sp. Y16C

Glyphosate is one of the most widely used herbicides worldwide. Unfortunately, the continuous use of glyphosate has resulted in serious environmental contamination and raised public concern about its impact on human health. In our previous study, Chryseobacterium sp. Y16C was isolated and characterized as an efficient degrader that can completely degrade glyphosate. However, the biochemical and molecular mechanisms underlying its glyphosate biodegradation ability remain unclear. In this study, the physiological response of Y16C to glyphosate stimulation was characterized at the cellular level. The results indicated that, in the process of glyphosate degradation, Y16C induced a series of physiological responses in the membrane potential, reactive oxygen species levels, and apoptosis. The antioxidant system of Y16C was activated to alleviate the oxidative damage caused by glyphosate. Furthermore, a novel gene, goW, was expressed in response to glyphosate. The gene product, GOW, is an enzyme that catalyzes glyphosate degradation, with putative structural similarities to glycine oxidase. GOW encodes 508 amino acids, with an isoelectric point of 5.33 and a molecular weight of 57.2 kDa, which indicates that it is a glycine oxidase. GOW displays maximum enzyme activity at 30 °C and pH 7.0. Additionally, most of the metal ions exhibited little influence on the enzyme activity except for Cu²⁺. Finally, with glyphosate as the substrate, the catalytic efficiency of GOW was higher than that of glycine, although opposite results were observed for the affinity. Taken together, the current study provides new insights to deeply understand and reveal the mechanisms of glyphosate degradation in bacteria.

Synthetic bacteria for the detection and bioremediation of heavy metals

Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Microbial degradation of organochlorine pesticide: 2,4-Dichlorophenoxyacetic acid by axenic and mixed consortium

The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and the ecosystem. Three potential strains having the capability to degrade 2,4-D were isolated from on site agricultural soil and identified as Arthrobacter sp. SVMIICT25, Sphingomonas sp. SVMIICT11 and Stenotrophomonas sp. SVMIICT13. Over 12 days of incubation, 81-90% of 100 mg/L of 2,4-D degradation was observed at 2% inoculum. A shorter lag phase with 80% of degradation efficiency was observed within 5 days when the inoculum size was increased to 10%. Six microbial consortia were prepared by combining the isolates along with in-house strains, Bacillus sp. and Pseudomonas sp. Consortia R3 (Arthrobacter sp. + Sphingomonas sp.), operated with 10% of inoculum, showed 85-90% degradation within 4 days and 98-100% in 9 days. Further, targeted exo-metabolite analysis confirmed the presence and catabolism of intermediate 2,4-dichlorophenol and 4-chlorophenol compounds.

Rapid Biodegradation of the Organophosphorus Insecticide Acephate by a Novel Strain Burkholderia sp. A11 and Its Impact on the Structure of the Indigenous Microbial Community

The acephate-degrading microbes that are currently available are not optimal. In this study, Burkholderia sp. A11, an efficient degrader of acephate, presented an acephate-removal efficiency of 83.36% within 56 h (100 mg·L^-1). The A11 strain has a broad substrate tolerance and presents a good removal effect in the concentration range 10-1600 mg·L^-1. Six metabolites from the degradation of acephate were identified, among which the main products were methamidophos, acetamide, acetic acid, methanethiol, and dimethyl disulfide. The main degradation pathways involved include amide bond breaking and phosphate bond hydrolysis. Moreover, strain A11 successfully colonized and substantially accelerated acephate degradation in different soils, degrading over 90% of acephate (50-200 mg·kg^-1) within 120 h. 16S rDNA sequencing results further confirmed that the strain A11 gradually occupied a dominant position in the soil microbial communities, causing slight changes in the diversity and composition of the indigenous soil microbial community structure.

Metaproteomic and gene expression analysis of interspecies interactions in a PAH-degrading synthetic microbial consortium constructed with the key microbes of a natural consortium

Polycyclic Aromatic Hydrocarbons (PAHs) impose adverse effects on the environment and human life. The use of synthetic microbial consortia is promising in bioremediation of contaminated sites with these pollutants. However, the design of consortia taking advantage of natural interactions has been poorly explored. In this study, a dual synthetic bacterial consortium (DSC_AB) was constructed with two key members (Sphingobium sp. AM and Burkholderia sp. Bk), of a natural PAH degrading consortium. DSC_AB showed significantly enhanced degradation of PAHs and toxic intermediary metabolites relative to the axenic cultures, indicating the existence of synergistic relationships. Metaproteomic and gene-expression analyses were applied to obtain a view of bacterial performance during phenanthrene removal. Overexpression of the Bk genes, naph, biph, tol and sal and the AM gene, ahdB, in DSC_AB relative to axenic cultures, demonstrated that both strains are actively participating in degradation, which gave evidence of cross-feeding. Several proteins related to stress response were under-expressed in DSC_AB relative to axenic cultures, indicating that the division of labour reduces cellular stress, increasing the efficiency of degradation. This is the one of the first works revealing bacterial relationships during PAH removal in a synthetic consortium applying an omics approach. Our findings could be used to develop criteria for evaluating the potential effectiveness of synthetic bacterial consortia in bioremediation.

The role of microorganisms in petroleum degradation: Current development and prospects

Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.

Bioremediation of the herbicide glyphosate in polluted soils by plant-associated microbes

Most productive lands worldwide base their crop production on the use of glyphosate (GLY)-resistant plants, and consequently, widespread use of this herbicide has led to environmental issues that need to be solved. Soil bioremediation technologies based on degradation of GLY by microorganisms are strategies that have been considered useful to solve this environmental problem. Recently, a further step has been taken considering the use of bacteria that interact with plants, either alone or both bacteria and plant together, for the removal of GLY herbicide. Plant-interacting microorganisms with plant growth-promoting traits can also enhance plant growth and contribute to successful bioremediation strategies.

Bioremediation potential of laccase for catalysis of glyphosate, isoproturon, lignin, and parathion: Molecular docking, dynamics, and simulation

The present study aimed to investigate the catalytic degradation produced by laccase in the detoxification of glyphosate, isoproturon, lignin polymer, and parathion. We explored laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion using molecular docking (MD) and molecular dynamics simulation (MDS) approaches. The results suggest that laccase interacts well with glyphosate, lignin polymer, isoproturon, and parathion during biodegradation. We calculated the root mean square deviations (RMSD) of laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion as 0.24 ± 0.02, 0.59 ± 0.32, 0.43 ± 0.07, and 0.43 ± 0.06 nm, respectively. In an aqueous solution, the stability of laccase with glyphosate, lignin polymer, isoproturon, and parathion is mediated through the formation of hydrophobic interactions, hydrogen bonds, and van der Waals interactions. The presence of xenobiotic toxic compounds in the active site changed the conformation of laccase. MDS of the laccase-substrate complexes confirmed their stability during catalytic degradation. Laccase assay results confirmed that the degradation of syringol, dihydroconiferyl alcohol, guaiacol, parathion, isoproturon, and glyphosate were 100%, 99.31%, 95.69%, 60.96%, 54.51%, and 48.34% within 2 h, respectively. Taken together, we describe a novel method to understand the molecular-level biodegradation of xenobiotic compounds through laccase and its potential application in contaminant removal.

Environmental occurrence, toxicity concerns, and biodegradation of neonicotinoid insecticides

Neonicotinoids (NEOs) are fourth generation pesticides, which emerged after organophosphates, pyrethroids, and carbamates and they are widely used in vegetables, fruits, cotton, rice, and other industrial crops to control insect pests. NEOs are considered ideal substitutes for highly toxic pesticides. Multiple studies have reported NEOs have harmful impacts on non-target biological targets, such as bees, aquatic animals, birds, and mammals. Thus, the remediation of neonicotinoid-sullied environments has gradually become a concern. Microbial degradation is a key natural method for eliminating neonicotinoid insecticides, as biodegradation is an effective, practical, and environmentally friendly strategy for the removal of pesticide residues. To date, several neonicotinoid-degrading strains have been isolated from the environment, including Stenotrophomonas maltophilia, Bacillus thuringiensis, Ensifer meliloti, Pseudomonas stutzeri, Variovorax boronicumulans, and Fusarium sp., and their degradation properties have been investigated. Furthermore, the metabolism and degradation pathways of neonicotinoids have been broadly detailed. Imidacloprid can form 6-chloronicotinic acid via the oxidative cleavage of guanidine residues, and it is then finally converted to non-toxic carbon dioxide. Acetamiprid can also be demethylated to remove cyanoimine (=N-CN) to form a less toxic intermediate metabolite. A few studies have discussed the neonicotinoid toxicity and microbial degradation in contaminated environments. This review is focused on providing an in-depth understanding of neonicotinoid toxicity, microbial degradation, catabolic pathways, and information related to the remediation process of NEOs. Future research directions are also proposed to provide a scientific basis for the risk assessment and removal of these pesticides.

Bacillus Consortia Modulate Transcriptional and Metabolic Machinery of Arabidopsis Plants for Salt Tolerance

Rhizobacteria that are helpful to plants can lessen the impacts of salt stress, and they may hold promise for the development of sustainable agriculture in the future. The present study was intended to explicate consortia of salt-tolerant plant-beneficial rhizobacteria for the amelioration of salinity stress in Arabidopsis plants. Inoculation with both the consortia positively influenced the growth of plants as indicated by total chlorophyll content, MDA content, and antioxidant enzyme activities under stressful conditions. Both the multi-trait consortia altered the expression profiles of stress-related genes including CSD1, CAT1, Wrky, Ein, Etr, and ACO. Furthermore, the metabolomic analysis indicated that inoculated plants modulated the metabolic profiles to stimulate physiological and biochemical responses in Arabidopsis plants to mitigate salt stress. Our study affirms that the consortia of salt-tolerant bacterial strains modulate the transcriptional as well as metabolic machinery of plants to protect them from salinity stress. Nevertheless, the findings of this study revealed that consortia are composed of salt-tolerant bacterial strains viz. Bacillus safensis NBRI 12M, B. subtilis NBRI 28B, and B. subtilis NBRI 33N demonstrated significant improvement in Arabidopsis plants under saline stress conditions.

Co-inducible Catabolism of 2-Naphthol Initiated by Hydroxylase CehC1C2 in Rhizobium sp. X9 Removed Its Ecotoxicity

2-Naphthol, which originates from various industrial activities, is widely disseminated through the discharge of industrial wastewater and is, thus, harmful to the water ecosystem, agricultural production, and human health. In this study, the carbaryl degrading strain Rhizobium sp. X9 was proven to be able to degrade 2-naphthol and reduce its toxicity to rice (Oryza sativa) and Chlorella ellipsoidea. Two-component hydroxylase CehC1C2 is responsible for the initial step of degradation and generates 1,2-dihydroxynaphthalene, which is further degraded by the ceh cluster. The transcription of gene cluster cehC1C2 could be induced when both 2-naphthol and glucose were added. A bioinformatic analysis revealed that two transcriptional regulators, the inhibitor CehR2 and the activator CehR3, could be involved in this process. Our study elucidated the molecular mechanism of microbial degradation of 2-naphthol and provided an effective strategy for the in situ remediation of 2-naphthol contamination in the environment.

Isolation and characterization of synthetic pyrethroids-degrading bacterial strains from agricultural soil

Pyrethroid pesticides are commonly used for pest control in agriculture setup, veterinary and home garden. They are now posing increased risks to non-targeted organisms associated to human beings due to their considerable use. The present work deals with the isolation of bacteria with tolerance to high concentrations of bifenthrin and cypermethrin from contaminated soil. Enrichment culture technique (bifenthrin concentration = 50-800 mg/L) was used for bacterial isolation. Bacteria that showed growth on minimal media with bifenthrin were also sub-cultured on minimal media with cypermethrin. Bacteria showing luxurious growth on both the pyrethroid, were screened out based on their morphological, biochemical parameters and by API 20NE Kit. Phylogenetic studies revealed that, one bacterial isolate (MG04) belonging to Acinetobacter lwoffii and other five bacterial isolates (MG06, MG05, MG01, MG03 and MG02) cluster with Pseudomonas aeruginosa, Pseudomonas putida respectively. Isolated members of genera Pseudomonas and Acinetobacter could be used for further detailed degradation studies by using FTIR, HPLC-MS or GC-MS analysis.

Pesticide contamination in agro-ecosystems: toxicity, impacts, and bio-based management strategies

Continuous rise in application of pesticides in the agro-ecosystems in order to ensure food supply to the ever-growing population is of greater concern to the human health and the environment. Once entered into the agro-ecosystem, the fate and transport of pesticides is determined largely by the nature of pesticides and the soil attributes, in addition to the soil-inhabiting microbes, fauna, and flora. Changes in the soil microbiological actions, soil properties, and enzymatic activities resulting from pesticide applications are the important factors substantially affecting the soil productivity. Disturbances in the microbial community composition may lead to the considerable perturbations in cycling of major nutrients, metals, and subsequent uptake by plants. Indiscriminate applications are linked with the accumulation of pesticides in plant-based foods, feeds, and animal products. Furthermore, rapid increase in the application of pesticides having long half-life has also been reported to contaminate the nearby aquatic environments and accumulation in the plants, animals, and microbes surviving there. To circumvent the negative consequences of pesticide application, multitude of techniques falling in physical, chemical, and biological categories are presented by different investigators. In the present study, important findings pertaining to the pesticide contamination in cultivated agricultural soils; toxicity on soil microbes, plants, invertebrates, and vertebrates; effects on soil characteristics; and alleviation of toxicity by bio-based management approaches have been thoroughly reviewed. With the help of bibliometric analysis, thematic evolution and research trends on the bioremediation of pesticides in the agro-ecosystems have also been highlighted.

Biodegradation of the Pesticides Bifenthrin and Fipronil by Bacillus Isolated from Orange Leaves

The pyrethroid bifenthrin and the phenylpyrazole fipronil are widely employed insecticides, and their extensive use became an environmental issue. Therefore, this study evaluated their biodegradation employing bacterial strains of Bacillus species isolated from leaves of orange trees, aiming at new biocatalysts with high efficiency for use singly and in consortium. Experiments were performed in liquid culture medium at controlled temperature and stirring (32 °C, 130 rpm). After 5 days, residual quantification by HPLC-UV/Vis showed that Bacillus amyloliquefaciens RFD1C presented 93% biodegradation of fipronil (10.0 mg.L^-1 initial concentration) and UPLC-HRMS analyses identified the metabolite fipronil sulfone. Moreover, Bacillus pseudomycoides 3RF2C showed a biodegradation of 88% bifenthrin (30.0 mg.L^-1 initial concentration). A consortium composed of the 8 isolated strains biodegraded 81% fipronil and 51% bifenthrin, showing that this approach did not promote better results than the most efficient strains employed singly, although high rates of biodegradation were observed. In conclusion, bacteria of the Bacillus genus isolated from leaves of citrus biodegraded these pesticides widely applied to crops, showing the importance of the plant microbiome for degradation of toxic xenobiotics.

Latest eco-friendly approaches for pesticides decontamination using microorganisms and consortia microalgae: A comprehensive insights, challenges, and perspectives

Pesticides are chemical compounds that are considered toxic to many organisms, including humans. Their elimination from polluted sites attracted the attention of Scientifics in the last decade; Among the various methods used to decontaminate pesticides from the environment, the microbial-algae consortium is a promising bioremediation technology, which implies several advantages as an eco-friendly process that generate biomass produced that could be valorized in the form of bioenergy, In this review, we will discuss the latest eco-friendly approaches using microorganisms to remediate sites contaminated by pesticides, and shows the ability of microbial, algae and their consortium to remove pesticides and the role of different enzymes in degradation processes.

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.

Effects of Free or Immobilized Bacterium Stenotrophomonas acidaminiphila Y4B on Glyphosate Degradation Performance and Indigenous Microbial Community Structure

The overuse of glyphosate has resulted in serious environmental contamination. Thus, effective techniques to remove glyphosate from the environment are required. Herein, we isolated a novel strain Stenotrophomonas acidaminiphila Y4B, which completely degraded glyphosate and its major metabolite aminomethylphosphonic acid (AMPA). Y4B degraded glyphosate over a broad concentration range (50-800 mg L^-1), with a degradation efficiency of over 98% within 72 h (50 mg L^-1). Y4B degraded glyphosate via the AMPA pathway by cleaving the C-N bond, followed by degradation of AMPA and subsequent metabolism. Y4B demonstrated strong competitiveness and substantially accelerated the degradation of glyphosate in different soils, degrading 71.93 and 89.81% of glyphosate (400 mg kg^-1) within 5 days in sterile and nonsterile soils, respectively. The immobilized cells of Y4B were more efficient than their free cells and they displayed excellent biodegradation efficiency in a sediment-water system. Taken together, Y4B is an ideal degrader for the bioremediation of glyphosate-contaminated sites.

Microbial degradation and transformation of benzo[a]pyrene by using a white-rot fungus Pleurotus eryngii F032

Polycyclic aromatic hydrocarbons (PAHs) are environmentally recalcitrant contaminants formed from naturally or incomplete combustion of organic materials and some of them are difficult to degrade due to their hydrophobicity and persistency. Benzo [a]pyrene (BaP), is one of PAHs that having five fused benzene and reported as mutagenic, carcinogenic and teratogenic compounds. Biodegradation is one of promising techniques due to its relatively low economic cost and microorganism is a natural capacity to consume hydrocarbons. In this investigation, Pleurotus eryngii F032 was grown in 20 mL of modified mineral salt broth (MSB) supplemented with BaP under static and agitated culture. Within 20 days, static culture removed 59% of BaP, whereas agitated culture removed the highest amount (73%). To expedite BaP elimination, the mechanism and behavior of BaP biosorption and biotransformation by Pleurotus eryngii F032 were additionally examined by gas chromatography-mass spectrometer (GC-MS). The optimal conditions for P. eryngii F032 to eliminate BaP were 25 °C, a C/N ratio of 8, pH 3 and 0.2% inoculum concentration. At an initial BaP content of 10 mg/L, more than 50% was effectively eliminated within 20 days under these conditions. Salinity, glucose, and rhamnolipids were the most important factors impacting BaP biodegradation. GC-MS found degradation products such as BaP-3,6-quinone, indicating plausible metabolic routes. Finally, it may be assumed that the primary mechanism by which white-rot fungi eliminate BaP is by the utilization of biotransformation enzymes such as laccase to mineralize the PAHs. Hence, Pleurotus eryngii F032 could be an ideal candidate to treat PAHs contaminated soils.

Novel mechanism and degradation kinetics of allethrin using Bacillus megaterium strain HLJ7 in contaminated soil/water environments

As a common pyrethroid insecticide, allethrin is widely used for various purposes in agriculture and home applications. At present, allethrin residues have been frequently detected worldwide, yet little is known about the kinetics and degradation mechanisms of this insecticide. In this study, a highly efficient allethrin-degrading bacterium, Bacillus megaterium strain HLJ7, was obtained through enrichment culture technology. Strain HLJ7 can remove 96.5% of 50 mg L^-1 allethrin in minimal medium within 11 days. The first-order kinetic analysis of degradation demonstrated that the half-life of allethrin degradation by strain HLJ7 was 3.56 days, which was significantly shorter than the 55.89 days of the control. The Box-Behnken design of the response surface method optimized the degradation conditions for strain HLJ7: temperature 32.18 °C, pH value 7.52, and inoculation amount 1.31 × 10⁷ CFU mL^-1. Using Andrews equation, the optimal concentration of strain HLJ7 to metabolize allethrin was determined to be 21.15 mg L^-1, and the maximum specific degradation rate (q_max), half-rate constant (K_s) and inhibition coefficient (K_i) were calculated to be 1.80 d^-1, 1.85 mg L^-1 and 68.13 mg L^-1, respectively. Gas chromatography-mass spectrometry identified five intermediate metabolites, suggesting that allethrin could be degraded firstly by cleavage of its carboxylester bond, followed by degradation of the five-carbon ring and subsequent metabolism. The results of soil remediation experiments showed that strain HLJ7 has excellent bioremediation potential in the soils. After 15 days of treatment, about 70.8% of the initial allethrin (50 mg kg^-1) was removed and converted into nontoxic intermediate metabolites, and its half-life was significantly reduced in the soils. Taken together, these findings shed light on the degradation mechanisms of allethrin and also highlight the promising potentials of B. megaterium HLJ7 in bioremediation of allethrin-comtaminated environment.

Indigenous bacterial consortium-mediated cypermethrin degradation in the presence of organic amendments and Zea mays plants

Cypermethrin is a toxic pyrethroid insecticide that is widely used in agricultural and household activities. One of the most serious issues is its persistence in the environment, because it is easily transported to the soil and aquatic ecosystem. The biodegradation of cypermethrin is emerging as an environmentally friendly method for large-scale treatment. This study examined the application of a novel binary bacterial combination-based (Bacillus thuringiensis strain SG4 and Bacillus sp. strain SG2) approach used for the enhanced degradation of cypermethrin from the environment. The bacterial strains degraded cypermethrin (80% and 85%) in the presence of external nitrogen sources (KNO₃ and NaNO₃). Furthermore, when immobilized in agar disc beads, the co-culture degraded cypermethrin (91.3%) with a half-life (t_1/2) of 4.3 days compared to 4.9 days using sodium alginate beads. Cereal straw, farmyard manure, press mud compost, fresh cow dung, and gypsum were used as organic amendments in the soil to stimulate cypermethrin degradation. Cereal straw promoted the fastest cypermethrin degradation among the different organic amendments tested, with a t_1/2 of 4.4 days. The impact of cypermethrin-degrading bacterial consortium on cypermethrin rhizoremediation was also investigated. Bacterial inoculums exhibited beneficial effects on plant biomass. Moreover, Zea mays and the bacterial partnership substantially enhanced cypermethrin degradation in soil. Six intermediate metabolites were detected during the degradation of cypermethrin, indicating that cypermethrin could be degraded first by the hydrolysis of its carboxyl ester bond, followed by the cleavage of the diaryl linkage and subsequent metabolism. Our findings highlight the promising potential and advantages of the bacterial consortium for the bioremediation of a cypermethrin-contaminated environment.

Current status of pesticide effects on environment, human health and it's eco-friendly management as bioremediation: A comprehensive review

Pesticides are either natural or chemically synthesized compounds that are used to control a variety of pests. These chemical compounds are used in a variety of sectors like food, forestry, agriculture and aquaculture. Pesticides shows their toxicity into the living systems. The World Health Organization (WHO) categorizes them based on their detrimental effects, emphasizing the relevance of public health. The usage can be minimized to a least level by using them sparingly with a complete grasp of their categorization, which is beneficial to both human health and the environment. In this review, we have discussed pesticides with respect to their global scenarios, such as worldwide distribution and environmental impacts. Major literature focused on potential uses of pesticides, classification according to their properties and toxicity and their adverse effect on natural system (soil and aquatic), water, plants (growth, metabolism, genotypic and phenotypic changes and impact on plants defense system), human health (genetic alteration, cancer, allergies, and asthma), and preserve food products. We have also described eco-friendly management strategies for pesticides as a green solution, including bacterial degradation, myco-remediation, phytoremediation, and microalgae-based bioremediation. The microbes, using catabolic enzymes for degradation of pesticides and clean-up from the environment. This review shows the importance of finding potent microbes, novel genes, and biotechnological applications for pesticide waste management to create a sustainable environment.