Identification of the key amino acid sites of the carbendazim hydrolase (MheI) from a novel carbendazim-degrading strain Mycobacterium sp. SD-4

Synergistic insights into pesticide persistence and microbial dynamics for bioremediation

Rampant use of fertilizers and pesticides for boosting agricultural crop productivity has proven detrimental impact on land, water, and air quality globally. Although fertilizers and pesticides ensure greater food security, their unscientific management negatively impacts soil fertility, structure of soil microbiome and ultimately human health and hygiene. Pesticides exert varying impacts on soil properties and microbial community functions, contingent on factors such as their chemical structure, mode of action, toxicity, and dose-response characteristics. The diversity of bacterial responses to different pesticides presents a valuable opportunity for pesticide remediation. In this context, OMICS technologies are currently under development, and notable advancements in gene editing, including CRISPR technologies, have facilitated bacterial engineering, opening promising avenues for reducing toxicity and enhancing biological remediation. This paper provides a holistic overview of pesticide dynamics, with a specific focus on organophosphate, organochlorine, and pyrethroids. It covers their occurrence, activity, and potential mitigation strategies, with an emphasis on the microbial degradation route. Subsequently, the pesticide degradation pathways, associated genes and regulatory mechanisms, associated OMICS approaches in soil microbes with a special emphasis on CRISPR/Cas9 are also being discussed. Here, we analyze key environmental factors that significantly impact pesticide degradation mechanisms and underscore the urgency of developing alternative strategies to diminish our reliance on synthetic chemicals.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Deciphering the degradation characteristics of the fungicides imazalil and penflufen and their effects on soil bacterial community composition, assembly, and functional profiles

The adsorption-desorption and degradation characteristics of two widely applied fungicides, imazalil and penflufen, and the responses of soil bacterial diversity, structure, function, and interaction after long-term exposure were systemically studied in eight different soils. The adsorption ability of imazalil in soil was significantly higher than that of penflufen. Both imazalil and penflufen degraded slowly in most soils following the order: imazalil > penflufen, with soil pH, silt, and clay content being the potential major influencing factors. Both imazalil and penflufen obviously inhibited the soil microbial functional diversity, altered the soil bacterial community and decreased its diversity. Although exposure to low and high concentrations of imazalil and penflufen strengthened the interactions among the soil bacterial communities, the functional diversity of the co-occurrence network tended to be simple at high concentrations, especially in penflufen treatment. Both imazalil and penflufen markedly disturbed soil nitrogen cycling, especially penflufen seriously inhibited most nitrogen cycling processes, such as nitrogen fixation and nitrification. Meanwhile, sixteen and ten potential degradative bacteria of imazalil and penflufen, respectively, were found in soils, including Kaistobacter and Lysobacter. Collectively, the long-term application of imazalil and penflufen could cause residual accumulation in soils and subsequently result in serious negative effects on soil ecology.

The long-acting herbicide mesosulfuron-methyl inhibits soil microbial community assembly mediating nitrogen cycling

Mesosulfuron-methyl is a widely used herbicide in wheat fields. We previously reported that mesosulfuron-methyl alters the bacterial/fungal community structure in experimental indoor microcosms, ultimately affecting NO₃^--N and NH₄⁺-N contents in soil nitrogen (N) cycling. However, how mesosulfuron-methyl application alter soil N cycling by changing microbial community assembly is unknown. Here, we designed an outdoor experiment comprising 2-month periods to investigate changes in soil N-cycle functional genes and structural shifts in the microbial community assembly in response to mesosulfuron-methyl applied at 11.25 and 112.5 g a.i. hm^-2. Results showed that high mesosulfuron-methyl input significantly decreased AOA amoA and nirK abundances within the initial 15 days, but increased AOB amoA on day 60. The nifH abundance displayed a stimulation-inhibition trend. Moreover, high mesosulfuron-methyl input decreased the network's complexity, and newly formed multiple network modules exhibited strong negative associations with nifH, AOB amoA, nirK and nirS. Further structural equation model demonstrated that mesosulfuron-methyl did reveal strong direct inhibition of nirK, and it indirectly affected nirK by changing nifH abundance and Planomicrobium. Thus mesosulfuron-methyl perturbs N-cycling processes by reshaping bacterial community assembly. Taken together, our study provides theoretical support for determining the microbiological mechanism by which mesosulfuron-methyl affects soil N cycling.

Untargeted Metabolomics Reveals Lipid Impairment in the Liver of Adult Zebrafish (Danio rerio) Exposed to Carbendazim

Carbendazim is a systemic fungicide used in several countries, particularly in Brazil. However, studies suggest that it is related to the promotion of tumors, endocrine disruption, and toxicity to organisms, among other effects. As a result, carbendazim is not allowed in the United States, Australia, and some European Union countries. Therefore, further studies are necessary to evaluate its effects, and zebrafish is a model routinely used to provide relevant information regarding the acute and long-term effects of xenobiotics. In this way, zebrafish water tank samples (water samples from aquari containing zebrafish) and liver samples from animals exposed to carbendazim at a concentration of 120 μg/L were analyzed by liquid chromatography coupled to high-resolution mass spectrometry, followed by multivariate and univariate statistical analyses, using the metabolomics approach. Our results suggest impairment of lipid metabolism with a consequent increase in intrahepatic lipids and endocrine disruption. Furthermore, the results suggest two endogenous metabolites as potential biomarkers to determine carbendazim exposure. Finally, the present study showed that it is possible to use zebrafish water tank samples to assess the dysregulation of endogenous metabolites to understand biological effects. Environ Toxicol Chem 2023;42:437-448. © 2022 SETAC.

Carbendazim: Ecological risks, toxicities, degradation pathways and potential risks to human health

Carbendazim is a highly effective benzimidazole fungicide and is widely used throughout the world. The effects of carbendazim contamination on the biology and environment should be paid more attention. We reviewed the published papers to evaluate the biological and environmental risks of carbendazim residues. The carbendazim has been frequently detected in the soil, water, air, and food samples and disrupted the soil and water ecosystem balances and functions. The carbendazim could induce embryonic, reproductive, developmental and hematological toxicities to different model animals. The carbendazim contamination can be remediated by photodegradation and chemical and microbial degradation. The carbendazim could enter into human body through food, drinking water and skin contact. Most of the existing studies were completed in the laboratory, and further studies should be conducted to reveal the effects of successive carbendazim applications in the field.

Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G

Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.

Effective Usage of Biochar and Microorganisms for the Removal of Heavy Metal Ions and Pesticides

The bioremediation of heavy metal ions and pesticides is both cost-effective and environmentally friendly. Microbial remediation is considered superior to conventional abiotic remediation processes, due to its cost-effectiveness, decrement of biological and chemical sludge, selectivity toward specific metal ions, and high removal efficiency in dilute effluents. Immobilization technology using biochar as a carrier is one important approach for advancing microbial remediation. This article provides an overview of biochar-based materials, including their design and production strategies, physicochemical properties, and applications as adsorbents and support for microorganisms. Microorganisms that can cope with the various heavy metal ions and/or pesticides that enter the environment are also outlined in this review. Pesticide and heavy metal bioremediation can be influenced by microbial activity, pollutant bioavailability, and environmental factors, such as pH and temperature. Furthermore, by elucidating the interaction mechanisms, this paper summarizes the microbe-mediated remediation of heavy metals and pesticides. In this review, we also compile and discuss those works focusing on the study of various bioremediation strategies utilizing biochar and microorganisms and how the immobilized bacteria on biochar contribute to the improvement of bioremediation strategies. There is also a summary of the sources and harmful effects of pesticides and heavy metals. Finally, based on the research described above, this study outlines the future scope of this field.

Effectiveness and mechanisms of the adsorption of carbendazim from wastewater onto commercial activated carbon

The wide application of fungicides is becoming one of the main causes of water pollution. Activated carbon (AC) is a frequently-used adsorbent in water treatment. In this work, aiming to obtain a better understanding of fungicides on AC, carbendazim was selected as a model fungicide in water. The effects of AC dosage, adsorption temperature, adsorption time and pH value of solution on carbendazim adsorption by AC were investigated. When the initial concentration of carbendazim was 500 mg L^-1 and the volume of wastewater was 25 mL, the optimum dosage of AC and reaction time was determined to be 0.3 g and 150 min, respectively. The pH ranging from 3.0 to 10.0 exhibited little effect on the adsorption capability of AC. The higher the adsorption temperature was, the better adsorption capacity was. Adsorption capacity could reach 32.31 mg g^-1 under the optimal adsorption conditions. The kinetics study reveals that the adsorption of carbendazim occurred on the surface of adsorbent during initial stage. The adsorption data was well fitted by Langmuir adsorption isotherm, indicating that the adsorption process was monolayer adsorption. The thermodynamic experiments confirmed that the adsorption of carbendazim was an endothermic process with the coexistence of physical and chemical adsorption. Because the main components of AC used in this research work is amorphous carbon with low impurity and its surface has not been modified with additional functional groups, the conclusion of the study was easy to be replicated by repeated experiments. Therefore, the findings of this study could guide the adsorption of carbendazim onto the other kinds of AC with high specific surface area, and provide useful information for application of commercial AC in treatment of fungicides wastewater.

Functional analysis, diversity, and distribution of carbendazim hydrolases MheI and CbmA, responsible for the initial step in carbendazim degradation

Strains Rhodococcus qingshengii djl-6 and Rhodococcus jialingiae djl-6-2 both harbor the typical carbendazim degradation pathway with the hydrolysis of carbendazim to 2-aminobenzimidazole (2-AB) as the initial step. However, the enzymes involved in this process are still unknown. In this study, the previous reported carbendazim hydrolase MheI was found in strain djl-6, but not in strain djl-6-2, then another carbendazim hydrolase CbmA was obtained by a four-step purification strategy from strain djl-6-2. CbmA was classified as a member of the amidase signature superfamily with conserved catalytic site residues Ser157, Ser181, and Lys82, while MheI was classified as a member of the Abhydrolase superfamily with conserved catalytic site residues Ser77 and His224. The catalytic efficiency (k_cat /K_m ) of MheI (24.0-27.9 μM^-1 min^-1 ) was 200 times more than that of CbmA (0.032-0.21 μM^-1 min^-1 ). The mheI gene (plasmid encoded) was highly conserved (> 99% identity) in the strains from different bacterial genera and its plasmid encoded flanked by mobile genetic elements. The cmbA gene was highly conserved only in strains of the genus Rhodococcus and it was chromosomally encoded. Overall, the function, diversity, and distribution of carbendazim hydrolases MheI and CbmA will provide insights into the microbial degradation of carbendazim.

Construction and Characterization of an Intergeneric Fusant That Degrades the Fungicides Chlorothalonil and Carbendazim

Bordetella sp. CTN-16 (GenBank FJ598326) can degrade chlorothalonil (CTN) but not carbendazim (MBC), and Microbacterium sp. MBC-3 (GenBank OK667229) can degrade MBC but not CTN. A functional strain BD2 was obtained by protoplast fusion of CTN-16 and MBC-3 to generate a fusant with improved degradation efficiency of CTN and MBC. Fusant-BD2 with eighth transfer on a medium containing CTN and two antibiotics was obtained. To identify and confirm the genetic relationship between parental strains and fusion strain BD2, scanning electron microscopy (SEM), random amplified polymorphic DNA (RAPD), and 16S ribosomal RNA (rRNA) gene sequences analysis were carried out. SEM analysis illustrated BD2 and its parents had some slight differences in the cell morphology. Fusant-BD2 not only possessed the same bands as parental strains but also had its specific bands analyzed through RAPD. The genetic similarity indices for BD2 and its parental strains CTN-16 and MBC-3 are 0.571 and 0.428, respectively. The degradation rates of CTN and MBC were 79.8% and 65.2% in the inorganic salt solution containing 50 mg·L−1 CTN and 50 mg·L−1 MBC, respectively, and the degradation efficiencies were better than the parental strains CTN-16 and MBC-3. This study provides a prospect for the application of fusion strain BD2 in bioremediation of CTN and MBC contaminated sites.

Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications

Recombinant enzyme expression in Escherichia coli is one of the most popular methods to produce bulk concentrations of protein product. However, this method is often limited by the inadvertent formation of inclusion bodies. Our analysis systematically reviews literature from 2010 to 2021 and details the methods and strategies researchers have utilized for expression of difficult to express (DtE), industrially relevant recombinant enzymes in E. coli expression strains. Our review identifies an absence of a coherent strategy with disparate practices being used to promote solubility. We discuss the potential to approach recombinant expression systematically, with the aid of modern bioinformatics, modelling, and ‘omics’ based systems-level analysis techniques to provide a structured, holistic approach. Our analysis also identifies potential gaps in the methods used to report metadata in publications and the impact on the reproducibility and growth of the research in this field.

Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome

As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg^-1 dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.

Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides

Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.

Characterization of the role of esterases in the biodegradation of organophosphate, carbamate, and pyrethroid pesticides

Ester-containing organophosphate, carbamate, and pyrethroid (OCP) pesticides are used worldwide to minimize the impact of pests and increase agricultural production. The toxicity of these chemicals to humans and other organisms has been widely reported. Chemically, these pesticides share an ester bond in their parent structures. A particular group of hydrolases, known as esterases, can catalyze the first step in ester-bond hydrolysis, and this initial regulatory metabolic reaction accelerates the degradation of OCP pesticides. Esterases can be naturally found in plants, animals, and microorganisms. Previous research on the esterase enzyme mechanisms revealed that the active sites of esterases contain serine residues that catalyze reactions via a nucleophilic attack on the substrates. In this review, we have compiled the previous research on esterases from different sources to determine and summarize the current knowledge of their properties, classifications, structures, mechanisms, and their applications in the removal of pesticides from the environment. This review will enhance the understanding of the scientific community when studying esterases and their applications for the degradation of broad-spectrum ester-containing pesticides.

Non-Target Site Mechanisms of Fungicide Resistance in Crop Pathogens: A Review

The rapid emergence of resistance in plant pathogens to the limited number of chemical classes of fungicides challenges sustainability and profitability of crop production worldwide. Understanding mechanisms underlying fungicide resistance facilitates monitoring of resistant populations at large-scale, and can guide and accelerate the development of novel fungicides. A majority of modern fungicides act to disrupt a biochemical function via binding a specific target protein in the pathway. While target-site based mechanisms such as alternation and overexpression of target genes have been commonly found to confer resistance across many fungal species, it is not uncommon to encounter resistant phenotypes without altered or overexpressed target sites. However, such non-target site mechanisms are relatively understudied, due in part to the complexity of the fungal genome network. This type of resistance can oftentimes be transient and noninheritable, further hindering research efforts. In this review, we focused on crop pathogens and summarized reported mechanisms of resistance that are otherwise related to target-sites, including increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations, regulation of stress response pathways, and single nucleotide polymorphisms (SNPs) or mutations. In addition, novel mechanisms of drug resistance recently characterized in human pathogens are reviewed in the context of nontarget-directed resistance.

Characterization of a novel carbendazim-degrading strain Rhodococcus sp. CX-1 revealed by genome and transcriptome analyses

The persistence and ecotoxicity of carbendazim residues pose a potential risk to environmental ecology and human health. Here, a novel and highly efficient carbendazim-degrading bacterium Rhodococcus sp. CX-1, capable of utilizing carbendazim as its sole source of carbon and energy, was isolated from contaminated soil. The biodegradation characteristics and metabolic pathways were studied by mass spectrometry, genomic annotation, and transcriptome analysis. The degradation rate of carbendazim by strain CX-1 was 3.98-9.90 mg/L/h under different conditions, and the optimum degradation conditions were 40 °C and pH 7.0. The addition of carbon sources (glucose, fructose, and sucrose, 100 mg/L) could accelerate carbendazim degradation. HPLC-MS/MS identification suggested that carbendazim is first hydrolyzed into 2-aminobenzimidazole and then to 2-hydroxybenzimidazole, and is ultimately mineralized to carbon dioxide. The genome of strain CX-1 contained 6,511,628 bp nucleotides, 2 linear plasmids, 2 circular plasmids, and 6437 protein coding genes. Genome annotation and transcriptome analysis indicated that carbendazim degradation may be regulated by the degradation genes harbored in the chromosome and in plasmid 2, and two different degradation pathways of carbendazim by imidazole ring cleavage or benzene ring cleavage were predicted. This study provided new insight to reveal the biodegradation mechanism of carbendazim; furthermore, strain CX-1 is a promising bioresource for carbendazim bioremediation.

An angular dioxygenase gene cluster responsible for the initial phenazine-1-carboxylic acid degradation step in Rhodococcus sp. WH99 can protect sensitive organisms from toxicity

A bacterial strain, Rhodococcus sp. WH99, capable of degrading phenazine-1-carboxylic acid (PCA) was isolated and characterized. Genome comparison revealed that a 21499-bp DNA fragment containing a putative angular dioxygenase gene cluster consisting of the dioxygenase-, ferredoxin reductase- and ferredoxin-encoding genes (pzcA1A2, pzcC and pzcD) is missed in the PCA degradation-deficient mutant WH99M. The pzcA1A2CD genes were expressed in Escherichia coli respectively and hydroxylation of PCA to 1,2-dihydroxyphenazine occurred in vitro only when all components were present. However, in vivo analyses showed that pzcA1A2 and pzcD were indispensable for PCA degradation, while PzcC can be partially replaced by other ferredoxin reductases. Hydroxylation of PCA not only initiates degradation of PCA in strain WH99 but also provides protection to sensitive organisms that would otherwise be inhibited by PCA toxicity. This study illustrates a new initial PCA degradation step in Gram-positive bacteria and enhances our understanding of the genes responsible for PCA hydroxylation, thus enabling targeted studies on protection by PCA degradation in diverse environments.

Removal of dimethachlon from soils using immobilized cells and enzymes of a novel potential degrader Providencia stuartii JD

The first potential degrader capable of detoxifying dimethachlon (NDPS) was isolated and identified as Providencia stuartii JD, whose free cells and freely crude enzymes degraded more than 80% and 90% of 50 mg L^-1 NDPS in liquid culture within 7 d and 2 h, respectively. Strain JD metabolized NDPS through the typical pathway, in which NDPS was firstly transformed into succinic acid and 3, 5-dichloroanilin, and the latter was then converted to phenol, which was subsequently degraded to muconic acid further subjected to the mineralization. The immobilization obviously improved the stability and adaptability of cells and enzymes. In laboratory non-sterile soils treated by free or immobilized cells and enzymes, 50 mg kg^-1 NDPS decreased to 15.66 and 13.32 mg kg^-1, or 8.32 and 2.18 mg kg^-1 within 7 d, respectively. In field, immobilized cells and enzymes exhibited significantly higher efficiencies in removing 20.250 kg a.i. ha^-1 NDPS wettable powder from soils after 9 d (96.02% and 98.56%) than free cells and enzymes (79.35% and 66.45%). This study highlights that strain JD promises the great potential to remove hazardous NDPS residues and its immobilized cells and enzymes possess the more promising advantages in the bioremediation of NDPS-contaminated soils in situ.

Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata

The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

Toxicity and Metabolic Fate of the Fungicide Carbendazim in the Typical Freshwater Diatom Navicula Species

Fungicides are frequently detected in natural water and have gained increasing attention as a result of their potential toxicity to non-target aquatic organisms. Carbendazim (CAR), a commonly used fungicide, was selected to explore its toxicity and biodegradation in a typical freshwater diatom Navicula sp. Results showed that the growth of Navicula sp. was inhibited by CAR, with a 24 h EC₅₀ value of 2.18 mg L^-1. Although the algal growth rate was recovered after 72 h of exposure, the chlorophyll a content remained significantly decreased when the concentration of CAR was above 0.5 mg L^-1. Moreover, Navicula sp. had a negative effect on the removal of CAR, and the acute toxicity by CAR was likely due to its rapid accumulation in algal cells. Mass spectrometric data revealed the transformation products of CAR from hydroxylation, methylation, decarboxylation, demethylation, and deamination in algal cultures. These results provide a better understanding of the environmental risks of CAR in water and point to the need for additional studies on the potential adverse biological effects of its intermediates.

Exploring bacterial communities and biodegradation genes in activated sludge from pesticide wastewater treatment plants via metagenomic analysis

Activated sludge (AS) has been regarded as the main driver in the removal of organic pollutants such as pesticides due to a high diversity and abundance of microorganisms. However, little is known about the biodegradation genes (BDGs) and pesticide degradation genes (PDGs) harbored in the AS from wastewater treatment plants (WWTPs). In this study, we explored the bacterial communities and BDGs/PDGs in the AS from five WWTPs affiliated with pesticide factories across four consecutive seasons based on high-throughput sequencing. The AS in pesticide WWTPs exhibited unique bacterial taxa at the genus level. Furthermore, a total of 17 BDGs and 68 PDGs were explored with a corresponding average relative abundance of 0.002-0.046% and 2.078-7.143% in each AS sample, respectively, and some BDGs/PDGs clusters were also identified in the AS. The bacterial communities and BDGs/PDGs were season-dependent, and the total variations of 50.4% and 76.8% were jointly explained by environmental variables (pesticide types, wastewater characteristics, and temperature). In addition, network analysis and distribution patterns suggested that the potential hosts of BDGs/PDGs were Thauera, Stenotrophomonas, Mycobacterium, Hyphomicrobium, Allochromatium, Ralstonia, and Dechloromonas. Our findings demonstrated the linkages of bacterial communities and BDGs/PDGs in the AS, and depended on the seasons and the pesticide wastewater characteristics.

Pesticide Detox by Design

Detoxification (detox) plays a major role in pesticide action and resistance. The mechanisms involved are sometimes part of the discovery and development process in seeking new biochemical targets and metabolic pathways. Genetically modified and chemical-safener-modified crops are a marked exception and often involve herbicide detox by design to achieve the required crop tolerance. This perspective evaluates the role of detox by design or chance and target-site-based selectivity in insecticide, herbicide, and fungicide action and human health and environmental effects.

Cloning and expression of the carbaryl hydrolase gene mcbA and the identification of a key amino acid necessary for carbaryl hydrolysis

Carbamate hydrolase is the initial and key enzyme for degradation of carbamate pesticides. In the present study, we report the isolation of a carbaryl-degrading strain Pseudomonas sp. XWY-1, the cloning of its carbaryl hydrolase gene (mcbA) and the characterization of McbA. Strain XWY-1 was able to utilize carbaryl as a sole carbon source and degrade it using 1-naphthol as an intermediate. Transposon mutagenesis identified a mutant of XWY-1M that was unable to hydrolyze carbaryl. The transposon-disrupted gene mcbA was cloned by self-formed adaptor PCR, then expressed in Escherichia coli BL21(DE3) and purified. McbA was able to hydrolyze carbamate pesticides including carbaryl, isoprocarb, fenobucarb, carbofuran efficiently, while it hydrolyzed aldicarb, and propoxur poorly. The optimal pH of McbA was 7.0 and the optimal temperature was 40°C. The apparent K_m and k_cat values of McbA for carbaryl were 77.67±12.31μM and 2.12±0.10s^-1, respectively. Three amino acid residues (His467, His477 and His504) in the predicted polymerase/histidinol phosphatase-like domain were shown to be closely related to the activity of McbA, with His504 being the most important, as a replacement of His504 led to the complete loss of activity. This is the first study to identify key amino acids in McbA.