Degradation of Phenylurea Herbicides by a Novel Bacterial Consortium Containing Synergistically Catabolic Species and Functionally Complementary Hydrolases

Biodegradation of acetochlor by microbial consortium AT1: microcosm centric microbiomic-metabolomics mechanisms and environmental remediation feasibility

The excessive use of herbicide acetochlor (ACT) threatens crop health and the environment, necessitating effective remediation strategies. This study focused on a consortium named AT1, enriched from ACT-contaminated soil. Under optimized conditions (25 °C, pH 7, 1 % inoculum), AT1 almost completely degraded ACT (50-1000 mg/L) within 6-12 days. High-throughput sequencing of 16S rRNA gene revealed a reduction in community diversity over time, with Sphingomonas (58.6 %) and Diaphorobacter (26.43 %) as dominant taxa. A structure model and network analysis indicated strong microbial competition during the peak degradation. Predicted functions and liquid chromatography-mass spectrometry based metabolomics data identified benzene ring intermediates during ACT degradation, including 2,6-dimethylaniline, resorcinol, phenol, 3-ethyl-1,2-benzenediol, 1,2,3-trihydroxybenzene, phloroglucinol, and benzene-1,2,4-triol. Joint omics analysis revealed that AT1 likely degrades ACT via N-dealkylation by Pseudomonas, amide bond hydrolysis by Diaphorobacter, and carboxylation and hydroxylation by Sphingomonas, leading to the formation of these intermediate metabolites. Moreover, AT1 efficiently degraded key intermediates, particularly 2,6-dimethylaniline, phenol, and resorcinol, further enhancing ACT mineralization. Notably, AT1 efficiently degraded ACT in soil, resulting in a significant decrease in ACT environmental residues. These findings provide valuable insights for the discovery and identification of herbicide-degrading bacterial resources and the metabolic transformation of herbicides, and developing approaches for pollution control and biodegradation of amide herbicides.

An exploration of bacterial consortia in chlorpyrifos degradation, soil remediation, and promotion of plant growth

The eleven combinations of four isolates, S. maltophilia, P. hibiscicola, P. aeruginosa, and P. monteilii, were prepared and screened for chlorpyrifos (CP) degradation. Among these combinations, four highly CP degrading consortia were identified: D: S. maltophilia, P. hibiscicola, P. monteilii, E: P. hibiscicola, P. aeruginosa, P. monteilii, F: S. maltophilia, P. hibiscicola, and G: S. maltophilia, P. aeruginosa. These combinations were found to be mutually compatible, exhibiting no lysis or inhibition zones. Their application significantly decreased in CP content from 37.6 to 68.6% as compared to control. Consortia-treated soil also displayed reduced bio-concentration factor and translocation of CP in W. somnifera. A significant increase in biomass (40-71.2%), protein content (38-66.6%), chlorophyll (24.7-52.3%), and secondary metabolite of W. somnifera was observed after the application of consortia. The activities of soil enzymes (alkaline phosphatase, dehydrogenase, and N-acetyl glucosaminidase), availability of nutrients, and soil microbial biomass carbon were also enhanced by the inoculation of consortia in soil. Overall, the results indicated that the consortium of S. maltophilia and P. aeruginosa exhibited the highest potential for CP degradation and plant growth promotion compared to the others. This consortium could be effectively utilized for the rapid degradation of CP in agricultural soil vis-a-vis improvement in the productivity of the plants.

Preparation of boric acid functionalized hyper-crosslinked polymer for efficient extraction of phenylurea herbicides from lake water, green tea drink and tomato samples

A boric acid functionalized hyper-crosslinked polymer (HCP), designated as NPCBA/TBM-HCP, was successfully synthesized via Friedel-Crafts reaction by copolymerizing N-phenylcarbazole-2-boronic acid (NPCBA) and 2,4,6-Tris(bromomethyl)mesitylene (TBM). The NPCBA/TBM-HCP showed a large surface area and a good adsorption property for phenylurea herbicides (PUHs). A method with NPCBA/TBM-HCP based solid phase extraction and high-performance liquid chromatographic detection was developed for the simultaneous analysis of PUHs in lake water, green tea drink and tomato samples. Under the optimized experimental conditions that the amount of the NPCBA/TBM-HCP was 30 mg, sample solution was 100 mL, sample loading rate was 4 mL min-1, and eluent was 0.3 mL acetonitrile, the linear response for the PUHs was in the range of 0.06-80.0 ng mL-1, 0.6-80.0 ng mL-1 and 0.9-200 ng g-1 for lake water, green tea drink and tomato samples, respectively, with a good linearity (the coefficients of determination (r2) ≥ 0.9916). The detection limits (S/N = 3) for lake water, green tea drink and tomato samples were 0.02-0.03 ng mL-1, 0.2 ng mL-1 and 0.3-0.5 ng g-1, respectively. The method recoveries for spiked samples were 80.0 %-119.1 % and RSDs were lower than 9.9 % for the determination. The method provides a new and feasible approach for the determination of phenylurea herbicide in real samples.

Molecular docking and mutation sites of CYP57A1 enzyme with Fomesafen

Fomesafen is a diphenyl ether herbicide developed by Zeneca Group PLC (UK), mainly used in soybean and peanut fields to control annual and perennial broad-leaved weeds. Fomesafen has strong persistence in the soil, slow degradation rate, and is prone to harm subsequent sensitive crops. This study utilized Autodock molecular docking technology to investigate the binding and interaction between degradation enzyme CYP57A1 and small molecules of fomesafen herbicides. The CYP57A1 gene cloned from a fomesafen-resistant fungus Fusarium verticilloids, belongs to a fragment of the P450 family, contains 587 bases, encodes 190 amino acids, and has an isoelectric point of 5.16. Visualization of the active surface of the protein receptor reveals that fomesafen is located in the cavity formed by the CYP57A1 protein and the cavity is small and tightly, the proteins are connected to small molecules through hydrogen bonds, halogen atom and π - cation interactions. Molecular modification of CYP57A1 enzyme was carried out using virtual amino acid mutation technology. Four key amino acids, LEU143, MET52, PHE176, and GLU177, were subjected to site-specific mutations. This study successfully constructed mutant engineered bacteria with stable protein expression. Mutations (1) MET52 > TRP showed a a decrease in enzyme activity, and the degradation rate of fomesafen was only 7.8 % of the wild-type. It is believed that MET52 is a key active site for the binding of CYP57A1 enzyme to small molecules of fomesafen, playing a crucial role in the degradation of fomesafen by this enzyme. This provides new insights into the impact on the degradation activity of fomesafen.

Chitinophaga defluvii sp. nov., a Cyhalofop-Butyl-Degrading Bacterium Isolated from Municipal Sludge

A yellow-colored, Gram-stain-negative, non-motile, and rod-shaped bacterium, designated strain H8T, was isolated from municipal sludge in Huaibei, China. Strain H8T was able to grow at 15-37 °C (optimum at 30 °C), pH 6.0-8.0 (optimum at pH 7.0), and 0-2.5% (w/v) NaCl concentration (optimum at 0%). This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain H8T represented to the genus Chitinophaga and shared highest sequence similarities with C. arvensicola DSM 3695T (97.5%), C. niastensis JS16-4T (97.3%), C. hostae 2R12T (97.1%), and C. ginsengisegetis Gsoil 040T (96.8%). The 16S rRNA gene similarities with other members of the genus Chitinophaga are less than 96.3%. The only respiratory quinone was a menaquinone with seven isoprene units (MK-7); the major polar lipid was phosphatidylethanolamine; and the predominant fatty acids were iso-C15:0 and C16:1 ω5c. The genome size of strain H8T was 7.6 Mb, with 44.3% G + C content. The DNA-DNA relatedness and the average nucleotide identity values among strain H8T and other relatives were all less than 19.7% and 72.6%, respectively, which fall below the threshold value of 70% and 95% for the strain to be considered as novel. The morphological, physiological, chemotaxonomic, and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbors. Thus, strain H8T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga defluvii sp. nov. is proposed. The type strain is H8T (= CCTCC AB 2023228T = KCTC 102174T).

Biodegradation of imidacloprid and diuron by Simplicillium sp. QHSH-33

Imidacloprid (IMI) and diuron (DIU) are widely used pesticides in agricultural production. However, their excessive use and high residues have caused harm to the ecological environment and human health. Microbial remediation as an efficient and low-toxic method has become a research hotspot for controlling environmental pollutants. A fungus QHSH-33, identified as Simplicillium sp., has the ability to degrade neonicotinoids IMI and phenylurea DIU. When QHSH-33 and pesticide were co-cultured in liquid medium for 7 days, the degradation rates of IMI and DIU by QHSH-33 in simulated field soil microenvironment were 50.19 % and 70.57 %, respectively. Through HPLC-MS analysis, it was found that the degradation of IMI mainly involved nitro reduction, hydroxylation and other reactions. Three degradation pathways and eight degradation products were identified, among which two metabolites were obtained by microbial transformation of IMI for the first time. The degradation of DIU mainly involved demethylation and dehalogenation reactions, and two degradation pathways and four degradation products were identified, one of which was a new degradation product of DIU. Toxicity assessment demonstrated that most of the degradation products might be considerably less harmful than IMI and DIU. Whole genome sequencing of QHSH-33 revealed a genome size of 33.2 Mbp with 11,707 genes. The genome of QHSH-33 was annotated by KEGG to reveal 128 genes related to exogenous degradation and metabolism. After local blast with reported IMI and DIU degrading enzymes, seven IMI-degrading related genes and seven DIU-degrading related genes were identified in the QHSH-33 genome. The results of this study will help to expand our knowledge on the microbial decomposition metabolism of IMI and DIU, and provide new insights into the degradation mechanism of IMI and DIU in soil and pure culture system, laying a foundation for QHSH-33 strain applied to the removal, biotransformation or detoxification of IMI and DIU.

Comprehensive toxicological, metabolomic, and transcriptomic analysis of the biodegradation and adaptation mechanism by Achromobacter xylosoxidans SL-6 to diuron

Biodegradation was considered a promising and environmentally friendly method for treating environmental pollution caused by diuron. However, the mechanisms of biodegradation of diuron required further research. In this study, the degradation process of diuron by Achromobacter xylosoxidans SL-6 was systematically investigated. The results suggested that the antioxidant system of strain SL-6 was activated by adding diuron, thereby alleviating their oxidative stress response. In addition, degradation product analysis showed that diuron in strain SL-6 was mainly degraded by urea bridge cleavage, dehalogenation, deamination, and ring opening, and finally cis, cis-muconic acid was generated. The combined analysis of metabolomics and transcriptomics revealed the biodegradation and adaptation mechanism of strain SL-6 to diuron. Metabolomics analysis showed that after the strain SL-6 was exposed to diuron, metabolic pathways such as tricarboxylic acid cycle (cis, cis-muconic acid), glutathione metabolism (oxidized glutathione), and urea cycle (arginine) were reprogrammed in the cells. Furthermore, diuron could induce the production of membrane transport proteins in strain SL-6 cells and overexpress antioxidant enzyme genes, finally ultimately promoting the up-regulation of genes encoding amide hydrolases and dioxygenases, which was revealed by transcriptomics studies. This work enriched the biodegradation mechanism of phenylurea herbicides and provided guidance for the removal of diuron residues in the environment and promoting agriculture sustainable development.

Nanoconfinement of functionalized ionic liquid for enhanced adsorption and rapid sensitive detection of phenylurea herbicides in food and environmental samples

The novel ILs@CNTs was synthesized by encapsulating task-specific ionic liquids (ILs) within carbon nanotubes (CNTs) derived from ZIF-67. These hybrid materials served as multifunctional adsorbents enabling simultaneous sorptive removal, sensitive detection, molecular sieve selection, and magnetic separation. In contrast to pristine CNTs, ILs@CNTs demonstrate significantly enhanced adsorption of phenylurea herbicides (PUHs). The complex interactions between ILs@CNTs and PUHs were comprehensively analyzed using a combination of experimental results and theoretical calculations. Furthermore, a magnetic solid phase extraction-high performance liquid chromatography (MSPE-HPLC) method was developed for the determination of multiple trace PUHs in real samples. The method exhibited lower detection limits (0.02-0.03 μg L-1) and higher enrichment factors (131 < EFs < 185). Interestingly, a portable lab-in-a-syringe device was developed to facilitate rapid on-site extraction and enrichment of PUHs. Additionally, the developed methods successfully applied in river water, tea drinks, and cucumber samples, highlighting its substantial potential for rapid PUH detection.

Metabolic insights into how multifunctional microbial consortium enhances atrazine removal and phosphorus uptake at low temperature

Agricultural soils in the black soil region of northeast China often face negative stress due to low temperatures, pesticide contamination, and inadequate nutrient supply. In this study, a new cold-tolerant strain of Peribacillus simplex C1 (C1) was selectively isolated from atrazine contaminated soil. The artificially constructed microbial consortium (CPD) [C1, phosphorus-solubilizing bacterium Enterobacter sp. P1, and atrazine-degrading bacterium Acinetobacter lwoffii DNS32] demonstrated the most effective performance in enhancing atrazine degradation and phosphorus-solubilizing capacity when the initial inoculation ratio of 5:1:2 at 15 °C. CPD enhanced energy-related metabolic pathways and increased choline production to regulate bacterial adaptation to temperature decrease. Additionally, the strains could selectively utilize carbon sources (low molecular weight organic acids) or nitrogen sources (some metabolites of atrazine) provided by each other to enhance growth. Furthermore, strain C1 enhanced membrane fluidity through increased expression of the unsaturated fatty acids. Pot experiments demonstrated that CPD assisted soybean seedlings in resisting dual stresses of low temperature and atrazine contamination by inducing the expression of genes related to photosynthesis, membrane permeability, phosphorus response, and cold tolerance.

Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia

Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation. To overcome these challenges, approaches that leverage knowledge from environmental bio-chem-informatics and metabolic engineering are crucial. Here, we propose a novel high-throughput bio-chem-informatics pipeline, to link chemicals and their predicted biotransformation pathways with potential enzymes and bacterial strains. Our framework systematically selects the most promising candidates for the degradation of chemicals with unknown biotransformation pathways and associated enzymes from the vast array of aquatic and soil bacteria. We substantiated our perspective by validating the pipeline for two chemicals with known or predicted pathways and show that our predicted strains are consistent with strains known to biotransform those chemicals. Such pipelines can be integrated with metabolic network analysis built upon genome-scale models and ecological principles to rationally design fit-for-purpose bacterial communities for augmenting deficient biotransformation functions and study operational and design parameters that influence their structure and function. We believe that research in this direction can pave the way for achieving our long-term goal of enhancing pollutant biodegradation.

Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5

The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had k_cat and K_m values of 5.7 s^-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.

Novel biodegradation pathway of insecticide flonicamid mediated by an amidase and its unusual substrate spectrum

The insecticide flonicamid (FLO) and its main degradation intermediate 4-trifluoromethylnicotinamide (TFNA-AM) are hazardous to the environment and animals. Microbial transformation of FLO has been well studied, but no study has yet reported on TFNA-AM degradation by a microorganism. Here, Pseudomonas stutzeri CGMCC 22915 effectively degraded TFNA-AM to 5-trifluoromethylnicotinic acid (TFNA). P. stutzeri CGMCC 22915 degraded 60.0% of TFNA-AM (1154.44 μmol/L) within 6 h with a half-life of just 4.5 h. Moreover, P. stutzeri CGMCC 22915 significantly promoted TFNA-AM decomposition in surface water. The reaction was catalyzed by an amidase, PsAmiA. PsAmiA is encoded in a novel nitrile-converting enzyme gene cluster. The enzyme shared only 20-44% identities with previously characterized signature amidases. PsAmiA was successfully expressed in Escherichia coli and its enzymatic properties were investigated using TFNA-AM as the substrate. PsAmiA was more active toward amides without hydrophilic groups, and did not hydrolyze another amide metabolite of FLO, N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM), which is structurally very similar to TFNA-AM. Molecular docking of PsAmiA and TFNA-AM indicated that hydrophobic residues Leu148, Ala150, Ala195, Ile225, Trp341, Leu460, and Ile463 may affect its substrate spectrum. This study provides new insights of the environmental fate of FLO at the molecular level and the structure-function relationships of amidases.

Aerobic Degradation Characteristics and Mechanism of Decabromodiphenyl Ether (BDE-209) Using Complex Bacteria Communities

Complex bacteria communities that comprised Brevibacillus sp. (M1) and Achromobacter sp. (M2) with effective abilities of degrading decabromodiphenyl ether (BDE-209) were investigated for their degradation characteristics and mechanisms under aerobic conditions. The experimental results indicated that 88.4% of 10 mg L^-1 BDE-209 could be degraded after incubation for 120 h under the optimum conditions of pH 7.0, 30 °C and 15% of the inoculation volume, and the addition ratio of two bacterial suspensions was 1:1. Based on the identification of BDE-209 degradation products via liquid chromatography-mass spectrometry (LC-MS) analysis, the biodegradation pathway of BDE-209 was proposed. The debromination, hydroxylation, deprotonation, breakage of ether bonds and ring-opening processes were included in the degradation process. Furthermore, intracellular enzymes had the greatest contribution to BDE-209 biodegradation, and the inhibition of piperyl butoxide (PB) for BDE-209 degradation revealed that the cytochrome P450 (CYP) enzyme was likely the key enzyme during BDE-209 degradation by bacteria M (1+2). Our study provided alternative ideas for the microbial degradation of BDE-209 by aerobic complex bacteria communities in a water system.

Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing

Excessive application of the herbicide chlorimuron-ethyl (CE) severely harms subsequent crops and poses severe risks to environmental health. Therefore, methods for efficiently decreasing and eliminating CE residues are urgently needed. Microbial consortia show potential for bioremediation due to their strong metabolic complementarity and synthesis. In this study, a microbial consortium entitled L1 was enriched from soil contaminated with CE by a “top-down” synthetic biology strategy. The consortium could degrade 98.04% of 100 mg L−1 CE within 6 days. We characterized it from the samples at four time points during the degradation process and a sample without degradation activity via metagenome and 16S rDNA sequencing. The results revealed 39 genera in consortium L1, among which Methyloversatilis (34.31%), Starkeya (28.60%), and Pseudoxanthomonas (7.01%) showed relatively high abundances. Temporal succession and the loss of degradability did not alter the diversity and community composition of L1 but changed the community structure. Taxon-functional contribution analysis predicted that glutathione transferase [EC 2.5.1.18], urease [EC 3.5.1.5], and allophanate hydrolase [EC 3.5.1.54] are relevant for the degradation of CE and that Methyloversatilis, Pseudoxanthomonas, Methylopila, Hyphomicrobium, Stenotrophomonas, and Sphingomonas were the main degrading genera. The degradation pathway of CE by L1 may involve cleavage of the CE carbamide bridge to produce 2-amino-4-chloro-6-methoxypyrimidine and ethyl o-sulfonamide benzoate. The results of network analysis indicated close interactions, cross-feeding, and co-metabolic relationships between strains in the consortium, and most of the above six degrading genera were keystone taxa in the network. Additionally, the degradation of CE by L1 required not only “functional bacteria” with degradation capacity but also “auxiliary bacteria” without degradation capacity but that indirectly facilitate/inhibit the degradation process; however, the abundance of “auxiliary bacteria” should be controlled in an appropriate range. These findings improve the understanding of the synergistic effects of degrading bacterial consortia, which will provide insight for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia. Furthermore, our results provide a new route for pollution control and biodegradation of sulfonylurea herbicides.

Concerted action of extracellular and cytoplasmic esterase and urethane-cleaving activities during Impranil biodegradation by Alicycliphilus denitrificans BQ1

The concerted action of commercial esterases, proteases and amidases has been demonstrated to be relevant in polyurethane (PU) degradation by in vitro experiments. However, the spatial and temporal dynamics of these activities during PU biodegradation by PU-degrading bacteria have not been addressed. Here, we examined the capability of Alicycliphilus denitrificans BQ1 to biodegrade the polyester (PS)-PU Impranil, analyzed the temporal and spatial coordination between the extracellular and cytoplasmic esterase and urethane-cleaving activities, and their independent and combined effects on Impranil biodegradation. A. denitrificans BQ1 grew in Impranil, and its clearing was correlated with the cleavage of ester and urethane groups since early times, with decrements of some Impranil compounds and the appearance of biodegradation products. While extracellular esterase was active at early times with its maximum at 18 h, urethanase appeared at this time and increased up to the end of the analysis (48 h), with the cytoplasmic activities behaving similarly but with lower levels than the extracellular ones. Both enzymatic activities exhibited distinct substrate specificity depending on their cellular localization and cultivation times, suggesting they cleave differentially located groups. As the urethane cleavage occurred since early times, when no urethane-cleaving activity was detected, different proteins should be acting at early and late times. In vitro experiments with independent or combined cellular protein fractions supported the previous deduction and confirmed the concerted action of extracellular and cytoplasmic esterase and urethane-cleaving activities. A two-stage process for Impranil degradation by A. denitrificans BQ1 is proposed.

Enhanced Biodegradation of Phenylurea Herbicides by Ochrobactrum anthrophi CD3 Assessment of Its Feasibility in Diuron-Contaminated Soils

The phenylurea herbicides are persistent in soil and water, making necessary the de-velopment of techniques for their removal from the environment. To identify new options in this regard, bacterial strains were isolated from a soil historically managed with pesticides. Ochrobactrum anthropi CD3 showed the ability to remove completely herbicides such as diuron, linuron, chlorotoluron and fluometuron from aqueous solution, and up to 89% of isoproturon. In the case of diuron and linuron, their main metabolite, 3,4-dichloroaniline (3,4-DCA), which has a higher toxicity than the parent compounds, was formed, but remained in solution without further degradation. O. anthropi CD3 was also tested for bioremediation of two different agricultural soils artificially contaminated with diuron, employing bioremediation techniques: (i) biostimulation, using a nutrient solution (NS), (ii) bioaugmentation, using O. anthropi CD3, and iii) bioavailability enhancement using 2-hydroxypropyl-β-cyclodextrin (HPBCD). When bioaugmentation and HPBCD were jointly applied, 50% of the diuron initially added to the soil was biodegraded in a range from 4.7 to 0.7 d. Also, 3,4-DCA was degraded in soil after the strain was inoculated. At the end of the soil biodegradation assay an ecotoxicity test confirmed that after inoculating O. anthropi CD3 the toxicity was drastically reduced.

Microbial Consortia Are Needed to Degrade Soil Pollutants

Soil pollution is one of the most serious environmental problems globally due to the weak self-purification ability, long degradation time, and high cost of cleaning soil pollution. The pollutants in the soil can be transported into the human body through water or dust, causing adverse effects on human health. The latest research has shown that the clean-up of soil pollutants through microbial consortium is a very promising method. This review provides an in-depth discussion on the efficient removal, bio-adsorption, or carbonated precipitation of organic and inorganic pollutants by the microbial consortium, including PAHs, BPS, BPF, crude oil, pyrene, DBP, DOP, TPHP, PHs, butane, DON, TC, Mn, and Cd. In view of the good degradation ability of the consortium compared to single strains, six different synergistic mechanisms and corresponding microorganisms are summarized. The microbial consortium obtains such activities through enhancing synergistic degradation, reducing the accumulation of intermediate products, generating the crude enzyme, and self-regulating, etc. Furthermore, the degradation efficiency of pollutants can be greatly improved by adding chemical materials such as the surfactants Tween 20, Tween 80, and SDS. This review provides insightful information regarding the application of microbial consortia for soil pollutant removal.

Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g^–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

Emerging Strategies for the Bioremediation of the Phenylurea Herbicide Diuron

Diuron (DUR) is a phenylurea herbicide widely used for the effective control of most annual and perennial weeds in farming areas. The extensive use of DUR has led to its widespread presence in soil, sediment, and aquatic environments, which poses a threat to non-target crops, animals, humans, and ecosystems. Therefore, the removal of DUR from contaminated environments has been a hot topic for researchers in recent decades. Bioremediation seldom leaves harmful intermediate metabolites and is emerging as the most effective and eco-friendly strategy for removing DUR from the environment. Microorganisms, such as bacteria, fungi, and actinomycetes, can use DUR as their sole source of carbon. Some of them have been isolated, including organisms from the bacterial genera Arthrobacter, Bacillus, Vagococcus, Burkholderia, Micrococcus, Stenotrophomonas, and Pseudomonas and fungal genera Aspergillus, Pycnoporus, Pluteus, Trametes, Neurospora, Cunninghamella, and Mortierella. A number of studies have investigated the toxicity and fate of DUR, its degradation pathways and metabolites, and DUR-degrading hydrolases and related genes. However, few reviews have focused on the microbial degradation and biochemical mechanisms of DUR. The common microbial degradation pathway for DUR is via transformation to 3,4-dichloroaniline, which is then metabolized through two different metabolic pathways: dehalogenation and hydroxylation, the products of which are further degraded via cooperative metabolism. Microbial degradation hydrolases, including PuhA, PuhB, LibA, HylA, Phh, Mhh, and LahB, provide new knowledge about the underlying pathways governing DUR metabolism. The present review summarizes the state-of-the-art knowledge regarding (1) the environmental occurrence and toxicity of DUR, (2) newly isolated and identified DUR-degrading microbes and their enzymes/genes, and (3) the bioremediation of DUR in soil and water environments. This review further updates the recent knowledge on bioremediation strategies with a focus on the metabolic pathways and molecular mechanisms involved in the bioremediation of DUR.

Isolation, Characterization, and Efficacy of Actinobacteria Associated with Arbuscular Mycorrhizal Spores in Promoting Plant Growth of Chili (Capsicum flutescens L.)

Nowadays, microorganisms that display plant growth promoting properties are significantly interesting for their potential role in reducing the use of chemical fertilizers. This research study proposed the isolation of the actinobacteria associated with arbuscular mycorrhizal fungi (AMF) spores and the investigation of their plant growth promoting properties in the in vitro assay. Three actinobacterial strains were obtained and identified to the genus Streptomyces (GETU-1 and GIG-1) and Amycolatopsis (GLM-2). The results indicated that all actinobacterial strains produced indole-3-acetic acid (IAA) and were positive in terms of siderophore, endoglucanase, and ammonia productions. In the in vitro assay, all strains were grown in the presence of water activity within a range of 0.897 to 0.998, pH values within a range of 5–11, and in the presence of 2.5% NaCl for the investigation of drought, pH, and salt tolerances, respectively. Additionally, all strains were able to tolerate commercial insecticides (propargite and methomyl) and fungicides (captan) at the recommended dosages for field applications. Only, Amycolatopsis sp. GLM-2 showed tolerance to benomyl at the recommended dose. All the obtained actinobacteria were characterized as plant growth promoting strains by improving the growth of chili plants (Capsicum flutescens L.). Moreover, the co-inoculation treatment of the obtained actinobacteria and AMF (Claroideoglomus etunicatum) spores could significantly increase plant growth, contribute to the chlorophyll index, and enhance fruit production in chili plants. Additionally, the highest value of AMF spore production and the greatest percentage of root colonization were observed in the treatment that had been co-inoculated with Streptomyces sp. GETU-1.

A Path Forward: Promoting Microbial-Based Methods in the Control of Invasive Plant Species

In this review, we discuss the unrealized potential of incorporating plant-microbe and microbe-microbe interactions into invasive plant management strategies. While the development of this as a viable strategy is in its infancy, we argue that incorporation of microbial components into management plans should be a priority and has great potential for diversifying sustainable control options. We advocate for increased research into microbial-mediated phytochemical production, microbial controls to reduce the competitiveness of invasive plants, microbial-mediated increases of herbicidal tolerance of native plants, and to facilitate increased pathogenicity of plant pathogens of invasive plants.

DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil

The frequent exposure of agricultural soils to pesticides can lead to microbial adaptation, including the development of dedicated microbial populations that utilize the pesticide compound as a carbon and energy source. Soil from an agricultural field in Halen (Belgium) with a history of linuron exposure has been studied for its linuron-degrading bacterial populations at two time points over the past decade and Variovorax was appointed as a key linuron degrader. Like most studies on pesticide degradation, these studies relied on isolates that were retrieved through bias-prone enrichment procedures and therefore might not represent the in situ active pesticide-degrading populations. In this study, we revisited the Halen field and applied, in addition to enrichment-based isolation, DNA stable isotope probing (DNA-SIP), to identify in situ linuron-degrading bacteria in linuron-exposed soil microcosms. Linuron dissipation was unambiguously linked to Variovorax and its linuron catabolic genes and might involve the synergistic cooperation between two species. Additionally, two novel linuron-mineralizing Variovorax isolates were obtained with high 16S rRNA gene sequence similarity to strains isolated from the same field a decade earlier. The results confirm Variovorax as a prime in situ degrader of linuron in the studied agricultural field soil and corroborate the genus as key for maintaining the genetic memory of linuron degradation functionality in that field.

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

The application of microbial strains as axenic cultures has frequently been employed in a diverse range of sectors. In the natural environment, microbes exist as multispecies and perform better than monocultures. Cell signaling and communication pathways play a key role in engineering microbial consortia, because in a consortium, the microorganisms communicate via diffusible signal molecules. Mixed microbial cultures have gained little attention due to the lack of proper knowledge about their interactions with each other. Some ideas have been proposed to deal with and study various microbes when they live together as a community, for biotechnological application purposes. In natural environments, microbes can possess unique metabolic features. Therefore, microbial consortia divide the metabolic burden among strains in the group and robustly perform pesticide degradation. Synthetic microbial consortia can perform the desired functions at naturally contaminated sites. Therefore, in this article, special attention is paid to the microbial consortia and their function in the natural environment. This review comprehensively discusses the recent applications of microbial consortia in pesticide degradation and environmental bioremediation. Moreover, the future directions of synthetic consortia have been explored. The review also explores the future perspectives and new platforms for these approaches, besides highlighting the practical understanding of the scientific information behind consortia.

Fabrication of carboxyl functionalized microporous organic network coated stir bar for efficient extraction and analysis of phenylurea herbicides in food and water samples

Fabrication of novel coatings continues to be an area of great interest and significance in the development and application of stir bar sorptive extraction (SBSE). In this work, a carboxyl-enriched microporous organic network (MON-2COOH) coated stir bar was designed and fabricated as a novel adsorbent for efficient extraction of four phenylurea herbicides (PUHs) before their determination by high-performance liquid chromatography coupled with photodiode array detector (HPLC-PDA). The MON-2COOH was represented as an effective adsorbent for PUHs due to its large surface area, rigid porous structure, aromatic pore walls and the desired hydrogen bonding sites of introduced carboxyl groups. Variables affecting the SBSE of target analytes were optimized in detail. Under the optimal extraction conditions, favorable correlation coefficients (R² > 0.996) in the linear range 0.10-250 μg L^-1, low limits of detection (LODs, S/N = 3) of 0.025-0.070 μg L^-1 and good enrichment factors (46-49) were obtained. Besides, the proposed SBSE-HPLC-PDA method was successfully applied to determine trace PUHs in food and environmental water samples with recoveries in the range of 80.0-104.8% and the precisions (relative standard deviations, RSDs) lower than 9.9% (n = 3). This work revealed the potential of MONs in SBSE of trace contaminants from environmental samples.

Culture-Independent Analysis of Linuron-Mineralizing Microbiota and Functions in on-Farm Biopurification Systems via DNA-Stable Isotope Probing: Comparison with Enrichment Culture

Our understanding of the microorganisms involved in in situ biodegradation of xenobiotics, like pesticides, in natural and engineered environments is poor. On-farm biopurification systems (BPSs) treat farm-produced pesticide-contaminated wastewater to reduce surface water pollution. BPSs are a labor and cost-efficient technology but are still mainly operated as black box systems. We used DNA-stable isotope probing (DNA-SIP) and classical enrichment to be informed about the organisms responsible for in situ degradation of the phenylurea herbicide linuron in a BPS matrix. DNA-SIP identified Ramlibacter, Variovorax, and an unknown Comamonadaceae genus as the dominant linuron assimilators. While linuron-degrading Variovorax strains have been isolated repeatedly, Ramlibacter has never been associated before with linuron degradation. Genes and mobile genetic elements (MGEs) previously linked to linuron catabolism were enriched in the heavy DNA-SIP fractions, suggesting their involvement in in situ linuron assimilation. BPS material free cultivation of linuron degraders from the same BPS matrix resulted in a community dominated by Variovorax, while Ramlibacter was not observed. Our study provides evidence for the role of Variovorax in in situ linuron biodegradation in a BPS, alongside other organisms like Ramlibacter, and further shows that cultivation results in a biased representation of the in situ linuron-assimilating bacterial populations.

Enantioselective Catabolism of the Two Enantiomers of the Phenoxyalkanoic Acid Herbicide Dichlorprop by Sphingopyxis sp. DBS4

Dichlorprop [(RS)-2-(2,4-dichlorophenoxy)propanoic acid; DCPP], an important phenoxyalkanoic acid herbicide (PAAH), is extensively used in the form of racemic mixtures (Rac-DCPP), and the environmental fates of both DCPP enantiomers [(R)-DCPP and (S)-DCPP] mediated by microorganisms are of great concern. In this study, a bacterial strain Sphingopyxis sp. DBS4 was isolated from contaminated soil and was capable of utilizing both (R)-DCPP and (S)-DCPP as the sole carbon source for growth. Strain DBS4 preferentially catabolized (S)-DCPP as compared to (R)-DCPP. The optimal conditions for Rac-DCPP degradation by strain DBS4 were 30 °C and pH 7.0. In addition to Rac-DCPP, other PAAHs such as (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid, 2,4-dichlorophenoxyacetic acid, 4-chloro-2-methylphenoxyacetic acid, and 2,4-dichlorophenoxyacetic acid butyl ester could also be catabolized by strain DBS4. Bioremediation of Rac-DCPP-contaminated soil by inoculation of strain DBS4 exhibited an effective removal of both (R)-DCPP and (S)-DCPP from the soil. Due to its broad substrate spectrum, strain DBS4 showed great potential in the bioremediation of PAAH-contaminated sites.

Characterization of a Linuron-Specific Amidohydrolase from the Newly Isolated Bacterium Sphingobium sp. Strain SMB

The phenylurea herbicide linuron is globally used and has caused considerable concern because it leads to environmental pollution. In this study, a highly efficient linuron-transforming strain Sphingobium sp. SMB was isolated, and a gene (lahB) responsible for the hydrolysis of linuron to 3,4-dichloroaniline and N,O-dimethylhydroxylamine was cloned from the genome of strain SMB. The lahB gene encodes an amidohydrolase, which shares 20-53% identity with other biochemically characterized amidohydrolases, except for the newly reported linuron hydrolase Phh (75%). The optimal conditions for the hydrolysis of linuron by LahB were determined to be pH 7.0 and 30 °C, and the K_m value of LahB for linuron was 37.3 ± 1.2 μM. Although LahB and Phh shared relatively high identity, LahB exhibited a narrow substrate spectrum (specific for linuron) compared to Phh (active for linuron, diuron, chlortoluron, etc.). Sequence analysis and site-directed mutagenesis revealed that Ala261 of Phh was the key amino acid residue affecting the substrate specificity. Our study provides a new amidohydrolase for the specific hydrolysis of linuron.

Fate, risk and removal of triclocarban: A critical review

The halogenated antimicrobial triclocarban (TCC) has large production and consumption over last decades. Its extensive utilization in personal care products and insufficient treatment in conventional wastewater treatment plants (WWTPs) has led to its listing as one of emerging organic contaminants (EOCs). Due to the hydrophobicity and chemical stability of TCC, it has been omnipresent detected in terrestrial and aquatic environments, and its prolonged exposure has thrown potential pernicious threat to ecosystem and human health. Considering its recalcitrance, especially under anoxic conditions, both biological and non-biological methods have been exploited for its removal. The efficiency of advanced oxidation processes was optimistic, but complete removal can rarely be realized through a single method. The biodegradation of TCC either with microbial community or pure culture is feasible but efficient bacterial degraders and the molecular mechanism of degradation need to be further explored. This review provides comprehensive information of the occurrence, potential ecological and health effects, and biological and non-biological removal of TCC, and outlines future prospects for the risk evaluation and enhanced bioremediation of TCC in various environments.

Microbial Degradation of Zearalenone by a Novel Microbial Consortium, NZDC-6, and Its Application on Contaminated Corncob by Semisolid Fermentation

A novel microbial consortium (NZDC-6) was screened and characterized to detoxify the estrogenic mycotoxin zearalenone (ZEA), which commonly contaminates maize and is a major threat to food and health security. We found NZDC-6 to be thermophilic and highly effective, with a 90.3% ZEA degradation ratio at an optimum temperature of 60 °C. NZDC-6 was also effective at degrading the more estrogenic ZEA cognates, α-zearalenol (α-ZAL) and β-zearalenol (β-ZAL), with >90% degradation ratios. To evaluate a practical application, ZEA-contaminated corncobs were treated with NZDC-6 via semisolid fermentation. Measurements of physicochemical parameters and 16S microbial diversity and redundancy analysis (RDA) indicated that ZEA removal was most efficient at a low corncob solid content (< 5%), as a high solid content overwhelmed the microbial metabolic load, leading to increased dissolved oxygen and lowered pH. Our results demonstrate that the control of environmental variables is crucial for effective ZEA microbial removal in practical applications.

Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep

BACKGROUND

Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported.

RESULTS

In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep.

CONCLUSIONS

These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.

Enantioselective Catabolism of Napropamide Chiral Enantiomers in Sphingobium sp. A1 and B2

Napropamide [ N, N-diethyl-2-(1-naphthalenyloxy)propenamide, NAP] is a highly efficient and broad-spectrum amide herbicide. Little is known about the bacterial catabolism of its different enantiomers. Here, we report the isolation of two NAP-degrading strains of Sphingobium sp., A1 and B2, and the different catabolic pathways of different enantiomers in these two strains. Strain A1 dioxygenated NAP at different positions of the naphthalene ring of different enantiomers, leading to the complete degradation of R-NAP while producing a dead-end product from S-NAP. Strain B2 cleaved the amido bonds of both enantiomers, but only the product from S-NAP could be further transformed to form α-naphthol and mineralize in strain B2. The degradation rates of R-NAP and S-NAP in the combination degradation by strains A1 and B2 were 24.8 and 7.5 times that in the single-strain degradation by strain B2 or A1, respectively, showing enhanced synergistic catabolism between strains A1 and B2. This study provides new insights into the enantioselective catabolic network of the chiral herbicide NAP in microorganisms.