Biodegradation of chlorpyrifos and its hydrolysis product 3,5,6-trichloro-2-pyridinol using a novel bacterium Ochrobactrum sp. JAS2: A proposal of its metabolic pathway

Rapid Screening of Indigenous Degrading Microorganisms for Enhancing In-Situ Bioremediation of Organic Pollutants-Contaminated Soil

Organic pollutants (OPs) have caused severe environmental contaminations in the world and aroused wide public concern. Autochthonous bioaugmentation (ABA) is considered a reliable bioremediation approach for OPs contamination. However, the rapid screening of indigenous degrading strains from in-situ environments remains a primary challenge for the practical application of ABA. In this study, 3,5,6-Trichloro-2-pyridinol (TCP, an important intermediate in the synthesis of various pesticides) was selected as the target OPs, and DNA stable isotope probing (DNA-SIP) combined with high-throughput sequencing was employed to explore the rapid screening of indigenous degrading microorganisms. The results of DNA-SIP revealed a significant enrichment of OTU557 (Cupriavidus sp.) in the 13C-TCP-labeled heavy DNA fractions, indicating that it is the key strain involved in TCP metabolism. Subsequently, an indigenous TCP degrader, Cupriavidus sp. JL-1, was rapidly isolated from native soil based on the analysis of the metabolic substrate spectrum of Cupriavidus sp. Furthermore, ABA of strain JL-1 demonstrated higher remediation efficacy and stable survival compared to the exogenous TCP-degrading strain Cupriavidus sp. P2 in in-situ TCP-contaminated soil. This study presents a successful case for the rapid acquisition of indigenous TCP-degrading microorganisms to support ABA as a promising strategy for the in-situ bioremediation of TCP-contaminated soil.

Comparative evaluation of biodegradation of chlorpyrifos by various bacterial strains: Kinetics and pathway elucidation

The present study focused on the isolation and identification of CP and TCP bacteria degrading bacteria from the rhizospheric zone of aromatic grasses i.e. palmarosa (Cymbopogon martinii (Roxb. Wats), lemongrass (Cymbopogon flexuosus) and vetiver (Chrysopogon zizaniodes (L.) Nash.). So that these isolates alone or in combination with the vegetation of aromatic grasses will be used to clean up CP-contaminated soils. The study also explored enzymatic activities, CO2 release, dechlorination potential, and degradation pathways of bacterial strains. A total of 53 CP-tolerant bacteria were isolated on their physical characteristics and their ability to degrade CP. The ten highly CP-tolerant isolates were Pseudomonas aeruginosa Pa608, three strains of Pseudomonas hibiscicola R4-721 from different rhizosphere, Enterococcus lectis PP2a, Pseudomonas monteilii NBFPALD_RAS131, Enterobacter cloacae L3, Stenotrophomonas maltophilia PEG-390, Escherichia coli ABRL132, and Escherichia coli O104:H4 strain FWSEC0009. The CO2 emission and phosphatase activities of the isolates varied from 3.1 to 8.6 μmol mL-1 and 12.3 to 31 μmol PNP h-1, respectively in the CP medium. The degradation kinetics of CP by these isolates followed a one-phase decay model with a dissipation rate ranging from 0.048 to 0.41 d-1 and a half-life of 1.7-14.3 days. The growth data fitted in the SGompertz equation showed a growth rate (K) of 0.21 ± 0.28 to 0.91 ± 0.33 d-1. The P. monteilii strain had a faster growth rate while E. coli ABRL132 had slower growth among the isolates. The rate of TCP accumulation calculated by the SGompertz equation was 0.21 ± 0.02 to 1.18 ± 0.19 d-1. The Pseudomonas monteilii showed a lower accumulation rate of TCP. Among these, four highly effective isolates were Pseudomonas aeruginosa Pa608, Pseudomonas monteilii NBFPALD_RAS131, Stenotrophomonas maltophilia PEG-390, and Pseudomonas hibiscicola R4-721. Illustrations of the degradation pathways indicated that the difference in metabolic pathways of each isolate was associated with their growth rate, phosphatase, dehydrogenase, oxidase, and dechlorination activities.

Adsorption, natural attenuation, and microbial community response of ofloxacin and oxolinic acid in marine sediments

The pollution of quinolone antibiotics in the marine environment has attracted widespread attention, especially for ofloxacin (OFL) and oxolinic acid (OXO) due to their frequent detection. However, few studies have been conducted to assess the behaviors and microbial community response to these antibiotics in marine sediments, particularly for potential antibiotic-resistant bacteria. In this work, the adsorption characteristics, natural attenuation characteristics, and variation of microbial communities of OFL and OXO in marine sediments were investigated. The adsorption process of antibiotics in sediments occurred on the surface and internal pores of organic matter, where OFL was more likely to be transferred from seawater to sediment compared with OXO. Besides, the adsorption of two antibiotics on sediment surfaces was attributed to physisorption (pore filling, electrostatic interaction) and chemisorption (hydrogen bonding). The natural attenuation of OFL and OXO in marine sediment followed second-order reaction kinetics with half-lives of 6.02 and 26.71 days, respectively, wherein biodegradation contributed the most to attenuation, followed by photolysis. Microbial community structure in marine sediments exposure to antibiotics varied by reducing abundance and diversity of microbial communities, as a whole displaying as an increase in the relative abundance of Firmicutes whereas a decrease of Proteobacteria. In detail, Escherichia-Shigella sp., Blautia sp., Bifidobacterium sp., and Bacillus sp. were those antibiotic-resistant bacteria with potential ability to degrade OFL, while Bacillus sp. may be resistant to OXO. Furthermore, functional predictions indicated that the microbial communities in sediment may resist the stress caused by OFL and OXO through cyano-amino acid metabolism, and ascorbate and aldarate metabolism, respectively. The research is key to understanding fate and bacterial resistance of antibiotics in marine sediments.

The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems

The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as Pseudomonas, Acinetobacter, Streptomyces, Serratia, Arthrobacter, and Rhodococcus can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms Acinetobacter, Arthrobacter, Enterobacter, Ochrobactrum, Pseudomonas, Rhodococcus, Serratia, Streptomyces, Biostimulants, Plant growth promoting rhizobactera, and Stenotrophomonas. The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.

Seed biopriming with Ochrobactrum ciceri mediated defense responses in Zea mays (L.) against Fusarium rot

Seed bio-priming is a simple and friendly technique to improve stress resilience against fungal diseases in plants. An integrated approach of maize seeds biopriming with Ochrobactrum ciceri was applied in Zn-amended soil to observe the response against Fusarium rot disease of Zea mays (L.) caused by Fusarium verticillioides. Initially, the pathogen isolated from the infected corn was identified as F. verticillioides based on morphology and sequences of the internally transcribed spacer region of the ribosomal RNA gene. Re-inoculation of maize seed with the isolated pathogen confirmed the pathogenicity of the fungus on the maize seeds. In vitro, the inhibitory potential of O. ciceri assessed on Zn-amended/un-amended growth medium revealed that antifungal potential of O. ciceri significantly improved in the Zn-amended medium, leading to 88% inhibition in fungal growth. Further assays with different concentrations (25, 50, and 75%) of cell pellet and the cultural filtrate of O. ciceri (with/without the Zn-amendment) showed a dose-dependent inhibitory effect on mycelial growth of the pathogen that also led to discoloration, fragmentation, and complete disintegration of the fungus hyphae and spores at 75% dose. In planta, biopriming of maize seeds with O. ciceri significantly managed disease, improved the growth and biochemical attributes (up to two-fold), and accelerated accumulation of lignin, polyphenols, and starch, especially in the presence of basal Zn. The results indicated that bioprimed seeds along with Zn as the most promising treatment for managing disease and improving plant growth traits through the enhanced accumulation of lignin, polyphenols, and starch, respectively.

Elimination of tetracyclines in seawater by laccase-mediator system

Long-term exposure of antibiotics at low level leads to the accumulation of antibiotics in environmental media and organisms, inducing the formation of antibiotic resistance genes. Seawater is an important sink for many contaminants. Here, laccase from Aspergillus sp. And mediators that follow different oxidation mechanisms were combined to degrade tetracyclines (TCs) at environmentally relevant levels (ng·L^-1-μg·L^-1) in coastal seawater. The high salinity and alkaline of seawater changed the enzymatic structure of laccase, resulting in a reduced affinity of laccase to the substrate in seawater (K_m of 0.0556 mmol L^-1) than that in buffer (K_m of 0.0181 mmol L^-1). Although the stability and activity of the laccase decreased in seawater, laccase at a concentration of 200 U·L^-1 with a laccase/syringaldehyde (SA) ratio of 1 U: 1 μmol could completely degrade TCs in seawater at initial concentrations of less than 2 μg L^-1 in 2 h. Molecular docking simulation showed that the interaction between TCs and laccase mainly includes hydrogen bond interaction and hydrophobic interaction. TCs were degraded into small molecular products through a series of reactions: demethylation, deamination, deamidation, dehydration, hydroxylation, oxidation, and ring-opening. Prediction of the toxicity of intermediates showed that the majority of TCs can be degraded into low-toxic or non-toxic, small-molecule products within 1 h, indicating that the degradation process of TCs by a laccase-SA system has good ecological safety. The successful removal of TCs by the laccase-SA system demonstrates its potential for the elimination of pollutants in marine environment.

Identification of two possible metabolic pathways responsible for the biodegradation of 3, 5, 6-trichloro-2-pyridinol in Micrococcus luteus ML

3, 5, 6-Trichloro-2-pyridinol (TCP) is a metabolite of the insecticide chlorpyrifos and the herbicide triclopyr, and it is higher toxic than the parent compounds. Microbially-mediated mineralization appears to be the primary degradative pathway and the important biological process of detoxification. However, little information is available on TCP complete metabolic pathways and mechanisms. In this study, the degradation of TCP was studied with a novel strain Micrococcus luteus ML isolated from a stable TCP degrading microbiota. Strain ML was capable of degrading 61.6% of TCP (50 mg/L) and 35.4% of chlorpyrifos (50 mg/L) at 24 h and 48 h under the optimal conditions (temperature: 35 °C; pH: 7.0), respectively. It could also degrade 3, 5-dichloro-2-pyridone, 6-chloropyridin-2-ol, 2-hydroxypyridine and phoxim when provided as sole carbon and energy sources. Seven TCP intermediate metabolites were detected in strain ML and two possible degradation pathways of TCP were proposed on the basis of LC-MS analysis. Both the hydrolytic-oxidative dechlorination pathway and the denitrification pathway might be involved in TCP biodegradation by strain ML. To the best of our knowledge, this is the first report on two different pathways responsible for TCP degradation in one strain, and this finding also provides novel information for studying the metabolic mechanism of TCP in pure culture.

Biodegradation mechanism of chlorpyrifos by halophilic bacterium Hortaea sp. B15

For decades, most of the developing nations have relied on chlorpyrifos for insecticidal activity in the agriculture sector. It is a common chlorinated organophosphorus pesticide that has been widely used to control insects to protect plants. This study aimed to investigate the effects of environmental characteristics such as salinity, pH, temperature, and surfactant on Hortaea sp. B15 mediated degradation of chlorpyrifos as well as enzyme activity and metabolic pathway. The highest bacterial growth (4.6 × 10¹⁶ CFU/mL) was achieved after 20 h of incubation in a 100 mg/L chlorpyrifos amended culture. The fit model and feasible way to express the chlorpyrifos biodegradation kinetics in normal condition and optimized was a first-order rate equation, with an R² value of 0.95-0.98. The optimum pH for chlorpyrifos biodegradation was pH 9, which resulted in a high removal rate (91.1%) and a maximum total count of 3.8 × 10¹⁶ CFU/mL. Increasing the temperature over 40 °C may inhibit microbial development and biodegradation. There was no significant effect of culture salinity on degradation and bacterial growth. In the presence of non-ionic surfactant Tween 80, the maximum chlorpyrifos degradation (89.5%) and bacterial growth (3.8 × 10¹⁶ CFU/mL) was achieved. Metabolites such as 3,5,6-trichloropyridin-2-ol and 2-pyridinol were identified in the Hortaea sp. B15 mediated degradation of chlorpyrifos. According to the findings, Hortaea sp. B15 should be recommended for use in the investigation of in situ biodegradation of pesticides.

Efficient and synergistic degradation of fluoroquinolones by bacteria and microalgae: Design of environmentally friendly substitutes, risk regulation and mechanism analysis

Fluoroquinolones (FQs) are widely used as antimicrobial agents, and their nonbiodegradable in sewage has become an increasingly concerning. High-biochemical substitutes of FQs were designed with bacteria and microalgae as driving forces of biodegradation, and this is the first study on efficient synergistic degradation of FQs by multiple microorganisms. Among 143 designed FQ substitutes, only one was screened with high biodegradability (increased by 120.51 %), improved functional properties (genotoxicity: 13.66 %), less environmental impacts (bio-accumulation: -44.81 %), less human health and ecological risk (hepatotoxicity: -106.21 %). The complex functional protein with the synergistic degradation effect of bacteria and microalgae was constructed, which proved their synergistic degradation and realized the effect of "1 + 1 > 2″. The best risk regulation scheme determined using molecular dynamics simulation proved the degradation ability of complex functional protein and found the CIP-129 was easy to be degraded in real environment compared with CIP, and the degradation rate increased by 70.42 %. The synthesis path of CIP-129 and CIP were inferred and calculated, and the results showed the Gibbs free energies of three CIP-129 synthetic paths (40.64 a.u.; 40.61 a.u.; 40.65 a.u.) were close to the energy required for the CIP (39.43 a.u.), indicating there was no significant difference in the energy consumption of CIP-129 in laboratory synthesis.

Biodegradation of 4-nitroaniline by novel isolate Bacillus sp. strain AVPP64 in the presence of pesticides

In this study, Bacillus sp. strain AVPP64 was isolated from diuron-contaminated soil. It showed 4-nitroaniline (4-NA) degradation, pesticide tolerance, and self-nutrient integration via nitrogen (N)-fixation and phosphate (P)-solubilization. The rate constant (k) and half-life period (t_1/2) of 4-NA degradation in the aqueous medium inoculated with strain AVPP64 were observed to be 0.445 d^-1 and 1.55 d, respectively. Nevertheless, in the presence of chlorpyrifos, profenofos, atrazine and diuron pesticides, strain AVPP64 degraded 4-NA with t_1/2 values of 2.55 d, 2.26 d, 2.31 d and 3.54 d, respectively. The strain AVPP64 fixed 140 μg mL^-1 of N and solubilized 103 μg mL^-1 of P during the presence of 4-NA. In addition, strain AVPP64 produced significant amounts of plant growth-promoting metabolites like indole 3-acetic acid, siderophores, exo-polysaccharides and ammonia. In the presence of 4-NA and various pesticides, strain AVPP64 greatly increased the growth and biomass of Vigna radiata and Crotalaria juncea plants. These results revealed that Bacillus sp. strain AVPP64 can be used as an inoculum for bioremediation of 4-NA contaminated soil and sustainable crop production even when pesticides are present.

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

Heavy metal and pesticide pollution have become an inevitable part of the modern industrialized environment that find their way into all ecosystems. Because of their persistent nature, recalcitrance, high toxicity and biological enrichment, metal and pesticide pollution has threatened the stability of the environment as well as the health of living beings. Due to the environmental persistence of heavy metals and pesticides, they get accumulated in the environs and consequently lead to food chain contamination. Therefore, remediation of heavy metals and pesticide contaminations needs to be addressed as a high priority. Various physico-chemical approaches have been employed for this purpose, but they have significant drawbacks such as high expenses, high labor, alteration in soil properties, disruption of native soil microflora and generation of toxic by-products. Researchers worldwide are focusing on bioremediation strategies to overcome this multifaceted problem, i.e., the removal, immobilization and detoxification of pesticides and heavy metals, in the most efficient and cost-effective ways. For a period of millions of evolutionary years, microorganisms have become resistant to intoxicants and have developed the capability to remediate heavy metal ions and pesticides, and as a result, they have helped in the restoration of the natural state of degraded environs with long term environmental benefits. Keeping in view the environmental and health concerns imposed by heavy metals and pesticides in our society, we aimed to present a generalized picture of the bioremediation capacity of microorganisms. We explore the use of bacteria, fungi, algae and genetically engineered microbes for the remediation of both metals and pesticides. This review summarizes the major detoxification pathways and bioremediation technologies; in addition to that, a brief account is given of molecular approaches such as systemic biology, gene editing and omics that have enhanced the bioremediation process and widened its microbiological techniques toward the remediation of heavy metals and pesticides.

Natural attenuation of sulfometuron-methyl in seawater: Kinetics, intermediates, toxicity change and ecological risk assessment

This research aims to evaluate the environmental feasibility of sulfometuron-methyl (SM) as a growth inhibitor for restricting the growth of Spartina alterniflora. To achieve this purpose, the natural attenuation characteristics, ecological risk, degradation pathway, and comprehensive toxicity changes of SM in seawater were investigated under the simulated marine environmental conditions of Jiaozhou Bay, China. The natural attenuation of SM in seawater followed first-order reaction kinetics with a rate constant (K) of 0.0694 d^-1 and a half-life of 9.99 days. When photolysis, hydrolysis, and biodegradation pathways act alone, the rate constants K of SM were 0.0167, 0.0143, and 0.0099 d^-1 respectively, indicating that their contributions to the total removal of SM decreased in turn. The calculation results of risk quotient (RQ) showed that the seawater containing 10 mg/L of SM demonstrated a very high risk to marine diatom Skeletonema costatum before and after 21 days of attenuation with RQ values of 24.46 and 6.32, respectively, however, the risk to other marine organisms (fish, crustaceans, and bivalves) decreased from moderate (RQ < 1) to low (RQ < 0.01). Four attenuation products of SM were identified and two degradation pathways of SM in seawater were proposed. Based on the rate of inhibition of bioluminescence, SM in seawater was not harmful to Photobacterium phosphoreum T3, whereas the toxicity of seawater containing SM increased with the extension of attenuation time, suggesting the formation of intermediate products with high aquatic toxicity. According to the toxicity values predicted by ECOSAR, the toxicity of one identified attenuation product was higher than that of SM. To the best of our knowledge, this is the first report on the attenuation characteristics and toxicity changes of SM in seawater. The results indicated that the toxicity of both SM and its degradation products to non-target marine organisms should be considered in evaluating the feasibility of SM in controlling coastal Spartina alterniflora.

A synergistic bacterial pool decomposes tebuthiuron in soil

This study aimed to propose an eco-compatible strategy to mitigate the possible environmental contamination caused by tebuthiuron. Therefore, we screened potential tebuthiuron-degrading microorganisms from conventional (CS) and no-till (NTS) systems producing sugarcane. Then, they were bioprospected for their ability of decomposing the target-molecule at 2.48 mmol g-1 and 4.96 mmol g-1 into CO2 via respirometry. Integrating microbiota from CS and NTS into an advantageously synergistic bacterial pool produced the highest specific-growth rate of CO2 of 89.60 mg day-1, so outstripped the other inoculum. The bacterial CN-NTS framework notably stabilized the sigmoidal Gompertz curve on microbial degradation earliest and enabled the seeds of Lactuca sativa to germinate healthiest throughout ecotoxicological bioassay for cross-validation. Our study is preliminary, but timely to provide knowledge of particular relevance to progress in the field's prominence in remediating terrestrial ecosystems where residual tebuthiuron can persist and contaminate. The analytical insights will act as an opening of solutions to develop high-throughput biotechnological strategies for environmental decontamination.

Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB

Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.

Study on degradation characteristics of imazamox by Streptomycetaceae

The residues of imazamox (IMX) will cause phytotoxicity to subsequent crops after long-term use, and will also pollute the soil and its surrounding environment. This study isolates and identifies two strains of Streptomycetaceae JX02 and JX06 that can effectively degrade IMX. Use response surface method Box-Behnken design to optimize physicochemical parameters. The optimal degradation conditions of strains JX02 and JX06 are obtained and verified: IMX concentration is 150 mg L^-1, the initial dosage is 9.9%, 9.1% (OD600 = 0.1), the temperature is 26.4 and 27.5 °C, and pH value is 7.0 and 7.7, respectively. The degradation rates of 150 mg L^-1 IMX detected by HPLC within 4 d were 99 and 94%, respectively. After adding strains JX02 and JX06, the half-life of IMX in the soil is shortened to 11 d and 13 d, indicating that Streptomycetaceae had a positive effect on the remediation of soil. It is expected to provide scientific information for the rational use, environmental safety evaluation of IMX, and provide a basis for future research and development of microbial agents.

Evidence for enhanced dissipation of chlorpyrifos in an agricultural soil inoculated with Serratia rubidaea strain ABS 10

The insecticide ¹⁴C-chlorpyrifos was found mineralized in a Tunisian soil with repeated exposure to it. From this soil, a bacterial strain was isolated that was able to grow in a minimal salt medium (MSM) supplemented with 25 mg L^-1 of chlorpyrifos. It was characterized as Serratia rubidaea strain ABS 10 using morphological and biochemical analyses, as well as 16S rRNA sequencing. In a liquid culture, the S. rubidaea strain ABS 10 was able to dissipate chlorpyrifos almost entirely within 48 h of incubation. Although the S. rubidaea strain ABS 10 was able to grow in an MSM supplemented with chlorpyrifos and dissipate it in a liquid culture, it was not able to mineralize ¹⁴C-chlorpyrifos. Therefore, it can be concluded that the dissipation capability of this bacteria might be attributed to its capacity to adsorb CHL. It can also be ascribed to other reasons such as the formation of biogenic non-extractable residues. In both non-sterile and sterile soil inoculated with S. rubidaea strain ABS 10, chlorpyrifos was more rapidly dissipated than in controls with DT₅₀ of 1.38 and 1.05 days, respectively.

Degradation insight of organophosphate pesticide chlorpyrifos through novel intermediate 2,6-dihydroxypyridine by Arthrobacter sp. HM01

Organophosphates (OPs) are hazardous pesticides, but an indispensable part of modern agriculture; collaterally contaminating agricultural soil and surrounding water. They have raised serious food safety and environmental toxicity that adversely affect the terrestrial and aquatic ecosystems and therefore, it become essential to develop a rapid bioremediation technique for restoring the pristine environment. A newly OPs degrading Arthrobacter sp. HM01 was isolated from pesticide-contaminated soil and identified by a ribotyping (16S rRNA) method. Genus Arthrobacter has not been previously reported in chlorpyrifos (CP) degradation, which shows 99% CP (100 mg L-1) degradation within 10 h in mMSM medium and also shows tolerance to a high concentration (1000 mg L-1) of CP. HM01 utilized a broad range of OPs pesticides and other aromatic pollutants including intermediates of CP degradation as sole carbon sources. The maximum CP degradation was obtained at pH 7 and 32 °C. During the degradation, a newly identified intermediate 2,6-dihydroxypyridine was detected through TLC/HPLC/LCMS analysis and a putative pathway was proposed for its degradation. The study also revealed that the organophosphate hydrolase (opdH) gene was responsible for CP degradation, and the opdH-enzyme was located intracellularly. The opdH enzyme was characterized from cell free extract for its optimum pH and temperature requirement, which was 7.0 and 50 °C, respectively. Thus, the results revealed the true potential of HM01 for OPs-bioremediation. Moreover, the strain HM01 showed the fastest rate of CP degradation, among the reported Arthrobacter sp.

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 detoxification of dimethoate through mediated hydrolysis by Brucella sp. PS4: molecular profiling and plant growth-promoting traits

High toxicity of dimethoate requires efficient ways for detoxification and removal of its residues in contaminated environments. Microbial remediation is a process that utilizes the degradation potential of microbes to provide a cost-effective and reliable approach for pesticide abatement. For this purpose, a dimethoate-degrading bacterium Brucella sp. was isolated from a contaminated agricultural soil sample in Multan, Pakistan. This isolate was found to tolerate up to 100 ppm of dimethoate in minimal salt medium and was further evaluated for plant growth-promoting traits. The strain gave positive results for amylase, ammonia, and catalase production, while other traits such as indole acetic acid production and potassium solubilization were also confirmed. Thus, the strain could play an important role for plant nutrient transmission in the plant rhizosphere. Optimization of growth parameters (i.e., pH and temperature) depicted the potential of PS4 to be best tolerating dimethoate, with maximum cell density at λ 600 nm. Optimum pH and temperature for growth were found to be 6 and 35 °C, respectively. Based on optimization results as well as different attributes, the rhizospheric bacterial isolate PS4 was further subjected to a batch degradation experiment under different concentrations of dimethoate (25, 50, 75, and 100 ppm). This promising dimethoate-degrading isolate was found to degrade 83% of dimethoate (at 100 ppm) within a period of 7 days. In addition, it degraded 88% of dimethoate at 50 ppm, indicating that the bacterial isolate utilized dimethoate solely as a source of energy. The strain followed the first order reaction kinetics, depicting its dependence on dimethoate as energy and carbon source. Molecular profiling further supported its role in plant growth promotion and multi-stress tolerance. This research showed that Brucella sp. is capable of degrading dimethoate, and therefore, it would be useful in the investigation of novel bioremediation techniques at pesticide-polluted sites.

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

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

Mesosulfuron-methyl influenced biodegradability potential and N transformation of soil

The wide application of mesosulfuron-methyl (MS) in soil may affect soil microbial community, yet the information is limited. In this work, two distinct soil types from Anyang (AY) and Nanjing (NJ) were spiked with MS (0, 0.006, 0.06, or 0.6 mg kg^-1) and incubated for 90 days. MS decreased bacterial and fungal (except the last sampling) abundance and altered their diversity and community. Five biomarkers of bacterial species may help MS degradation and more increased xenobiotics biodegradation pathways were also observed in 0.6 mg kg^-1 treatment in AY soil. A co-occurrence network revealed the biomarkers grouped in one module in all AY soils, suggesting these biomarkers act in concert to degrade MS. MS impacted soil N transformation with increasing N₂-fixing bacteria in both soils and ammonia-oxidising bacteria (AOB) in NJ and decreasing ammonia-oxidizing archaea (AOA) in AY. The contents of NO₃^--N and NH₄⁺-N were increased by MS. Structural equation models revealed that the abundance of bacteria and fungi was responsible for the NO₃^--N and NH₄⁺-N contents. In conclusion, this work aids safety assessments and degradation-related research of MS in soil.

Bioremediation of Agricultural Soils Polluted with Pesticides: A Review

Pesticides are chemical compounds used to eliminate pests; among them, herbicides are compounds particularly toxic to weeds, and this property is exploited to protect the crops from unwanted plants. Pesticides are used to protect and maximize the yield and quality of crops. The excessive use of these chemicals and their persistence in the environment have generated serious problems, namely pollution of soil, water, and, to a lower extent, air, causing harmful effects to the ecosystem and along the food chain. About soil pollution, the residual concentration of pesticides is often over the limits allowed by the regulations. Where this occurs, the challenge is to reduce the amount of these chemicals and obtain agricultural soils suitable for growing ecofriendly crops. The microbial metabolism of indigenous microorganisms can be exploited for degradation since bioremediation is an ecofriendly, cost-effective, rather efficient method compared to the physical and chemical ones. Several biodegradation techniques are available, based on bacterial, fungal, or enzymatic degradation. The removal efficiencies of these processes depend on the type of pollutant and the chemical and physical conditions of the soil. The regulation on the use of pesticides is strictly connected to their environmental impacts. Nowadays, every country can adopt regulations to restrict the consumption of pesticides, prohibit the most harmful ones, and define the admissible concentrations in the soil. However, this variability implies that each country has a different perception of the toxicology of these compounds, inducing different market values of the grown crops. This review aims to give a picture of the bioremediation of soils polluted with commercial pesticides, considering the features that characterize the main and most used ones, namely their classification and their toxicity, together with some elements of legislation into force around the world.

Biodegradation of chlorpyrifos using isolates from contaminated agricultural soil, its kinetic studies

Extensive pesticides use is negatively disturbing the environment and humans. Pesticide bioremediation with eco-friendly techniques bears prime importance. This study evaluates the bioremediation of chlorpyrifos in soil using indigenous Bacillus cereus Ct3, isolated from cotton growing soils. Strains were identified through ribotyping (16s rRNA) by Macrogen (Macrogen Inc. Geumchen-gu, South Korea). Bacillus cereus Ct3 was resistant up to 125 mg L⁻¹ of chlorpyrifos and successfully degraded 88% of chlorpyfifos in 8 days at pH 8. Bacillus cereus Ct3 tolerated about 30–40 °C of temperature, this is a good sign for in situ bioremediation. Green compost, farmyard manure and rice husk were tested, where ANOVA (P < 0.05) and Plackett–Burman design, results indicated that the farm yard manure has significant impact on degradation. It reduced the lag phase and brought maximum degradation up to 88%. Inoculum size is a statistically significant (P < 0.05) factor and below 10⁶ (CFU g⁻¹) show lag phase of 4–6 days. Michaelis–Menten model results were as follows; R² = 0.9919, V_max = 18.8, K_s = 121.4 and V_max/K_s = 0.1546. GC–MS study revealed that chlorpyrifos first converted into diethylthiophosphoric acid and 3,5,6-trichloro-2-pyridinol (TCP). Later, TCP ring was broken and it was completely mineralized without any toxic byproduct. Plackett–Burman design was employed to investigate the effect of five factors. The correlation coefficient (R²) between experimental and predicted value is 0.94. Central composite design (CBD) was employed with design matrix of thirty one predicted and experimental values of chlorpyrifos degradation, having “lack of fit P value” of “0.00”. The regression coefficient obtained was R² = 0.93 which indicate that the experimental vales and the predicted values are closely fitted. The most significant factors highlighted in CBD/ANOVA and surface response plots were chlorpyrifor concentration and inoculum size. Bacillus cereus Ct3 effectively degraded chlorpyrifos and can successfully be used for bioremediation of chlorpyrifos contaminated soils.

Insights into the microbial degradation and catalytic mechanisms of chlorpyrifos

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

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.

New insights into the biodegradation of chlorpyrifos by a novel bacterial consortium: Process optimization using general factorial experimental design

Himalayan mountains are subjected to the intensive and unjudicial application of chlorpyrifos (CP) in agricultural practices; hence it has spurred concerns over food safety and environmental consequences. These low-temperature mountainous regions are foremost ecosystems, representing the large-scale distribution of cold trapped CP residues. A bacterial consortium ECO-M was formed by isolating the CP degrading bacterial strains viz Agrobacterium tumefaciens strain ECO1, Cellulosimicrobium funkei strain ECO2, Shinella zoogloeoides strain ECO3 and Bacillus aryabhattai strain ECO4. At an initial concentration of 50 mg L^-1, consortium ECO-M degraded 100% of CP within 6 days. Emergence and subsequent degradation of the two metabolites, 3, 5, 6-trichloro-2-pyridinol (TCP) and 2-hydroxypyridine were confirmed by GC-MS analysis. A degradation pathway of CP by isolated strains has been proposed. A general factorial experimental design was effectuated to prognosticate the optimum biodegradation by manifesting the optimal biological and physicochemical factors. Fitness of the experimental design was affirmed experimentally by employing optimized factors i.e., temperature 30 °C, CP concentration 50 mg L^-1 and an inoculum size of 10% (v/v). The model appropriacy and the rationality of the optimization procedure were appraised by installing an in-situ microcosms experiment using the real contaminated soil collected from the Himalayan mountain ecosystem. The augmentation culture seems to be effectively conspicuous in stimulating maximum degradation up to 94.3% in the CP contaminated soil.

Biodegradation of hydrophobic pesticides by microalgae: Transformation products and impact on algae biochemical methane potential

Intensive and extensive use of pesticides has contributed to their wide distribution in soil, air, and water. Due to their detrimental effects on non-target organisms, different technologies have been considered for their removal. In this work, three hydrophobic pesticide active compounds, namely, chlorpyrifos, cypermethrin, and oxadiazon, were selected to study the potential for their removal from aqueous media by a microalgae consortium. An abiotic and a killed control (thermally inactivated dead microalgae biomass) were employed to clarify their removal pathways, and pesticide content was quantified in liquid and biomass phases for 7 days. At the final time, total degradation (biodegradation plus photodegradation) contributed to the removal of 55% of oxadiazon, 35% of chlorpyrifos, and 14% of cypermethrin. Furthermore, more than 60% of chlorpyrifos and cypermethrin were removed by sorption onto microalgae biomass. Overall, the three pesticides showed high removal from the liquid phase. O,O-diethyl thiophosphate was identified in the liquid phase as a transformation product of chlorpyrifos formed by microalgae degradation. Phycoremediation was coupled with anaerobic degradation of the microalgae biomass containing the retained pesticides by sorption through biochemical methane potential tests. Anaerobic digestion was not inhibited by the pesticides as verified by methane production yields. The removal efficiency of the pesticides in the digestate was as follows: chlorpyrifos > cypermethrin > oxadiazon. These results highlight the potential of low-cost algal-based systems for the treatment of wastewater or effluents from agrochemical industries. The integration of wastewater treatment with biogas production through anaerobic digestion is a biorefinery approach that facilitates the economic feasibility of the process.

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

Influence of plant beneficial Stenotrophomonas rhizophila strain CASB3 on the degradation of diuron-contaminated saline soil and improvement of Lactuca sativa growth

Diuron is one of the major hazardous pollutants which posses severe risk to the environment and human healthiness. On the other hand, salinity is the most severe environmental stressor that limits crop productivity. Therefore, it is required to address this co-existing abiotic stresses in agricultural soil. Plant growth-promoting rhizobacteria have gained an engaging role in the degradation of pesticides in agricultural soil. However, their role against the restoration of diuron-contaminated saline soil is still not known. Thus, in this study, diuron-degrading, salinity-tolerant Stenotrophomonas rhizophila strain CASB3 was isolated and characterized. Strain CASB3 showed important PGP traits under normal and diuron or salt stresses. Complete degradation of 10-50 mg L-1 diuron in the aqueous medium under normal and salinity stress conditions was achieved within 48-120 h and 48-192 h, respectively. A unique pathway for diuron biodegradation was proposed based on GC-MS analysis. In a greenhouse study, CASB3 inoculated into diuron-contaminated saline soil efficiently degraded diuron (50 mg kg-1) by 94% in 42 days and simultaneously resulted in an enhancement of root-shoot length (47.22-63.41%), fresh-dry biomass (136.36-156.66%), and photosynthetic pigments (36.93-92.28%) in Lactuca sativa plants. These results suggest the strain CASB3 could be used as a bioresource for the reclamation of diuron-contaminated saline soils.

Co-presence of the anionic surfactant sodium lauryl ether sulphate and the pesticide chlorpyrifos and effects on a natural soil microbial community

There is a growing concern about the simultaneous presence in the environment of different kinds of pollutants, because of the possible synergic or additive effects of chemical mixtures on ecosystems. Chlorpyrifos (CPF) is an organophosphate insecticide extensively used in agricultural practices. The anionic surfactant sodium lauryl ether sulphate (SLES) is the main component of several commercial products, including foaming agents used in underground mechanised excavation. Both compounds are produced and sold in high amounts worldwide and can be found in the environment as soil contaminants. The persistence of SLES and CPF in agricultural soils and their possible effects on the natural microbial community was evaluated in microcosms. The experimental set consisted of soil samples containing the autochthonous microbial community and treated with only SLES (70 mg/kg), only CPF (2 mg/kg) or with a mix of both compounds. Control microcosms (without the contaminants) were also performed. Soil samples were collected over the experimental period (0, 7, 14, 21 and 28 days) and analysed for CPF, SLES and the main metabolite of CPF (3, 5, 6-trichloropyridinol, TCP). The half-life time (DT50) of each parent compound was estimated in all experimental conditions. At the same time, the abundance, activity and structure of the microbial community were also evaluated. The results showed that the co-presence of SLES and CPF did not substantially affect their persistence in soil (DT50 of 11 and 9 days with co-presence and 13 and 10 days, respectively, when alone); however, in the presence of SLES, a higher amount of the metabolite TCP was found. Interestingly, some differences were found in the bacterial community structure, abundance and activity among the various conditions.

Biodegradation of CP/TCP by a constructed microbial consortium after comparative bacterial community analysis of long-term CP domesticated activated sludge

The objective of this study was to construct a microbial consortium for effective biodegradation of chlorpyrifos (CP) and its hydrolysis product, 3,5,6-Trichloro-2-pyridinol (TCP). A activated sludge from an organophosphorus pesticide factory was domesticated under long-term (20 weeks) CP stress, and the dynamic change in bacterial communities was analyzed by high-throughput sequencing. Then, a microbial consortium MC-BSPK was constructed of Bacillus sp. MC-B, Serratia sp. MC-S, Pseudomonas sp. MC-P, and Klebsiella sp. MC-K, which were significantly enriched during the domestication process. The biodegradation capacities of the microbial consortium MC-BSPK reached 100% for CP within 9 days and 88.61% for TCP within 15 days under the optimized degradation conditions (pH 8.0 and 31 °C). High-performance liquid chromatography (HPLC) revealed that CP could be degraded by the microbial consortium MC-BSPK into TCP, probably through hydrolysis of the P-O ester bond, and further degraded into other small molecules. A bioassay revealed that the virulence of CP toward Drosophila melanogaster W1118 was clearly reduced by the microbial consortium MC-BSPK biodegradation. Thus, the easily constructed microbial consortium MC-BSPK with high CP/TCP degradation capacities has the potential for application in pesticide-contaminated bioremediation.

Biodegradation of carbendazim by a potent novel Chryseobacterium sp. JAS14 and plant growth promoting Aeromonas caviae JAS15 with subsequent toxicity analysis

In the present study, carbendazim (MBC) degrading bacterial strains were isolated and identified as Chryseobacterium sp. JAS14 and Aeromonas caviae JAS15. Both the strains completely degraded 200 mg l^-1 of MBC in the aqueous medium and soil within 4-9 days of incubation. In an aqueous medium, the degradation process was characterized by a rate constant of 53.16 day^-1 and 42.60 day^-1, following zero order model and DT₅₀ was 1.8 days and 2.34 days for Chryseobacterium sp. JAS14 and A. caviae JAS15, respectively. A Chryseobacterium sp. JAS14 and A. caviae JAS15 inoculated into the soil without the addition of nutrients showed the degradation rate constant of 27.30 day^-1 and 23.87 day^-1, and DT₅₀ was 3.66 days and 4.18 days, respectively. The metabolites during MBC biodegradation by Chryseobacterium sp. JAS14 and A. caviae JAS15 were identified as 2-aminobenzimidazole, 2-hydroxybenzimidazole, 1, 2 diaminobenzene and catechol. To our knowledge, this is the first study of the detailed biodegradation pathway of MBC by Chryseobacterium sp. JAS14 was proposed. Phytotoxicity and cytogenotoxicity assays showed that the toxicity of the MBC reduced after biodegradation by Chryseobacterium sp. JAS14 and A. caviae JAS15. In addition, A. caviae JAS15 possess important plant growth promoting traits under normal and MBC stress condition. These results suggest the Chryseobacterium sp. JAS14 and A. caviae JAS15 could be used as a bioresource for the reclamation of MBC contaminated soil.

Alternative Bioremediation Agents against Haloacids, Haloacetates and Chlorpyrifos Using Novel Halogen-Degrading Bacterial Isolates from the Hypersaline Lake Tuz

The indiscriminate use of chemical pesticides alongside the expansion of large-scale industries globally can critically jeopardize marine ecology and the well-being of mankind. This is because the agricultural runoffs and industrial effluents eventually enter waterways before flowing into highly saline environments i.e., oceans. Herein, the study assessed two novel bacterial isolates, Bacillus subtilis strain H1 and Bacillus thuringiensis strain H2 from the hypersaline Lake Tuz in Turkey to degrade recalcitrant haloalkanoic acids, haloacetates and chlorpyrifos, and consequently, identify their optimal pollutant concentrations, pH and temperature alongside salt-tolerance thresholds. Bacillus strains H1 and H2 optimally degraded 2,2-dichloropropionic acid (2,2-DCP) under similar incubation conditions (pH 8.0, 30 °C), except the latter preferred a higher concentration of pollutants as well as salinity at 30 mM and 35%, respectively, while strain H1 grew well on 20 mM at <30%. While both isolates could degrade all substrates used, the dehalogenase gene from strain H1 could not be amplified. Capacity of the H2 bacterial isolate to degrade 2,2-DCP was affirmed by the detection of the 795 bp putative halotolerant dehalogenase gene after a successful polymerase chain reaction (PCR) amplification. Hence, the findings envisage the potential of both isolates as bio-degraders of recalcitrant halogenated compounds and those of the same chemical family as chlorpyrifos, in saline environments.

Pan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links

Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species of this genus, O. intermedium and O. anthropi were documented for causing infections mostly in the immunocompromised patients. Despite such ubiquitous presence, study of adaptation in various niches is still lacking. Thus, to gain insights into the niche adaptation strategies, pan-genome analysis was carried out by comparing 67 genome sequences belonging to Ochrobactrum species. Pan-genome analysis revealed it is an open pan-genome indicative of the continuously evolving nature of the genus. The presence/absence of gene clusters also illustrated the unique presence of antibiotic efflux transporter genes and type IV secretion system genes in the clinical strains while the genes of solvent resistance and exporter pumps in the environmental strains. A phylogenomic investigation based on 75 core genes depicted better and robust phylogenetic resolution and topology than the 16S rRNA gene. To support the pan-genome analysis, individual genomes were also investigated for the mobile genetic elements (MGE), antibiotic resistance genes (ARG), metal resistance genes (MRG) and virulence factors (VF). The analysis revealed the presence of MGE, ARG, and MRG in all the strains which play an important role in the species evolution which is in agreement with the pan-genome analysis. The average nucleotide identity (ANI) based on the genetic relatedness between the Ochrobactrum species indicated a distinction between individual species. Interestingly, the ANI tool was able to classify the Ochrobactrum genomes to the species level which were assigned till the genus level on the NCBI database.

Comparative Genomics of a Paddy Field Bacterial Isolate Ochrobactrum sp. CPD-03: Analysis of Chlorpyrifos Degradation Potential

Ochrobactrum genus is known to catabolize aromatic compounds. This study reports a complete genome sequence of Ochrobactrum sp. CPD-03 (~ 4.6 Mb of chromosomal features) responsible for chlorpyrifos (CP) isolated form a paddy field (20.3588° N, 85.8333° E) in Bhubaneswar, India. A comparative genomics approach was performed between CPD-03 and eight closely related genomes of other Ochrobactrum strains in order to deepen our knowledge, to establish its phylogenetic and functional relationships. The involvement of CP degrading genes indicated a versatile role of CPD-03 in additional field trails. This research would provide the genetic information for its use in natural environment for the depletion of organophosphorus (OP) compounds.

Minute-Speed Biodegradation of Organophosphorus Insecticides by Cupriavidus nantongensis X1T

Organophosphorus insecticides (OPs) have been widely used to control agricultural pests, which has raised concerns about OP residues in crops and the environment. In this study, we investigated the degradation kinetics and pathways of 8 OPs by Cupriavidus nantongensis X1^T and identified the enzyme via gene cloning and in vitro assays. The degradation half-life of methyl parathion, triazophos, and phoxim was only 5, 9, and 43 min, respectively. It was 46 fold faster than that of triazophos by Bacillus sp. TAP-1, a well-studied triazophos-degrader. Strain X1^T completely degraded not only chlorpyrifos, methyl parathion, parathion, fenitrothion, triazophos, and phoxim at 50 mg/L within 48 h but also the phenolic metabolites. This was the fastest degradation of OPs by bacterial whole cells reported thus far. The OPs were first hydrolyzed by an OP hydrolase encoded by the opdB gene in strain X1^T, followed by further degradation of the metabolites. The crude enzyme maintained a full activity.

Rapid Biodegradation of the Organophosphorus Insecticide Chlorpyrifos by Cupriavidus nantongensis X1T

Chlorpyrifos was one of the most widely used organophosphorus insecticides and the neurotoxicity and genotoxicity of chlorpyrifos to mammals, aquatic organisms and other non-target organisms have caused much public concern. Cupriavidus nantongensis X1^T, a type of strain of the genus Cupriavidus, is capable of efficiently degrading 200 mg/L of chlorpyrifos within 48 h. This is ~100 fold faster than Enterobacter B-14, a well-studied chlorpyrifos-degrading bacterial strain. Strain X1^T can tolerate high concentrations (500 mg/L) of chlorpyrifos over a wide range of temperatures (30–42 °C) and pH values (5–9). RT-qPCR analysis showed that the organophosphorus hydrolase (OpdB) in strain X1^T was an inducible enzyme, and the crude enzyme isolated in vitro could still maintain 75% degradation activity. Strain X1^T can simultaneously degrade chlorpyrifos and its main hydrolysate 3,5,6-trichloro-2-pyridinol. TCP could be further metabolized through stepwise oxidative dechlorination and further opening of the benzene ring to be completely degraded by the tricarboxylic acid cycle. The results provide a potential means for the remediation of chlorpyrifos- contaminated soil and water.

NanoFe3O4 accelerates anoxic biodegradation of 3, 5, 6-trichloro-2-pyridinol

3, 5, 6-trichloro-2-pyridinol (TCP) is a widespread organic pollutant with persistent, mobile and high antimicrobial effects. Here, nanoFe₃O₄ was firstly introduced into the anoxic biodegradation of TCP. It was found that nanoFe₃O₄ significantly accelerated TCP biodegradation. The removal rate of TCP (100 mg L^-1) increased from 83.03% to 98.74% within 12 h in the presence of nanoFe₃O₄, and the addition of nanoFe₃O₄ also promoted the accumulation of CO₂. Reductive dechlorination mechanism was involved in anoxic biodegradation of TCP. Molecular approaches further revealed that nanoFe₃O₄ distinctly induced the shifts of bacterial community. The dominant genus Ochrobactrum was converted to genus Delftia in nanoFe₃O₄ treatment, and the relative abundance of Delftia increased from 10.26% to 44.62%. Meanwhile, the total relative abundance of bacteria related to TCP dechlorination and degradation significantly increased in the presence of nanoFe₃O₄. These results indicated that nanoFe₃O₄ induced the enrichment of TCP-degrading bacteria to promote the anoxic biodegradation of TCP.

First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina

We report here on a high-quality draft genome sequence of Ochrobactrum haematophilum strain P6BS-III (DSM 106071), a Gram negative, non-sporulating bacterium isolated from a pastureland (Buenos Aires province, Argentina) which had been chronically exposed to the herbicide glyphosate. The genome of 5.25 Mb with a DNA G+C content of 56.63% size was estimated to contain 5,291 protein coding genes and 57 RNA genes. Genome analysis revealed the presence of the phn operon, which is involved in the phosphonate degradation pathway, and a class II 5-enolpyruvylshikimate-3-phosphate synthase (EPSP) that confers tolerance to glyphosate. Genes related to plant growth promotion traits are also present, and include genes for phosphorus metabolism, calcium phosphate and phytate solubilization, siderophore production, organic acid biosynthesis and indole acetic acid (IAA) production.

Biodegradation of fipronil and its metabolite fipronil sulfone by Streptomyces rochei strain AJAG7 and its use in bioremediation of contaminated soil

Fipronil is a most widely used insecticide. It has been found to be highly toxic to insects with alarming decline in honey bees' population. It has shown to cause severe contamination of soil and water. The present study was undertaken to understand the degradation of fipronil and its metabolite fipronil sulfone using actinomycetes. Fipronil degrading actinomycetes strain AJAG7 was isolated from fipronil contaminated agricultural field by enrichment method. Molecular identification by 16S rRNA gene sequencing identified strain AJAG7 as Streptomyces rochei. The biodegradation of fipronil and its metabolite fipronil sulfone by strain AJAG7 was examined by HPLC. Biodegradation pathway of fipronil by strain AJAG7 was deduced with GC-MS analysis. Scanning electron microscopy was used to investigate the surface morphological changes of strain AJAG7 upon fipronil degradation. Apart from fipronil degradation, low cost powder formulation of strain AJAG7 was prepared using agricultural waste to remediate the fipronil contaminated agricultural field. Results of the present study suggest that strain AJAG7 qualifies as an ideal candidate for biodegradation of fipronil contaminated environment.

Kinetics and Catabolic Pathways of the Insecticide Chlorpyrifos, Annotation of the Degradation Genes, and Characterization of Enzymes TcpA and Fre in Cupriavidus nantongensis X1T

Chlorpyrifos is one of the most used organophosphorus insecticides. It is commonly degraded to 3,5,6-trichloro-2-pyridinol (TCP), which is water-soluble and toxic. Bacteria can degrade chlorpyrifos and TCP, but the biodegradation mechanism has not been well-characterized. Recently isolated Cupriavidus nantongensis X1^T can completely degrade 100 mg/L chlorpyrifos and 20 mg/L TCP with half-lives of 6 and 8 h, respectively. We annotated a complete gene cluster responsible for TCP degradation in recently sequenced strain X1^T. Two key genes, tcpA and fre, were cloned from X1^T and transferred and expressed in Escherichia coli BL21(DE3). Degradation of TCP by X1^T whole cell was compared with that by the enzymes 2,4,6-trichlorophenol monooxygenase and NAD(P)H:flavin reductase expressed and purified from E. coli BL21(DE3). Novel metabolites of TCP were isolated and characterized, indicating stepwise dechlorination of TCP, which was confirmed by TCP disappearance, mass balance, and detection and formation kinetics of chloride ion from TCP.

Biodegradation of chlorpyrifos and 3,5,6-trichloro-2-pyridinol by the epiphytic yeasts Rhodotorula glutinis and Rhodotorula rubra

The possible involvement of the epiphytic yeasts Rhodotorula glutinis and Rhodotorula rubra in the biodegradation of the insecticide chlorpyrifos and its metabolite 3,5,6-trichloro-2-pyridinol (TCP), in pure cultures and in plant surfaces (tomato fruits) was investigated. Higher biodegradation rates were observed as the concentration of chlorpyrifos and the inoculum of the microorganisms were increased, while the yeasts proved to be more active at 25 and 15 °C. The presence of glucose in the mineral nutrient medium, as an extra source of carbon, delayed the biodegradation by Rhodotorula glutinis, while Rhodotorula rubra proved to be more active. The detection and quantification of the parent compound and TCP was successfully achieved using a LC/MS/MS chromatographic system. The in vitro enzymatic assays applied suggested that esterases may be involved in the biodegradation of chlorpyrifos, a fact that was further enhanced after the addition of the synergists triphenyl phosphate, diethyl maleate and piperonyl butoxide in the biodegradation trials. The decrease of chlorpyrifos residues on tomato fruits confirmed the corresponding on pure cultures, resulting in the suggestion that the yeasts R. glutinis and R. rubra can possibly be used successfully for the removal or detoxification of chlorpyrifos residues on tomatoes.

Treatment of olive mill wastewater through employing sequencing batch reactor: performance and microbial diversity assessment

This work describes the performance of a sequencing batch reactor (SBR) and the involvement of a novel reconstituted bacterial consortium in olive mill wastewater (OMW) treatment. The organic loading rate applied to the SBR was serially increased in terms of initial COD from 10 to 75 g L^-1 to allow gradual acclimatization of activated sludge to high concentrations of toxic compounds in OMW. After the acclimatization period, up to 60% of the total COD content were effectively biodegraded from OMW at 75 g L^-1 COD within 30 day hydraulic retention time. The diversity and community composition of cultivable bacteria participating in the aerobic process of treating OMW were further assessed. A total of 91 bacterial strains were isolated from the reactor and analyzed by amplification of the 16S-23S rRNA internal transcribed spacer (ITS) region and by 16S rRNA gene sequencing. The most abundant phylum was Firmicutes (57.1%) followed by Proteobacteria (35.2%) and Actinobacteria (7.7%). The use of the Biolog® Phenotype Microarray system to evaluate the ability of isolated strains to utilize OMW phenolic compounds is reported in this work for the first time. Interestingly, results showed that all species tested were able to utilize phenolics as sole carbon and energy sources. The removals of COD and phenolics from undiluted OMW by the reconstituted bacterial consortium were almost similar to those obtained by the acclimatized activated sludge, which suggest that cultivable bacteria play the major role in OMW biodegradation. Phytotoxicity assays using tomato seeds showed a significant improvement of seed germination values for treated OMW. Our overall results suggest that the novel developed bacterial consortium could be considered as a good prospect for phenolics-rich wastewaters bioremediation applications.

A review on pesticide removal through different processes

The main organic pollutants worldwide are pesticides, persistent chemicals that are of concern owing to their prevalence in various ecosystems. In nature, pesticide remainders are subjected to the chemical, physical, and biochemical degradation process, but because of its elevated stability and some cases water solubility, the pesticide residues persist in the ecosystem. The removal of pesticides has been performed through several techniques classified under biological, chemical, physical, and physicochemical process of remediation from different types of matrices, such as water and soil. This review provides a description of older and newer techniques and materials developed to remove specific pesticides according to previous classification, which range from bioremediation with microorganisms, clay, activated carbon, and polymer materials to chemical treatment based on oxidation processes. Some types of pesticides that have been removed successfully to large and small scale include, organophosphorus, carbamates, organochlorines, chlorophenols, and synthetic pyrethroids, among others. The most important characteristics, advantages, and disadvantages of techniques and materials for removing pesticides are described in this work.

Phylogeny and polycyclic aromatic hydrocarbons degradation potential of bacteria isolated from crude oil-contaminated site

This study employed the use of 16S rRNA gene sequence analysis to identify three of four native bacterial strains isolated from crude oil-contaminated site in Poza Rica, Veracruz, Mexico. The identified bacteria were Ochrobactrum intermedium, Pandoraea pnomenusa and Ochrobactrum sp., but SA2-09 strain was not identified. The ability of the isolates to degrade polycyclic aromatic hydrocarbons (PAHs) was evaluated at 31.61 and 54.52 mg/kg PAHs in soil, when used as crude oil in soil microcosm during 80 days of incubation at 30°C. The results demonstrated that O. intermedium biodegraded many PAHs, including the high molecular weight (HMW) PAHs fluoranthene (100% equivalent 0.24 mg/kg), benzo [b] fluoranthene (81.8% equal 0.18 mg/kg), Benzo[a]pyrene (87.0%, 0.20 mg/kg) and Benzo[g,h,i]perylene (52.7%, 0.39 mg/kg). P. pnomenusa had a degradation profile of HMW PAHs, which was similar to O. intermedium, while Ochrobactrum sp. and the strain SA-09 exhibited lower degradation rates of HMW.