Isolation and characterization of atrazine-degrading strain Shewanella sp. YJY4 from cornfield soil

A comparative evaluation of biochar and Paenarthrobacter sp. AT5 for reducing atrazine risks to soybeans and bacterial communities in black soil

Application of biochar and inoculation with specific microbial strains offer promising approaches for addressing atrazine contamination in agricultural soils. However, determining the optimal method necessitates a comprehensive understanding of their effects under similar conditions. This study aimed to evaluate the effectiveness of biochar and Paenarthrobacter sp. AT5, a bacterial strain known for its ability to degrade atrazine, in reducing atrazine-related risks to soybean crops and influencing bacterial communities. Both biochar and strain AT5 significantly improved atrazine degradation in both planted and unplanted soils, with the most substantial reduction observed in soils treated with strain AT5. Furthermore, bioaugmentation with strain AT5 outperformed biochar in enhancing soybean growth, photosynthetic pigments, and antioxidant defenses. While biochar promoted higher soil bacterial diversity compared to strain AT5, the latter selectively enriched specific bacterial populations. Additionally, soil inoculated with strain AT5 displayed a notable increase in the abundance of key genes associated with atrazine degradation (trzN, atzB, and atzC), surpassing the effects observed with biochar addition, thus highlighting its effectiveness in mitigating atrazine risks in soil.

Whole genome sequencing analysis and Box-Behnken design for the optimization of the decolourization of mixture textile dyes by halotolerant microbial consortium

The use of dyes in textile industries has resulted in substantially contaminated soil, water and ecosystem including fauna and flora. So, the application of eco-friendly approach for dyes removal is in great demand. The goal of this research was to develop and test a bacterial consortium for biodegrading dyes in artificial textile effluent (ATE) derived from mixture of Indigo carmine (40 mg/l); Malachite green (20 mg/l); Cotton bleu (40 mg/l); Bromocresol green (20 mg/l) and CI Reactive Red 66 (40 mg/l) dissolved in artificial seawater. The Box-Behnken design (BBD) which combine six variables with three levels each was used to determine the potential removal of dyes in ATE, by the selected microbial consortium (M31 and M69b). The experimental process indicated that decolourization of ATE reached 77.36 % under these conditions values: salinity (30 g/l), pH (9), peptone (5 g/l), inoculum size (1.5 108 CFU/ml), agitation (150 rpm) and contact time (72 h). The decolourization was confirmed by FTIR spectrum analysis of ATE before and after bacterial treatment. Bacterial strains used in this study were identified as Halomonas pacifica M31 and Shewanella algae M69b using 16 rDNA sequences. Moreover, the total genome analysis of M31 and M69b validated the implication of bacterial genes in mixture dyes removal. Therefore, the effect of the selected bacterial consortium on ATE removal was confirmed and it may be used in industrial wastewater treatment to issuing environmental safety.

Characterization and novel pathway of atrazine catabolism by Agrobacterium rhizogenes AT13 and its potential for environmental bioremediation

Agrobacterium rhizogenes AT13, a novel bacterial strain that was isolated from contaminated soil, could utilize atrazine as the sole nitrogen, thereby degrading it. Optimization of the degradation reaction using a Box-Behnken design resulted in 99.94% atrazine degradation at pH 8.57, with an inoculum size of 3.10 × 10⁹ CFU/mL and a concentration of 50 mg/L atrazine. Ultra-high performance liquid chromatography-electrospray ionization-high resolution mass spectrometry (UPLC-ESI-HRMS), liquid chromatography tandem mass spectrometry (LC-MS/MS) and high performance liquid chromatography (HPLC) analyses identified and quantified six reported metabolites and a novel metabolite (2-hydroxypropazine) from atrazine degradation by AT13. On the basis of these metabolites, we propose an atrazine degradation pathway that includes dichlorination, hydroxylation, deamination, dealkylation and methylation reactions. The toxicity of the degradation products was evaluated by Toxicity Estimation Software Tool (T.E.S.T). Bioaugmentation of atrazine-polluted soils/water with strain AT13 significantly improved the atrazine removal rate. Thus, AT13 has potential applications in bioremediation.

Biodegradation of Crystalline and Nonaqueous Phase Liquid-Dissolved ATRAZINE by Arthrobacter sp. ST11 with Cd2+ Resistance

A newly isolated cadmium (Cd)-resistant bacterial strain from herbicides-polluted soil in China could use atrazine as the sole carbon, nitrogen, and energy source for growth in a mineral salt medium (MSM). Based on 16S rRNA gene sequence analysis and physiochemical tests, the bacterium was identified as Arthrobacter sp. and named ST11. The biodegradation of atrazine by ST11 was investigated in experiments, with the compound present either as crystals or dissolved in di(2-ethylhexyl) phthalate (DEHP) as a non-aqueous phase liquid (NAPL). After 48 h, ST11 consumed 68% of the crystalline atrazine in MSM. After being dissolved in DEHP, the degradation ratio of atrazine was reduced to 55% under the same conditions. Obviously, the NAPL-dissolved atrazine has lower bioavailability than the crystalline atrazine. Cd2+ at concentrations of 0.05–1.5 mmol/L either had no effect (<0.3 mmol/L), slight effects (0.5–1.0 mmol/L), or significantly (1.5 mmol/L) inhibited the growth of ST11 in Luria-Bertani medium. Correspondingly, in the whole concentration range (0.05–1.5 mmol/L), Cd2+ promoted ST11 to degrade atrazine, whether crystalline or dissolved in DEHP. Refusal to adsorb Cd2+ may be the main mechanism of high Cd resistance in ST11 cells. These results may provide valuable insights for the microbial treatment of arable soil co-polluted by atrazine and Cd.

Managing the efficiencies of three different bacterial isolates for removing atrazine from wastewater

Three individual bacterial isolates previously isolated from two types of soil with a different history of atrazine applications were chosen, purified, and subjected to subsequent work. Identification of the individual bacterial isolates was conducted using molecular methods 16S rRNA and then tested for their atrazine degradation potentials. Effects of different parameters like mixing, starvation, UV exposure, and sodium citrate for enhancing the atrazine bioremediation process by identified bacteria were also studied. The molecular method identified individual bacterial isolates as Stenotrophomonas sp. strain SD2 (strain SD2), Bacillus cereus strain BC3 (strain BC3), and Paenarthrobacter ureafaciens strain AD3 (strain AD3). The bacterial isolate strain AD3 was able to degrade 47.95% of atrazine after 28 days. Mixing strain AD3 with strain BC3 showed almost doubled of atrazine degradation percentage (61.39%) of using strain BC3 as an individual isolate (36.59%). The atrazine degradation efficacy for Stenotrophomonas sp. strain SD2, Bacillus cereus strain BC3, and Paenarthrobacter ureafaciens strain AD3 was increased between 1.28 and 4.32 folds after the starvation process. The UV exposure enhanced the efficiencies of the tested isolates either individual or mixtures (from 1.08 to 4.63-fold). Adding sodium citrate as a stimulator to the media of growing the tested isolates enhanced their potential for atrazine degradation.

Soil bacterial community dynamics following bioaugmentation with Paenarthrobacter sp. W11 in atrazine-contaminated soil

Atrazine is one of the most widely used herbicides, however it and its metabolites cause widespread contamination in soil and ground water. Bioaugmentation is an effective method for remediation of environmental organic pollutants. High-throughput sequencing provides an important tool for understanding the changes of microbial community and function in response to pollutants degradation based on bioaugmentation. In this study, the effect of biodegradation with Paenarthrobacter sp. W11 and the change of microbial community during atrazine degradation were investigated. The results showed that bioaugmentation significantly accelerated the degradation rate of atrazine in soil and reduced the toxic effect of atrazine residues on wheat growth. The extra available NH₄⁺ through atrazine mineralization could serve as a nitrogen source to increase microbial numbers. High-throughput sequencing further revealed that the microbial community restored a new balance. The function of microbial community predicted by PICRUSt2 suggested that the biodegradation process of atrazine affected not only the atrazine degradation pathway, but also the nitrogen metabolism pathway. Methylobacillus and Pseudomonas were considered as the most important indigenous atrazine-degrading microorganisms, because their relative abundances were positively correlated with the relative abundance of Paenarthrobacter and atrazine degradation pathway. This study provides insight into the cooperation between indigenous microorganisms and external inoculums on atrazine degradation process.

Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1

The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.

Isolation and Identification of Pseudomonas sp. Strain DY-1 from Agricultural Soil and Its Degradation Effect on Prometryne

Prometryne is a widely used herbicide in China to control annual grasses and broadleaf weeds. However, the stability of prometryne makes it difficult to be degraded, which poses a threat to human health. This study presents a bacterial strain isolated from soil samples with a prometryne application history, designated strain DY-1. Strain DY-1, identified as Pseudomonas sp., is capable of utilizing prometryne as a sole carbon source for growth and degrading 100% of prometryne within 48 h from an initial concentration of 50 mg L^-1. To further optimize the degradation of prometryne, the prometryne concentration, temperature, pH, and salt concentration were examined. The optimal conditions for degradation of prometryne by strain DY-1 were an initial prometryne concentration of 50 mg L^-1, 30 °C, pH 7-8, and NaCl concentration of 200 mg L^-1. The same strain also degraded other s-triazine herbicides, including simetryne, ametryne, desmetryne, and metribuzin, under the same conditions. The biodegradation pathway of prometryne was established by isolating sulfoxide prometryne as the first metabolite and by the identification of sulfone prometryne and 2-hydroxy prometryne by liquid chromatography-mass spectrometry (LC-MS/MS). The results illustrated that strain DY-1 achieved the removal of prometryne by gradually oxidizing and hydrolyzing the methylthio groups. A bioremediation trial with contaminated soil and pot experiments showed that after treating the prometryne-contaminated soil with strain DY-1, the content of prometryne was significantly reduced (P < 0.05). This study provides an efficient bacterial strain and approach that could be potentially useful for detoxification and bioremediation of prometryne analogs.

Purification, characterization, and catalytic mechanism of N-Isopropylammelide isopropylaminohydrolase (AtzC) involved in the degradation of s-triazine herbicides

Deamination is ubiquitous in nature and has important biological significance. Leucobacter triazinivorans JW-1, recently isolated from sludge, can rapidly degrade s-triazine herbicides. The responsible enzymes, however, have not been purified and characterized. Herein, we purified an amidohydrolase, i.e., N-isopropylammelide isopropylaminohydrolase (AtzC) from JW-1 cells by ammonium sulfate precipitation and three chromatography steps. The purified AtzC catalyzed amidohydrolysis of N-isopropylammelide to cyanuric acid. The optimal catalytic conditions of the purified AtzC were 42 °C and pH 7.0, and the K_m and V_max of AtzC was 0.811 mM and 28.19 mmol/min·mg. AtzC could catalyze amidohydrolysis of an N-alkyl substituent from dihydroxy s-triazines to cyanuric acid. Molecular docking and structural alignments were used to infer AtzC catalytic mechanism. The structural architecture of AtzC resembled that of cytosine deaminase in class III amidohydrolase, with a single Zn²⁺ coordinated by His and Asp. Interestingly, the AtzC lacks an acidic residue putatively to activate water for hydrolysis as compared to the other amidohydrolases. His253 in AtzC probably functions as a single general acid-base catalyst. These findings further enhance our understanding how aminohydrolases catalyze the metabolism of s-triazine herbicides.

Influence of the herbicide haloxyfop-R-methyl on bacterial diversity in rhizosphere soil of Spartina alterniflora

Haloxyfop-R-methyl (haloxyfop) can efficiently control Spartina alterniflora in coastal ecosystems, but its effect on soil microbial communities is not known. In the present study, the impact of the haloxyfop on rhizosphere soil bacterial communities of S. alterniflora over the dissipation process of the herbicide has been studied in a coastal wetland. The response of the bacterial community in the rhizoplane (iron plaque) of S. alterniflora subjected to haloxyfop treatment was also investigated. Results showed that the persistence of haloxyfop in the rhizosphere soil followed an exponential decay with a half-life of 2.6-4.9 days, and almost all of the haloxyfop dissipated on Day 30. The diversity of rhizosphere soil bacteria was decreased at the early stages (Days 1, 3 & 7) and recovered at late stages (Days 15 & 30) of the haloxyfop treatment. Application of haloxyfop treatment increased the relative abundance of the genera Pseudomonas, Acinetobacter, Pontibacter, Shewanella and Aeromonas. Strains isolated from these genera can degrade herbicides efficiently, which possibly played a role in the degradation of haloxyfop. The rhizoplane bacterial diversity was reduced on Day 15 while being vastly enhanced on Day 30. Soil variables, including the electric conductivity, redox potential, and soil moisture, along with the soil haloxyfop residue, jointly shape the bacterial community in rhizosphere soil.

Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Enhancement of atrazine biodegradation by marine isolate Bacillus velezensis MHNK1 in presence of surfactin lipopeptide

Atrazine is one of the widely used toxic herbicide and considered as serious environmental contaminant worldwide due to its long term use in crop production. In this study, the effect of surfactin lipopeptide produced by Bacillus velezensis MHNK1 on atrazine biodegradation was investigated. B. velezensis MHNK1 produced 0.83 ± 0.07 g/L of anionic biosurfactant that reduced surface tension from 72.12 ± 0.02 to 33.2 ± 0.61 mN/m and CMC was 40 mg/L with 85.21 ± 1.60% emulsification index. Further, biosurfactant was characterized as surfactin by TLC, HPLC, FTIR, ¹H and ¹³C NMR and LCMS-ESI. B. velezensis MHNK1 showed 87.10 ± 3.10% atrazine biodegradation within 5 days which was revealed by HPLC and MS analysis. Atrazine biodegradation using a combination of B. velezensis MHNK1 (2%) and surfactin (2 CMC) resulted in 100 ± 1.20% degradation within 4 days. Presence of atrazine degrading genes in B. velezensis MHNK1 was also confirmed by PCR. To the best of our knowledge, there are no previous reports available on atrazine degradation using B. velezensis strain and also in combination with surfactin. The results of this study reveal that strain B. velezensis MHNK1 and surfactin can be potential source of ecofriendly application for removal of atrazine from contaminated sites.

Concentration and Community of Airborne Bacteria in Response to Cyclical Haze Events During the Fall and Midwinter in Beijing, China

Since 2013, severe haze events frequently have occurred in Beijing between October and March, which have created a significant public health threat. Although variations in the chemical composition of these haze events have been studied widely, information pertaining to airborne bacteria in such haze events remains limited. In this study, we characterized the concentration, community structure, and composition of the airborne bacteria in response to nine haze events that occurred between October 1, 2015, and January 5, 2016. We also analyzed the correlations of airborne bacteria (concentration, community structure, and composition) with pollution levels and meteorological factors. The results indicated that airborne bacterial concentration showed a positive cyclical correlation with the haze events, but the bacterial concentration plateaued at the yellow pollution level. In addition, we found particulate matter (PM₁₀) and relative humidity to be key factors that significantly affected the airborne bacterial concentration and community structure. Moreover, Halomonas and Shewanella were enriched on haze days for all nine of the haze events. Finally, the correlations between haze pollution and airborne bacteria in midwinter were weaker than those in fall and early winter, indicating an obvious staged distinction among the effects of haze on airborne bacteria. Our study illuminated the dynamic variation of bioaerosols corresponding to the cyclical haze events and revealed the interactions among air pollution, climate factors (mainly relative humidity), and airborne bacteria. These results imply that different strategies should be applied to deal with the potential threat of airborne bacteria during haze events in different seasons.

Biodegradation of atrazine by the novel Citricoccus sp. strain TT3

A previously undescribed atrazine-degrading bacterial strain TT3 capable of growing with atrazine as its sole nitrogen source was isolated from soil at the wastewater outfall of a pesticide factory in China. Phenotypic characterization and 16S rRNA gene sequencing indicated that the isolate belonged to the genus Citricoccus. Polymerase chain reaction (PCR) analysis revealed that TT3 contained the atrazine-degrading genes trzN, atzB, and atzC. The range for growth and atrazine degradation of TT3 was found to be pH 6.0-11.0, with a preference for alkaline conditions. At 30°C and pH 7.0, the strain removed 50mg/L atrazine in 66h with 1% inoculum. These results demonstrate that Citricoccus sp. TT3 has great potential for bioremediation of atrazine-contaminated sites, particularly in alkaline environments. To the best of our knowledge, there are no previous reports of Citricoccus strains that degrade atrazine, and therefore this work provides a novel candidate for atrazine bioremediation.

Characterisation of an efficient atrazine-degrading bacterium, Arthrobacter sp. ZXY-2: an attempt to lay the foundation for potential bioaugmentation applications

BACKGROUND

The isolation of atrazine-degrading microorganisms with specific characteristics is fundamental for bioaugmenting the treatment of wastewater containing atrazine. However, studies describing the specific features of such microorganisms are limited, and further investigation is needed to improve our understanding of bioaugmentation.

RESULTS AND CONCLUSIONS

In this study, strain Arthrobacter sp. ZXY-2, which displayed a strong capacity to degrade atrazine, was isolated and shown to be a potential candidate for bioaugmentation. The factors associated with the biodegrading capacity of strain ZXY-2 were investigated, and how these factors likely govern the metabolic characteristics that control bioaugmentation functionality was determined. The growth pattern of Arthrobacter sp. ZXY-2 followed the Haldane-Andrews model with an inhibition constant (K_i) of 52.76 mg L^-1, indicating the possible augmentation of wastewater treatment with relatively high atrazine concentrations (> 50 ppm). Real-time quantitative PCR (RT-qPCR) results showed a positive correlation between the atrazine degradation rate and the expression levels of three functional genes (trzN, atzB, and atzC), which helped elucidate the role of strain ZXY-2 in bioaugmentation. In addition, multiple copies of the atzB gene were putatively identified, explaining the higher expression levels of this gene than those of the other functional genes. Multiple copies of the atzB gene may represent a compensatory mechanism that ensures the biodegradation of atrazine, a feature that should be exploited in future bioaugmentation applications.