Microbial attenuation of atrazine in agricultural soils: Biometer assays, bacterial taxonomic diversity, and catabolic genes

Nitrogen fertiliser-domesticated microbes change the persistence and metabolic profile of atrazine in soil

Pesticides and fertilisers are frequently used and may co-exist on farmlands. The overfertilisation of soil may have a profound influence on pesticide residues, but the mechanism remains unclear. The effects of chemical fertilisers on the environmental behaviour of atrazine and their underlying mechanisms were investigated. The present outcomes indicated that the degradation of atrazine was inhibited and the half-life was prolonged 6.0 and 7.6 times by urea and compound fertilisers (NPK) at 1.0 mg/g (nitrogen content), respectively. This result, which was confirmed in both sterilised and transfected soils, was attributed to the inhibitory effect of nitrogen fertilisers on soil microorganisms. The abundance of soil bacteria was inhibited by nitrogen fertilisers, and five families of potential atrazine degraders (Micrococcaceae, Rhizobiaceae, Bryobacteraceae, Chitinophagaceae, and Sphingomonadaceae) were strongly and positively (R > 0.8, sig < 0.05) related to the decreased functional genes (atzA and trzN), which inhibited hydroxylation metabolism and ultimately increased the half-life of atrazine. In addition, nitrogen fertilisers decreased the sorption and vertical migration behaviour of atrazine in sandy loam might increase the in-situ residual and ecological risk. Our findings verified the weakened atrazine degradation with nitrogen fertilisers, providing new insights into the potential risks and mechanisms of atrazine in the context of overfertilisation.

Epilithic biofilms as a discriminating matrix for long-term and growing season pesticide contamination in the aquatic environment: Emphasis on glyphosate and metabolite AMPA

The indiscriminate use of pesticides represents high ecological risk in aquatic systems. Recently, the inclusion of epilithic biofilms as a reactive matrix has shown potential in diagnosing the health of water resources. The objective of this study was to use multiple matrices (water, suspended sediments, and biofilms) to discriminate contamination degrees in catchments with long and recent history of intensive pesticide use and to monitor growing season pesticides transfer to watercourses. Two catchments were monitored: one representative of "modern agriculture" in a subtropical environment, and another representative of recent agricultural expansion over the Pampa Biome in subtropical Brazil. Glyphosate and AMPA were accumulated in the biofilms and were detected at all sites and at all monitoring times, in concentrations ranging from 195 to 7673 μg kg-1 and from 225 to 4180 μg kg-1, respectively. Similarly, the fungicide tebuconazole has always been found in biofilms. The biofilms made it possible to discriminate the long-term history of pesticide use in the catchments and even to identify the influx pulses of pesticides immediately after their application to crops, which was not possible with active water sampling and even with suspended sediment monitoring. It is strongly recommended that, in regions with intensive cultivation of soybeans and other genetically modified crops, the presence of glyphosate and its metabolite AMPA be permanently monitored, a practice still very scarce in the literature.

Impact of Paenarthrobacter ureafaciens ZF1 on the soil enzyme activity and microbial community during the bioremediation of atrazine-contaminated soils

Bioremediation of atrazine-contaminated soil is considered a safe and effective approach in removing contaminates from the soil. However, the effects of adding foreign organisms to assist bioremediation on soil environmental quality and ecosystem are unclear. Here, the ecological remediation potential of strain Paenarthrobacter ureafaciens ZF1 on atrazine-contaminated soil was investigated through miniature experiments using variations in soil enzymes and bacterial communities as indicators. The results showed that strain ZF1 accelerated atrazine degradation, which could completely degrade atrazine at concentrations of 100 mg·L^− 1 atrazine within 2 h in liquid medium and could remove up to 99.3% of atrazine (100 mg·kg^− 1 in soil) within 6 days. During soil bioremediation, atrazine promoted the activities of urease and cellulase, and inhibited the activities of sucrase and catalase, while the strain ZF1 significantly promoted the activities of these four enzymes. High-throughput sequencing of 16S rRNA genes showed that ZF1 affected the relative abundance and bacterial community structure, and promoted bacterial diversity and evenness. Furthermore, redundancy analysis revealed a certain correlation among the strain ZF1, atrazine residue, soil enzyme activity, and soil bacterial community. The strain ZF1 in this work demonstrated remarkable potential for ecological restoration, and can be an effective and environmentally friendly alternative in remediating atrazine-contaminated soil.

Impacts of earthworm casts on atrazine catabolism and bacterial community structure in laterite soil

Atrazine accumulation in agricultural soil is prone to cause serious environmental problems and pose risks to human health. Vermicomposting is an eco-friendly approach to accelerating atrazine biodegradation, but the roles of earthworm cast in the accelerated atrazine removal remains unclear. This work aimed to investigate the roles of earthworm cast in promoting atrazine degradation performance by comprehensively exploring the change in atrazine metabolites and bacterial communities. Our results showed that earthworm cast amendment significantly increased soil pH, organic matters, humic acid, fulvic acid and humin, and achieved a significantly higher atrazine removal efficiency. Earthworm cast addition also remarkably changed soil microbial communities by enriching potential soil atrazine degraders (Pseudomonadaceae, Streptomycetaceae, and Thermomonosporaceae) and introducing cast microbial degraders (Saccharimonadaceae). Particularly, earthworm casts increased the production of metabolites deethylatrazine and deisopropylatrazine, but not hydroxyatrazine. Some bacterial taxa (Gaiellaceaea and Micromonosporaceae) and humus (humic acid, fulvic acid and humin) were strongly correlated with atrazine metabolism into deisopropylatrazine and deethylatrazine, whereas hydroxyatrazine production was benefited by higher pH. Our findings verified the accelerated atrazine degradation with earthworm cast supplement, providing new insights into the influential factors on atrazine bioremediation in vermicomposting.

Isolation of 2 simazine-degrading bacteria and development of a microbial agent for bioremediation of simazine pollution

Simazine was one of the most commonly used herbicides and was widely used to control broadleaf weeds in agriculture and forestry. Its widespread use had caused wide public concern for its high ecological toxicity. In order to remove simazine residues, 2 strains capable of effectively degrading simazine were isolated from the soil and named SIMA-N5 and SIMA-N9. SIMA-N5 was identified as Bacillus licheniformis by 16SrRNA sequence analysis, and SIMA-N9 was Bacillus altitudinis. According to the degradation ratio of simazine in a certain period of time, the degradation ability of different strains was evaluated. The degradation efficiency of simazine (5 mg/L) by SIMA-N9 could reach about 98% in 5d, and the strain SIMA-N5 could reach 94% under the same conditions. In addition, the addition of Pennisetum rhizosphere soil during the process of degrading simazine by strain SIMA-N9 could effectively improve the degradation efficiency. The strain SIMA-N9 has been developed as a microbial agent for the bioremediation of simazine contamination in soil. The new microbial agent developed by using SIMA-N9 has achieved satisfactory application effects. Based on the research results already obtained in this study, it was considered that strain SIMA-N9 and its live bacterial agent could play an important role in bioremediation of simazine pollution. This study could not only provide a set of solutions to the simazine pollution, but also provide a reference for the treatment of other pesticide pollution.

Coexisting antibiotic changes the persistence and metabolic profile of atrazine in the environment

Pesticides are widely used in agriculture to control weeds, pests and plant diseases. Antibiotics may be introduced to the agricultural environment by manure fertilizer or wastewater irrigation. Co-existence of antibiotics in field may lead to profound impacts on pesticide residue. In this study, the impacts of oxytetracycline on the environmental fate and metabolic profile of atrazine was investigated, and the disturbance of oxytetracycline on functional genes related to atrazine degradation in soils was also studied. Oxytetracycline could inhibit the degradation of atrazine significantly and prolong the half-life to 1.27 and 1.59 times longer at 5 mg/kg and 50 mg/kg. Also, oxytetracycline altered the composition of atrazine metabolites, including three chloro-s-triazine metabolites (DEA, DIA, DDA) and three hydroxyl metabolites (OH-ATZ, OH-DEA, OH-DIA). Oxytetracycline decreased the ratio of hydroxyl metabolites, while increased the chloro-s-triazine metabolites which had higher toxicity and were easily leached in soil. Atrazine hydrolase genes atzA and trzN were down-regulated by oxytetracycline, which might decrease the hydroxyl metabolite formation and detoxification of atrazine. Oxytetracycline changed the degradation of atrazine and the composition of the metabolites probably by altering the soil microorganisms. The increased persistence and the percentage of the chloro-s-triazine metabolites induced by oxytetracycline might result in increased environmental problems.

Metagenomic analysis reveals mechanisms of atrazine biodegradation promoted by tree species

Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.

Potential for the Biodegradation of Atrazine Using Leaf Litter Fungi from a Subtropical Protection Area

The intense use of pesticides in agricultural activities for the last several decades has caused contamination of the ecosystems connected with crop fields. Despite the well-documented occurrence of pesticide biodegradation by microbes, natural attenuation of atrazine (ATZ), and its effects on ecological processes in subtropical forested areas, such as Iguaçu National Park located in Brazil, has been poorly investigated. Subtropical environments sustain a great degree of fungal biodiversity, and the patterns and roles of these organisms should be better understood. This work aimed to evaluate nine ligninolytic-producer fungi isolated from the INP edge to degrade and detoxify ATZ solutions. ATZ degradation and the main metabolites produced, including deisopropylatrazine and deethylatrazine (DEA), were analyzed using dispersive liquid-liquid microextraction followed by gas chromatography-mass spectrometer. Four fungi were able to degrade ATZ to DEA, and the other five showed potential to grow and facilitate ATZ biodegradation. Furthermore, two strains of Fusarium spp. showed an enhanced potential for detoxification according to the Allium cepa (onion) test. Although the isolates produced ligninolytic enzymes, no ligninolytic activity was observed in the biodegradation of ATZ, a feature with ecological significance. In conclusion, Ascomycota fungi from the INP edge can degrade and detoxify ATZ in solution. Increasing the knowledge of biodiversity in subtropical protected areas, such as ecosystem services provided by microbes, enhances ecosystem conservation.

Transcriptome Analysis of Ice Plant Growth-Promoting Endophytic Bacterium Halomonas sp. Strain MC1 to Identify the Genes Involved in Salt Tolerance

Salt stress is an important adverse condition encountered during plant and microbe growth in terrestrial soil ecosystems. Currently, how ice plant (Mesembryanthemum crystallinum) growth-promoting endophytic bacteria (EB) cope with salt stress and regulate growth and the genes responsible for salt tolerance remain unknown. We applied RNA-Seq technology to determine the growth mechanism of the EB Halomonas sp. MC1 strain and the genes involved in salt tolerance. A total of 893 genes were significantly regulated after salt treatment. These genes included 401 upregulated and 492 downregulated genes. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis revealed that the most enriched genes included those related to the outer membrane-bounded periplasmic space, ATPase activity, catabolic process, and proton transmembrane transport. The quantitative real-time polymerase chain reaction data were similar to those obtained from RNA-Seq. The MC1 strain maintained survival under salt stress by regulating cellular and metabolic processes and pyruvate metabolism pathways such as organic and carboxylic acid catabolic pathways. We highlighted the response mechanism of Halomonas sp. MC1 to fully understand the dynamics of complex salt-microbe interactions.

Self-immobilized biomixture with pellets of Aspergillus niger Y3 and Arthrobacter. sp ZXY-2 to remove atrazine in water: A bio-functions integration system

The microorganism Arthrobacter. ZXY-2 exhibits excellent degradation efficiency for atrazine in free cells. However, its poor fixability makes it hard to be kept and recycled in water. To conquer the problem, this work employed mycelial pellets of Aspergillus niger Y3 to immobilize ZXY-2, which formed a self-immobilized biomixture (SIB) to remove atrazine. SIB could completely degrade 57.3 mg/L atrazine within 10 h. The SIB exhibited the highest degradation efficiency at pH = 7 and 40 °C. Degradation of atrazine with initial concentrations of 57.3 mg/L and 17.5 mg/L was described well by zero and first-order reaction kinetics, respectively. The recycling experiments demonstrated that SIB could be recycled for 5 batches. The results of SEM, FT-IR, and zeta potential analysis showed that porous structure, functional groups, and electronegativity of SIB all contributed to its stable formation. Therefore, this study demonstrates that SIB could be formed stably and could remove atrazine efficiently.

Enhanced biodegradation of atrazine at high infiltration rates in agricultural soils

The objective of this study was to assess the persistence and transport of atrazine at high infiltration rates expected from higher intensity precipitation associated with climate change scenarios in the midwestern U.S. The transport and transformation of atrazine was monitored in column experiments at high infiltration rates (64-119 mm d-1) associated with increased precipitation intensity. The optimum linear sorption and the lumped Monod biokinetic parameters were determined by inverting observed break-through curves (BTCs) using the advection-dispersion-sorption-degradation model. Batch microcosm studies were also conducted to examine the effect of moisture content (5%, 15% and 25%) on atrazine degradation and support the column results. BTCs from both soil types with continuous atrazine input showed a characteristic pattern of a pulse input i.e. lag phase prior to rapid atrazine degradation. The rate of atrazine leaching at higher infiltration rates was not fast enough to counteract the effect of enhanced degradation. Higher infiltration rates enriched the distribution of hydroxyatrazine in the soil profile for sandy loam, but their effect was minimal in loam soil. The pattern of degradation obtained in batch microcosms agreed with the column results. In both soils, mean half-life of atrazine was lower (4-8 days) at high soil moisture contents. Under future climate change scenarios, where more intense precipitation is likely to result in higher infiltration rates and increased soil moisture, the potential for groundwater pollution from atrazine may be reduced, especially in areas with a long history of atrazine application to soil.

Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1

Exploring adaptive strategies by which microorganisms function and survive in low-energy natural environments remains a grand goal of microbiology, and may help address a prime challenge of the 21st century: degradation of man-made chemicals at low concentrations (“micropollutants”). Here we explore physiological adaptation and maintenance energy requirements of a herbicide (atrazine)-degrading microorganism (Arthrobacter aurescens TC1) while concomitantly observing mass transfer limitations directly by compound-specific isotope fractionation analysis. Chemostat-based growth triggered the onset of mass transfer limitation at residual concentrations of 30 μg L⁻¹ of atrazine with a bacterial population doubling time (t_d) of 14 days, whereas exacerbated energy limitation was induced by retentostat-based near-zero growth (t_d = 265 days) at 12 ± 3 μg L⁻¹ residual concentration. Retentostat cultivation resulted in (i) complete mass transfer limitation evidenced by the disappearance of isotope fractionation (ε¹³C = −0.45‰ ± 0.36‰) and (ii) a twofold decrease in maintenance energy requirement compared with chemostat cultivation. Proteomics revealed that retentostat and chemostat cultivation under mass transfer limitation share low protein turnover and expression of stress-related proteins. Mass transfer limitation effectuated slow-down of metabolism in retentostats and a transition from growth phase to maintenance phase indicating a limit of ≈10 μg L⁻¹ for long-term atrazine degradation. Further studies on other ecosystem-relevant microorganisms will substantiate the general applicability of our finding that mass transfer limitation serves as a trigger for physiological adaptation, which subsequently defines a lower limit of biodegradation.

Changes in atrazine speciation and the degradation pathway in red soil during the vermiremediation process

Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a triazine herbicide intensively used in agricultural production and is often detected in different environmental matrices at concentrations above the permitted limit. This study investigated the influence of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) on atrazine speciation and the degradation pathway. Our results revealed that both earthworms significantly accelerated atrazine degradation in a 28-day vermiremediation, and the residual atrazine declined from 4.23 ± 0.21 mg/kg in bulk soils to 0.51 ± 0.29 mg/kg (E. foetida) and 0.43 ± 0.19 mg/kg (A. robustus). By consuming organic matter (from 40.37 ± 1.14 to 36.31 ± 1.55 and 34.59 ± 1.13 g/kg for E. foetida and A. robustus) and neutralizing the soil pH (from 5.37 ± 0.27 to 6.36 ± 0.11 and 6.61 ± 0.30 for E. foetida and A. robustus), both earthworms reduced humus-fixed atrazine and increased the available atrazine. The percentage of available atrazine increased from 8.80 ± 0.21% in bulk soil to 10.30 ± 0.29% and 16.42 ± 0.18% in the vermiremediation treatments. Both earthworms promoted the hydroxyatrazine pathway by consuming soil organic matter and encouraged the deethylatrazine/deisopropylatrazine pathway by neutralizing the soil pH. Our findings unravel a new mechanism of vermiremediation by improving the soil physical-chemical properties and altering the atrazine degradation pathway, providing new insights into the influential factors on atrazine bioremediation in red soil.

Phytoextraction and biodegradation of atrazine by Myriophyllum spicatum and evaluation of bacterial communities involved in atrazine degradation in lake sediment

The accumulation of atrazine in lake sediments leads to persistent contamination, which may damage the succeeding submerged plants and create potential threats to the lake eco-environment. In this study, the degradation characteristics of atrazine and its detoxication by Myriophyllum spicatum and the associated bacterial community in lake sediments were evaluated. M. spicatum absorbed more than 18-fold the amount of atrazine in sediments and degraded atrazine to hydroxyatrazine (HA), deelthylatrazine (DEA), didealkylatrazine (DDA), cyanuric acid (CYA) and biuret. The formation of biuret suggested for the first time, the ring opening of atrazine in an aquatic plant. The residual rate of atrazine was 6.5 ± 2.0% in M. spicatum-grown sediment, which was significantly lower than the 18.0 ± 2.5% in unplanted sediments on day 60 (P < 0.05). Moreover, on day 15, the increase in contents of HA, CYA and biuret in M. spicatum-grown sediment indicated that M. spicatum promoted the degradation and removal of atrazine following rapid dechlorination. The colonization of M. spicatum and the addition of atrazine altered the structure of the dominant bacterial community in sediments, including effects on Nitrospirae and Acidobacteria. Based on the maximum amount among the genera of atrazine-degrading bacteria, Acetobacter was most likely responsible for the degradation of atrazine. Our findings reveal the natural attenuation of atrazine by aquatic organisms.

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Vermicomposting is an effective and environmentally friendly approach for eliminating soil organic contamination. Atrazine is one of the most commonly applied triazinic herbicides and frequently detected in agricultural soils. This study investigated the roles and mechanisms of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) in microbial degradation of atrazine. Both earthworms accelerated atrazine degradation performance from 39.0% in sterile soils to 94.9%-95.7%, via neutralizing soil pH, consuming soil humus, altering bacterial community structure, enriching indigenous atrazine degraders and excreting the intestinal atrazine-degrading bacteria. Rhodoplanes and Kaistobacter were identified as soil indigenous degraders for atrazine mineralization and stimulated by both earthworm species. A. robustus excreted the intestinal Cupriavidus and Pseudomonas, whereas Flavobacterium was released by E. foetida. This study provides a comprehensive understanding of the distinct effects of two earthworm species on soil microbial community and atrazine degradation, offering technical supports to apply vermicomposting in effective soil bioremediation.

Addressing the mycotoxin deoxynivalenol contamination with soil-derived bacterial and enzymatic transformations targeting the C3 carbon

The search for feasible biological means of detoxifying mycotoxins has attained successful accomplishments in the past twenty years due to the involvement of many teams coming from diverse backgrounds and research expertise. The recently witnessed breakthroughs in the field of bacterial genomics (including next-generation sequencing), proteomics, and computational biology helped all in shaping the current understanding of how microorganisms/mycotoxins/environmental factors intertwined and interact together, hence paving the road for some substantial discoveries. This perspective review summarises the advances that were observed in the past two decades within the deoxynivalenol (DON) bio-detoxification field. It highlights the research efforts and progresses that were made in the arena of the aerobic oxidation and epimerization of this mycotoxin at the C3 carbon carried out by multiple Devosia species. Moreover, it sets practical examples and discusses how the recent standing-knowledge of bacterial detoxifications of this mycotoxin has evolved into a fascinating potential of empirical bacterial and enzymatic solutions aiming at addressing DON contamination. The obtained results argue for determining the involved enzyme’s co-factors and defining the chemistry behind the established catalytic activity at an early stage of investigation to maximise the chances of isolating the responsible enzymes.