atz gene expressions during atrazine degradation in the soil drilosphere

One of the various ecosystemic services sustained by soil is pollutant degradation mediated by adapted soil bacteria. The pathways of atrazine biodegradation have been elucidated but in situ expression of the genes involved in atrazine degradation has yet to be demonstrated in soil. Expression of the atzA and atzD genes involved in atrazine dechlorination and s‐triazine ring cleavage, respectively, was investigated during in situ degradation of atrazine in the soil drilosphere and bulked samples from two agricultural soils that differed in their ability to mineralize atrazine. Interestingly, expression of the atzA gene, although present in both soils, was not detected. Atrazine mineralization was greatest in Epoisses soil, where a larger pool of atzD mRNA was consistently measured 7 days after atrazine treatment, compared with Vezin soil (146 vs. 49 mRNA per 10 ⁶ 16S rRNA, respectively). Expression of the atzD gene varied along the degradation time course and was profoundly modified in soil bioturbated by earthworms. The atzD mRNA pool was the highest in the soil drilosphere (casts and burrow‐linings) and it was significantly different in burrow‐linings compared with bulk soil (e.g. 363 vs. 146 mRNA per 10 ⁶ 16S rRNA, 7 days after atrazine treatment in Epoisses soil). Thus, consistent differences in atrazine mineralization were demonstrated between the soil drilosphere and bulk soil. However, the impact of bioturbation on atrazine mineralization depended on soil type. Mineralization was enhanced in casts, compared with bulk soil, from Epoisses soil but in burrow‐linings from Vezin soil. This study is the first to report the effects of soil bioturbation by earthworms on s‐triazine ring cleavage and its spatial variability in soil.     

Assessment of Bioavailability of Soil-Sorbed Atrazine

Bioavailability of pesticides sorbed to soils is an important determinant of their environmental fate and impact. Mineralization of sorbed atrazine was studied in soil and clay slurries, and a desorption-biodegradation-mineralization (DBM) model was developed to quantitatively evaluate the bioavailability of sorbed atrazine. Three atrazine-degrading bacteria that utilized atrazine as a sole N source (Pseudomonas sp. strain ADP, Agrobacterium radiobacter strain J14a, and Ralstonia sp. strain M91-3) were used in the bioavailability assays. Assays involved establishing sorption equilibrium in sterile soil slurries, inoculating the system with organisms, and measuring the CO₂ production over time. Sorption and desorption isotherm analyses were performed to evaluate distribution coefficients and desorption parameters, which consisted of three desorption site fractions and desorption rate coefficients. Atrazine sorption isotherms were linear for mineral and organic soils but displayed some nonlinearity for K-saturated montmorillonite. The desorption profiles were well described by the three-site desorption model. In many instances, the mineralization of atrazine was accurately predicted by the DBM model, which accounts for the extents and rates of sorption/desorption processes and assumes biodegradation of liquid-phase, but not sorbed, atrazine. However, for the Houghton muck soil, which manifested the highest sorbed atrazine concentrations, enhanced mineralization rates, i.e., greater than those expected on the basis of aqueous-phase atrazine concentration, were observed. Even the assumption of instantaneous desorption could not account for the elevated rates. A plausible explanation for enhanced bioavailability is that bacteria access the localized regions where atrazine is sorbed and that the concentrations found support higher mineralization rates than predicted on the basis of aqueous-phase concentrations. Characteristics of high sorbed-phase concentration, chemotaxis, and attachment of cells to soil particles seem to contribute to the bioavailability of soil-sorbed atrazine.     

Enzymatic Degradation of Chlorodiamino-s-Triazine

2-Chloro-4,6-diamino-s-triazine (CAAT) is a metabolite of atrazine biodegradation in soils. Atrazine chlorohydrolase (AtzA) catalyzes the dechlorination of atrazine but is unreactive with CAAT. In this study, melamine deaminase (TriA), which is 98% identical to AtzA, catalyzed deamination of CAAT to produce 2-chloro-4-amino-6-hydroxy-s-triazine (CAOT). CAOT underwent dechlorination via hydroxyatrazine ethylaminohydrolase (AtzB) to yield ammelide. This represents a newly discovered dechlorination reaction for AtzB. Ammelide was subsequently hydrolyzed by N-isopropylammelide isopropylaminohydrolase to produce cyanuric acid, a compound metabolized by a variety of soil bacteria.     

Impact of Polyacrylamide Treatment on Sorptive Dynamics and Degradation of 2,4-D and Atrazine in Agricultural Soil

High-molecular-weight, anionic polyacrylamide (PAM) is added to irrigation water to reduce soil erosion during furrow irrigation of crops. The chemical nature of PAM, together with the observation that the polymer can be biotransformed by soil bacteria, led us to question the impact of PAM treatment on the fate of coapplied agrochemicals. The herbicides, atrazine (nonionic) and 2,4-D (anionic), were tested for pesticide sorption, desorption, and degradation in PAM-treated and untreated soils. Sorption of atrazine and 2,4-D in soil was unaffected by PAMtreatment, as was atrazine desorption. However, 2,4-D desorbedmore readily from the PAM-treated soil than from untreated soil. With respect to pesticide degradation, mineralization of the 2,4-D aromatic ring was not impacted by PAM treatment, but decarboxylation of the 2,4-D carboxylic acid side chain was significantly reduced in the PAM-treated soil. Limited mineralization (7 to 10%) of atrazine was observed in both soils. However, in PAM-treated soils atrazine conversion to ¹⁴CO₂ and bound residue components was significantly reduced, and there was an increase in the level of methanol extractable metabolites. These results may indicate that PAM application can alter the environmental fate of some pesticides in soils, especially under the high dose treatment conditions examined in this study.     

Atrazine biodegradation by a bacterial community immobilized in two types of packed-bed biofilm reactors

Through selective enrichment of atrazine-metabolizing microorganisms, a microbial community was selected from agricultural soil. Bacterial isolates, identified by their closest similarity with 16S rDNA sequences stored in NCBI GeneBank, belonged to the genera: Massilia, Stenotrophomonas, Klebsiella, Sphingomonas, Ochrobactrum, Arthrobacter, Microbacterium, Xanthomonas and Ornithinimicrobium. From these strains, only the first six used atrazine as nitrogen and carbon source. The microbial community attached to a non-porous support was evaluated for its atrazine biodegradation rate and removal efficiency under aerobic conditions in two types of packed-bed biofilm reactors fed with a mineral salt medium containing glucose plus atrazine, or atrazine as the sole carbon and nitrogen source. Removal efficiencies near 100% were obtained at loading rates up to 10 mg l⁻¹ h⁻¹. After long periods of continuous operation, the richness of microbial species in biofilm reactors diminished to only three bacterial strains; Stenotrophomonas sp., Ochrobactrum sp. and Arthrobacter sp. By PCR analysis of their DNA, the presence of atzABC genes codifying for the enzymes of the upper catabolic pathway of atrazine, was confirmed in the three strains. The gene atzD that encodes for the cyanuric acid amidohydrolase enzyme was detected only in Stenotrophomonas sp.     

Mineralization Potential of Atrazine and Degradation Intermediates from Clustered Characteristics in Inoculated Soils

Soil properties impact pesticide persistence. Because these characteristics operate together in situ, identification of their clustered associations can help explain pesticide fate. Factor analysis was used to reduce the dimensionality of soil characteristics by grouping them into clustered independent factors, which were then related to the mineralization of atrazine and selected degradation intermediates. A Sharpsburg silty clay loam, Ortello sandy loam, and Hord silt loam were inoculated with a Hord soil that had a high capacity for atrazine mineralization. The soils were spiked with ¹⁴C-radiolabeled atrazine, deethylatrazine, hydroxyatrazine, N-isopropylammeline, N-isopropylammelide or cyanuric acid and sampled during incubation for 80 d (atrazine) or 40 d (degradation intermediates) at 22°C. Low mineralization in uninoculated soils demonstrated that the absence of atrazine-mineralizing microorganisms was most limiting. In inoculated soils, regression analysis indicated mineralization of atrazine (R² = 0.88) and its degradation intermediates (R² ≥ 0.89) was related to factors associated with bioavailability and microbial activity. For atrazine, this relationship indicated mineralization may be positively influenced by higher pH and available phosphorus, lower NO₃-N, organic carbon and clay contents, and lower adsorption. Our results show how factor analysis can be used in conjunction with multiple regression to determine mineralization potential and thus help identify soils with limited degradation capacities and possible long-term persistence.     

Nitrogen Control of Atrazine Utilization in Pseudomonas sp. Strain ADP

Pseudomonas sp. strain ADP uses the herbicide atrazine as the sole nitrogen source. We have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. The atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that support rapid growth of Pseudomonas sp. strain ADP compared to cells cultivated on growth-limiting nitrogen sources. The presence of atrazine in addition to the nitrogen sources did not stimulate degradation. High degradation rates obtained in the presence of ammonium plus the glutamine synthetase inhibitor MSX and also with an Nas⁻ mutant derivative grown on nitrate suggest that nitrogen regulation operates by sensing intracellular levels of some key nitrogen-containing metabolite. Nitrate amendment in soil microcosms resulted in decreased atrazine mineralization by the wild-type strain but not by the Nas⁻ mutant. This suggests that, although nitrogen repression of the atrazine catabolic pathway may have a strong impact on atrazine biodegradation in nitrogen-fertilized soils, the use of selected mutant variants may contribute to overcoming this limitation.     

Isolation and Characterization of Atrazine Mineralizing Bacillus subtilis Strain HB-6

Atrazine is a widely used herbicide with great environmental concern due to its high potential to contaminate soil and waters. An atrazine-degrading bacterial strain HB-6 was isolated from industrial wastewater and the 16S rRNA gene sequencing identified HB-6 as a Bacillus subtilis. PCR assays indicated that HB-6 contained atrazine-degrading genes trzN, atzB and atzC. The strain HB-6 was capable of utilizing atrazine and cyanuric acid as a sole nitrogen source for growth and even cleaved the s-triazine ring and mineralized atrazine. The strain demonstrated a very high efficiency of atrazine biodegradation with a broad optimum pH and temperature ranges and could be enhanced by cooperating with other bacteria, suggesting its huge potential for remediation of atrazine-contaminated sites. To our knowledge, there are few Bacillus subtilis strains reported that can mineralize atrazine, therefore, the present work might provide some new insights on atrazine remediation.     

Denitrifying capacity of rhizobial strains of Argentine soils and herbicide sensitivity

Agrochemical application in soils is a matter of environmental concern, and among soil microorganisms, rhizobia and their action before different pesticides are interesting to study, due to their taxonomic and functional diversity. The objectives of the present work were to assess the capacity of rhizobial populations to use herbicides as source of nutrients, as well as their ability to reduce nitrates and / or denitrify. Eighty-one strains belonging to four populations of different genera of rhizobia (Rhizobium, Mesorhizobium, Ensifer and Bradyrhizobium) were assessed. The effect of glyphosate, 2,4-dichlorophenoxyacetic acid, and atrazine on growth of the strains, as well as the ability of the strains to act on herbicide transformation to reduce nitrate and denitrify, were evaluated. The genera studied showed different responses to pesticides. Bradyrhizobium had the greater capacity to utilize the herbicides and among the compounds evaluated, atrazine was the most used as a source of energy. To conclude, some Bradyrhizobium strains were able both to denitrify and to use the atrazine herbicide. The results obtained in this study increase expectations of the use of rhizobia as inoculants, causing changes at the agricultural and environmental level and allowing an appropriate management of agricultural soil fertilization, efficiency in nitrogen fixation and a faster biodegradation of pesticides in soil.     

Evidence of atrazine mineralization in a soil from the Nile Delta: Isolation of Arthrobacter sp. TES6, an atrazine-degrading strain

The s-triazine herbicide atrazine was rapidly mineralized (i.e., about 60% of ¹⁴C-ring-labelled atrazine released as ¹⁴CO₂ within 21 days) by an agricultural soil from the Nile Delta (Egypt) that had been cropped with corn and periodically treated with this herbicide. Seven strains able to degrade atrazine were isolated by enrichment cultures of this soil. DNA fingerprint and phylogenetic studies based on 16S rRNA analysis showed that the seven strains were identical and belonged to the phylogeny of the genus Arthrobacter (99% similarity with Arthrobacter sp. AD38, EU710554). One strain, designated Arthrobacter sp. strain TES6, degraded atrazine and mineralized the ¹⁴C-chain-labelled atrazine. However, it was unable to mineralize the ¹⁴C-ring-labelled atrazine. Atrazine biodegradation ended in a metabolite that co-eluted with cyanuric acid in HPLC. This was consistent with its atrazine-degrading genetic potential, shown to be dependent on the trzN, atzB, and atzC gene combination. Southern blot analysis revealed that the three genes were located on a large plasmid of about 175 kb and clustered on a 22-kb SmaI fragment. These results reveal for the first time the adaptation of a North African agricultural soil to atrazine mineralization and raise interesting questions about the pandemic dispersion of the trzN, atzBC genes among atrazine-degrading bacteria worldwide.     

Screening of valid reference genes for real-time RT-PCR data normalization in Hevea brasiliensis and expression validation of a sucrose transporter gene HbSUT3

Real-time RT-PCR (RT-qPCR) is a sensitive and precise method of quantifying gene expression, however, suitable reference genes are required. Here, a systematic reference gene screening was performed by RT-qPCR on 22 candidate genes in Hevea brasiliensis. Two ubiquitin-protein ligases (UBC2a and UBC4) were the most stable when all samples were analyzed together. A mitosis protein (YLS8) and a eukaryotic translation initiation factor (eIF1Aa) were the most stable in response to tapping. UBC2b and UBC1 were the most stable among different genotypes. UBC2b and a DEAD box RNA helicase (RH2b) were the most stable across individual trees. YLS8 and RH8 were most stably expressed in hormone-treated samples. Expression of the candidate reference genes varied significantly across different tissues, and at least four genes (RH2b, RH8, UBC2a and eIF2) were needed for expression normalization. In addition, examination of relative expression of a sucrose transporter HbSUT3 in different RNA samples demonstrated the importance of additional reference genes to ensure accurate quantitative expression analysis. Overall, our work serves as a guide for selection of reference genes in RT-qPCR gene expression studies in H. brasiliensis.     

Coriolus hirsutus laccase effect on atrazine adsorption and desorption by different types of soil

Study of adsorption-desorption behavior of herbicide atrazine in soils of different geographical zones in the presence of Coriolus hirsutus laccase was performed. Laccase was shown to significantly increase adsorption coefficient and to facilitate irreversible adsorption of atrazine to soil. Supposably, laccase catalyzes oxidative binding of atrazine to soil.     

Microbial community responses to atrazine exposure and nutrient availability: Linking degradation capacity to community structure

Repeated pesticide exposure may enhance biodegradation through selective enrichment of pesticide-metabolizing microorganisms, particularly when the compound is used as a C and energy source. The relationship between pesticide application history and degradation rate is unclear when the chemical is utilized as a nutrient source other than C. Atrazine, a poor source of C and energy, was chosen as a model compound because it can serve as an N source for some microorganisms. Soils with (H-soil) and without (NH-soil) prior s-triazine treatment history were repeatedly exposed to atrazine and a variety of C and N source amendments. Exposure to atrazine and inorganic-N availability were the dominant factors leading to the development of microbial communities with an enhanced capacity to degrade atrazine. The density of the atrazine-degrading microorganisms increased immediately, up to 1000-fold, with atrazine exposure in the H-soil, but comparable increases were not observed in the NH-soil until 12 weeks following laboratory acclimation, despite high rates of atrazine mineralization in these soils immediately following the acclimation period. Whole-soil fatty acid methyl ester (FAME) analysis showed that the application of alternative C and N sources in addition to atrazine resulted in a microbial community composition that was distinctly different from that in either the atrazine-alone treatment or water controls for both the H- and NH-soils. These data suggest that the microbial communities in both soils were altered differently in response to the treatments but developed a similar enhanced capacity to mineralize atrazine.     

Biodegradation of Atrazine by Agrobacterium radiobacter J14a and Use of This Strain in Bioremediation of Contaminated Soil

We examined the ability of a soil bacterium, Agrobacterium radiobacter J14a, to degrade the herbicide atrazine under a variety of cultural conditions, and we used this bacterium to increase the biodegradation of atrazine in soils from agricultural chemical distribution sites. J14a cells grown in nitrogen-free medium with citrate and sucrose as carbon sources mineralized 94% of 50 μg of [¹⁴C-U-ring]atrazine ml⁻¹ in 72 h with a concurrent increase in the population size from 7.9 × 10⁵ to 5.0 × 10⁷ cells ml⁻¹. Under these conditions cells mineralized the [ethyl-¹⁴C]atrazine and incorporated approximately 30% of the ¹⁴C into the J14a biomass. Cells grown in medium without additional carbon and nitrogen sources degraded atrazine, but the cell numbers did not increase. Metabolites produced by J14a during atrazine degradation include hydroxyatrazine, deethylatrazine, and deethyl-hydroxyatrazine. The addition of 10⁵ J14a cells g⁻¹ into soil with a low indigenous population of atrazine degraders treated with 50 and 200 μg of atrazine g⁻¹ soil resulted in two to five times higher mineralization than in the noninoculated soil. Sucrose addition did not result in significantly faster mineralization rates or shorten degradation lag times. However, J14a introduction (10⁵ cells g⁻¹) into another soil with a larger indigenous atrazine-mineralizing population reduced the atrazine degradation lag times below those in noninoculated treatments but did not generally increase total atrazine mineralization.     

Validation of reference genes for gene expression analysis in Valsa mali var. mali using real-time quantitative PCR

Valsa mali var. mali (Vmm), is the predominant species of apple valsa canker in China. Modern analysis of genes involved in virulence or pathogenicity usually implicate gene expression analysis most often performed using real-time quantitative polymerase chain reaction (RT-qPCR). However, for relative gene expression analysis pertinent reference genes have to be validated before using them as internal reference. This has not been reported for Vmm, so far. Therefore, eight commonly used housekeeping genes (ACT, CYP, EF1-α, G6PDH, GAPDH, L13, TUB, and UBQ) were cloned and evaluated for their expression stability by geNorm and NormFinder. Overall, all of the candidate reference genes were found to be suitable for gene expression analysis. After analysis of 10 samples from different strains and abiotic stress treatments, G6PDH appeared to be the most suitable reference gene, whereas GAPDH was the least suitable. Moreover, taking G6PDH combined with L13 or CYP as reference genes, improved the reliability of RT-qPCR significantly. The influence of the reference system on expression data was demonstrated by analyzing Vmmpg-1 encoding an endo-polygalacturonase gene. Pectinases are considered key pathogenicity factors for this fungus. In order to better understand the role of pectinases in pathogenicity of Vmm, RT-qPCR was used for expression analysis. Our results may provide a guideline for future studies on gene expression of V. mali var. mali by using RT-qPCR.