Arthrobacter aurescens TC1 metabolizes diverse s-triazine ring compounds

Degradation of Atrazine by an Anaerobic Microbial Consortium Enriched from Soil of an Herbicide-Manufacturing Plant

Atrazine is an important herbicide that has been widely used for weed control in recent decades. However, with the extensive use of atrazine, its residue seriously pollutes the environment. Therefore, the microbial degradation and detoxification of atrazine have received extensive attention. To date, the aerobic degradation pathway of atrazine has been well studied; however, little is known about its anaerobic degradation in the environment. In this study, an anaerobic microbial consortium capable of efficiently degrading atrazine was enriched from soil collected from an herbicide-manufacturing plant. Six metabolites including hydroxyatrazine, deethylatrazine, N-isopropylammelide, deisopropylatrazine, cyanuric acid, and the novel metabolite 4-ethylamino-6-isopropylamino-1,3,5-triazine (EIPAT) were identified, and two putative anaerobic degradation pathways of atrazine were proposed: a hydrolytic dechlorination pathway is similar to that seen in aerobic degradation, and a novel pathway initiated by reductive dechlorination. During enrichment, Denitratisoma, Thiobacillus, Rhodocyclaceae_unclassified, Azospirillum, and Anaerolinea abundances significantly increased, dominating the enriched consortium, indicating that they may be involved in atrazine degradation. These findings provide valuable evidence for elucidating the anaerobic catabolism of atrazine and facilitating anaerobic remediation of residual atrazine pollution.

Physiological and transcriptomic changes drive robust responses in Paenarthrobacter sp. AT5 to co-exposure of sulfamethoxazole and atrazine

Agricultural waterways are often contaminated with herbicide and antibiotic residues due to the widespread use of these chemicals in modern agriculture. The search for resistant bacterial strains that can adapt to and degrade these mixed contaminants is essential for effective in situ bioremediation. Herein, by integrating chemical and transcriptomic analyses, we shed light on mechanisms through which Paenarthrobacter sp. AT5, a well-known atrazine-degrading bacterial strain, can adapt to sulfamethoxazole (SMX) while degrading atrazine. When exposed to SMX and/or atrazine, strain AT5 increased the production of extracellular polymeric substances and reactive oxygen species, as well as the rate of activity of antioxidant enzymes. Atrazine and SMX, either alone or combined, increased the expression of genes involved in antioxidant responses, multidrug resistance, DNA repair, and membrane transport of lipopolysaccharides. Unlike atrazine alone, co-exposure with SMX reduced the expression of genes encoding enzymes involved in the lower part of the atrazine degradation pathway. Overall, these findings emphasize the complexity of bacterial adaptation to mixed herbicide and antibiotic residues and highlight the potential of strain AT5 in bioremediation efforts.

Occurrence, ecological risk, and advanced removal methods of herbicides in waters: a timely review

Coastal pollution caused by the importation of agricultural herbicides is one of the main environmental problems that directly affect the coastal primary productivity and even the safety of human seafood. It is urgent to evaluate the ecological risk objectively and explore feasible removal strategies. However, existing studies focus on the runoff distribution and risk assessment of specific herbicides in specific areas, and compared with soil environment, there are few studies on remediation methods for water environment. Therefore, we systematically reviewed the current situation of herbicide pollution in global coastal waters and the dose-response relationships of various herbicides on phytoplankton and higher trophic organisms from the perspective of ecological risks. In addition, we believe that compared with the traditional single physical and chemical remediation methods, biological remediation and its combined technology are the most promising methods for herbicide pollution remediation currently. Therefore, we focus on the application prospects, challenges, and management strategies of new bioremediation systems related to biology, such as constructed wetlands, membrane bioreactor processes, and microbial co-metabolism, in order to provide more advanced methods for reducing herbicide pollution in the water environment.

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

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

Retracing the Rapid Evolution of an Herbicide-Degrading Enzyme by Protein Engineering

The mechanisms underlying the rapid evolution of novel enzymatic activities from promiscuous side activities are poorly understood. Recently emerged enzymes catalyzing the catabolic degradation of xenobiotic substances that have been spread out into the environment during the last decades provide an exquisite opportunity to study these mechanisms. A prominent example is the herbicide atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine), which is degraded through a number of enzymatic reactions constituting the Atz pathway. Here, we analyzed the evolution of the hydroxyatrazine ethylaminohydrolase AtzB, a Zn(II)-dependent metalloenzyme that adopts the amidohydrolase fold and catalyzes the second step of the Atz pathway. We searched for promiscuous side activities of AtzB, which might point to the identity of its progenitor. These investigations revealed that AtzB has low promiscuous guanine deaminase activity. Furthermore, we found that the two closest AtzB homologues, which have not been functionally annotated up to now, are guanine deaminases with modest promiscuous hydroxyatrazine hydrolase activity. Based on sequence comparisons with the closest AtzB homologues, the guanine deaminase activity of AtzB could be increased by three orders of magnitude through the introduction of only four active site mutations. Interestingly, introducing the inverse four mutations into the AtzB homologues significantly enhanced their hydroxyatrazine hydrolase activity, and in one case is even equivalent to that of wild-type AtzB. Molecular dynamics simulations elucidated the structural and molecular basis for the mutation-induced activity changes. The example of AtzB highlights how novel enzymes with high catalytic proficiency can evolve from low promiscuous side activities by only few mutational events within a short period of time.

Investigation of the Persistence, Toxicological Effects, and Ecological Issues of S-Triazine Herbicides and Their Biodegradation Using Emerging Technologies: A Review

S-triazines are a group of herbicides that are extensively applied to control broadleaf weeds and grasses in agricultural production. They are mainly taken up through plant roots and are transformed by xylem tissues throughout the plant system. They are highly persistent and have a long half-life in the environment. Due to imprudent use, their toxic residues have enormously increased in the last few years and are frequently detected in food commodities, which causes chronic diseases in humans and mammals. However, for the safety of the environment and the diversity of living organisms, the removal of s-triazine herbicides has received widespread attention. In this review, the degradation of s-triazine herbicides and their intermediates by indigenous microbial species, genes, enzymes, plants, and nanoparticles are systematically investigated. The hydrolytic degradation of substituents on the s-triazine ring is catalyzed by enzymes from the amidohydrolase superfamily and yields cyanuric acid as an intermediate. Cyanuric acid is further metabolized into ammonia and carbon dioxide. Microbial-free cells efficiently degrade s-triazine herbicides in laboratory as well as field trials. Additionally, the combinatorial approach of nanomaterials with indigenous microbes has vast potential and considered sustainable for removing toxic residues in the agroecosystem. Due to their smaller size and unique properties, they are equally distributed in sediments, soil, water bodies, and even small crevices. Finally, this paper highlights the implementation of bioinformatics and molecular tools, which provide a myriad of new methods to monitor the biodegradation of s-triazine herbicides and help to identify the diverse number of microbial communities that actively participate in the biodegradation process.

Triazine Herbicides Risk Management Strategies on Environmental and Human Health Aspects Using In-Silico Methods

As an effective herbicide, 1, 3, 5-Triazine herbicides (S-THs) are used widely in the pesticide market. However, due to their chemical properties, S-THs severely threaten the environment and human health (e.g., human lung cytotoxicity). In this study, molecular docking, Analytic Hierarchy Process—Technique for Order Preference by Similarity to the Ideal Solution (AHP-TOPSIS), and a three-dimensional quantitative structure-active relationship (3D-QSAR) model were used to design S-TH substitutes with high herbicidal functionality, high microbial degradability, and low human lung cytotoxicity. We discovered a substitute, Derivative-5, with excellent overall performance. Furthermore, Taguchi orthogonal experiments, full factorial design of experiments, and the molecular dynamics method were used to identify three chemicals (namely, the coexistence of aspartic acid, alanine, and glycine) that could promote the degradation of S-THs in maize cropping fields. Finally, density functional theory (DFT), Estimation Programs Interface (EPI), pharmacokinetic, and toxicokinetic methods were used to further verify the high microbial degradability, favorable aquatic environment, and human health friendliness of Derivative 5. This study provided a new direction for further optimizations of novel pesticide chemicals.

Engineering artificial microbial consortia based on division of labor promoted simultaneous removal of Cr(VI)-atrazine combined pollution

Combined pollution caused by organic pollutants and heavy metals is common in polluted sites and wastewater. Engineering artificial microbial consortia offers a promising approach to address this complex issue. However, the mutualistic interactions and the critical function of specific microbe within microbial consortia remain unclear. In this study, based on division of labor, we respectively co-cultured two Cr(VI)-reducing strains, Paenarthrobacter nitroguajacolicus C1 and Pseudomonas putida C2, with an atrazine-degrading strain, Paenarthrobacter ureafaciens AT. After 5 days, up to 95 % Cr(VI) and 100 % atrazine were removed from the cocultures. Strain AT degraded nearly all atrazine and contributed only to a fraction of Cr(VI) reduction, whereas C1 promoted 41 % Cr(VI) transformation to Cr(III) fixed in cells, and C2 promoted 91 % Cr(VI) transformation to soluble Cr(III). Metabolic analyses of the cocultures and monocultures demonstrated that AT provided C1 with isopropylamine by passive diffusion and C2 with other effective nitrogen resources by cell-cell surface contact to promote their growth. Soil experiments also showed that treatments with AT and C2 achieved the highest Cr(VI) reduction and no atrazine residue. Our results indicate that engineering artificial microbial consortia based on division of labor and metabolic interactions is effective in promoting highly efficient bioremediation of combined pollution.

Noval bio-organic fertilizer containing Arthrobacter sp. DNS10 alleviates atrazine-induced growth inhibition on soybean by improving atrazine removal and nitrogen accumulation

Herbicide atrazine restricts nutrient accumulation and thus inhibits the growth of sensitive crops. The application of organic fertilizer is a common measure that contributes to modulating abiotic tolerance of crops and providing nutrients, but its advantages in combination with atrazine degrading microorganisms as bio-organic fertilizer to alleviate atrazine stress on sensitive crops and the associated mechanisms are unknown. We investigated the beneficial effects of organic and bio-organic fertilizer (named DNBF10) containing Arthrobacter sp. DNS10 applications on growth, leaf nitrogen accumulation, root surface structure and root physiological properties of soybean seedlings exposed to 20 mg kg^-1 atrazine in soil. Compared with organic fertilizer, bio-organic fertilizer DNBF10 exhibited more reduction in soil atrazine residue and plant atrazine accumulation, as well as alleviation in atrazine-induced root oxidative stress and damaged cells of soybean roots. Transcriptome analysis revealed that DNBF10 application enhanced nitrogen utilization by improving the expression of genes involved in nitrogen metabolism in soybean leaves. Besides, genes expression of cytochrome P450 and ABC transporters involved in atrazine detoxification and transport in soybean leaves were also down-regulated by DNBF10 to diminish phytotoxicity of atrazine to soybean seedlings. These results illustrate the molecular mechanism by which the application of DNBF10 alleviates soybean seedlings growth under atrazine stress, providing a step forward for mitigate the atrazine induced inhibition on soybean seedlings growth through decreasing atrazine residues as well as enhancing damaged root repair and nitrogen accumulation.

Pesticide contamination in agro-ecosystems: toxicity, impacts, and bio-based management strategies

Continuous rise in application of pesticides in the agro-ecosystems in order to ensure food supply to the ever-growing population is of greater concern to the human health and the environment. Once entered into the agro-ecosystem, the fate and transport of pesticides is determined largely by the nature of pesticides and the soil attributes, in addition to the soil-inhabiting microbes, fauna, and flora. Changes in the soil microbiological actions, soil properties, and enzymatic activities resulting from pesticide applications are the important factors substantially affecting the soil productivity. Disturbances in the microbial community composition may lead to the considerable perturbations in cycling of major nutrients, metals, and subsequent uptake by plants. Indiscriminate applications are linked with the accumulation of pesticides in plant-based foods, feeds, and animal products. Furthermore, rapid increase in the application of pesticides having long half-life has also been reported to contaminate the nearby aquatic environments and accumulation in the plants, animals, and microbes surviving there. To circumvent the negative consequences of pesticide application, multitude of techniques falling in physical, chemical, and biological categories are presented by different investigators. In the present study, important findings pertaining to the pesticide contamination in cultivated agricultural soils; toxicity on soil microbes, plants, invertebrates, and vertebrates; effects on soil characteristics; and alleviation of toxicity by bio-based management approaches have been thoroughly reviewed. With the help of bibliometric analysis, thematic evolution and research trends on the bioremediation of pesticides in the agro-ecosystems have also been highlighted.

Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil

Extensive use of agrochemicals is emerging as a serious environmental issue coming at the cost of the pollution of soil and water resources. Bioremediation techniques such as biostimulation are promising strategies used to remove pollutants from agricultural soils by supporting the indigenous microbial degraders. Though considered cost-effective and eco-friendly, the success rate of these strategies typically varies, and consequently, they are rarely integrated into commercial agricultural practices. In the current study, we applied metabolic-based community-modeling approaches for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Efficacy of biostimulants as enhancers of the indigenous degrader Paenarthrobacter was ranked through simulation and validated in pot experiments. A two-dimensional simulation matrix predicting the effect of different biostimulants on additional potential indigenous degraders (Pseudomonas, Clostridium, and Geobacter) was crossed with experimental observations. The overall ability of the models to predict the compounds that act as taxa-selective stimulants indicates that computational algorithms can guide the manipulation of the soil microbiome in situ and provides an additional step toward the educated design of biostimulation strategies. IMPORTANCE Providing the food requirements of a growing population comes at the cost of intensive use of agrochemicals, including pesticides. Native microbial soil communities are considered key players in the degradation of such exogenous substances. Manipulating microbial activity toward an optimized outcome in efficient biodegradation processes conveys a promise of maintaining intensive yet sustainable agriculture. Efficient strategies for harnessing the native microbiome require the development of approaches for processing big genomic data. Here, we pursued metabolic modeling for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Our genomic-based predictions point at strategies for optimizing biodegradation by the native community. Developing a systematic, data-guided understanding of metabolite-driven targeted enhancement of selected microorganisms lays the foundation for the design of ecologically sound methods for optimizing microbiome functioning.

Degradation of dimethachlon by a newly isolated bacterium Paenarthrobacter sp. strain JH-1 relieves its toxicity against Chlorella ellipsoidea

Dimethachlon, a broad-spectrum dicarboximide fungicide, poses a hazard to the safety of human and ecosystem due to its residue in the environment. A high-efficient dimethachlon degrading bacteria JH-1 belonging to Paenarthrobacter sp. was isolated and characterized. Strain JH-1 can utilize high concentration of dimethachlon as sole carbon source for growth and degrade 98.53% of 300 mg·L^-1 dimethachlon within 72 h. Crude enzyme of strain JH-1 could degrade 99.76% of 100 mg·L^-1 dimethachlon within 2 h. The optimum degradation condition of dimethachlon by strain JH-1 was at 35 °C and pH 7.0. Dimethachlon was degraded in Paenarthrobacter sp. JH-1 as following: it was firstly converted to 4-(3,5-dichloroanilino)-4-oxobutanoic acid and then subjected to the hydrolysis to 3,5-dichloroaniline and succinic acid, the latter was further degraded. Dimethachlon inhibited the growth of Chlorella ellipsoidea, while Paenarthrobacter sp. JH-1 could degrade dimethachlon to relieve its toxicity. This work facilitates our knowledge of the degradation mechanism of dimethachlon and offers potential resource of microbial strains for the bioremediation of dimethachlon-contaminated environments in the future.

Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6

Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h^-1, 88 mg L^-1) and ε(C) = -2.1 ± 0.5‰ in batch (c₀ = 220 mg L^-1) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L^-1. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h^-1. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.

Arthrobacter is a universal responder to di-n-butyl phthalate (DBP) contamination in soils from various geographical locations

Plasticizer phthalic acid esters (PAEs) are commonly found as contaminants in various soils. Previous studies indicated that their natural degradation can substantially differ among soil types; however, potential implications of the soil microbiome remained largely unexplored. Here, we have collected ten soil types from nine different geographical regions of China to investigate the degradation of DBP therein and role of bacteria in this process. Results showed that the degradation rate of DBP was lowest in nutrient-poor red soils from Jiangxi Province, while it was highest in fluvo-aquatic soil from Hebei Province. Bacterial community responses to DBP substantially differed in each of the analyzed soils. Arthrobacter is known for its broad-spectrum activity in terms of DBP degradation in soil and was therefore implemented as bioremediating inoculant in many polluted environments. In the present study, network analyses indicated that synergism between soil bacteria increased following exposure to DBP. Arthrobacter and Sphingomonas were found to expand their positive interactions with other members of the microbiome in DBP-contaminated soils. The overall findings of our study provide a basis for biomarker development for detection of DBP contaminations and an extended basis for future bioremediation approaches based on beneficial bacteria.

Actinobacteria: An eco-friendly and promising technology for the bioaugmentation of contaminants

Over the past two decades, various eco-friendly approaches utilizing microbial species to clean up contaminated environments have surfaced. In this aspect, actinobacteria have demonstrated their potential in contaminant degradation. The members of actinobacteria phylum exhibits a cosmopolitan distribution, which means that they can be found widely in both aquatic and terrestrial ecosystems. Actinobacteria play important ecological roles in the environment, such as degrading complex polymers, recycling compounds, and producing bioactive molecules. Hence, using actinobacteria to clean up contaminants is an attractive method in the field of biotechnology. This can be achieved through the green technology of bioaugmentation, whereby the degradative capacity of contaminated areas can be greatly improved through the introduction of specific microorganisms. This review describes actinobacteria as an eco-friendly and a promising technology for the bioaugmentation of contaminants, with focus on pesticides and heavy metals.

Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance

Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.

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.

Four families of folate-independent methionine synthases

Although most organisms synthesize methionine from homocysteine and methyl folates, some have “core” methionine synthases that lack folate-binding domains and use other methyl donors. In vitro, the characterized core synthases use methylcobalamin as a methyl donor, but in vivo, they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.

Methionine is one of the amino acids that make up proteins, and the final step in methionine synthesis is the transfer of a methyl group. In most organisms, the methyl group is obtained from methyl folates, but some anaerobic bacteria and archaea are thought to use corrinoid (vitamin B12-binding) proteins instead. By analyzing the sequences of the potential methionine synthases across the genomes of diverse bacteria and archaea, we identified four families of folate-independent methionine synthases. For three of these families, we can use co-occurrence with corrinoid proteins to predict their likely partners. We show that the fourth family does not require vitamin B12; instead, it obtains methyl groups from an oxygen-dependent partner protein. Our results will help us understand the growth requirements of diverse bacteria and archaea.

Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions

To guarantee the supply of critical elements in the future, the development of new technologies is essential. Siderophores have high potential in the recovery and recycling of valuable metals due to their metal-chelating properties. Using the Chrome azurol S assay, 75 bacterial strains were screened to obtain a high-yield siderophore with the ability to complex valuable critical metal ions. The siderophore production of the four selected strains Nocardioides simplex 3E, Pseudomonas chlororaphis DSM 50083, Variovorax paradoxus EPS, and Rhodococcus erythropolis B7g was optimized, resulting in significantly increased siderophore production of N. simplex and R. erythropolis. Produced siderophore amounts and velocities were highly dependent on the carbon source. The genomes of N. simplex and P. chlororaphis were sequenced. Bioinformatical analyses revealed the occurrence of an achromobactin and a pyoverdine gene cluster in P. chlororaphis, a heterobactin and a requichelin gene cluster in R. erythropolis, and a desferrioxamine gene cluster in N. simplex. Finally, the results of the previous metal-binding screening were validated by a proof-of-concept development for the recovery of metal ions from aqueous solutions utilizing C₁₈ columns functionalized with siderophores. We demonstrated the recovery of the critical metal ions V(III), Ga(III), and In(III) from mixed metal solutions with immobilized siderophores of N. simplex and R. erythropolis.

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.

Pesticide bioremediation in liquid media using a microbial consortium and bacteria-pure strains isolated from a biomixture used in agricultural areas

Microorganisms' role in pesticide degradation has been studied widely. Insitu treatments of effluents containing pesticides such as biological beds (biobeds) are efficient biological systems where biomixture (mixture of substrates) and microorganisms are the keys in pesticide treatment; however, microbial activity has been studied poorly, and its potential beyond biobeds has not been widely explored. In this study, the capacity of microbial consortium and bacteria-pure strains isolated from a biomixture (soil-straw; 1:1, v/v) used to treat agricultural effluents under real conditions were evaluated during a bioremediation process of five pesticides commonly used Yucatan Mexico. Atrazine, carbofuran, and glyphosate had the highest degradations (>90%) using the microbial consortium; 2,4-D and diazinon were the most persistent (DT50 = 8.64 and 6.63 days). From the 21 identified bacteria species in the microbial consortium, Pseudomonas nitroreducens was the most abundant (52%) according to identified sequences. For the pure strains evaluation 2,4-D (DT50 = 9.87 days), carbofuran (DT50 = 8.27 days), diazinon (DT50 = 8.80 days) and glyphosate (DT50 = 8.59 days) were less persistent in the presence of the mixed consortium (Ochrobactrum sp. DGG-1-3, Ochrobactrum sp. Ge-14, Ochrobactrum sp. B18 and Pseudomonas citronellolis strain ADA-23B). Time, pesticide, and strain type were significant (P < 0.05) in pesticide degradation, so this process is multifactorial. Microbial consortium and pure strains can be used to increase the biobed efficiency by inoculation, even in the remediation of soil contaminated by pesticides in agricultural areas.

Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism’s phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as bio-stimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation.

Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions

Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.

Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis

Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L^-1. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.

Compound-specific chlorine isotope fractionation in biodegradation of atrazine

Atrazine is a frequently detected groundwater contaminant. It can be microbially degraded by oxidative dealkylation or by hydrolytic dechlorination. Compound-specific isotope analysis is a powerful tool to assess its transformation. In previous work, carbon and nitrogen isotope effects were found to reflect these different transformation pathways. However, chlorine isotope fractionation could be a particularly sensitive indicator of natural transformation since chlorine isotope effects are fully represented in the molecular average while carbon and nitrogen isotope effects are diluted by non-reacting atoms. Therefore, this study explored chlorine isotope effects during atrazine hydrolysis with Arthrobacter aurescens TC1 and oxidative dealkylation with Rhodococcus sp. NI86/21. Dual element isotope slopes of chlorine vs. carbon isotope fractionation (Λ = 1.7 ± 0.9 vs. Λ = 0.6 ± 0.1) and chlorine vs. nitrogen isotope fractionation (Λ = -1.2 ± 0.7 vs. Λ = 0.4 ± 0.2) provided reliable indicators of different pathways. Observed chlorine isotope effects in oxidative dealkylation (ε_Cl = -4.3 ± 1.8‰) were surprisingly large, whereas in hydrolysis (ε_Cl = -1.4 ± 0.6‰) they were small, indicating that C-Cl bond cleavage was not the rate-determining step. This demonstrates the importance of constraining expected isotope effects of new elements before using the approach in the field. Overall, the triple element isotope information brought forward here enables a more reliable identification of atrazine sources and degradation pathways.

Influence of terminal electron-accepting conditions on the soil microbial community and degradation of organic contaminants of emerging concern

Better understanding of the fate and persistence of trace organic contaminants of emerging concern (CEC) in agricultural soils is critical for assessing the risks associated with using treated wastewater effluent to irrigate crops and land application of wastewater biosolids. This study reports on the influence of prevailing terminal electron-accepting processes (TEAPs, i.e., aerobic, nitrate-reducing, iron(III)-reducing, and sulfate-reducing conditions) and exposure to a mixture of nine trace CEC (90 ng/g each) on both the microbial community structure and CEC degradation in agricultural soil. DNA analysis revealed significant differences in microbial community composition following establishment of different TEAPs, but no significant change upon exposure to the mixture of CEC. The largest community shift was observed after establishing nitrate-reducing conditions and the smallest shift for sulfate-reducing conditions. Two of the CEC (atrazine and sulfamethoxazole) showed significant degradation in both bioactive and abiotic (i.e., sterilized) conditions, with half-lives ranging from 1 to 64 days for different TEAPs, while six of the CEC (amitriptyline, atenolol, trimethoprim, and three organophosphate flame retardants) only degraded in bioactive samples, with half-lives ranging from 27 to 90 days; carbamazepine did not degrade appreciably within 90 days in any of the incubations. Amplicon sequence variants (ASVs) from Firmicutes Hydrogenispora, Gemmatimonadetes Gemmatimonadaceae, and Verrucomicrobia OPB34 soil group were identified as potentially responsible for the biodegradation of organophosphate flame retardants, and ASVs from other taxa groups were suspected to be involved in biodegrading the other target CEC. These results demonstrate that CEC fate and persistence in agricultural soils is influenced by the prevailing TEAPs and their influence on the microbial community, suggesting the need to incorporate these factors into contaminant fate models to improve risk assessment predictions.

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.

Nitrogen-dependent induction of atrazine degradation pathway in Pseudomonas sp. strain AKN5

Soil isolate Pseudomonas sp. strain AKN5 degrades atrazine as the sole source of nitrogen. The strain showed expeditious growth on medium containing citrate as the carbon source and ammonium chloride as the nitrogen source as compared to citrate plus atrazine or cyanuric acid. Biochemical and nitrogen-source-dependent enzyme induction studies revealed that atrazine is metabolized through hydrolytic pathway and has two segments: the upper segment converts atrazine into cyanuric acid while the lower segment metabolizes cyanuric acid to CO2 and ammonia. Bioinformatics and co-transcriptional analyses suggest that atzA, atzB and atzC were transcribed as three independent transcripts while atzDEF were found to be transcribed as a single polycistronic mRNA indicating operonic arrangement. Transcriptional analysis showed inducible expression of atzA/B/C/DEF from atrazine grown cells while cyanuric acid grown cells showed significantly higher expression of atzDEF. Interestingly, growth profiles and enzyme activity measurements suggests that strain utilizes a simple nitrogen source (ammonium chloride) over the complex (atrazine or cyanuric acid) when grown on dual nitrogen source. These results suggest that atrazine degradation genes were up-regulated in the presence of atrazine but repressed in the presence of simple nitrogen source like ammonium chloride.

Biodegradation of Atrazine by the Novel Klebsiella variicola Strain FH-1

Bacterial strain FH-1 with high efficiency of degrading Atrazine is separated by means of enrichment culture from the soil applied with Atrazine for many years. FH-1, recognized as Klebsiella variicola based on phylogenetic analysis of 16S rDNA sequences, can grow with Atrazine which is the sole nitrogen source. In fluid inorganic salt medium, the optimal degradation temperature, pH value, and initial concentration of Atrazine are 25°C, 9.0, and 50 mg L^–1, respectively, and the degradation rate of Atrazine by strain FH-1 reached 81.5% in 11 d of culture. The degrading process conforms to the kinetics equation of pesticide degradation. Among the metal ions tested, Zn²⁺ (0.2 mM) has the most significant effect of facilitation on the degradation of Atrazine. In the fluid medium with Zn²⁺, the degradation rate of Atrazine is increased to 72.5%, while the Cu²⁺ (0.2 mM) inhibits the degradation of Atrazine. The degradation products of Atrazine by strain FH-1 were identified as HEIT (2-hydroxyl-4-ethylamino-6-isopropylamino-1,3,5-triazine), MEET (2-hydroxyl-4,6-bis(ethylamino)-1,3,5-triazine), and AEEO (4,6-bis(ethylamino)-1,3,5-triazin-2(1H)-one) by HPLC-MS/MS. Three genes (atzC, trzN, and trzD) encoding for Atrazine degrading enzymes were identified by PCR and sequencing in strain FH-1. This study provides additional theoretical support for the application of strain FH-1 in bioremediation of fields polluted by Atrazine.

Evaluating formulation and storage of Arthrobacter aurescens strain TC1 as a bioremediation tool for terbuthylazine contaminated soils: Efficacy on abatement of aquatic ecotoxicity

Recently, a bioremediation tool consisting of freshly grown cells of the Arthrobacter aurescens strain TC1 proved successful in the cleanup of terbuthylazine (TBA) contaminated soil, with potential to prevent TBA dispersal via the soil-water pathway. The present work aimed at examining the feasibility of preparing and formulating bioaugmentation bacterial cells in advance which retain adequate viability and herbicide-degrading activity during storage and transport to contaminated sites. Three different types of formulation of A. aurescens TC1 cells were performed, namely cell paste, lyophilized, and adsorbed onto the mineral carrier vermiculite. Vermiculite-based cell material and cell paste offered survival rates significantly higher (≥78% of cells recovered viable, when compared to the initial numbers) than lyophilized cells (≥65%) after storage at 4 °C for up to a maximum period of 30 days. Inocula prepared from the three types of formulated and stored cells supported adequate levels of herbicide-biodegradation activity, ultimately allowing an almost complete removal of TBA from either liquid buffer or soil. In soil microcosms, the efficacy of bioremediation of TBA-contaminated soil in terms of decontamination (%) based on the ecotoxicity assessment of soil eluates towards a freshwater microalga was found to differ within formulations in the order: lyophilized cells (~100% efficacy at the end of one or two weeks of bioremediation treatment with an initial inoculum of ~2.5 × 10⁷ viable cells/g of soil; similar to fresh cells) > vermiculite-adsorbed cells (81% with ~2.4 × 10⁸ cells/g) > cell paste (68% with ~2.4 × 10⁸ cells/g). The limitations and advantages of each type of bacterial formulation, together with the prediction of their applicability in the field are discussed.

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.

Identification and characterization of cytochrome P450 1232A24 and 1232F1 from Arthrobacter sp. and their role in the metabolic pathway of papaverine

Cytochrome P450 monooxygenases (P450s) play crucial roles in the cell metabolism and provide an unsurpassed diversity of catalysed reactions. Here, we report the identification and biochemical characterization of two P450s from Arthrobacter sp., a Gram-positive organism known to degrade the opium alkaloid papaverine. Combining phylogenetic and genomic analysis suggested physiological roles for P450s in metabolism and revealed potential gene clusters with redox partners facilitating the reconstitution of the P450 activities in vitro. CYP1232F1 catalyses the para demethylation of 3,4-dimethoxyphenylacetic acid to homovanillic acid while CYP1232A24 continues demethylation to 3,4-dihydroxyphenylacetic acid. Interestingly, the latter enzyme is also able to perform both demethylation steps with preference for the meta position. The crystal structure of CYP1232A24, which shares only 29% identity to previous published structures of P450s helped to rationalize the preferred demethylation specificity for the meta position and also the broader substrate specificity profile. In addition to the detailed characterization of the two P450s using their physiological redox partners, we report the construction of a highly active whole-cell Escherichia coli biocatalyst expressing CYP1232A24, which formed up to 1.77 g l−1 3,4-dihydroxyphenylacetic acid. Our results revealed the P450s’ role in the metabolic pathway of papaverine enabling further investigation and application of these biocatalysts.

Rate-Limiting Mass Transfer in Micropollutant Degradation Revealed by Isotope Fractionation in Chemostat

Biodegradation of persistent micropollutants like pesticides often slows down at low concentrations (μg/L) in the environment. Mass transfer limitations or physiological adaptation are debated to be responsible. Although promising, evidence from compound-specific isotope fractionation analysis (CSIA) remains unexplored for bacteria adapted to this low concentration regime. We accomplished CSIA for degradation of a persistent pesticide, atrazine, during cultivation of Arthrobacter aurescens TC1 in chemostat under four different dilution rates leading to 82, 62, 45, and 32 μg/L residual atrazine concentrations. Isotope analysis of atrazine in chemostat experiments with whole cells revealed a drastic decrease in isotope fractionation with declining residual substrate concentration from ε(C) = -5.36 ± 0.20‰ at 82 μg/L to ε(C) = -2.32 ± 0.28‰ at 32 μg/L. At 82 μg/L ε(C) represented the full isotope effect of the enzyme reaction. At lower residual concentrations smaller ε(C) indicated that this isotope effect was masked indicating that mass transfer across the cell membrane became rate-limiting. This onset of mass transfer limitation appeared in a narrow concentration range corresponding to about 0.7 μM assimilable carbon. Concomitant changes in cell morphology highlight the opportunity to study the role of this onset of mass transfer limitation on the physiological level in cells adapted to low concentrations.

Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments

Arthrobacter spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.

Chattonella subsalsa (Raphidophyceae) growth and hemolytic activity in response to agriculturally-derived estuarine contaminants

The potential for toxic contaminants and nutrient pollution to alter natural cycles of estuarine phytoplankton blooms is well known, yet few studies have examined how these combined stressors affect harmful algal species. Here, a robust testing protocol was developed to enable an ecotoxicological assessment of responses to commonly co-occurring estuarine contaminants by harmful algal bloom species. The population growth and toxicity (as cell density and hemolytic activity, respectively) of a cultured strain of the toxigenic raphidiophycean, Chattonella subsalsa, were assessed in two experiments (duration 10 days and 28 days) across a gradient of atrazine concentrations and N:P ratios simulating nutrient-rich versus nutrient-depleted regimes. The response of this large-celled, slowly growing alga to atrazine × nutrients depended on growth phase; atrazine was most inhibitory during early exponential population growth (day 10), whereas nutrient regime was a more important influence during later phases of growth (day 28). Without atrazine, toxicity toward fish was highest in low-P cultures. At atrazine levels >25 μg L^-1, hemolytic activity was highest in low-N cultures, and increased with increasing atrazine concentration in all nutrient-limited cultures. Hemolytic activity varied inversely with atrazine concentration in N,P-replete conditions. Overall, atrazine inhibitory effects on population growth of this C. subsalsa strain depended on the growth phase and the nutrient regime; hemolytic activity was higher and further enhanced by atrazine in low N-P regimes; and atrazine inhibited hemolytic activity in nutrient-replete conditions. The data suggest that, depending on the growth phase and nutrient regime, atrazine can help promote toxic C. subsalsa blooms.

Lignin peroxidase ligand access channel dysfunction in the presence of atrazine

Studies have determined that the white-rot basidiomycete Phanerochaete chrysosporium is capable of biodegrading the atrazine herbicide with its broad-specificity enzymes, but the particular role of biocatalysts is still unclear. In the case of lignin peroxidase, a ligand access channel connected to the active heme cofactor provides access to the active site for potential small-sized substrates. Experimental results show that lignin peroxidase is unable to degrade atrazine, therefore, the primary goal was to determine whether there is any connection between the structural and dynamical properties of the enzyme and its incapability to degrade atrazine. The results of protein-ligand docking and molecular dynamics study correlate with relevant, published NMR and molecular dynamics data, and give the answer to the lack of atrazine degradation by lignin peroxidase which has already been established by numerous authors using experimental methods. Atrazine has no access to heme edge due to the electric charges of the delocalized s-triazine ring. The detected phenomenon suggests that the small size of the ligands only is not a sufficient condition to access the active site. Their physicochemical properties influence the structural behaviour of the channel.

Assessment of atrazine toxicity to the estuarine phytoplankter, Dunaliella tertiolecta (Chlorophyta), under varying nutrient conditions

Anthropogenic inputs of chemical environmental contaminants are frequently associated with developing harmful algal blooms, but little is known about how estuarine phytoplankton assemblages respond to multiple, co-occurring chemical stressors in chronically disturbed habitats. The goals of this research were to establish a robust protocol for testing the effects of atrazine on estuarine phytoplankton, and then to use that protocol to compare the effects of atrazine exposure with and without nutrient enrichment on a cosmopolitan estuarine/marine alga, Dunaliella tertiolecta (Chlorophyta). Atrazine sensitivity in nutrient-replete media (96-h growth inhibition [Formula: see text]) was 159.16 μg l^-1, but sensitivity was influenced by exposure duration, and inhibitory effects of herbicide on algal growth decreased under imbalanced nutrient regimes and low nitrogen and phosphorus supplies. These findings advance knowledge about how nutrient regimes and herbicides interact to control estuarine phytoplankton population dynamics.

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.

Biodegradation of a commercial mixture of the herbicides atrazine and S-metolachlor in a multi-channel packed biofilm reactor

Atrazine and S-metolachlor are two of the most widely used herbicides for agricultural purposes; consequently, residues of both compounds and their metabolites had been detected in ground and superficial waters. Unlike atrazine, the complete degradation of metolachlor has not been achieved. Hence, the purpose of this research is to study the biodegradation of a commercial mixture of atrazine and S-metolachlor in a prototype of a multi-channel packed-bed-biofilm reactor (MC-PBR) designed with the aim of solving the problems of pressure drop and oxygen transfer, typically found on this type of bioreactors.Because the removal efficiency of the herbicides was increased when Candida tropicalis was added to the original microbial community isolated, the reactor was inoculated with this enriched community. The operational conditions tested in batch and continuous mode did not affect the removal efficiency of atrazine; however, this was not the case for S-metolachlor. The removal rates and efficiencies showed a notable variation along the MC-PBR operation.

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

The purpose of this study was to examine the potential biomineralization of atrazine and identification of atrazine-degrading bacteria in agricultural soils. Different atrazine application histories of soils impacted the kinetics of biomineralization but not the presence of catabolic genes of two atrazine degradative pathways (Trz and Atz). Biomineralization was based on the measurement of ¹⁴CO₂ from [U-ring-¹⁴C]-atrazine in surface soil (0-7 cm) samples incubated in biometers. Aerobic atrazine biomineralization rate constants (k) varied in the range of 0.004-0.508 d^-1 depending on the specific soil sample and glucose amendment. The corresponding k-values for anaerobic biometers ± nitrate, ferrihydrite or sulfate were 0.002-0.360 d^-1. Glucose enhancement of atrazine biomineralization was not consistent. Aerobic enrichments from soil samples and in-situ incubated BioSep beads yielded mixed cultures, four of which were characterized by 16S rRNA gene amplification, cloning and sequencing. Twelve pure cultures were isolated from enrichments and they were primarily Arthrobacter spp. (10/12). The presence of eight atrazine catabolic genes representing two degradative pathways was investigated in seven bacterial isolates by PCR amplification and sequencing. Several combinations of atrazine catabolic genes were detected; each contained at least atzBC. A complete set of genes for the Atz pathway was not found among the isolates. Our data indicate that atrazine metabolism involves multiple microorganisms and cooperative pathways diverging from atrazine metabolites.

Bioaugmentation as a strategy for the remediation of pesticide-polluted soil: A review

Bioaugmentation, a green technology, is defined as the improvement of the degradative capacity of contaminated areas by introducing specific microorganisms, has emerged as the most advantageous method for cleaning-up soil contaminated with pesticides. The present review discusses the selection of pesticide-utilising microorganisms from various sources, their potential for the degradation of pesticides from different chemical classes in liquid media as well as soil-related case studies in a laboratory, a greenhouse and field conditions. The paper is focused on the microbial degradation of the most common pesticides that have been used for many years such as organochlorinated and organophosphorus pesticides, triazines, pyrethroids, carbamate, chloroacetamide, benzimidazole and derivatives of phenoxyacetic acid. Special attention is paid to bacterial strains from the genera Alcaligenes, Arthrobacter, Bacillus, Brucella, Burkholderia, Catellibacterium, Pichia, Pseudomonas, Rhodococcus, Serratia, Sphingomonas, Stenotrophomonas, Streptomyces and Verticillum, which have potential applications in the bioremediation of pesticide-contaminated soils using bioaugmentation technology. Since many factors strongly influence the success of bioaugmentation, selected abiotic and biotic factors such as pH, temperature, type of soil, pesticide concentration, content of water and organic matter, additional carbon and nitrogen sources, inoculum size, interactions between the introduced strains and autochthonous microorganisms as well as the survival of inoculants were presented.

Microbial changes linked to the accelerated degradation of the herbicide atrazine in a range of temperate soils

Accelerated degradation is the increased breakdown of a pesticide upon its repeated application, which has consequences for the environmental fate of pesticides. The herbicide atrazine was repeatedly applied to soils previously untreated with s-triazines for >5 years. A single application of atrazine, at an agriculturally relevant concentration, was sufficient to induce its rapid dissipation. Soils, with a range of physico-chemical properties and agricultural histories, showed similar degradation kinetics, with the half-life of atrazine decreasing from an average of 25 days after the first application to <2 days after the second. A mathematical model was developed to fit the atrazine-degrading kinetics, which incorporated the exponential growth of atrazine-degrading organisms. Despite the similar rates of degradation, the repertoire of atrazine-degrading genes varied between soils. Only a small portion of the bacterial community had the capacity for atrazine degradation. Overall, the microbial community was not significantly affected by atrazine treatment. One soil, characterised by low pH, did not exhibit accelerated degradation, and atrazine-degrading genes were not detected. Neutralisation of this soil restored accelerated degradation and the atrazine-degrading genes became detectable. This illustrates the potential for accelerated degradation to manifest when conditions become favourable. Additionally, the occurrence of accelerated degradation under agriculturally relevant concentrations supports the consideration of the phenomena in environmental risk assessments.

Novel hydrolytic de-methylthiolation of the s-triazine herbicide prometryn by Leucobacter sp. JW-1

s-Triazine herbicides have been widely used in recent decades and caused serious concern over contamination of groundwater, surface water and soil. A novel bacterial strain JW-1 was isolated from activated sludge and identified as Leucobacter sp. based on comparative morphology, physiological characteristics and comparison of the 16S rDNA gene sequence. JW-1 was capable of using methylthio-s-triazine prometryn as a sole source of carbon and energy in pure culture. Favorable conditions for prometryn degradation were found at pH7.0-9.0 and temperature of 37-42°C. The degradation half-life of prometryn at 50mgL^-1 was remarkably as short as 1.1h, and increased to 6.0h when the initial concentration increased to 400mgL^-1. The strain JW-1 could degrade 100% of ametryn, 99% of simetryn, 41% of propazine, 43% of atrazine, 28% of simazine, 12% of terbutylhylazine, 10% of prometon and 13% of atraton at 50mgL^-1 of each herbicide in 2days. Prometryn was converted to 2-hydroxypropazine and methanthiol via a novel hydrolysis pathway. 2-Hydroxypropazine was then transformed to N-isopropylammelide and the final product cyanuric acid via two sequential deamination reactions. In addition to biodegradation by Leucobacter sp. JW-1, the hydrolytic de-methylthiolation would be valuable in biocatalysis.

Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China

Background

Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.

Methods

Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA.

Results

A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins.

Conclusions

Direct plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0868-3) contains supplementary material, which is available to authorized users.

Bacterial biodegradation of melamine-contaminated aged soil: influence of different pre-culture media or addition of activation material

This study aimed to investigate the biodegrading potential of Arthrobacter sp. MCO, Arthrobacter sp. CSP, and Nocardioides sp. ATD6 in melamine-contaminated upland soil (melamine: approx. 10.5 mg/kg dry weight) after 30 days of incubation. The soil sample used in this study had undergone annual treatment of lime nitrogen, which included melamine; it was aged for more than 10 years in field. When R2A broth was used as the pre-culture medium, Arthrobacter sp. MCO could degrade 55 % of melamine after 30 days of incubation, but the other strains could hardly degrade melamine (approximately 25 %). The addition of trimethylglycine (betaine) in soil as an activation material enhanced the degradation rate of melamine by each strain; more than 50 % of melamine was degraded by all strains after 30 days of incubation. In particular, strain MCO could degrade 72 % of melamine. When the strains were pre-cultured in R2A broth containing melamine, the degradation rate of melamine in soil increased remarkably. The highest (72 %) melamine degradation rate was noted when strain MCO was used with betaine addition.

Degradation of Swainsonine by the NADP-Dependent Alcohol Dehydrogenase A1R6C3 in Arthrobacter sp. HW08

Swainsonine is an indolizidine alkaloid that has been found in locoweeds and some fungi. Our previous study demonstrated that Arthrobacter sp. HW08 or its crude enzyme extract could degrade swainsonie efficiently. However, the mechanism of swainsonine degradation in bacteria remains unclear. In this study, we used label-free quantitative proteomics method based on liquid chromatography-electrospray ionization-tandem mass spectrometry to dissect the mechanism of swainsonine biodegradation by Arthrobacter sp. HW08. The results showed that 129 differentially expressed proteins were relevant to swainsonine degradation. These differentially expressed proteins were mostly related to the biological process of metabolism and the molecular function of catalytic activity. Among the 129 differentially expressed proteins, putative sugar phosphate isomerase/epimerase A1R5X7, Acetyl-CoA acetyltransferase A0JZ95, and nicotinamide adenine dinucleotide phosphate (NADP)-dependent alcohol dehydrogenase A1R6C3 were found to contribute to the swainsonine degradation. Notably, NADP-dependent alcohol dehyrodgenase A1R6C3 appeared to play a major role in degrading swainsonine, but not as much as Arthrobacter sp. HW08 did. Collectively, our findings here provide insights to understand the mechanism of swainsonine degradation in bacteria.