Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils

Biochar modification accelerates soil atrazine biodegradation by altering bacterial communities, degradation-related genes and metabolic pathways

Atrazine is one of the most used herbicides, posing non-neglectable threats to ecosystem and human health. This work studied the performance and mechanisms of surface-modified biochar in accelerating atrazine biodegradation by exploring the changes in atrazine metabolites, bacterial communities and atrazine degradation-related genes. Among different types of biochar, nano-hydroxyapatite modified biochar achieved the highest degradation efficiency (85.13 %), mainly attributing to the increasing pH, soil organic matter, soil humus, and some enriched indigenous bacterial families of Bradyrhizobiaceae, Rhodospirillaceae, Methylophilaceae, Micrococcaceae, and Xanthobacteraceae. The abundance of 4 key atrazine degradation-related genes (atzA, atzB, atzC and triA) increased after biochar amendment, boosting both dechlorination and dealkylation pathways in atrazine metabolism. Our findings evidenced that biochar amendment could accelerate atrazine biodegradation by altering soil physicochemical properties, microbial composition and atrazine degradation pathways, providing clues for improving atrazine biodegradation performance at contaminated sites.

Assessing the impact of soil microbial fuel cells on atrazine removal in soil

Widespread pesticide use in agriculture is a major source of soil pollution, driving biodiversity loss and posing serious threads to human health. The recalcitrant nature of most of these pesticides demands for effective remediation strategies. In this study, we assess the ability of soil microbial fuel cell (SMFC) technology to bioremediate soil polluted by the model pesticide atrazine. To elucidate the degradation mechanism and consequently define effective implementation strategies, we provide the first comprehensive investigation of the SMFC performance, in which the monitoring of the electrochemical performance of the system is combined with Quadrupole Time-of-Flight (QTOF) mass spectrometry and microbial analyses. Our results show that, while both SMFC and natural attenuation lead to a reduction on atrazine levels, the SMFC modulates the activity of different microbial pathways. As a result, atrazine degradation by natural attenuation leads to high levels of deisoproylatrazine (DIPA), a very toxic degradation metabolite, while DIPA levels in soil treated by SMFC remain comparatively low. The beta diversity and differential abundance analyses revealed how the microbial community evolves over time in the SMFCs degrading atrazine, demonstrating the enrichment of electroactive taxa on the anode, and the enrichment of a mixture of electroactive and atrazine-degrading taxa at the cathode. The detection and taxonomic classification of peripheral atrazine degrading genes, atzA, atzB and atzC, was carried out in combination with the differential abundance analysis. Results revealed that these genes are likely harboured by members of the order Rhizobiales enriched at the cathode, thus promoting atrazine degradation via the conversion of hydroxyatrazine (HA) into N-isopropylammelide (NIPA), as confirmed by mass spectrometry data. Overall, the comprehensive approach adopted in this work, provides fundamental insights into the degradation pathways of atrazine in soil by SMFC technology, which is critical for practical applications, thus suggesting an effective approach to advance research in the field.

Tracking atrazine degradation in soil combining 14C-mineralisation assays and compound-specific isotope analysis

The quantification of pesticide dissipation in agricultural soil is challenging. In this study, we investigated atrazine biodegradation in both liquid and soil experiments bioaugmented with distinct atrazine-degrading bacterial isolates. This was achieved by combining 14C-mineralisation assays and compound-specific isotope analysis of atrazine. In liquid experiments, the three bacterial isolates mineralised over 40% of atrazine, demonstrating their potential for extensive degradation. However, the kinetics of mineralisation and degradation varied among the isolates. Carbon stable isotope fractionation was similar for Pseudomonas isolates ADPT34 and ADP2T0, but slightly higher for Chelatobacter SR27. In soil experiments, atrazine primarily degraded into atrazine-desethyl, while atrazine-hydroxy was mainly observed in experiments with SR27. Atrazine mineralisation in soil by ADPT34 and SR27 exceeded 40%, whereas ADP2T0 exhibited a mineralisation rate of 10%. In experiments with ADPT34 and SR27, atrazine 14C-residues were predominantly found in the non-extractable fraction, whereas they accumulated in the extractable fraction in the experiment with ADP2T0. Compound-specific isotope analysis (CSIA) relies on changes of stable isotope ratios and holds potential to evaluate herbicide transformation in soil. CSIA of atrazine indicated atrazine biodegradation in water and solvent extractable soil fractions and varied between 29% and 52%, depending on the bacterial isolate. Despite atrazine degradation in both soil fractions, a significant portion of atrazine residues persisted, depending on the bacterial degrader, initial cell concentration, and mineralisation and degradation rates. Overall, our approach can aid in quantifying atrazine persistence and degradation in soil, and in optimizing bioaugmentation strategies for remediating soils contaminated with persistent herbicides.

Fibrobacter sp. HC4, a newly isolated strain, demonstrates a high cellulolytic activity as revealed by enzymatic measurements and in vitro assay

Despite their low quantity and abundance, the cellulolytic bacteria that inhabit the equine large intestine are vital to their host, as they enable the crucial use of forage-based diets. Fibrobacter succinogenes is one of the most important intestinal cellulolytic bacteria. In this study, Fibrobacter sp. HC4, one cellulolytic strain newly isolated from the horse cecum, was characterized for its ability to utilize plant cell wall fibers. Fibrobacter sp. HC4 consumed only cellulose, cellobiose, and glucose and produced succinate and acetate in equal amounts. Among genes coding for CAZymes, 26% of the detected glycoside hydrolases (GHs) were involved in cellulolysis. These cellulases belong to the GH5, GH8, GH9, GH44, GH45, and GH51 families. Both carboxymethyl cellulase and xylanase activities of Fibrobacter sp. HC4 were detected using the Congo red method and were higher than those of F. succinogenes S85, the type strain. The in vitro addition of Fibrobacter sp. HC4 to a fecal microbial ecosystem of horses with large intestinal acidosis significantly enhanced fibrolytic activity as measured by the increase in gas and volatile fatty acids production during the first 48 h. According to this, the pH decreased and the disappearance of dry matter increased at a faster rate with Fibrobacter sp. HC4. Our data suggest a high specialization of the new strain in cellulose degradation. Such a strain could be of interest for future exploitation of its probiotic potential, which needs to be further determined by in vivo studies.IMPORTANCECellulose is the most abundant of plant cell wall fiber and can only be degraded by the large intestine microbiota, resulting in the production of volatile fatty acids that are essential for the host nutrition and health. Consequently, cellulolytic bacteria are of major importance to herbivores. However, these bacteria are challenged by various factors, such as high starch diets, which acidify the ecosystem and reduce their numbers and activity. This can lead to an imbalance in the gut microbiota and digestive problems such as colic, a major cause of mortality in horses. In this work, we characterized a newly isolated cellulolytic strain, Fibrobacter sp. HC4, from the equine intestinal microbiota. Due to its high cellulolytic capacity, reintroduction of this strain into an equine fecal ecosystem stimulates hay fermentation in vitro. Isolating and describing cellulolytic bacteria is a prerequisite for using them as probiotics to restore intestinal balance.

Performance of atrazine adsorption behavior and microbial community structure in Mollisol aggregate fraction

Owing to complex pore systems and chemical substances, soil aggregates provide a spatially heterogeneous microenvironment for adsorption capacity and microbial survival. As the widely used pesticide in farmlands, atrazine environmental behavior is not well known at the aggregate scale. In this study, Mollisol soil samples were sieved into four aggregate-size classes: large macroaggregates (>2 mm, LMa), small macroaggregates (1-2 mm, SMa), microaggregates (0.25-1 mm, Mia) and primary particles (<0.25 mm, P). The pore characteristics of each aggregate fraction was visualized by non-invasive X-ray three-dimensional microscopic computed tomography (3D-CT) combined with pore network extraction. The adsorption kinetics of atrazine in each aggregate-size fraction can be described well by a pseudo-second-order kinetic model. The adsorption isothermal process of atrazine can be better fitted by the Langmuir isotherm model than Freundlich isotherm model. There was an obvious linear correlation between the maximum atrazine adsorption capacity and aggregate SOC content as well as TN. In addition, the abundance of bacteria, actinomycetes and anaerobic bacteria in P was totally higher than those in SMa and Mia. Although pH is strongly linked to the bacterial community in the aggregate fraction, aggregate particle size explained 18 % for shaping the microbial community. Therefore, chemical properties and pore characteristics of each soil aggregate fraction both contributed to performance of atrazine adsorption behavior and microbial community.

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

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

Enhanced phytoremediation of atrazine-contaminated soil by vetiver (Chrysopogon zizanioides L.) and associated bacteria

The intensive and long-term use of atrazine (ATZ) has led to the contamination of agricultural soils and non-target organisms, posing a series of threats to human health through the transmission of the food chain. In this study, a 60-day greenhouse pot experiment was carried out to explore the phytoremediation by Chrysopogon zizanioides L. (vetiver). The uptake, accumulation, distribution, and removal of ATZ were investigated, and the degradation mechanisms were elucidated. The results showed that the growth of vetiver was inhibited in the first 10 days of the incubation; subsequently, the plant recovered rapidly with time going. Vetiver grass was capable of taking up ATZ from the soil, with root concentration factor ranging from 2.36 to 15.55, and translocating to the shoots, with shoot concentration factor ranging from 7.51 to 17.52. The dissipation of ATZ in the rhizosphere soil (97.51%) was significantly higher than that in the vetiver-unplanted soil (85.14%) at day 60. Metabolites were identified as hydroxyatrazine (HA), deethylatrazine (DEA), deisopropylatrazine (DIA), and didealkylatrazine (DDA) in the samples of the shoots and roots of vetiver as well as the soils treated with ATZ. HA, DEA, DIA, and DDA were reported first time as metabolites of ATZ in shoots and roots of vetiver grown in soil. The presence of vetiver changed the formation and distribution of the dealkylated products in the rhizosphere soil, which remarkably enhanced the occurrence of DEA, DIA, and DDA. Arthrobacter, Bradyrhizobium, Nocardioides, and Rhodococcus were the major atrazine-degrading bacterial genera, which might be responsible for ATZ degradation in the rhizosphere soil. Our findings suggested that vetiver grass can significantly promote ATZ degradation in the soil, and it could be a strategy for remediation of the atrazine-contaminated agricultural soil.

Whole-Genome Sequencing and Annotation of Fibrobacter succinogenes HC4, Isolated from the Horse Cecum

Fibrobacter succinogenes is a major cellulolytic bacterial species living in the large intestines of herbivores. This study reports the genome sequencing, assembly, and annotation of F. succinogenes HC4 (DSM 33656), a strain isolated from horse cecal contents. The genome comprised a total of 3.74 Mbp, with a G+C content of 48.96%.

Degradation of Residual Herbicide Atrazine in Agri-Food and Washing Water

Atrazine, an herbicide used to control grassy and broadleaf weed, has become an essential part of agricultural crop protection tools. It is widely sprayed on corn, sorghum and sugar cane, with the attendant problems of its residues in agri-food and washing water. If ingested into humans, this residual atrazine can cause reproductive harm, developmental toxicity and carcinogenicity. It is therefore important to find clean and economical degradation processes for atrazine. In recent years, many physical, chemical and biological methods have been proposed to remove atrazine from the aquatic environment. This review introduces the research works of atrazine degradation in aqueous solutions by method classification. These methods are then compared by their advantages, disadvantages, and different degradation pathways of atrazine. Moreover, the existing toxicological experimental data for atrazine and its metabolites are summarized. Finally, the review concludes with directions for future research and major challenges to be addressed.

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

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

Accelerated atrazine degradation and altered metabolic pathways in goat manure assisted soil bioremediation

The intensive and long-term use of atrazine in agriculture has resulted in serious environmental pollution and consequently endangered ecosystem and human health. Soil microorganisms play an important role in atrazine degradation. However, their degradation efficiencies are relatively low due to their slow growth and low abundance, and manure amendment as a practice to improve soil nutrients and microbial activities can solve these problems. This study investigated the roles of goat manure in atrazine degradation performance, metabolites and bacterial community structure. Our results showed that atrazine degradation efficiencies in un-amended soils were 26.9-35.7% and increased to 60.9-84.3% in goat manure amended treatments. Hydroxyatrazine pathway was not significantly altered, whereas deethylatrazine and deisopropylatrazine pathways were remarkably enhanced in treatments amended with manure by encouraging the N-dealkylation of atrazine side chains. In addition, goat manure significantly increased soil pH and contents of organic matters and humus, explaining the change of atrazine metabolic pathway. Nocardioides, Sphingomonas and Massilia were positively correlated with atrazine degradation efficiency and three metabolites, suggesting their preference in atrazine contaminated soils and potential roles in atrazine degradation. Our findings suggested that goat manure acts as both bacterial inoculum and nutrients to improve soil microenvironment, and its amendment is a potential practice in accelerating atrazine degradation at contaminated sites, offering an efficient, cheap, and eco-friendly strategy for herbicide polluted soil remediation.

Effects of different parameters on the removal of atrazine in a water environment by Aspergillus oryzae biosorption

Atrazine is the most extensively used herbicide in the agricultural and forestry sectors. Nevertheless, along with the increasing usage amount of Atrazine, its harm exposed gradually, the main problem is its residues in the environment. Microbial adsorption may effectively reduce the pollution caused by atrazine residue in the environment. In this study, a strain of fungi with the function of adsorbing atrazine was selected using microbial screening technology. According to its phenotypic characteristics and 18S rDNA gene sequencing, this strain was of the species genus Aspergillus and was named ECUST-TXZC2018. By studying the dynamic adsorption effect of this strain on atrazine, we found that this strain adsorbed atrazine after 36 hr at pH=5-7, and 20-30°C with more than 70% adsorption. These results demonstrated that ECUST-TXZC2018 had potential application ability to control atrazine residue pollution through the biosorption function.

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA-DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95-96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, "Bartonella mastomydis," and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) "Bartonella vinsonii" subsp. arupensis and "B. vinsonii" subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 ("Mesorhizobium loti LMG 6,125T"), GCF_003024595.1 ("Mesorhizobium plurifarium LMG 11,892T"), GCF_003096615.1 ("Methylobacterium organophilum DSM 760T"), and GCF_000373025.1 ("R. gallicum R-602 spT") are not from the genuine type strains used for the respective species descriptions; and v) "Xanthobacter autotrophicus" Py2 and "Aminobacter aminovorans" KCTC 2,477T represent cases of misuse of the term "type strain". Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust ("Prokaryotic Clusters"), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

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.

Labour sharing promotes coexistence in atrazine degrading bacterial communities

Microbial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

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.

Whole Cell Actinobacteria as Biocatalysts

Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.

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

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

Evidence for photolytic and microbial degradation processes in the dissipation of leptospermone, a natural β-triketone herbicide

Bioherbicides appear as an ecofriendly alternative to synthetic herbicides, generally used for weed management, because they are supposed to have low side on human health and ecosystems. In this context, our work aims to study abiotic (i.e., photolysis) and biotic (i.e,. biodegradation) processes involved in the fate of leptospermone, a natural β-triketone herbicide, by combining chemical and microbiological approaches. Under controlled conditions, the photolysis of leptospermone was sensitive to pH. Leptospermone has a half-life of 72 h under simulated solar light irradiations. Several transformation products, including hydroxy-leptospermone, were identified. For the first time, a bacterial strain able to degrade leptospermone was isolated from an arable soil. Based on its 16S ribosomal RNA (rRNA) gene sequence, it was affiliated to the Methylophilus group and was accordingly named as Methylophilus sp. LS1. Interestingly, we report that the abundance of OTUs, similar to the 16S rRNA gene sequence of Methylophilus sp. LS1, was strongly increased in soil treated with leptospermone. The leptospermone was completely dissipated by this bacteria, with a half-life time of 6 days, allowing concomitantly its growth. Hydroxy-leptospermone was identified in the bacterial culture as a major transformation product, allowing us to propose a pathway of transformation of leptospermone including both abiotic and biotic processes.

Atrazine Triggers Mitochondrial Dysfunction and Oxidative Stress in Quail ( Coturnix C. coturnix) Cerebrum via Activating Xenobiotic-Sensing Nuclear Receptors and Modulating Cytochrome P450 Systems

The residues from the widely used broad-spectrum environmental herbicide, atrazine (ATR), result in the exposure of nontarget organisms and persist as a global major public health hazard. ATR is neurotoxic and may cause adverse health effects in mammals, birds, and fishes. Nevertheless, the molecular mechanism of ATR induced neurotoxicity remains unclear. To assess the molecular mechanisms of ATR-induced cerebral toxicity through potential oxidative damage, quail were treated with ATR by oral gavage administration at doses of 0, 50, 250, and 500 mg/kg body weight daily for 45 days. Markedly, increases in the amount of swelling of neuronal cells, the percentage of mean damaged mitochondria, mitochondrial malformation, and mitochondrial vacuolar degeneration as well as decreases in the mitochondrial cristae and mitochondrial volume density were observed by light and electron microscopy in the cerebrum of quail. ATR induced toxicities in the expression of mitochondrial function-related genes and promoted oxidative damage, as indicated by effects on oxidative stress indices. These results indicated that ATR exposure can cause neurological disorders and cerebral injury. ATR may initiate apoptosis by activating Bcl-2, Bax, and Caspase3 protein expression but failed to induce autophagy (LC3B has not cleaved to LC3BI/II). Furthermore, ATR induced CYP-related enzymes metabolism disorders by activating the nuclear xenobiotic receptors response (NXRs including AHR, CAR, and PXR) and increased expression of several CYP isoforms (including CYP1B1 and CYP2C18) and thereby producing mitochondrial dysfunction. In this study, we observed ATR exposure resulted in oxidative stress and mitochondrial dysfunction by activating the NXR response and interfering the CYP450s homeostasis in quail cerebrum that supported the molecular mechanism of ATR induced cerebrum toxicity. In conclusion, these results provided new evidence on molecular mechanism of ATR induced neurotoxicity.

Diuron degradation by bacteria from soil of sugarcane crops

The isolation of microorganisms from soil impacted by xenobiotic chemicals and exposing them in the laboratory to the contaminant can provide important information about their response to the contaminants. The purpose of this study was to isolate bacteria from soil with historical application of herbicides and to evaluate their potential to degrade diuron. The isolation media contained either glucose or diuron as carbon source. A total of 400 bacteria were isolated, with 68% being Gram-positive and 32% Gram-negative. Most isolates showed potential to degrade between 10 and 30% diuron after five days of cultivation; however Stenotrophomonas acidophila TD4.7 and Bacillus cereus TD4.31 were able to degrade 87% and 68%, respectively. The degradation of diuron resulted in the formation of the metabolites DCPMU, DCPU, DCA, 3,4-CAC, 4-CA, 4-CAC and aniline. Based on these results it was proposed that Pseudomonas aeruginosa TD2.3, Stenotrophomonas acidaminiphila TD4.7, B. cereus TD4.31 and Alcaligenes faecalis TG 4.48, act on 3,4-DCA and 4-CA by alkylation and dealkylation while Micrococcus luteus and Achromobacter sp follow dehalogenation directly to aniline. Growth on aniline as sole carbon source demonstrates the capacity of strains to open the aromatic ring. In conclusion, the results show that the role of microorganisms in the degradation of xenobiotics in the environment depends on their own metabolism and also on their synergistic interactions.

Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil

Propazine is a s-triazine herbicide widely used for controlling weeds for crop production. Its persistence and contamination in environment nagatively affect crop growth and food safety. Elimination of propazine residues in the environment is critical for safe crop production. This study identified a microbial community able to degrade propazine in a farmland soil. About 94% of the applied propazine was degraded within 11 days of incubation when soil was treated with 10mgkg^-1 propazine as the initial concentration. The process was accompanied by increased microbial biomass and activities of soil enzymes. Denaturing gradient gel electrophoresis (DGGE) revealed multiple bacterial strains in the community as well as dynamic change of the composition of microbial community with a reduced microbial diversity (H' from 3.325 to 2.78). Tracking the transcript level of degradative genes AtzB, AtzC and TrzN showed that these genes were induced by propazine and played important roles in the degradation process. The activities of catalase, dehydrogenase and phenol oxidase were stimulated by propazine exposure. Five degradation products (hydroxyl-, methylated-, dimeric-propazine, ammeline and ammelide) were characterized by UPLC-MS², revealing a biodegradation of propazine in soil. Several novel methylated and dimeric products of propazine were characterized in thepropazine-exposed soil. These data help understand the pathway, detailed mechanism and efficiency of propazine biodegradation in soil under realistic field condition.

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.

Fast atrazine degradation by the mixed cultures enriched from activated sludge and analysis of their microbial community succession

In this study, fast atrazine degradation by the mixed bacterial cultures from sewage sludge was investigated. The acquired activated cultures showed great capability in atrazine degradation. The biodegradation process was well fitted into a pseudo-first reaction kinetic model. Atrazine could inhibit the propagation of ammonium oxidation bacteria and nitrite oxidation bacteria, decreasing the ammonium removal rate and the accumulation of nitrite. Only 162-172 reads of Nitrosomonadaceae and no Nitrospirales were detected after atrazine was exposed to the mixed cultures. The bacterial community structures in the cultures under different inoculation conditions (with or without atrazine) were investigated to explore the mechanism of atrazine degradation. Our results show that the genera Thiobacillus and Ferruginibacter were the most possible candidates responsible for the degradation of atrazine.

Rapid preconcentration of viable bacteria using magnetic ionic liquids for PCR amplification and culture-based diagnostics

In this study, a series of magnetic ionic liquids (MILs) were investigated for the extraction and preconcentration of bacteria from aqueous samples. By dispersing small volumes (e.g., 15 μL) of MIL within an aqueous cell suspension, bacteria were rapidly extracted and isolated using a magnetic field. Of the seven hydrophobic MILs examined, the trihexyl(tetradecyl)phosphonium Ni(II) hexafluoroacetylacetonate ([P₆₆₆₁₄⁺][Ni(hfacac)₃^-]) MIL exhibited the greatest enrichment of viable Escherichia coli K12 when coupled with microbiological culture as the detection method. The MIL-based strategy was applied for the preconcentration of E. coli from aqueous samples to obtain enrichment factors (E _F) as high as 44.6 in less than 10 min. The MIL extraction approach was also interfaced with polymerase chain reaction (PCR) amplification where the positive detection of E. coli was achieved with the [P₆₆₆₁₄⁺][Co(hfacac)₃^-], [P₆₆₆₁₄⁺][Ni(hfacac)₃^-], [P₆₆₆₁₄⁺][Dy(hfacac)₄^-], and [P₆₆₆₁₄⁺][Nd(hfacac)₄^-] MILs. While direct sampling of an aqueous cell suspension at a concentration of 1.68 × 10⁴ colony-forming units (CFUs) mL^-1 yielded no amplicon when subjected to PCR, extraction of the sample with the [P₆₆₆₁₄⁺][Ni(hfacac)₃^-] MIL under optimized conditions provided sufficient enrichment of E. coli for amplicon detection. Importantly, the enrichment of bacteria using the Ni(II)-, Co(II)-, and Dy(III)-based MILs was compatible with real-time quantitative PCR amplification to dramatically improve sample throughput and lower detection limits to 1.0 × 10² CFUs mL^-1. The MIL-based method is much faster than existing enrichment approaches that typically require 24-h cultivation times prior to detection and could potentially be applied for the preconcentration of a variety of Gram-negative bacteria from aqueous samples. Graphical abstract Magnetic ionic liquid solvents rapidly preconcentrate viable E. coli cells for unambiguous pathogen detection using microbiological culture and qPCR.

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.

Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere

The 'biochar effect' depicts a phenomenon in which biochar soil amendment enhances plant performance by promoting growth and suppressing disease. Although this phenomenon has been observed in numerous studies, the mode of action that explains it is currently unknown. In order to elucidate mechanisms responsible for the 'biochar effect', we comprehensively monitored tomato plant development and resistance to the foliar fungal pathogen Botrytis cinerea, in biochar-amended and nonamended soils using native biochar and washed biochar, striped of labile chemical constituents. We concomitantly assessed bacterial community succession in the rhizosphere by high-throughput 16S rRNA gene amplicon sequencing and carbon-source utilization profiling. Biochar had little impact on plant physiological parameters. However, both native and washed biochar treatments were characterized by higher rhizosphere bacterial diversity and enhanced carbohydrate and phenolic compound utilization rates coupled to stimulation of bacteria known to degrade phenolic compounds. This study indicates that the 'biochar effect' is at least partially dictated by increased diversity and changes in metabolic potential in the rhizosphere microbiome, which is primarily triggered by the recalcitrant carbon backbone of the biochar and tightly bound compounds. It corresponds to the growing consensus that soil amendments which enhance microbial diversity have important benefits to ecosystem functioning.

Novel insights into the metabolic pathway of iprodione by soil bacteria

Microbial degradation constitutes the key soil dissipation process for iprodione. We recently isolated a consortium, composed of an Arthrobacter sp. strain C1 and an Achromobacter sp. strain C2, that was able to convert iprodione to 3,5-dichloroaniline (3,5-DCA). However, the formation of metabolic intermediates and the role of the strains on iprodione metabolism remain unknown. We examined the degradation of iprodione and its suspected metabolic intermediates, 3,5-dichlorophenyl-carboxamide (metabolite I) and 3,5-dichlorophenylurea-acetate (metabolite II), by strains C1 and C2 and their combination under selective (MSM) and nutrient-rich conditions (LB). Bacterial growth during degradation of the tested compounds was determined by qPCR. Strain C1 rapidly degraded iprodione (DT₅₀ = 2.3 h) and metabolite II (DT₅₀ = 2.9 h) in MSM suggesting utilization of isopropylamine, transiently formed by hydrolysis of iprodione, and glycine liberated during hydrolysis of metabolite II, as C and N sources. In contrast, strain C1 degraded metabolite I only in LB and growth kinetics suggested the involvement of a detoxification process. Strain C2 was able to transform iprodione and its metabolites only in LB. Strain C1 degraded vinclozolin, a structural analog of iprodione, and partially propanil, but not procymidone and phenylureas indicating a structure-dependent specificity related to the substituents of the carboxamide moiety.

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.

Carbaryl degradation by bacterial isolates from a soil ecosystem of the Gaza Strip

Carbaryl is an important and widely used insecticide that pollutes soil and water systems. Bacteria from the local soil ecosystem of the Gaza Strip capable of utilizing carbaryl as the sole source of carbon and nitrogen were isolated and identified as belonging to Bacillus, Morganella, Pseudomonas, Aeromonas and Corynebacterium genera. Carbaryl biodegradation by Bacillus, Morganella and Corynebacterium isolates was analyzed in minimal liquid media supplemented with carbaryl as the only source of carbon and nitrogen. Bacillus and Morganella exhibited 94.6% and 87.3% carbaryl degradation, respectively, while Corynebacterium showed only moderate carbaryl degradation at 48.8%. These results indicate that bacterial isolates from a local soil ecosystem in the Gaza Strip are able to degrade carbaryl and can be used to decrease the risk of environmental contamination by this insecticide.

Effects of soil moisture depletion on vegetable crop uptake of pharmaceuticals and personal care products (PPCPs)

Agricultural crops have a long history of being irrigated with recycled wastewater (RW). However, its use on vegetable crops has been of concern due to the potential prevalence of microcontaminants, such as pharmaceuticals and personal care products (PPCPs) in the latter, which represents a possible health hazard to consumers. We investigated the uptake of three PPCPs (atenolol, diclofenac, and ofloxacin), at three different concentrations in irrigation water (0.5, 5, and 25 μg L^-1) in relation to three varying volumetric soil moisture depletion levels of 14 % (-4.26 kPa), 10 % (-8.66 kPa), and 7 % (-18.37 kPa) by various vegetable crop species. Experiments were conducted in a split-split block completely randomized design. PPCPs were extracted using a developed method of accelerated solvent extraction and solid phase extraction and analyzed via liquid chromatography mass spectrometry (LCMS). Results indicate that all treated crops were capable of PPCP uptake at nanogram per gram concentrations independent of the applied soil moisture depletion levels and PPCP concentrations. Ofloxacin was the chemical with the highest uptake amounts, followed by atenolol and then diclofenac. Although the results were not statistically significant, higher concentrations of PPCPs were detected in plants maintained under higher soil moisture levels of 14 % (-4.26 kPa).

Genomic Potential of Stenotrophomonas maltophilia in Bioremediation with an Assessment of Its Multifaceted Role in Our Environment

The gram negative bacterium Stenotrophomonas is rapidly evolving as a nosocomial pathogen in immuno-compromised patients. Treatment of Stenotrophomonas maltophilia infections is problematic because of their increasing resistance to multiple antibiotics. This article aims to review the multi-disciplinary role of Stenotrophomonas in our environment with special focus on their metabolic and genetic potential in relation to bioremediation and phytoremediation. Current and emerging treatments and diagnosis for patients infected with S. maltophilia are discussed besides their capability of production of novel bioactive compounds. The plant growth promoting characteristics of this bacterium has been considered with special reference to secondary metabolite production. Nano-particle synthesis by Stenotrophomonas has also been reviewed in addition to their applications as effective biocontrol agents in plant and animal pathogenesis.

Isolation and characterization of Bradyrhizobium sp. SR1 degrading two β-triketone herbicides

In this study, a bacterial strain able to use sulcotrione, a β-triketone herbicide, as sole source of carbon and energy was isolated from soil samples previously treated with this herbicide. Phylogenetic study based on16S rRNA gene sequence showed that the isolate has 100 % of similarity with several Bradyrhizobium and was accordingly designated as Bradyrhizobium sp. SR1. Plasmid profiling revealed the presence of a large plasmid (>50 kb) in SR1 not cured under nonselective conditions. Its transfer to Escherichia coli by electroporation failed to induce β-triketone degrading capacity, suggesting that degrading genes possibly located on this plasmid cannot be expressed in E. coli or that they are not plasmid borne. The evaluation of the SR1 ability to degrade various synthetic (mesotrione and tembotrione) and natural (leptospermone) triketones showed that this strain was also able to degrade mesotrione. Although SR1 was able to entirely dissipate both herbicides, degradation rate of sulcotrione was ten times higher than that of mesotrione, showing a greater affinity of degrading-enzyme system to sulcotrione. Degradation pathway of sulcotrione involved the formation of 2-chloro-4-mesylbenzoic acid (CMBA), previously identified in sulcotrione degradation, and of a new metabolite identified as hydroxy-sulcotrione. Mesotrione degradation pathway leads to the accumulation of 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4 methylsulfonylbenzoic acid (AMBA), two well-known metabolites of this herbicide. Along with the dissipation of β-triketones, one could observe the decrease in 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibition, indicating that toxicity was due to parent molecules, and not to the formed metabolites. This is the first report of the isolation of bacterial strain able to transform two β-triketones.

Veterinary Antibiotic Effects on Atrazine Degradation and Soil Microorganisms

Veterinary antibiotics (VAs) in manure applied to agricultural lands may change agrichemical degradation by altering soil microbial community structure or function. The objectives of this study were to investigate the influence of two VAs, sulfamethazine (SMZ) and oxytetracycline (OTC), on atrazine (ATZ) degradation, soil microbial enzymatic activity, and phospholipid fatty acid (PLFA) markers. Sandy loam soil with and without 5% swine manure (w/w) was amended with 0 or 500 μg kgC radiolabeled ATZ and with 0, 100, or 1000 μg kg SMZ or OTC and incubated at 25°C in the dark for 96 d. The half-life of ATZ was not significantly affected by VA treatment in the presence or absence of manure; however, the VAs significantly ( < 0.05) inhibited ATZ mineralization in soil without manure (25-50% reduction). Manure amendment decreased ATZ degradation by 22%, reduced ATZ mineralization by 50%, and increased the half-life of ATZ by >10 d. The VAs had limited adverse effects on the microbial enzymes β-glucosidase and dehydrogenase in soils with and without manure. In contrast, manure application stimulated dehydrogenase activity and altered chlorinated ATZ metabolite profiles. Concentrations of PLFA markers were reduced by additions of ATZ, manure, OTC, and SMZ; adverse additive effects of combined treatments were noted for arbuscular mycorrhizal fungi and actinobacteria. In this work, the VAs did not influence persistence of the ATZ parent compound or chlorinated ATZ metabolite formation and degradation. However, reduced CO evolved from VA-treated soil suggests an inhibition to the degradation of other ATZ metabolites due to an altered soil microbial community structure.

Ancient Evolution and Recent Evolution Converge for the Biodegradation of Cyanuric Acid and Related Triazines

Cyanuric acid was likely present on prebiotic Earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the United States. In light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. The initial reaction that opens the s-triazine ring is catalyzed by the unusual enzyme cyanuric acid hydrolase. This enzyme is in a rare protein family that consists of only cyanuric acid hydrolase (CAH) and barbiturase, with barbiturase participating in pyrimidine catabolism by some actinobacterial species. The X-ray structures of two cyanuric acid hydrolase proteins show that this family has a unique protein fold. Phylogenetic, bioinformatic, enzymological, and genetic studies are consistent with the idea that CAH has an ancient protein fold that was rare in microbial populations but is currently becoming more widespread in microbial populations in the wake of anthropogenic synthesis of cyanuric acid and other s-triazine compounds that are metabolized via a cyanuric acid intermediate. The need for the removal of cyanuric acid from swimming pools and spas, where it is used as a disinfectant stabilizer, can potentially be met using an enzyme filtration system. A stable thermophilic cyanuric acid hydrolase from Moorella thermoacetica is being tested for this purpose.

The Antisense RNA Approach: a New Application for In Vivo Investigation of the Stress Response of Oenococcus oeni, a Wine-Associated Lactic Acid Bacterium

Oenococcus oeni is a wine-associated lactic acid bacterium mostly responsible for malolactic fermentation in wine. In wine, O. oeni grows in an environment hostile to bacterial growth (low pH, low temperature, and ethanol) that induces stress response mechanisms. To survive, O. oeni is known to set up transitional stress response mechanisms through the synthesis of heat stress proteins (HSPs) encoded by the hsp genes, notably a unique small HSP named Lo18. Despite the availability of the genome sequence, characterization of O. oeni genes is limited, and little is known about the in vivo role of Lo18. Due to the lack of genetic tools for O. oeni, an efficient expression vector in O. oeni is still lacking, and deletion or inactivation of the hsp18 gene is not presently practicable. As an alternative approach, with the goal of understanding the biological function of the O. oeni hsp18 gene in vivo, we have developed an expression vector to produce antisense RNA targeting of hsp18 mRNA. Recombinant strains were exposed to multiple stresses inducing hsp18 gene expression: heat shock and acid shock. We showed that antisense attenuation of hsp18 affects O. oeni survival under stress conditions. These results confirm the involvement of Lo18 in heat and acid tolerance of O. oeni. Results of anisotropy experiments also confirm a membrane-protective role for Lo18, as previous observations had already suggested. This study describes a new, efficient tool to demonstrate the use of antisense technology for modulating gene expression in O. oeni.

Comparative study on the biodegradability of morpholinium herbicidal ionic liquids

This study focused on evaluating the toxicity as well as primary and ultimate biodegradability of morpholinium herbicidal ionic liquids (HILs), which incorporated MCPA, MCPP, 2,4-D or Dicamba anions. The studied HILs were also subjected to determination of surface active properties in order to assess their influence on toxicity and biodegradability. The study was carried out with microbiota isolated from different environmental niches: sediments from river channel, garden soil, drainage trench collecting agricultural runoff stream, agricultural soil and municipal waste repository. The obtained results revealed that resistance to toxicity and biodegradation efficiency of the microbiota increased in the following order: microbiota from the waste repository > microbiota from agricultural soil ≈ microbiota from an agricultural runoff stream > microbiota from garden soil > microbiota from the river sludge. It was observed that the toxicity of HILs increased with the hydrophobicity of the cation, however the influence of the anion was more notable. The highest toxicity was observed when MCPA was used as the anion (EC₅₀ values ranging from 60 to 190 mg L⁻¹). The results of ultimate biodegradation tests indicated that only HILs with 2,4-D as the anion were mineralized to some extent, with slightly higher values for HILs with the 4-decyl-4-ethylmorpholinium cation (10–31 %) compared to HILs with the 4,4-didecylmorpholinium cation (9–20 %). Overall, the cations were more susceptible (41–94 %) to primary biodegradation compared to anions (0–61 %). The obtained results suggested that the surface active properties of the studied HILs may influence their toxicity and biodegradability by bacteria in different environmental niches.

Isolation and Characterization of a Novel Imidacloprid-Degrading Mycobacterium sp. Strain MK6 from an Egyptian Soil

Thus far, only a small number and types of bacteria with limited ability in degrading imidacloprid have been reported. Also, genes regulating imidacloprid (IMDA) degradation have yet to be discovered. To study this in more detail, an enrichment technique was used to isolate consortia and pure cultures of IMDA-degrading bacteria. Through this approach, we successfully isolated a novel bacterium capable of completely degrading IMDA as a sole nitrogen source. The bacterium was subsequently identified as Mycobacterium sp. strain MK6 by sequence analysis of its 16S rRNA gene (Genbank accession number KR052814 ). BLASTn searches indicated that 16S rRNA gene from Mycobacterium sp. strain MK6 was 99% identical to several Mycobacterium spp. Mycobacterium sp. strain MK6 transformed 99.7% added IMDA (150 μg mL(-1)) in <2 weeks (t1/2 = 1.6 days) to 6-chloronicotinic acid (6-CNA) as its major metabolite. Although the isolated strain and mixed bacterial consortia were able to degrade IMDA, they failed to grow further on 6-CNA, indicating a lack of IMDA mineralization to carbon dioxide. Small amounts of the desnitro-olefin and desnitro-degradates of IMDA were observed during the incubation but did not accumulate in culture medium.

Microbial aerobic and anaerobic degradation of acrylamide in sludge and water under environmental conditions--case study in a sand and gravel quarry

Polyacrylamides (PAMs) are used in sand and gravel quarries as water purification flocculants for recycling process water in a recycling loop system where the flocculants remove fine particles in the form of sludge. The PAM-based flocculants, however, contain residual amounts of acrylamide (AMD) that did not react during the polymerization process. This acrylamide is released into the environment when the sludge is discharged into a settling basin. Here, we explore the microbial diversity and the potential for AMD biodegradation in water and sludge samples collected in a quarry site submitted to low AMD concentrations. The microbial diversity, analyzed by culture-dependent methods and the denaturing gradient gel electrophoresis approach, reveals the presence of Proteobacteria, Cyanobacteria, and Actinobacteria, among which some species are known to have an AMD biodegradation activity. Results also show that the two main parts of the water recycling loop-the washing process and the settling basin-display significantly different bacterial profiles. The exposure time with residual AMD could, thus, be one of the parameters that lead to a selection of specific bacterial species. AMD degradation experiments with 0.5 g L(-1) AMD showed a high potential for biodegradation in all parts of the washing process, except the make-up water. The AMD biodegradation potential in samples collected from the washing process and settling basin was also analyzed taking into account on-site conditions: low (12 °C) and high (25 °C) temperatures reflecting the winter and summer seasons, and AMD concentrations of 50 μg L(-1). Batch tests showed rapid (as little as 18 h) AMD biodegradation under aerobic and anaerobic conditions at both the winter and summer temperatures, although there was a greater lag time before activity started with the AMD biodegradation at 12 °C. This study, thus, demonstrates that bacteria present in sludge and water samples exert an in situ and rapid biodegradation of AMD at low concentration, whatever the season, and in both the aerobic and anaerobic parts of the water recycling system.

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.

The biofilm mode of life boosts the anti-inflammatory properties of Lactobacillus

The predominant form of life for microorganisms in their natural habitats is the biofilm mode of growth. The adherence and colonization of probiotic bacteria are considered as essential factors for their immunoregulatory function in the host. Here, we show that Lactobacillus casei ATCC334 adheres to and colonizes the gut of zebrafish larvae. The abundance of pro-inflammatory cytokines and the recruitment of macrophages were low when inflammation was induced in probiotic-fed animals, suggesting that these bacteria have anti-inflammatory properties. We treated human macrophage-differentiated monocytic THP-1 cells with supernatants of L. casei ATCC334 grown in either biofilm or planktonic cultures. TNF-α production was suppressed and the NF-κB pathway was inhibited only in the presence of supernatants from biofilms. We identified GroEL as the biofilm supernatant compound responsible, at least partially, for this anti-inflammatory effect. Gradual immunodepletion of GroEL demonstrated that the abundance of GroEL and TNF-α were inversely correlated. We confirmed that biofilm development in other Lactobacillus species affects the immune response. The biofilms supernatants of these species also contained large amounts of GroEL. Thus, our results demonstrate that the biofilm enhances the immunomodulatory effects of Lactobacillus sp. and that secreted GroEL is involved in this beneficial effect.

Microbial degradation of herbicides

Herbicides remain the most effective, efficient and economical way to control weeds; and its market continues to grow even with the plethora of generic products. With the development of herbicide-tolerant crops, use of herbicides is increasing around the world that has resulted in severe contamination of the environment. The strategies are now being developed to clean these substances in an economical and eco-friendly manner. In this review, an attempt has been made to pool all the available literature on the biodegradation of key herbicides, clodinafop propargyl, 2,4-dichlorophenoxyacetic acid, atrazine, metolachlor, diuron, glyphosate, imazapyr, pendimethalin and paraquat under the following objectives: (1) to highlight the general characteristic and mode of action, (2) to enlist toxicity in animals, (3) to pool microorganisms capable of degrading herbicides, (4) to discuss the assessment of herbicides degradation by efficient microbes, (5) to highlight biodegradation pathways, (6) to discuss the molecular basis of degradation, (7) to enlist the products of herbicides under degradation process, (8) to highlight the factors effecting biodegradation of herbicides and (9) to discuss the future aspects of herbicides degradation. This review may be useful in developing safer and economic microbiological methods for cleanup of soil and water contaminated with such compounds.

Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil

Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography (HPLC) and mass spectrometry. Nine cultures JS01.Deg01 to JS09.Deg01 were identified as the degrader of atrazine in the enrichment culture. The three isolates JS04.Deg01, JS07.Deg01, and JS08.Deg01 were identified as efficient atrazine metabolizers. Isolates JS04.Deg01 and JS07.Deg01 produced hydroxyatrazine (HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate JS08.Deg01 generated deethylatrazine (DEA), deisopropylatrazine (DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by JS08.Deg01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain JS08.Deg01. The highest atrazine mineralization was observed in case of isolate JS08.Deg01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain JS08.Deg01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process.

Biodegradation of atrazine by Rhodococcus sp. BCH2 to N-isopropylammelide with subsequent assessment of toxicity of biodegraded metabolites

Atrazine is a persistent organic pollutant in the environment which affects not only terrestrial and aquatic biota but also human health. Since its removal from the environment is needed, atrazine biodegradation is achieved in the present study using the bacterium Rhodococcus sp. BCH2 isolated from soil, long-term treated with atrazine. The bacterium was capable of degrading about 75 % atrazine in liquid medium having pH 7 under aerobic and dark condition within 7 days. The degradation ability of the bacterium at various temperatures (20-60 °C), pH (range 3-11), carbon (glucose, fructose, sucrose, starch, lactose, and maltose), and nitrogen (ammonium molybdate, sodium nitrate, potassium nitrate, and urea) sources were studied for triumph optimum atrazine degradation. The results indicate that atrazine degradation at higher concentrations (100 ppm) was pH and temperature dependent. However, glucose and potassium nitrate were optimum carbon and nitrogen source, respectively. Atrazine biodegradation analysis was carried out by using high-performance thin-layer chromatography (HPTLC), Fourier transform infrared spectroscopy (FTIR), and liquid chromatography quadrupole time-of-flight (LC/Q-TOF-MS) techniques. LC/Q-TOF-MS analysis revealed formation of various intermediate metabolites including hydroxyatrazine, N-isopropylammelide, deisopropylhydroxyatrazine, deethylatrazine, deisopropylatrazine, and deisopropyldeethylatrazine which was helpful to propose biochemical degradation pathway of atrazine. Furthermore, the toxicological studies of atrazine and its biodegraded metabolites were executed on earthworm Eisenia foetida as a model organism with respect to enzymatic (SOD and Catalase) antioxidant defense mechanism and lipid peroxidation studies. These results suggest innocuous degradation of atrazine by Rhodococcus sp. BCH2 in nontoxic form. Therefore the Rhodococcus sp.BCH2 could prove a valuable source for the eco-friendly biodegradation of atrazine pesticide.

Dichlobenil and 2,6-dichlorobenzamide (BAM) dissipation in topsoil and deposits from groundwater environment within the boreal region in southern Finland

BAM (2,6-dichlorobenzamide) is a metabolite of pesticide dichlobenil and a common groundwater contaminant. Dichlobenil and BAM half-lives were determined in five Finnish subsurface deposits and in topsoil. Aerobic and anaerobic conditions with sterilized controls were included in this 1.4-year incubation experiment. In subsurface deposits, dichlobenil half-life varied from 157 days to no degradation and that of BAM from 314 days to no degradation. Microbes and oxygen enhanced dichlobenil and BAM dissipation rates in some deposits. However, dichlobenil and BAM concentrations were most significantly affected by deposit characteristics, especially carbon and nitrogen amounts. Also low pH, cadmium, iron, zinc, manganese and lead correlated with low dichlobenil and/or BAM concentrations. In mineral topsoil, dissipation was faster with half-lives of 41-54 days for dichlobenil, and 182-261 days for BAM. Dichlobenil was depleted completely in surface soil, but BAM was not dissipated below 55-81 % of the initial concentration. Generally, dichlobenil and BAM dissipation in samples from the northern boreal region was similar to that reported for the temperate region. BAM was persistent in topsoil and subsurface deposits, indicating long-term persistence problems in groundwater also within the northern boreal region.

High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments

Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS1071, two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil. Comparison of IncP-1/IS1071 prevalence between pesticide-treated and nontreated soil and BPS microcosms suggested that both IncP-1 and IS1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS1071-specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS1071 and especially IncP-1, MGE were less abundant in field ecosystems without pesticide history although some of them still showed a high IS1071 abundance. Our data suggest that MGE-containing organisms were enriched in pesticide-contaminated environments like BPS where they might contribute to spreading of catabolic genes and to pathway assembly.