Isolation and characterization of fenobucarb-degrading bacteria from rice paddy soils

The novel hydrolase IpcH initiates the degradation of isoprocarb in a newly isolated strain Rhodococcus sp. D-6

Isoprocarb (IPC), a representative monocyclic carbamate insecticide, poses risks of environmental contamination and harm to non-target organisms. However, its degradation mechanism has not been reported. In this study, a newly IPC-degrading strain D-6 was isolated from the genus Rhodococcus, and its degradation characteristics and pathway of IPC were analyzed. A novel hydrolase IpcH, responsible for hydrolyzing IPC to 2-isopropylphenol (IPP), was identified. IpcH exhibited low similarity (< 27 %) with other reported hydrolases, including previously characterized carbamate insecticides hydrolases, indicating its novelty. The Km and kcat values of IpcH towards IPC were 69.99 ± 8.33 μM and 95.96 ± 4.02 s-1, respectively. Also, IpcH exhibited catalytic activity towards various types of carbamate insecticides, including monocyclic carbamates (IPC, fenobucarb and propoxur), bicyclic carbamates (carbaryl and carbofuran), and linear carbamates (oxamyl and aldicarb). The molecular docking and site-directed mutagenesis revealed that His254, His256, His329 and His376 were essential for IpcH activity. Strain D-6 can effectively reduce the toxicity of IPC and IPP towards sensitive organisms through its degradation ability. This study presents the initial report on IPC degradation pathway and molecular mechanism of IPC degradation, and provides a good potential strain for bioremediating IPC and IPP-contaminated environments.

Design, Synthesis, Herbicidal Activity, and Molecular Docking Study of 2-Thioether-5-(Thienyl/Pyridyl)-1,3,4-Oxadiazoles as Potent Transketolase Inhibitors

Transketolase (TK) has been regarded as a new target for the development of novel herbicides. In this study, a series of 2-thioether-5-(thienyl/pyridyl)-1,3,4-oxadiazoles were designed and synthesized based on TK as the new target. The preliminary bioassay results indicated that compounds 4l and 4m displayed the best herbicidal activities against Amaranthus retroflexus (AR) and Digitaria sanguinalis (DS), with the inhibition exceeding 90% at 100-200 mg/L in vitro. Moreover, they also displayed higher postemergence herbicidal activities (90% control) against AR and DS than all of the positive controls at 45-90 g [active ingredient (ai)]/ha in a greenhouse. Notably, compounds 4l and 4m showed a broad spectrum of weed control at 90 g ai/ha. More significantly, compound 4l exhibited good crop selectivity against maize at 90 g ai/ha. Both fluorescent binding experiments and molecular docking analyses indicated that compounds 4l and 4m exhibited strong TK inhibitory activities with superior binding affinities than the others. Preliminary mechanism studies suggested that they might exert their TK inhibitory effects by occupying the active cavity of At TK and forming more strong interactions with amino acids in the active site. Taken together, these results suggested that compound 4l was a potential herbicide candidate for weed control in maize fields targeting TK.

Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides

Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.

Fenobucarb-induced developmental neurotoxicity and mechanisms in zebrafish

Fenobucarb (2-sec-butylphenyl methylcarbamate, BPMC) is an extensively used carbamate insecticide. Its developmental neurotoxicity and the underlying mechanisms have not been well investigated. In this study, zebrafish embryos were exposed to various concentrations of BPMC from 6 hpf (hours post fertilization, hpf) to 120 hpf. BPMC induced developmental toxicity with reduced motility in larval zebrafish. The spinal cord neutrophil infiltration, increased ROS production, caspase 3 and 9 activation, central nerve and peripheral motor neuron damage, axon and myelin degeneration were observed in zebrafish treated with BPMC generally in a dose-dependent manner. The expression of eight marker genes for nervous system function or development, namely, a1-tubulin, shha, elavl3, gap43, syn2a, gfap, mbp and manf, was significantly downregulated following BPMC exposure. AChE activity reduction and ache gene expression suppression was also found significantly in BPMC-treated zebrafish. These results indicate that BPMC is highly toxic to zebrafish and that BPMC induces zebrafish developmental neurotoxicity through pathways involved in inflammation, oxidative stress, degeneration and apoptosis.

Flavobacterium sandaracinum sp. nov., Flavobacterium caseinilyticum sp. nov., and Flavobacterium hiemivividum sp. nov., novel psychrophilic bacteria isolated from Arctic soil

This study presents taxonomic description of strains LB-D12T, AT-3-2T, AT-3–7, and TSA-D2T isolated from Arctic soil. All strains were psychrophilic, Gram-stain-negative, aerobic, non-motile, and rod-shaped. Phylogenetic analysis showed that these strains belonged to the genus Flavobacterium . Strains LB-D12T, AT-3-2T and AT-3–7 were closest to Flavobacterium psychrolimnae LMG 22018T (98.5–98.8% sequence similarity). Strain TSA-D2T was closest to Flavobacterium degerlachei DSM 15718T (98.3 % sequence similarity). These strains shared common chemotaxonomic features comprising MK-6 as a sole quinone, phosphatidylethanolamine as the principal polar lipid, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C16 : 0 3-OH, C15 : 1ω6c, iso-C16 : 0, and anteiso-C15 : 0 as the main fatty acids. The ANI and dDDH values between these novel isolates and their closest relatives were below the cut-off values of 95 and 70 %, respectively used for species demarcation. The DNA G+C content of all strains ranged from 34.2 to 34.6 mol%. The obtained polyphasic taxonomic data suggested that the isolated strains represent novel species within the genus Flavobacterium , for which the names Flavobacterium sandaracinum sp. nov. (type strain LB-D12T=KEMB 9005-737T=KACC 21180T=NBRC 113784T), Flavobacterium caseinilyticum sp. nov. (type strain AT-3–2T=KEMB 9005-738T=KACC 21176T=NBRC 113785T), and Flavobacterium hiemivividum sp. nov. (type strain TSA-D2T=KEMB 9005-741T=KACC 21179T=NBRC 113788T) are proposed.

Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities

Fifteen isolates of the genus Pedobacter were obtained from Arctic soil samples. All isolates were Gram-stain-negative and rod-shaped. Cells were strictly aerobic, psychrotolerant and grew optimally at 15–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all the isolated strains formed a lineage within the family Sphingobacteriaceae and clustered as members of the genus Pedobacter . The sole respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (iso-C15 : 02-OH/C16 : 1ω7c/ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of the novel strains was 33.9–41.8 mol%. In addition, the average nucleotide identity and in silico DNA–DNA hybridization relatedness values between the novel type strains and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, phylogenetic and phylogenomic analyses, the isolated strains represent novel species in the genus Pedobacter , for which the names Pedobacter cryotolerans sp. nov. (type strain AR-2-6T=KEMB 9005-717T=KACC 19998T=NBRC 113826T), Pedobacter cryophilus sp. nov. (type strain AR-3-17T=KEMB 9005-718T=KACC 19999T=NBRC 113827T), Pedobacter frigiditerrae sp. nov. (type strain RP-1-13T=KEMB 9005-720T=KACC 21147T=NBRC 113829T), Pedobacter psychroterrae sp. nov. (type strain RP-1-14T=KEMB 9005-721T=KACC 21148T=NBRC 113830T), Pedobacter hiemivivus sp. nov. (type strain RP-3-8T=KEMB 9005-724T=KACC 21152T=NBRC 113833T), Pedobacter frigidisoli sp. nov. (type strain RP-3-11T=KEMB 9005-725T=KACC 21153T=NBRC 113927T), Pedobacter frigoris sp. nov. (type strain RP-3-15T=KEMB 9005-726T=KACC 21154T=NBRC 113834T), Pedobacter psychrodurus sp. nov. (type strain RP-3-21T=KEMB 9005-728T=KACC 21156T=NBRC 113835T) and Pedobacter polaris sp. nov. (type strain RP-3-22T=KEMB 9005-729T=KACC 21157T=NBRC 113836T) are proposed.

Gut microbiome: An intermediary to neurotoxicity

There is growing recognition that the gut microbiome is an important regulator for neurological functions. This review provides a summary on the role of gut microbiota in various neurological disorders including neurotoxicity induced by environmental stressors such as drugs, environmental contaminants, and dietary factors. We propose that the gut microbiome remotely senses and regulates CNS signaling through the following mechanisms: 1) intestinal bacteria-mediated biotransformation of neurotoxicants that alters the neuro-reactivity of the parent compounds; 2) altered production of neuro-reactive microbial metabolites following exposure to certain environmental stressors; 3) bi-directional communication within the gut-brain axis to alter the intestinal barrier integrity; and 4) regulation of mucosal immune function. Distinct microbial metabolites may enter systemic circulation and epigenetically reprogram the expression of host genes in the CNS, regulating neuroinflammation, cell survival, or cell death. We will also review the current tools for the study of the gut-brain axis and provide some suggestions to move this field forward in the future.

Fenobucarb induces heart failure and cerebral hemorrhage in zebrafish

The potential risk and toxic mechanisms of fenobucarb (2-sec-butylphenyl methylcarbamate, BPMC) to animals and humans have not been fully elucidated. In this study, zebrafish embryos were exposed to various concentrations of BPMC from 48 hpf (hour post fertilization, hpf) to 72 hpf. We found that BPMC induced severe heart failure with bradycardia, reduced heart contractions, cardiac output and blood flow dynamics；and myocardial apoptosis. BPMC also induced cerebral hemorrhages and blood erythrocyte reduction in a dose-dependent manner. Also observed were increased ROS production and capase 9 and 3/7 activation. The mRNA levels of the ATPase-related gene (atp2a1l), calcium channel-related gene (cacna1ab), sodium channel-related gene (scn5Lab), potassium channel-related gene (kcnq1), the regulatory gene (tnnc1a) for cardiac troponin C, and several apoptosis-related genes were significantly downregulated in zebrafish following BPMC exposure. These results suggest that exposure to BPMC is a possible risk factor to cardiovascular and cerebrovascular systems in animals.

Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil

This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri-42^T and Kopri-43, isolated during screening of oil-degrading psychrotrophs from oil-contaminated Arctic soil. A preliminary 16S rRNA gene sequence and phylogenetic tree analysis indicated that these Arctic strains belonged to the genus Flavobacterium, with the nearest relative being Flavobacterium psychrolimnae LMG 22018^T (98.9% sequence similarity). The pairwise 16S rRNA gene sequence identity between strains Kopri-42^T and Kopri-43 was 99.7%. The DNA-DNA hybridization value between strain Kopri-42^T and Kopri-43 was 88.6 ± 2.1% indicating that Kopri-42^T and Kopri-43 represents two strains of the same genomospecies. The average nucleotide identity and in silico DNA-DNA hybridization values between strain Kopri-42^T and nearest relative F. psychrolimnae LMG 22018^T were 92.4% and 47.9%, respectively. These values support the authenticity of the novel species and confirmed the strain Kopri-42^T belonged to the genus Flavobacterium as a new member. The morphological, physiological, biochemical and chemotaxonomic data also distinguished strain Kopri-42^T from its closest phylogenetic neighbors. Based on the polyphasic data, strains Kopri-42^T and Kopri-43 represents a single novel species of the genus Flavobacterium, for which the name Flavobacterium petrolei sp. nov. is proposed. The type strain is Kopri-42^T (=KEMB 9005-710^T = KACC 19625^T = NBRC 113374^T).

Simultaneous biodegradation of mixture of carbamates by newly isolated Ascochyta sp. CBS 237.37

In this study, a mixture of carbamates (CRBs) degrading Carb.1b strain was isolated from soil. Based on the morphology and 18S rRNA sequence analysis, the strain was identified as an Ascochyta sp. CBS 237.37 with accession number MG786925. The isolate was employed in two growth mediums (added carbon and carbon-free) enriched with varied concentrations of CRBs ranging from 25 to 85 mg L^-1 to assess its degradation efficacy. As determined by the Response Surface Methodology (RSM), optimum parameters for the degradation were: pH value of 7.5 and temperature of 28 °C. The degradation was inhibited at higher concentrations and was found to be 91.2%/94.8%, 67.25%/71.75%, 55.81%/59.81%, 46.85%/49.57% and 36%/40.80% (in carbon-free/added carbon) after 20 d. The removal of the higher concentration CRBs was comparatively slower, and the obtained degradation rate constant (K_avg) 0.03412 d^-1. Added carbon and carbon-free medium removed over 86.7%/90.15% of CRBs (85 mgL^-1) with the half-life (t_1/2) of 26 d and R² ranging from 0.982 to 0.999; indicating the high tolerance of carb.1b strain towards CRBs. Residual analysis of CRBs biodegradation was performed using GC/MS analysis. This is the first report of degradation of a mixture of CRBs by Ascochyta sp. CBS 237.37. The results of this study can possibly impact the development strategies of bioremediation for the elimination of CRBs.

Identification of two pesticide-tolerant bacteria isolated from Medicago sativa nodule useful for organic soil phytostabilization

Plant-microbe interactions such as rhizobacteria legumes are interesting in organic farming that has undergone significant expansion in the world. The organic agriculture is as an environment-friendly technique and a sustainable alternative to intensive agricultural system. Three types of soil were chosen, organic (ORG), conventional (CON), and fallow land (NA) to isolate soil bacteria-nodulating Medicago sativa, in order to develop microbial inoculants for use in agricultural sustainable system. Soil analysis revealed significant higher amounts of total nitrogen, organic carbon, total phosphorus, and matter detected in ORG. As for heavy metals, ORG showed high Cu content due to the authorized chemical use in organic farming. A sample of 130 bacteria was isolated from Medicago sativa nodule, genetically characterized by PCR/RFLP of ribosomal 16S RNAs, and a great dominance of Sinorhizobium meliloti (88.4%, 73.8%, and 55.5%) is obtained among NA-, CON-, and ORG-managed soils, respectively. The ORG showed the high bacterial diversity with 13.3% of non-identified strains. The resistance against five pesticides (Prosper, Cuivox, Fungastop, Nimbecidine, and Maneb) revealed a maximum of inhibitory concentration about 10 mg l^-1 of Prosper, 12 mg l^-1 of Cuivox, 6 ml l^-1 of Fungastop, 7.5 ml l^-1of Nimbecidine, and 25 ml l^-1 of Maneb. The analysis of the symbiotic properties and plant growth-promoting potential revealed two efficient strains significantly increased alfalfa dry weight through producing siderophores, phosphorus, and indole acetic acid (13.6 mg ml^-1 and 19.9 mg ml^-1 respectively). Hence, we identify two tolerant and efficient strains, Achromobacter spanium and Serratia plymuthica, isolated from Medicago sativa nodule with valuable potential able to phytostabilize pesticide-contaminated soils.

Discovery of carbamate degrading enzymes by functional metagenomics

Bioremediation of pollutants is a major concern worldwide, leading to the research of new processes to break down and recycle xenobiotics and environment contaminating polymers. Among them, carbamates have a very broad spectrum of uses, such as toxinogenic pesticides or elastomers. In this study, we mined the bovine rumen microbiome for carbamate degrading enzymes. We isolated 26 hit clones exhibiting esterase activity, and were able to degrade at least one of the targeted polyurethane and pesticide carbamate compounds. The most active clone was deeply characterized. In addition to Impranil, this clone was active on Tween 20, pNP-acetate, butyrate and palmitate, and on the insecticide fenobucarb. Sequencing and sub-cloning of the best target revealed a novel carboxyl-ester hydrolase belonging to the lipolytic family IV, named CE_Ubrb. This study highlights the potential of highly diverse microbiota such as the ruminal one for the discovery of promiscuous enzymes, whose versatility could be exploited for industrial uses.

Removal of environmental estrogens by bacterial cell immobilization technique

Contamination of steroidal estrogens in the environment has raised a great public concern, and therefore, developing an effective method for removal of trace amount of environmental estrogens is necessary. In this study, two estrogen-degrading bacteria were isolated from activated sludge and were identified as strain Sphingomonas sp. AHC-F and strain Sphingobium sp. AX-B. They were capable of utilizing estrone (E1) and 17ß-estradiol (E2) as sole carbon and energy source. Cell immobilization technique was applied to these two estrogen-degrading bacteria. Confocal laser-scanning microscopy images with live and dead staining of entrapped bacterial cells showed that most bacteria were present inside the porous structure and were mostly viable after immobilization procedures. Batch estrogen degradation study showed that immobilized strains AHC-F and AX-B could effectively degrade 2 mg/L of E2 and its metabolite E1. Immobilized bacteria column reactors using pure culture of strain AHC-F were set up for continuous-flow removal of 850 ng/L of E2 in the influent. The removal efficiency of E2 and equivalent estrogenic quantity of E2 (EEQ) could achieve 94 and 87% under 12 h hydraulic retention time (HRT), respectively. Increasing HRT could further improve the removal efficiency of EEQ. When the HRT increased to 72 h, the effluent concentrations of E2 and E1 were not detectable by gas chromatography-mass spectrometry. Our results also proved that most of the estrogen removal was due to biodegradation. This study has demonstrated the potential use of immobilized bacteria technique for the removal of environmental estrogens.

Groundwater screening for 940 organic micro-pollutants in Hanoi and Ho Chi Minh City, Vietnam

Groundwater is the main source of drinking water for more than half of the residents of Hanoi (HN). It also provides about one third of the total water demand for residents of Ho Chi Minh City (HCM). However, due to rapid urbanization and frequent discharges of untreated urban wastewater to surface water, freshwater is widely contaminated by man-made chemicals, which may result in groundwater pollution. As part of an ongoing campaign to collect baseline information on the occurrence of organic micro-pollutants (OMPs) in the aquatic environment in Vietnam, 43 water samples were collected from 26 groundwater wells in HN (22) and HCM (4) in September 2013 and August 2014. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS) and the resulting chromatograms were screened for 940 OMPs by an automated identification and quantification system (AIQS) within a GC-MS database. A total of 74 compounds were detected, with between 4 and 43 (median 18) compounds found at each site. Overall, contamination levels were low, with over 89 % of the detected concentrations that were less than 0.5 μg L(-1). Results suggest that most of the sampled aquifers have been impacted by non-point source pollution. Most of the contaminants detected are either currently not regulated in drinking water or are present at low levels. A health risk assessment for detected contaminants implied that there were no risks to humans. Since this study was based on a limited number of samples, especially in HCM, further, more detailed studies on the occurrence of OMPs in groundwater in HCM and a full risk assessment of detected contaminants should be prioritized.

Bioremediation using Novosphingobium strain DY4 for 2,4-dichlorophenoxyacetic acid-contaminated soil and impact on microbial community structure

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly used for weed control. The ubiquity of 2,4-D has gained increasing environmental concerns. Biodegradation is an attractive way to clean up 2,4-D in contaminated soil. However, information on the bioaugmentation trial for remediating contaminated soil is still very limited. The impact of bioaugmentation using 2,4-D-degraders on soil microbial community remains unknown. The present study investigated the bioremediation potential of a novel degrader (strain DY4) for heavily 2,4-D-polluted soil and its bioaugmentation impact on microbial community structure. The strain DY4 was classified as a Novosphingobium species within class Alphaproteobacteria and harbored 2,4-D-degrading TfdAα gene. More than 50 and 95 % of the herbicide could be dissipated in bioaugmented soil (amended with 200 mg/kg 2,4-D) respectively in 3-4 and 5-7 days after inoculation of Novosphingobium strain DY4. A significant growth of the strain DY4 was observed in bioaugmented soil with the biodegradation of 2,4-D. Moreover, herbicide application significantly altered soil bacterial community structure but bioaumentation using the strain DY4 showed a relatively weak impact.