Rhodococcus wratislaviensis strain 9: An efficient p-nitrophenol degrader with a great potential for bioremediation

Soil-derived cellulose-degrading bacteria: screening, identification, the optimization of fermentation conditions, and their whole genome sequencing

Straw cellulose is an abundant renewable resource in nature. In recent years, the conversion of cellulose from waste straw into biofuel by specific microorganisms' fragmentation has attracted extensive attention. Although many bacteria with the ability to degrade cellulose have been identified, comprehensive bioinformatics analyses of these bacteria remain limited, and research exploring optimal fragmentation conditions is scarce. Our study involved the isolation and screening of bacteria from various locations in Yangzhou using carboxymethyl cellulose (CMC) media. Then, the cellulose-degrading bacteria were identified using 16S rRNA and seven candidate bacterial strains with cellulose degrading ability were identified in Yangzhou city for the first time. The cellulase activity was determined by the 3,5-dinitrosalicylic acid (DNS) method in different fragmentation conditions, and finally two bacteria strains with the strongest cellulose degradation ability were selected for whole genome sequencing analysis. Sequencing results revealed that the genome sizes of Rhodococcus wratislaviensis YZ02 and Pseudomonas Xanthosomatis YZ03 were 8.51 Mb and 6.66 Mb, containing 8,466 and 5,745 genes, respectively. A large number of cellulose degradation-related genes were identified and annotated using KEGG, GO and COG analyses. In addition, genomic CAZyme analysis indicated that both R. wratislaviensis YZ02 and P. Xanthosomatis YZ03 harbor a series of glycoside hydrolase family (GH) genes and other genes related to cellulose degradation. Our finding provides new options for the development of cellulose-degrading bacteria and a theoretical basis for improving the cellulose utilization of straw.

Application of cold-adapted microbial agents in soil contaminate remediation: biodegradation mechanisms, case studies, and safety assessments

The microbial agent technology has made significant progress in remediating nitro-aromatic compounds (NACs), such as p-nitrophenol, 2,4-dinitrophenol, and 2,4,6-Trinitrotoluene, in farmland soil over the past decade. However, there are still gaps in our understanding of the bioavailability and degradation mechanisms of these compounds in low-temperature environments. In this review, we provide a comprehensive summary of the strategies employed by cold-adapted microorganisms and elucidate the degradation pathways of NACs pollutants. To further analyze their metabolic mechanisms, we propose using mass balance to improve our understanding of biochemical processes and refine the degradation pathways through stoichiometry analysis. Additionally, we suggest employing 13C-metabolic flux analysis to track enzyme activity and intermediate products during bio-degradation processes with the aim of accelerating the remediation of nitro-aromatic compounds, particularly in cold regions. Through a comprehensive analysis of pollutant metabolic activities and a commitment to the 'One Health' approach, with an emphasis on selecting non-pathogenic strains, the environmental management strategies for soil remediation could be positioned to develop and implement safe and effective measure.

RhB-Embedded Mn-MOF with Cyclotriphosphazene Skeleton as Dual-Emission Sensor for Putrescine as well as Smart Fluorescent Response of Aromatic Diamines and Nitrophenol

Luminescent metal-organic framework composites with multiple luminescence emissions have been efficient sensing platforms. Herein, a fluorescent sensor (RhB@1-0.4) with dual-emission fluorescence properties was prepared by introducing rhodamine B (RhB) into the framework of complex 1, [Mn2.5(HCPCP)(H2O)4]·(CH3CN)0.5 [HCPCP = hexa-(4-carboxyl-phenoxy)-cyclotriphosphazene and CH3CN = acetonitrile), which is a novel crystalline two-dimensional (2D) coordinated organic framework material. It is a highly desirable material, realizing a ratiometric fluorescence response to putrescine with a high signal-to-noise ratio, and the detection limit can be as low as 6.8 μM. In addition, RhB@1-0.4 exhibited a better fluorescent sensing performance for aromatic diamines and nitrophenols compared with that of complex 1. It is a potential functionalized MOF material for the application of multichannel fluorescence sensing.

A Highly Selective Pyrene Appended Oxacalixarene Receptor for MNA and 4-NP Detection: an Experimental and Computational Study

A novel pyrene-substituted oxacalixarene was designed and synthesized as a selective probe for the simultaneous detection of MNA and 4-NP. Utilizing 1H-NMR, 13C-NMR, and FT-IR analysis techniques, its structure was characterized. The binding property of BPOC to a variety of NACs, including 1,3-DNB, 2,3-DNT, 2,4-DNT, 2,6-DNT, 4-NP, 4-NT, and PA, revealed that the sensor binds to MNA and 4-NP with remarkable selectivity. Binding constant reveals lower detection limits of MNA is 0.2 µM and 0.3 µM for 4-NP. Using docking and density functional theory (DFT), computational insights were provided for investigating the stability and spectroscopic analysis of the inclusion complex. From molecular docking study, we observed the best docking score of BPOC with 4-NT and MNA complex. The calculations supplement the findings significantly and clarify the structural geometry and mode of interactions in supramolecular complexation. In an MTT experiment on human PBMC to check for cytotoxicity, this chemical was found to influence 1 × 105 cell viability dose-dependently.

Effects of Cadmium Stress on Bacterial and Fungal Communities in the Whitefly Bemisia tabaci

Heavy metal contamination is among the most prominent environmental problems in China, posing serious threats to both ecosystem and human health. Among the diverse heavy metal contaminants, cadmium is the most serious. The whitefly Bemisia tabaci is a cosmopolitan pest capable of causing severe damage to a broad range of agricultural crops, especially vegetables. At present, little is known about the effects of cadmium stress on B. tabaci, including on its bacterial and fungal communities. In the current study, we investigated the effects of cadmium on bacterial and fungal communities in whiteflies. Meta-barcode sequencing of the 16S rRNA gene revealed that the whitefly bacterial community contained 264 operational taxonomic units (OTUs) belonging to 201 known genera and 245 known species. The top five most frequent bacterial genera were Rickettsia, Rhodococcus, Candidatus Portiera, Candidatus Hamiltonella, and Achromobacter. Meta-barcode sequencing of the fungal ITS locus revealed that the whitefly fungal community contained 357 OTUs belonging to 187 known genera and 248 known species. The top five most frequent fungal genera were Wallemia, unclassified_f_Dipodascaceae, Apiotrichum, Penicillium, and unclassified_o_Saccharomycetales. Cadmium exposure reduced the fungal OTU richness but increased the bacterial Shannon and Simpson diversity indices in whiteflies. In addition, upon exposure to cadmium, the microbial community composition in whiteflies changed significantly, with increased prevalence of the bacterial genera Rhodococcus and Exiguobacterium and fungal genus Wallemia. Our results indicate that the whitefly microbiota likely contributed to their adaptation and resistance to cadmium and suggested that whiteflies may contain microbes that could help remediate cadmium contamination in natural environments and agricultural fields.

Detoxification of p-nitrophenol (PNP) using Enterococcus gallinarum JT-02 isolated from animal farm waste sludge

Enterococcus gallinarum (JT-02) isolated and identified from the animal farm waste sludge was found to be capable of biodegrading p-nitrophenol (PNP), an organic compound used to manufacture drugs, fungicides, insecticides, dyes, and to darken leather. The intention of this study was to optimize the biodegradation by finding the optimal conditions for the specific strain through single-factor experiments. The bacterial strain was grown in Luria Bertani broth and various parameters were optimized to achieve the prime settings for the p-nitrophenol (PNP) biodegradation. The results indicated that the best setups for the biodegradation by the strain JT-02 was 100 mg/L of PNP; pH 7; 30 °C; 150 rpm in a shaker incubator and 3% (v/v) of inoculum dose. Once the optimal conditions were found, the bacteria were capable of degrading p-nitrophenol (98.21%) in 4 days. Intermediates produced during PNP biodegradation were identified using High Performance Liquid Chromatography (HPLC) analysis and the biodegradation pathway was elucidated. Phytotoxicity studies were carried out with Vigna radiata seeds to confirm the applicability and efficiency of PNP biodegradation.

Incorporation of g-C3N4 nanosheets and CuO nanoparticles on polyester fabric for the dip-catalytic reduction of 4 nitrophenol

In the present work, we present the preparation of a new emerged heterogeneous catalyst (PE/g-C3N4/CuO) by in situ deposition of copper oxide nanoparticles (CuO) over the graphitic carbon nitride (g-C3N4) as the active catalyst and polyester (PE) fabric as the inert support. The synthesized sample (PE/g-C3N4/CuO) "dip catalyst" was studied by using various analytical techniques (Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy and dispersive X-ray spectroscopy (SEM/EDX), and transmission electron microscopy (TEM). The nanocomposite is utilized as heterogeneous catalysts for the 4-nitrophenol reduction in the presence of NaBH4, in aqueous solutions. According to experimental results, PE/g-C3N4/CuO with a surface of 6 cm2 (3 cm × 2 cm) demonstrated the catalyst exhibit excellent catalytic activity with 95% reduction efficiency for only 4 min of reaction and an apparent reaction rate constant (Kapp) of 0.8027 min-1. Further evidence that this catalyst based on prepared PE support can be a good contender for long-lasting chemical catalysis comes from the remarkable stability after 10 repetitions reaction cycles without a noticeably loss in catalytic activity. The novelty of this work consists to fabricate of catalyst based of CuO nanoparticles stabilized with g-C3N4 on the surface of an inert substrate PE, which results in an heterogenous dip-catalyst that can be easily introduced and isolated from the reaction solution with good retention of high catalytic performance in the reduction of 4-nitrophenol.

Removal of organic pollutants in shale gas fracturing flowback and produced water: A review

Shale gas has been developed as an alternative to conventional energy worldwide, resulting in a large amount of shale gas fracturing flowback and produced water (FPW). Previous studies focus on total dissolved solids reduction using membrane desalination. However, there is a lack of efficient and stable techniques to remove organic pollutants, resulting in severe membrane fouling in downstream processes. This review focuses on the concentration and chemical composition of organic matter in shale gas FPW in China, as well as the hazards of organic pollutants. Organic removal techniques, including advanced oxidation processes, coagulation, sorption, microbial degradation, and membrane treatment are systematically reviewed. In particular, the influences of high salt on each technique are highlighted. Finally, different treatment techniques are evaluated in terms of energy consumption, cost, and organic removal efficiency. It is concluded that integrated coagulation-sorption-Fenton-membrane filtration represents a promising treatment process for FPW. This review provides valuable information for the feasible design, practical operation, and optimization of FPW treatment.

Bioaccumulation and Bioremediation of Heavy Metals in Fishes-A Review

Heavy metals, the most potent contaminants of the environment, are discharged into the aquatic ecosystems through the effluents of several industries, resulting in serious aquatic pollution. This type of severe heavy metal contamination in aquaculture systems has attracted great attention throughout the world. These toxic heavy metals are transmitted into the food chain through their bioaccumulation in different tissues of aquatic species and have aroused serious public health concerns. Heavy metal toxicity negatively affects the growth, reproduction, and physiology of fish, which is threatening the sustainable development of the aquaculture sector. Recently, several techniques, such as adsorption, physio-biochemical, molecular, and phytoremediation mechanisms have been successfully applied to reduce the toxicants in the environment. Microorganisms, especially several bacterial species, play a key role in this bioremediation process. In this context, the present review summarizes the bioaccumulation of different heavy metals into fishes, their toxic effects, and possible bioremediation techniques to protect the fishes from heavy metal contamination. Additionally, this paper discusses existing strategies to bioremediate heavy metals from aquatic ecosystems and the scope of genetic and molecular approaches for the effective bioremediation of heavy metals.

Characterization and Biological Activities of Four Biotransformation Products of Diosgenin from Rhodococcus erythropolis

Diosgenin (DSG), a steroidal sapogenin derived from the tuberous roots of yam, possesses multiple biological properties. DSG has been widely used as a starting material for the industrial production of steroid drugs. Despite its significant pharmacological activities, moderate potency and low solubility hinder the medicinal application of DSG. Biotransformation is an efficient method to produce valuable derivatives of natural products. In this work, we performed the biotransformation of DSG using five Rhodococcus strains. Compounds 1–4 were isolated and identified from Rhodococcus erythropolis. Compounds 1 and 2 showed potent cytotoxicity against the A549, MCF-7, and HepG2 cell lines. Compounds 3 and 4 are novel entities, and each possesses a terminal carboxyl group attached to the spiroacetal ring. Remarkably, 4 exhibited significant cell protective effects for kidney, liver, and vascular endothelial cells, suggesting the therapeutic potential of this compound in chronic renal diseases, atherosclerosis, and hypertension. We further optimized the fermentation conditions aiming to increase the titer of compound 4. Finally, the yield of compound 4 was improved by 2.9-fold and reached 32.4 mg/L in the optimized conditions. Our study lays the foundation for further developing compound 4 as a cell protective agent.

The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests

Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.

Complete Genome Sequence of Rhodococcus sp. Strain 9, Isolated from Contaminated Australian Groundwater

Here, we report the 7.7-Mbp genome sequence of Rhodococcus sp. strain 9, which was isolated from Australian groundwater contaminated with phenols and trichloroethylene. This strain has previously been shown to efficiently degrade p-nitrophenol and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs).

Cage Bismuth Metal-Organic Framework Materials Based on a Flexible Triazine-Polycarboxylic Acid: Subgram Synthesis, Application for Sensing, and White Light Tuning

Bismuth-based metal-organic frameworks (MOFs) have always attracted the attention of many researchers. Here, we first report a crystalline Bi-MOF (Bi-TDPAT) based on a flexible triazine-polycarboxylic linker 2,4,6-tris(3,5-dicarboxylphenylamino)-1,3,5-triazine (H₆TDPAT) and bismuth nitrate; its crystallite quality is adequately good and the diffraction data can be collected directly by single crystal X-ray diffraction rather than 3D electron diffraction. The structure of Bi-TDPAT belongs to a novel topology type btt. Notably, the synthesis scale of Bi-TDPAT can be expanded, and sub-gram synthesis can be realized. At the same time, we synthesized a microcrystalline material Bi-TATAB utilizing 2,4,6-tris(4-carboxylphenylamino)-1,3,5-triazine (H₃TATAB). The structures of the two materials were characterized by several microanalysis tools. Considering that Bi-TDPAT is a blue light-emitting material with a broad emission peak, we prepared a white light emitting composite material Eu/Tb@Bi-TDPAT by encapsulating Eu(III)/Tb(III) in Bi-TDPAT. In addition, the fluorescence sensing functions of Bi-TDPAT and Bi-TATAB were explored. The results showed that they could detect and recognize various nitrophenols, and the optimal limit of detection is as low as 0.21 μM, which can be reused even after five cycles. Energy competitive absorption (CA) and photo-induced electron transfer are the main sensing mechanisms. By comparing and analyzing the properties of these two bismuth-based crystalline materials, we believe that this work also provides inspiration for the synthesis and development of bismuth-based MOF in the future.

“Unity and Struggle of Opposites” as a Basis for the Functioning of Synthetic Bacterial Immobilized Consortium That Continuously Degrades Organophosphorus Pesticides

This work was aimed at the development of an immobilized artificial consortium (IMAC) based on microorganisms belonging to the Gram-positive and Gram-negative bacterial cells capable of jointly carrying out the rapid and effective degradation of different organophosphorus pesticides (OPPs): paraoxon, parathion, methyl parathion, diazinon, chlorpyrifos, malathion, dimethoate, and demeton-S-methyl. A cryogel of poly(vinyl alcohol) was applied as a carrier for the IMAC. After a selection was made between several candidates of the genera Rhodococcus and Pseudomonas, the required combination of two cultures (P. esterophilus and R. ruber) was found. A further change in the ratio between the biomass of the cells inside the granules of IMAC, increasing the packing density of cells inside the same granules and decreasing the size of the granules with IMAC, gave a 225% improvement in the degradation activity of the cell combination. The increase in the velocity and the OPP degradation degree was 4.5 and 16 times greater than the individual P. esterophilus and R. ruber cells, respectively. Multiple uses of the obtained IMAC were demonstrated. The increase in IMAC lactonase activity confirmed the role of the cell quorum in the action efficiency of the synthetic biosystem. The co-inclusion of natural strains in a carrier during immobilization strengthened the IMAC activities without the genetic enhancement of the cells.

Biodegradation and Subsequent Toxicity Reduction of Co-contaminants Tribenuron Methyl and Metsulfuron Methyl by a Bacterial Consortium B2R

AllyMax is a widely used herbicide formulation in wheat-rice cropping areas of the world. The residues of its active ingredients, tribenuron methyl (TBM) and metsulfuron methyl (MET), persist in soil and water as co-contaminants, and cause serious threats to nontarget organisms. This study was performed to assess the potential of a bacterial consortium for the degradation and detoxification of TBM and MET individually and as co-contaminants. A bacterial consortium (B2R), comprising Bacillus cereus SU-1, Bacillus velezensis OS-2, and Rhodococcus rhodochrous AQ1, capable of degrading TBM and MET in liquid cultures was developed. Biodegradation of TBM and MET was optimized using the Taguchi design of experiment. Optimum degradation of both TBM and MET was obtained at pH 7 and 37 °C. Regarding media composition, optimum degradation of TBM and MET was obtained in minimal salt medium (MSM) supplemented with glucose, and MSM without glucose, respectively. The consortium simultaneously degraded TBM and MET (94.8 and 80.4%, respectively) in cultures containing the formulation AllyMax, where TBM and MET existed as co-contaminants at 2.5 mg/L each. Mass spectrometry analysis confirmed that during biodegradation, TBM and MET were metabolized into simpler compounds. Onion (Allium cepa) root inhibition and Comet assays revealed that the bacterial consortium B2R detoxified TBM and MET separately and as co-contaminants. The consortium B2R can potentially be used for the remediation of soil and water co-contaminated with TBM and MET.

Microbial Interventions in Bioremediation of Heavy Metal Contaminants in Agroecosystem

Soil naturally comprises heavy metals but due to the rapid industrialization and anthropogenic events such as uncontrolled use of agrochemicals their concentration is heightened up to a large extent across the world. Heavy metals are non-biodegradable and persistent in nature thereby disrupting the environment and causing huge health threats to humans. Exploiting microorganisms for the removal of heavy metal is a promising approach to combat these adverse consequences. The microbial remediation is very crucial to prevent the leaching of heavy metal or mobilization into the ecosystem, as well as to make heavy metal extraction simpler. In this scenario, technological breakthroughs in microbes-based heavy metals have pushed bioremediation as a promising alternative to standard approaches. So, to counteract the deleterious effects of these toxic metals, some microorganisms have evolved different mechanisms of detoxification. This review aims to scrutinize the routes that are responsible for the heavy metal(loid)s contamination of agricultural land, provides a vital assessment of microorganism bioremediation capability. We have summarized various processes of heavy metal bioremediation, such as biosorption, bioleaching, biomineralization, biotransformation, and intracellular accumulation, as well as the use of genetically modified microbes and immobilized microbial cells for heavy metal removal.

Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment

The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.

Iron carriers promote biofilm formation and p-nitrophenol degradation

Vertical baffled biofilm reactors (VBBR) equipped with Plastic-carriers and Fe-carriers were employed to explore the effect of biofilm carriers on biofilm formation and p-nitrophenol (PNP) degradation. The results showed that Fe-carriers enhanced biofilm formation and PNP degradation. The maximum thickness of biofilm grown on the Fe-carriers was 1.5-fold higher than that on the Plastic-carriers. The Fe-VBBR reached a maximum rate of PNP removal at 13.02 μM L^-1 h^-1 with less sodium acetate addition (3 mM), while the maximum rate of PNP removal was 11.53 μM L^-1 h^-1 with more sodium acetate addition (6 mM) in the Plastic-based VBBR. High-throughput sequencing suggested that the Fe-VBBR had a higher biodiversity of the bacterial community in evenness, and the Achromobacter genus and Xanthobacteraceae family were as main PNP degraders. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology analysis suggested more abundances of iron uptake genes were expressed to transport iron into the cytoplasm under an iron-limited condition in two VBBRs, and the metabolic pathway of PNP degradation went through 4-nitrocatechol and 1,2,4-benzenetriol. Our results provide a new insight for iron enhancing biofilm formation and PNP degradation.

Unique bacterial communities associated with components of an artificial aquarium ecosystem and their possible contributions to nutrient cycling in this microecosystem

In order to better understand the bacterial distribution characteristics in a whole microecosystem, the bacterial communities in different components of an artificial aquarium (i.e., plants, fishes, sand and water) were characterized using high throughput sequencing of bacterial 16S rRNA genes. Across all samples, 2873 operational taxonomic units were identified and assigned to 771 genera in 36 phyla. In a principle coordinate analysis, samples clustered according to their origin, indicating that bacterial communities from the same component were most similar. Further taxonomic analysis revealed that most dominant genera, even those with the similar functions, were biased to one component: Nitrospira and Rhodobacter were mainly abundant in plant samples; Rhodococcus, Serratia, Ralstonia, Sphingobacterium and Pseudomonas were most common in sand samples; Cetobacterium and Aeromonas dominated fish samples; and Flavobacterium, Alpinimonas and Limnobacter were especially common in water samples. Functional predictions performed by PICRUSt and the dominant genera exhibited that bacteria detected in each component could participate in all nutrient cycles in the aquarium. However, those involved in carbon and nitrogen cycling were most common in plant and fish samples, while phosphate metabolism-related pathways were more abundant in sand and water samples. Moreover, the aquarium plants, in association with their bacterial communities might be the most important component in the aquarium, as indicated by their highest bacterial richness and diversity. This study adds to our understanding on the differences in the microbiome of different components and their possible contributions to nutrient cycling in a self-sustaining aquarium.

Hierarchical ZIF-decorated nanoflower-covered 3-dimensional foam for enhanced catalytic reduction of nitrogen-containing contaminants

Metal Organic Frameworks (MOFs) represent a promising class of metallic catalysts for reduction of nitrogen-containing contaminants (NCCs), such as 4-nitrophenol (4-NP). Nevertheless, most researches involving MOFs for 4-NP reduction employ noble metals in the form of fine powders, making these powdered noble metal-based MOFs impractical and inconvenient for realistic applications. Thus, it would be critical to develop non-noble-metal MOFs which can be incorporated into macroscale and porous supports for convenient applications. Herein, the present study proposes to develop a composite material which combines advantageous features of macroscale/porous supports, and nanoscale functionality of MOFs. In particular, copper foam (CF) is selected as a macroscale porous medium, which is covered by nanoflower-structured CoO to increase surfaces for growing a cobaltic MOF, ZIF-67. The resultant composite comprises of CF covered by CoO nanoflowers decorated with ZIF-67 to form a hierarchical 3D-structured catalyst, enabling this ZIF-67@Cu foam (ZIF@CF) a promising catalyst for reducing 4-NP, and other NCCs. Thus, ZIF@CF can readily reduce 4-NP to 4-AP with a significantly lower E_a of 20 kJ/mol than reported values. ZIF@CF could be reused over 10 cycles and remain highly effective for 4-NP reduction. ZIF@CF also efficiently reduces other NCCs, such as 2-nitrophenol, 3-nitrophenol, methylene blue, and methyl orange. ZIF@CF can be adopted as catalytic filters to enable filtration-type reduction of NCCs by passing NCC solutions through ZIF@CF to promptly and conveniently reduce NCCs. The versatile and advantageous catalytic activity of ZIF@CF validates that ZIF@CF is a promising and practical heterogeneous catalyst for reductive treatments of NCCs.

Impact of electrical stimulation modes on the degradation of refractory phenolics and the analysis of microbial communities in an anaerobic-aerobic-coupled upflow bioelectrochemical reactor

An electrically stimulated anaerobic-aerobic coupled system was developed to improve the biodegradation of refractory phenolics. Expected 4-nitrophenol, 2, 4-dinitrophenol, and COD removals in the system with aerobic cathodic and anaerobic anodic chambers were approximately 53.7%, 45.4%, 22.3% (intermittent mode) and 37.9%, 19.8%, 17.3% (continuous mode) higher than that in the control system (26.0 ± 6.4%, 30.7 ± 7.1%, 49.8 ± 3.0%). 2, 4-dichlorophenol removal in the system with aerobic anodic and anaerobic cathodic chambers was approximately 28.5% higher than that in the control system (71.4 ± 5.7%). The contribution of the aerobic cathodic/anodic chambers to the removal of phenolic compounds was higher than that of the anaerobic cathodic/anodic chambers. The species related to phenolic biodegradation (Rhodococcus, Achromobacter, PSB-M-3, and Sphingobium) were enriched in the cathodic and anodic chambers of the system. These results showed that intermittent electrical stimulation could be a potential alternative for the efficient degradation of refractory phenolics.

Bioremediation process optimization and effective reclamation of mixed carbamate-contaminated soil by newly isolated Acremonium sp

Global pollution from excessive pesticide use has become a serious environmental and public health problem. The aim of the study was to optimize the fungal mediated simultaneous removal of carbofuran and carbaryl from soil. Carb-PV5 strain was isolated from contaminated soil following enrichment culture technique; based on 18S rRNA sequencing, strain was identified as Acremonium sp. (MK514615); Field Emission Scanning Electron Microscopic analysis reflected its morphology. Towards the development of bioaugmentation strategy for the bioremediation of carbamate-contaminated soil, the process parameters were optimized employing Central Composite Rotatable Method. The experimental studies were performed in the range of biomass (0.2-0.6 g kg^-1), temperature (23-33 °C), pH (6-9) and moisture (10-30%). The degradation rate parameters, k and t_1/2 were determined to as 0.475, 0.325 d^-1 and 5.39, 2.1 d with the corresponding r² of 0.9491, 0.9964 for zero and first order, respectively. The cube root growth kinetic constant k of Acremonium sp. varied from 0.0469 to 0.0512 (g^1/3 L^-1/3 h^-1) and 0.0378 to 0.0415 (g^1/3 L^-1/3 h^-1) for carbofuran and carbaryl, respectively. To confirm the model appropriacy and sustainability of the optimization procedure, bioremediation experiments were conducted onto real carbamate-contaminated soils. UPLC and GCMS analysis confirmed the successful removal of carbamates. The current study presents the first report on the bioaugmentation studies carried out on the mixed carbamate contaminated soil using newly isolated Acremonium sp.

Ultrasonically assisted synthesis of barium stannate incorporated graphitic carbon nitride nanocomposite and its analytical performance in electrochemical sensing of 4-nitrophenol

We describe the ultrasonic assisted preparation of barium stannate-graphitic carbon nitride nanocomposite (BSO-gCN) by a simple method and its application in electrochemical detection of 4-nitrophenol via electro-oxidation. A bath type ultrasonic cleaner with ultrasonic power and ultrasonic frequency of 100 W and 50 Hz, respectively, was used for the synthesis of BSO-gCN nanocomposite material. The prepared BSO-gCN nanocomposite was characterized by employing several spectroscopic and microscopic techniques such as X-ray diffraction, X-ray photoelectron spectroscopy, fourier transform infra-red, field emission scanning electron microscopy, and high resolution transmission electron microscopy, to unravel the structural and electronic features of the prepared nanocomposite. The BSO-gCN was drop-casted on a pre-treated glassy carbon electrode (GCE), and their sensor electrode was utilized for electrochemical sensing of 4-nitrophenol (4-NP). The BSO-gCN modified GCE exhibited better electrochemical sensing behavior than the bare GCE and other investigated electrodes. The electroanalytical parameters such as charge transfer coefficient (α = 0.5), the rate constant for electron transfer (k_s = 1.16 s^-1) and number of electron transferred were calculated. Linear sweep voltammetry (LSV) exhibited increase in peak current linearly with 4-NP concentration in the range between 1.6 and 50 μM. The lowest detection limit (LoD) was calculated to be 1 μM and sensitivity of 0.81 μA μM^-1 cm^-2_. A 100-fold excess of various ions, such as Ca²⁺, Na⁺, K⁺, Cl^-, I^-, CO₃^2-, NO₃, NH₄⁺ and SO₄^2- did not able to interfere with the determination of 4-NP and high sensitivity for detecting 4-NP in real samples was achieved. This newly developed BSO-gCN could be a potential candidate for electrochemical sensor applications.

An angular dioxygenase gene cluster responsible for the initial phenazine-1-carboxylic acid degradation step in Rhodococcus sp. WH99 can protect sensitive organisms from toxicity

A bacterial strain, Rhodococcus sp. WH99, capable of degrading phenazine-1-carboxylic acid (PCA) was isolated and characterized. Genome comparison revealed that a 21499-bp DNA fragment containing a putative angular dioxygenase gene cluster consisting of the dioxygenase-, ferredoxin reductase- and ferredoxin-encoding genes (pzcA1A2, pzcC and pzcD) is missed in the PCA degradation-deficient mutant WH99M. The pzcA1A2CD genes were expressed in Escherichia coli respectively and hydroxylation of PCA to 1,2-dihydroxyphenazine occurred in vitro only when all components were present. However, in vivo analyses showed that pzcA1A2 and pzcD were indispensable for PCA degradation, while PzcC can be partially replaced by other ferredoxin reductases. Hydroxylation of PCA not only initiates degradation of PCA in strain WH99 but also provides protection to sensitive organisms that would otherwise be inhibited by PCA toxicity. This study illustrates a new initial PCA degradation step in Gram-positive bacteria and enhances our understanding of the genes responsible for PCA hydroxylation, thus enabling targeted studies on protection by PCA degradation in diverse environments.

Adsorption and regeneration of leaf-based biochar for p-nitrophenol adsorption from aqueous solution

As an environmentally friendly and low-cost adsorbent, biochar has great potential in wastewater treatment. This study investigated biochar derived from Platanus orientalis L. leaves (PLB) activated by KOH in terms of its capacity and reusability to adsorb p-nitrophenol (PNP). PLB had a large specific surface area and total pore volume, and exhibits good PNP removal with a maximal adsorption capacity of 622.73 mg g-1 at 298 K. Batch experiments showed that PLB had a high PNP adsorption capacity under acidic conditions. Experimental results were well described by the pseudo-second-order kinetic model and the Langmuir adsorption isotherm model. The thermodynamic study showed that PNP adsorption was a spontaneously exothermic process, and increasing temperature was not conducive to adsorption. In addition, PNP adsorption was mainly attributed to hydrophobic interaction. The regeneration experiment showed that PLB had good reusability. After the fifth regeneration, the adsorption capacity of PLB still reached 557.05 mg g-1. The deactivation of oxygen-containing functional groups and pore blockage were the causes for the decrease in adsorption capacity of the recycled PLB. Moreover, the biochar showed good adsorption efficiency and reusability, thereby suggesting its potential to serve as an efficient PNP adsorbent for wastewater treatment.

Hazardous waste treatment technologies

This is a review of the literature published in 2018 on topics related to hazardous waste management in water, soils, sediments, and air. The review covers treatment technologies applying physical, chemical, and biological principles for contaminated water, soils, sediments, and air. PRACTITIONER POINTS: The management of waters, wastewaters, and soils contaminated by various hazardous chemicals including inorganic (e.g., oxyanions, salts, and heavy metals), organic (e.g., halogenated, pharmaceuticals and personal care products, pesticides, and persistent organic chemicals) was reviewed according to the technology applied, namely, physical, chemical and biological methods. Physical methods for the management of hazardous wastes including adsorption, coagulation (conventional and electrochemical), sand filtration, electrosorption (or CDI), electrodialysis, electrokinetics, membrane (RO, NF, MF), photocatalysis, photoelectrochemical oxidation, sonochemical, non-thermal plasma, supercritical fluid, electrochemical oxidation, and electrochemical reduction processes were reviewed. Chemical methods including ozone-based, hydrogen peroxide-based, persulfate-based, Fenton and Fenton-like, and potassium permanganate processes for the management of hazardous were reviewed. Biological methods such as aerobic, anaerobic, bioreactor, constructed wetlands, soil bioremediation and biofilter processes for the management of hazardous wastes, in mode of consortium and pure culture were reviewed.

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

Simultaneous p-nitrophenol and nitrogen removal in PNP wastewater treatment: Comparison of two integrated membrane-aerated bioreactor systems

The chemical p-nitrophenol (PNP) is a priority pollutant, and PNP wastewater is highly toxic and resistant to biodegradation. The traditional physical and chemical methods (adsorption, extraction, and oxidation) for treating PNP wastewater have the disadvantages of complicated processes, high costs and secondary pollution generation. In this study, two integrated membrane-aerated bioreactor systems (RA and RB) with anoxic and aerated zones were constructed to enhance PNP biodegradation. The results showed that a helical silicone rubber membrane module displayed a high oxygen supply rate under a low membrane aeration pressure, and the hydraulic flow state of the reactor approached ideal mixing. At an influent PNP concentration of 500 mg/L, the average removal rates of PNP, chemical oxygen demand (COD) and total nitrogen (TN) reached 95.86%, 89.77%, and 94.81%, respectively, for RA and 89.48%, 74.26% and 64.78%, respectively, for RB, indicating efficient simultaneous PNP and nitrogen removal. Compared with that of RB, the pre-anoxic zone in RA not only performed detoxification pretreatment but also enhanced PNP degradation and denitrification effects, which relieved the biological treatment burden of the subsequent aerated zone. Based on these comprehensive analyses of reactor performance, the hydroquinone pathway might be the main route in the aerobic degradation of PNP.

Effects of aeration on microbes and intestinal bacteria in bioaerosols from the BRT of an indoor wastewater treatment facility

The generation and emission of airborne bacteria from a biochemical reaction tank (BRT) for wastewater treatment was investigated by altering the aeration rate. The levels of bioaerosols increased from 715 ± 69 to 1597 ± 135 CFU/m³ (total airborne bacteria) and from 78 ± 6 to 359 ± 18 CFU/m³ (intestinal bacteria) as the aeration rate increased from 0.3 to 1.2 m³/h. Most airborne bacteria were attached to particles smaller than 4.7 μm at an aeration rate of 0.3 m³/h. They were found attached to larger particles (>4.7 μm) when the aeration rate increased to 1.2 m³/h. A similar phenomenon was observed for intestinal bacteria. The high-throughput sequencing technique was used to assay the microbial populations of the bioaerosols. Both microbial counts and diversity increased as the aeration rate increased. Brevundimonas (63.82%), Chryseobacterium (16.54%), and Micrococcaceae (12.37%) were the dominant intestinal bacteria at an aeration rate of 0.3 m³/h. Pseudochrobactrum (33.10%), Citrobacter (21.28%), and Yersinia (18.21%) were the dominant intestinal bacteria at an aeration rate of 1.2 m³/h. The level, particle size distribution, population structure, and diversity of the bioaerosols were all affected by aeration rate. The source tracker results indicated that water and the surrounding air were the two main bioaerosol sources. The contribution of water is greater at larger levels of aeration. Inhalation was the main pathway of microbial aerosol intake for people in the surrounding area. The exposure hazard quotients for adult males were generally higher than those for adult females. Necessary measures should be taken to ensure worker safety.

Crystal structure of hydroxyquinol 1,2-dioxygenase PnpC from Pseudomonas putida DLL-E4 and its role of N-terminal domain for catalysis

Hydroxyquinol 1,2-dioxygenase is a key enzyme in the hydroxyquinol pathway of p-nitrophenol (PNP) degradation, and catalyzes the ring cleavage of benzenetriol to maleylacetate. Here, we report the first structure of a hydroxyquinol 1,2-dioxygenase from the Gram-negative bacterium Pseudomonas putida DLL-E4 (PnpC) at the resolution of 2.1 Å. The tertiary structure of PnpC resembles that of the homologous intradiol dioxygenases. The catalytic Fe(III) is pentacoordinated by the conserved Tyr160, Tyr194, His218 and His220, the citrate anion and one water molecule. Among the residues expected to interact with the substrate, structural comparison with the (chloro)catechol dioxygenases suggested that Asp80, Thr81 and Val248 are responsible for the substrate specificity. Moreover, truncation of the N-terminal α-helix of PnpC suggested the N-terminal domain is required for its soluble expression and enzyme catalysis. Our results might provide insights in the substrate recognition and rational design of this enzyme class to be used in bioremediation.

Bioaugmented soil aquifer treatment for P-nitrophenol removal in wastewater unique for cold regions

P-nitrophenol (PNP) is a toxic and recalcitrant organic pollutant and a usual intermediate in the production of fine chemicals, which has posed a significant threat to subsurface environment safety. Soil aquifer treatment (SAT) is a promising method to remove and remediate contamination in vadose zone with low cost and high efficiency. However, there are still research gaps for the treatment of recalcitrant contaminants by SAT in cold regions, such as un-robust indigenous microbes and low temperature constraint in vadose zone. The bioaugmentation technology was first introduced into SAT in order to enhance the removal ability of PNP by SAT operated in cold regions in this study. A high-efficiency PNP-degrading bacterium was successfully isolated, which can efficiently degrade PNP below 200 mg L^-1 with a degradation rate above 99% at 15 °C close to the real subsurface temperature in cold regions, and added into SAT for bioaugmentation. The feasibility of bioaugmented SAT and associated PNP removal process were investigated by laboratory sand columns, along with effects of the SAT operative parameters (namely PNP loading concentration, flow rate and soil saturation level of SAT). Within the range of PNP loading stresses tested (1-200 mg L^-1), PNP removal efficiency was optimal at constant flow rate of 219 mL d^-1 in unsaturated operating condition of SAT under 15 °C among all the investigated experimental conditions. Longer hydraulic residence time increased the PNP removal rate, although the accumulated mass removed reduced and the removal efficiencies remained constant in unsaturated operating condition of SAT. It is found from the comparison between the PNP removals via both unsaturated and saturated columns that slight difference only in the removal rate of PNP was observed and the highly efficient bioaugmented SAT can completely degrade PNP of 10 mg L^-1 within 5 wetting/drying cycles under both scenarios.

Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4: The key enzyme involved in p-nitrophenol degradation

p-Nitrophenol 4-monooxygenase PnpA, the key enzyme in the hydroquinone pathway of p-nitrophenol (PNP) degradation, catalyzes the monooxygenase reaction of PNP to p-benzoquinone in the presence of FAD and NADH. Here, we determined the first crystal structure of PnpA from Pseudomonas putida DLL-E4 in its apo and FAD-complex forms to a resolution of 2.04 Å and 2.48 Å, respectively. The PnpA structure shares a common fold with hydroxybenzoate hydroxylases, despite a low amino sequence identity of 14-18%, confirming it to be a member of the Class A flavoprotein monooxygenases. However, substrate docking studies of PnpA indicated that the residues stabilizing the substrate in an orientation suitable for catalysis are not observed in other homologous hydroxybenzoate hydroxylases, suggesting PnpA employs a unique catalytic mechanism. This work expands our understanding on the reaction mode for this enzyme class.