Bioremediation Of Organic Pollutants Research Articles

Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa

Trametes villosa is a remarkable white-rot fungus (WRF) with the potential to be applied in lignocellulose conversion to obtain chemical compounds and biofuels. Lignocellulose breakdown by WRF is carried out through the secretion of oxidative and hydrolytic enzymes. Despite the existing knowledge about this process, the complete molecular mechanisms involved in the regulation of this metabolic system have not yet been elucidated. Therefore, in order to understand the genes and metabolic pathways regulated during lignocellulose degradation, the strain T. villosa CCMB561 was cultured in media with different carbon sources (lignin, sugarcane bagasse, and malt extract). Subsequently, biochemical assays and differential gene expression analysis by qPCR and high-throughput RNA sequencing were carried out. Our results revealed the ability of T. villosa CCMB561 to grow on lignin (AL medium) as the unique carbon source. An overexpression of Cytochrome P450 was detected in this medium, which may be associated with the lignin O-demethylation pathway. Clusters of up-regulated CAZymes-encoding genes were identified in lignin and sugarcane bagasse, revealing that T. villosa CCMB561 acts simultaneously in the depolymerization of lignin, cellulose, hemicellulose, and pectin. Furthermore, genes encoding nitroreductases and homogentisate-1,2-dioxygenase that act in the degradation of organic pollutants were up-regulated in the lignin medium. Altogether, these findings provide new insights into the mechanisms of lignocellulose degradation by T. villosa and confirm the ability of this fungal species to be applied in biorefineries and in the bioremediation of organic pollutants.

The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads.

Microbial cell surface hydrophobicity (CSH) reflects nonspecific adhesion ability and affects various physiological processes, such as biofilm formation and pollutant biodegradation. Understanding the regulation mechanisms of CSH will contribute to illuminating microbial adaptation strategies and provide guidance for controlling CSH artificially to benefit humans. Sphingomonads, a common bacterial group with great xenobiotic-degrading ability, generally show higher CSH than typical Gram-negative bacteria, which plays a positive role in organic pollutant capture and cell colonization. This study verified that the variations of two native plasmids involved in synthesizing outer membrane proteins and polysaccharides greatly affected the CSH of sphingomonads. It is feasible to control their CSH by changing the plasmid copy number and sequences. Additionally, considering that plasmids are likely to evolve faster than chromosomes, the CSH of sphingomonads may evolve quickly to respond to environmental changes. Our results provide valuable insights into the CSH regulation and evolution of sphingomonads.

Metagenomic analysis reveals the distribution, function, and bacterial hosts of degradation genes in activated sludge from industrial wastewater treatment plants

For comprehensive insights into the bacterial community and its functions during industrial wastewater treatment, with a particular emphasis on its pivotal role in the bioremediation of organic pollutants, this study utilized municipal samples as a control group for metagenomic analysis. This approach allowed us to investigate the distribution, function, and bacterial hosts of biodegradation genes (BDGs) and organic degradation genes (ODGs), as well as the dynamics of bacterial communities during the industrial wastewater bioprocess. The results revealed that BDGs and ODGs associated with the degradation of benzoates, biphenyls, triazines, nitrotoluenes, and chlorinated aromatics were notably more abundant in the industrial samples. Specially, genes like clcD, linC, catE, pcaD, hbaB, hcrC, and badK, involved in the peripheral pathways for the catabolism of aromatic compounds, benzoate transport, and central aromatic intermediates, showed a significantly higher abundance of industrial activated sludge (AS) than municipal AS. Additionally, the BDG/ODG co-occurrence contigs in industrial samples exhibited a higher diversity in terms of degradation gene carrying capacity. Functional analysis of Clusters of Orthologous Groups (COGs) indicated that the primary function of bacterial communities in industrial AS was associated with the category of “metabolism”. Furthermore, the presence of organic pollutants in industrial wastewater induced alterations in the bacterial community, particularly impacting the abundance of key hosts harboring BDGs and ODGs (e.g. Bradyrhizobium, Hydrogenophaga, and Mesorhizobium). The specific hosts of BDG/ODG could explain the distribution characteristics of degradation genes. For example, the prevalence of the Adh1 gene, primarily associated with Mesorhizobium, was notably more prevalent in the industrial AS. Overall, this study provides valuable insights into the development of more effective strategies for the industrial wastewater treatment and the mitigation of organic pollutant contamination.

The Role of Peroxidases in the Bioremediation of Organic Pollutants

The emergence of organic pollutants such as phenolic acids, pesticides, dyes, petrochemicals, pharmaceuticals, and industrial wastes threatens our environment, including biodiversity, ecosystems of terrestrial and aquatic animals, and human health. It is well known that toxicants disrupt the biochemical balance of organisms and cause physiological effects in individuals. Emerging Organic Pollutants (OPs) have varied levels of lethality depending on their chemical nature and byproducts, properties and composition of the compound fractions, mode of exposure, levels of exposure, and time of exposure. Accordingly, risk mitigation measures should be taken with constant environmental changes. The peroxidases are groups of heme-proteins, which at present are considered the most efficient biocatalysts for the bioremediation of the environment. To overcome the numerous disadvantages of conventional biological remediation methods, peroxidases require a more thorough interpretation for broadly understanding their potential uses in organic transformations as an efficient biocatalyst. Peroxidases are susceptible to the breakdown of polyaromatic hydrocarbons, dyes, pharmaceutical compounds, agrochemicals, phenols, and other highly hazardous organic pollutants found in industrial effluents. In this review, we focus on recent advances in the applications and the efficiency of peroxidases as eco-friendly catalysts.

Coupling phenol bioremediation and biodiesel production by Tetradesmus obliquus: Optimization of phenol removal, biomass productivity and lipid content

There is a growing interest for the utilization of microalgae in the bioremediation of organic pollutants and the use of biomass as a biofuel feedstock. This study investigated the influence of phenol exposure and culture conditions on the phenol removal efficiency, biomass productivity and lipid contents of Tetradesmus obliquus. Plackett-Burman design identified CaCl2, NaNO3, and initial phenol concentration as the most important variables affecting on phenol removal. The optimum conditions to maximize biomass productivity, phenol removal and lipid content were determined using the Box-Behnken experimental design as 150.1 mg L−1 phenol, 0.1 g L−1 NaNO3, and 0.03 g L−1 CaCl2. Under these conditions, phenol was completely removed from the optimized medium after 3 days and the biomass productivity and lipid content were 19.53 mg L−1 day−1 and 27.85% (w/w) after 10 days, respectively. Phenol treatment promoted algal biomass productivity to ∼1.3-folds and lipid productivity to ∼ 1.6-folds higher than the control treatment without adding phenol (negative control). Additionally, phenol altered the fatty acid methyl ester composition and increased the saturated and polyunsaturated fatty acid contents with concomitant decrease in the monounsaturated fatty acids. The predicted biodiesel characteristics viz. iodine value, cetane number, oxidation stability, kinematic viscosity, and flash point, in the presence of phenol were in accordance with the international standards. Accordingly, the present study indicated that phenol could be effectively bioremediated by T. obliquus with simultaneous promotion of the algal biomass and lipid productivity for biofuel production.

Factors Influencing the Bioavailability of Organic Molecules to Bacterial Cells-A Mini-Review.

The bioavailability of organic compounds to bacterial cells is crucial for their vital activities. This includes both compounds that are desirable to the cells (e.g., sources of energy, carbon, nitrogen, and other nutrients) and undesirable compounds that are toxic to the cells. For this reason, bioavailability is an issue of great importance in many areas of human activity that are related to bacteria, e.g., biotechnological production, bioremediation of organic pollutants, and the use of antibiotics. This article proposes a classification of factors determining bioavailability, dividing them into factors at the physicochemical level (i.e., those related to the solubility of a chemical compound and its transport in aqueous solution) and factors at the microbiological level (i.e., those related to adsorption on the cell surface and those related to transport into the cell). Awareness of the importance of and the mechanisms governing each of the factors described allows their use to change bioavailability in the desired direction.

Bioremediation of organic pollutants: a mini review on current and critical strategies for wastewater treatment

The release and prevalence of organic pollutants in an aqueous environment due to industrial discharges, agricultural operations, or inappropriate waste disposal is a huge threat to attaining sustainable development. As a result, wastewater treatment has attained a huge scope as it is evident from the number of articles published in recent years. Among the various techniques, bioremediation is one of the economical and eco-friendly means of wastewater treatment for the removal of organic pollutants. Microbial community and microalgae are the front runners of this process as they result in treated water and sludge or biomass formation. This mini review put forwards the types of organic pollutants and the bioremediation strategies using microbes and micro-algae, the role of genetically engineered microbes on the bio-remediation of organic pollutants and the recent applications of Artificial Intelligence (AI) techniques that have been implemented for improving the efficiency of the methods. The gap between practicability and applicability of the bioremediation process was also identified in this review. In addition, the economics and future research needs are discussed as outcomes.

Nocardioides humilatus sp. nov., isolated from farmland soil in the Republic of Korea.

A Gram-stain positive, aerobic, irregularly rod-shaped, non-spore-forming bacterium, designated as BN130099T, was isolated from farmland soil sampled in Goesan-gun, Chungbuk, Republic of Korea. Phylogenetic analysis of its 16S rRNA gene sequence showed that the strain is closely related to Nocardioides pelophilus KACC 19192T with 98.11 % similarity. The DNA G+C content of strain BN130099T was 68.84 mol% (draft genome sequence). The genome sequence of BN130099T displayed key enzymes involved in bioremediation of organic pollutants and biosynthetic clusters of saquayamycin. The strain contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as the major respiratory quinone. The predominant fatty acid was iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The results of physiological and biochemical characterization allowed the phenotypic differentiation of strain BN130099T from N. pelophilus KACC 19192T. The strain represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides humilatus sp. nov. The type strain is BN130099T (=KCTC 49079T=CCTCC AB 2018135T).

Dual‐Propelled Sporopollenin‐Exine‐Capsule Micromotors for Near‐Infrared Light Triggered Degradation of Organic Pollutants

AbstractTowards on‐site degradation of organic pollutants, dual‐propelled sporopollenin‐exine‐capsule (SEC) micromotors loaded with horseradish peroxidase (HRP) have been developed. The magnetic propulsion of SEC micromotors enables them to follow predesignated paths to arrive the pollution site, while the chemical propulsion on the site accelerates the degradation process taking advantage of the fluid mixing effect induced by their movement and bubble generation. Near‐infrared (NIR) light is employed to trigger the rupture of the magnetic polydopamine (PDA) outer coating and release the platinum‐coated SECs loaded with HRP enzyme. The dual propulsion system combined with the biocompatible nature of the components paves the way for on‐site bioremediation of organic pollutants.

Nocardioides antri sp. nov., Isolated from Soil in a Rock Cave.

A Gram-positive, aerobic, rod-shaped, non-spore-forming bacterium, designated as BN140041T, was isolated from cave soil at Gubyeongsan Mountain, Boeun-gun, Chungbuk province in Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides silvaticus S-34T, N. pelophilus THG-T63T, and N. immobilis FLL521T with 97.4%, 97.1%, and 96.8% similarity. The draft genome length was 4.27Mb containing 424 contigs with a DNA G + C content of 70.5mol%. The ANI value between strain BN140044T and its closely related species N. silvaticus S-34T was 82.6%. The genome sequence of BN140041T displayed a key enzyme involved in the bioremediation of organic pollutants. The diagnostic diamino acid of peptidoglycan was LL-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the major fatty acids (> 5% of the total fatty acids) were iso-C16:0 (55.3%), C18:1ω9c (7.7%) and iso-C17:0 (5.7%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol. The results of genotypical, physiological, and biochemical characterization allow the phenotypic differentiation of strain BN140041T from related the Nocardioides strains. Therefore, strain BN140041T represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides antri sp. nov. The type strain is BN140041T (= KCTC 49080T = CCTCC AB 2018226T).

Insights into Advancements and Electrons Transfer Mechanisms of Electrogens in Benthic Microbial Fuel Cells.

Benthic microbial fuel cells (BMFCs) are a kind of microbial fuel cell (MFC), distinguished by the absence of a membrane. BMFCs are an ecofriendly technology with a prominent role in renewable energy harvesting and the bioremediation of organic pollutants through electrogens. Electrogens act as catalysts to increase the rate of reaction in the anodic chamber, acting in electrons transfer to the cathode. This electron transfer towards the anode can either be direct or indirect using exoelectrogens by oxidizing organic matter. The performance of a BMFC also varies with the types of substrates used, which may be sugar molasses, sucrose, rice paddy, etc. This review presents insights into the use of BMFCs for the bioremediation of pollutants and for renewable energy production via different electron pathways.

Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil

Bioremediation of organic pollutants has been identified as an economically efficient and environmentally friendly method. Here, a pot experiment was conducted to evaluate the bioremediation efficiency of dibutyl phthalate (DBP) by Gordonia phthalatica sp. nov. QH-11 in agricultural soils, along with the effect of this exogenous organism on the native microbial community and ecosystem functions during the bioremediation process. The results showed that inoculation with strain QH-11 accelerated DBP degradation in the soil and decreased DBP accumulation in plants, thereby reducing the health risks associated with vegetables grown in those soils. High-throughput sequencing demonstrated that both DBP contamination and the bioremediation process significantly altered prokaryotic community composition, structure, and network interactions; however, these effects were greatly reduced after 30 d. Dibutyl phthalate affected the prokaryotic community by influencing soil properties rather than directly impacting on microorganisms. In addition, ecosystem functions, like the nitrogen cycle, were significantly altered. Contamination with DBP promoted nitrogen fixation and the denitrification processes while inhibiting nitrification. Bioremediation may mitigate some of the changes to nitrogen cycling, helping to maintain the balance of prokaryotic community function. According to this study, bioremediation through highly efficient degradation bacteria may be a safe and promising method for reducing PAEs contamination in soil-vegetable systems.

Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil

Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm−3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.

Cytoplasmic Localization of Sulfide:Quinone Oxidoreductase and Persulfide Dioxygenase of Cupriavidus pinatubonensis JMP134.

Heterotrophic bacteria have recently been reported to oxidize sulfide to sulfite and thiosulfate by using sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO). In chemolithotrophic bacteria, both SQR and PDO have been reported to function in the periplasmic space, with SQR as a peripheral membrane protein whose C terminus inserts into the cytoplasmic membrane and PDO as a soluble protein. Cupriavidus pinatubonensis JMP134, best known for its ability to degrade 2,4-dichlorophenoxyacetic acid and other aromatic pollutants, has a gene cluster of sqr and pdo encoding C. pinatubonensis SQR (CpSQR) and CpPDO2. When cloned in Escherichia coli, the enzymes are functional. Here we investigated whether they function in the periplasmic space or in the cytoplasm in heterotrophic bacteria. By using sequence analysis, biochemical detection, and green fluorescent protein (GFP)/PhoA fusion proteins, we found that CpSQR was located on the cytoplasmic side of the membrane and CpPDO2 was a soluble protein in the cytoplasm with a tendency to be peripherally located near the membrane. The location proximity of these proteins near the membrane in the cytoplasm may facilitate sulfide oxidation in heterotrophic bacteria. The information may guide the use of heterotrophic bacteria in bioremediation of organic pollutants as well as H2S.IMPORTANCE Sulfide (H2S, HS-, and S2-), which is common in natural gas and wastewater, causes a serious malodor at low levels and is deadly at high levels. Microbial oxidation of sulfide is a valid bioremediation method, in which chemolithotrophic bacteria that use sulfide as the energy source are often used to remove sulfide. Heterotrophic bacteria with SQR and PDO have recently been reported to oxidize sulfide to sulfite and thiosulfate. Cupriavidus pinatubonensis JMP134 has been extensively characterized for its ability to degrade organic pollutants, and it also contains SQR and PDO. This paper shows the localization of SQR and PDO inside the cytoplasm in the vicinity of the membrane. The information may provide guidance for using heterotrophic bacteria in sulfide bioremediation.

Analytical study of effective biodegradation of p-cresol using Serratia marcescens ABHI001: application in bioremediation.

This study evaluated the capability of Serratia marcescens ABHI001 to effectively degrade p-cresol through different techniques. The molecular identity of the laboratory isolate S. marcescens ABHI001 was confirmed through the 16S ribosomal DNA gene pattern, and its morphological features were investigated through field-emission scanning electron microscopy. In addition, the degradation behavior of the isolate for cresol was verified using several techniques, including UV-visible spectroscopy, followed by high-performance liquid chromatography (HPLC), gas chromatography, and Fourier transform infrared spectroscopy. The maximum degradation percentage of 85% for p-cresol could be achieved after 18h of incubation with S. marcescens ABHI001. The formation of p-hydroxybenzaldehyde, p-hydroxybenzoate, and protocatechuate metabolites was confirmed through HPLC. The study results indicate that S. marcescens ABHI001 may have applications in the bioremediation of organic pollutants, such as p-cresol.

Ligninolytic Activity of White Rot Fungi from GGV campus as Bioremediation of Organic Pollutants

White rot fungi constitute a diverse physiological group are capable of transforming and mineralizing a wide range of organopollutants. The Ligninolytic enzymes of white rot fungi are substrate specific, essential for Lignin degradation and organic pollutant remediation. In the present study white rot fungi were collected from the north region of Chhattisgarh of Guru Ghasidas Vishwavidyalaya (GGV) Campus. 40 species were collected and isolated then Qualitative and Quantitative screening for the Ligninolytic enzyme assaywere carried out. Out of 40 species, 5 species show potent Ligninolytic activity. In future we can utilize these fungi for the degradation of organic pollutants.

The effect of anthracene on total dry matter and extracellular enzyme analysis of a starch-amended composting process

ABSTRACTComposting technology has been widely used as a cost-effective, eco-friendly, and efficient solid waste management option for the bioremediation of organic pollutants. Most studies have focused on the use of compost in the bioremediation of organic pollutants, without any attention being paid to the effect of the organic pollutants on the composting process. Therefore, in this study, the effect of an organic pollutant (anthracene) on a starch-amended composting process is reported. In order to determine the effect, the total dry matter and the extracellular enzyme analysis (EEA) of starch-specific (α-glucosidase) and -nonspecific (β-glucosidase) substrates were monitored. Over the course of the experiments, there appeared to be some form of anthracene effect on the progression in the total dry matter and the extracellular enzyme analysis (EEA) of the α-glucosidase, particularly in the starch and anthracene–amended composts. The interactions between the starch and the anthracene consistently increased the total dry matter and the α-glucosidase activity of the starch and anthracene–amended composts. This observation is novel, and the kind of interaction is yet unknown. Therefore, detailed investigation to understand the magnitude of such interaction is necessary to potentially resolve these issues.

Yeast Extract as the Most Preferable Substrate for Optimized Biosurfactant Production by rhlB Gene Positive Pseudomonas putida SOL-10 Isolate

Oil contaminated sites are enriched source of microorganisms that produce a variety of surface active amphiphilic compounds known as biosurfactants. Pseudomonas putida SOL-10 strain isolated from oil contaminated soil of Fimkassar oil field, Chakwal, Pakistan, was identified by standard morphological, biochemical and 16S rRNA sequence analysis methods. SOL-10 strain was initially screened for biosurfactant production using oil spreading test and then manifestation of rhlB (rhamnolipid) gene was confirmed by PCR using gene-specific primers. Maximum biosurfactant production in terms of surface tension (29.9 mN m-1) and emulsification index (E24, 73.45%), was achieved when the strain was grown in MSM supplemented with yeast extract (1.5-2 %, w/v) and urea (0.1 %, w/v) as carbon and nitrogen sources, respectively, and the physical parameters were adjusted at pH 7.0, temperature 30°C, 150 rpm agitation speed. The biosurfactant emulsified various hydrocarbons tested, being more effective against xylene and kerosene (85.19% and 70.59%, respectively). The crude biosurfactant also showed stability at a wide range of temperature (25-80°C), pH (1-9) and salt concentration (1-5%, w/v). The stability and hydrocarbon emulsifying potential of the biosurfactant indicated its possible use as decent contender for future environmental applications like biodegradation and bioremediation of organic pollutants.

Kinetic Modelling of Phenol Oxidation in a Bioremediation Medium Using Fenton's Reagent

The present study is aimed at kinetic modeling of phenol oxidation using Fenton’s reagent in a medium suitable for bioremediation of organic pollutants. Batch experiments were conducted to study the effects of H2O2 concentration (29.26 to 146.31 mM), temperature (5 to 35°C), and to compare the oxidation of phenol in a bioremediation medium to that in pure water. The reaction mechanism used for kinetic modeling is based on the intermediate oxidation products identified in this study using LC-MS and ion chromatography. Progress of the chemical oxidation by Fenton’s reagent was monitored by determining the residual phenol concentration and concentrations of evolved intermediate compounds (catechol and hydroquinone) at regular time intervals. The rate of phenol oxidation and ultimate conversion of phenol were found to increase with increase in hydrogen peroxide concentration. The increase in temperatures has a positive effect on phenol oxidation and the rate of phenol oxidation was found to increase with temperature in the range of 5-35°C. Kinetic parameters, namely rate constants and activation energies for reactions involved, were determined by best-fitting the experimental data to the proposed reaction model. The values of the rate constants for oxidation of phenol and intermediate compounds, k1 (phenol to catechol), k2 (phenol to hydroquinone), k3 (catechol to maleic acid), k4 (hydroquinone to maleic acid) at 25°C were found to be 7.02x10-5±4.63x10-5, 7.22x10-4±6.09x10-4, 1.82x10-4±1.08x10-4, 1.68x10-3±1.29x10-3 L/mM min, respectively.

Bioavailable cadmium during the bioremediation of phenanthrene-contaminated soils using the diffusive gradients in thin-film technique

To study the impact of fungal bioremediation of phenanthrene on trace cadmium solid-solution fluxes and solution phase concentration. The bioremediation of phenanthrene in soils was performed using the fungus Penicillium frequentans. Metal behaviour was evaluated by the techniques of diffusive gradient in thin-films (DGT) and filtration. Fluxes of cadmium (Cd) show a significant (P < 0.002) increase after the start of bioremediation, indicating that the bioremediation process itself releases significant amount of Cd into solution from the soil solid-phase. Unlike DGT devices, the solution concentration from filtration shows a clear bimodal distribution. We postulate that the initial action of the fungi is most likely to breakdown the surface of the solid phase to smaller, 'solution-phase' material (<0.45 microm) leading to a peak in Cd concentration in solution. Phenanthrene removal from soils by bioremediation ironically results in the mobilization of another toxic pollutant (Cd). Bioremediation of organic pollutants in contaminated soil will likely lead to large increases in the mobilization of toxic metals, increasing metal bio-uptake and incorporation into the wider food chain. Bioremediation strategies need to account for this behaviour and further research is required both to understand the generality of this behaviour and the operative mechanisms.