Showing papers on "Microbial biodegradation published in 2019"
TL;DR: This study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils, and concludes that plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level.
Abstract: Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.
67 citations
TL;DR: In this review, the genes involved in the biodegrading of hydrocarbons and several emerging plasticizer compounds in Rhodococcus strains are described in detail and the metabolic biodegradation networks predicted from omics-derived data along with the catabolic enzymes exploited in diverse biotechnological and bioremediation applications are characterized.
Abstract: The past few years observed a breakthrough of genome sequences of bacteria of Rhodococcus genus with significant biodegradation abilities. Invaluable knowledge from genome data and their functional analysis can be applied to develop and design strategies for attenuating damages caused by hydrocarbon contamination. With the advent of high-throughput -omic technologies, it is currently possible to utilize the functional properties of diverse catabolic genes, analyze an entire system at the level of molecule (DNA, RNA, protein, and metabolite), simultaneously predict and construct catabolic degradation pathways. In this review, the genes involved in the biodegradation of hydrocarbons and several emerging plasticizer compounds in Rhodococcus strains are described in detail (aliphatic, aromatics, PAH, phthalate, polyethylene, and polyisoprene). The metabolic biodegradation networks predicted from omics-derived data along with the catabolic enzymes exploited in diverse biotechnological and bioremediation applications are characterized.
51 citations
TL;DR: The results suggest that these plant species are particularly efficient in increasing soil PCB bioavailability and in stimulating microbial degradation and could be used in field rhizoremediation strategies to enhance the natural attenuation process and reduce PCB levels in historically contaminated sites.
48 citations
TL;DR: 13C isotope fractionations of CH4 and CO2 in biogas and microbial community composition were analyzed in 5 different feedstocks and it showed that grass silage, maize silage and swine manure fed reactors had similar δ 13C values and methanogenic community composition, dominated by Methanosarcinaceae.
46 citations
TL;DR: In aged seawater that was presumably depleted of labile dissolved organic carbon and inorganic P, alkaline phosphatase activities significantly decreased when OPEs were added, indicating a relief on P stress, consistent with the role of O PEs as potential P sources.
Abstract: The anthropogenic perturbation of the phosphorus (P) marine biogeochemical cycle due to synthetic organophosphorus compounds remains unexplored. The objective of this work was to investigate the microbial degradation of organophosphate triesters (OPEs), widely used as plasticizers and flame retardants, in seawater and their effects on the physiology and composition of microbial communities. Experiments were performed in July 2014 using surface seawater from the Blanes Bay Microbial Observatory (NW Mediterranean) to which OPEs were added at environmentally relevant concentrations. The concentrations of OPEs in the dissolved-phase generally decreased after 24 hours of incubation at in situ conditions. The fitted first order reaction constants were significantly different than zero for the trihaloalkyl phosphate, tris(2-chloroethyl) phosphate and trialyl phosphate tricresyl phosphate. In general, OPEs triggered an increase of the percentage of actively respiring bacteria, total bacterial activity, and the number of low-nucleic acid bacteria, and a decrease in the percentage of membrane-compromised bacteria. Members of some bacterial groups, in particular Flavobacteria, increased their specific activity, indicating that seawater contains bacteria with the potential to degrade OPEs. In aged seawater that was presumably depleted of labile dissolved organic carbon and inorganic P, alkaline phosphatase activities significantly decreased when OPEs were added, indicating a relief on P stress, consistent with the role of OPEs as potential P sources.
43 citations
TL;DR: The result demonstrated that more toxic products may be produced during the biodegradation processes of OPs, and more attention should be put not only on the pesticides themselves, but also on the toxic effects of their degradation products.
Abstract: Farmland soil sprayed with organophosphorus pesticides (OPs) annually was investigated for the identification and characterization of OP-degrading microorganisms. Six bacterial strains were identified, including Brevundimonas faecalis MA-B12 and Alcaligenes faecalis subsp. parafaecalis MA-B13 for methamidophos degradation, Citrobacter freundii TF-B21 and Ochrobactrum intermedium TF-B23 for trichlorfon degradation, Ochrobactrum intermedium DV-B31 for dichlorvos degradation, and Bacillus cereus for dimethoate degradation. The optimal biodegradation conditions for OPs were obtained at pH 7.0 and incubation temperature ranging from 28 to 37 °C. In an 8-day batch test, biodegradation of the four OPs all followed first-order kinetics, with biodegradation rates ranging from 58.08 to 96.42%. Functional genes responsible for OPs degradation were obtained, including ophB, ampA, opdE, opd, opdA, and mpd. As these strains were indigenous strains isolated from farmland soils, they can be potentially used as bacterial consortium for the bioremediation of mixed OP-contaminated soils. A time-course genotoxicity assessment of the degradation products was done by a bacterial whole-cell bioreporter, revealing that biodegradation of trichlorfon, dichlorvos, and dimethoate resulted a decreased genotoxicity within 5 days, which, however, significantly increased on day 8. The result demonstrated that more toxic products may be produced during the biodegradation processes of OPs, and more attention should be put not only on the pesticides themselves, but also on the toxic effects of their degradation products. To the best of our knowledge, this is for the first time that the genotoxicity of OP degradation products was evaluated by the bioreporter assay, broadening our understanding on the genotoxic risks of OPs during biodegradation process. Graphical Abstract.
40 citations
01 Jan 2019
TL;DR: This chapter focuses on the metabolic steps and enzymes involved in the degradation pathway of aromatic compounds that are used in cosmetics, pharmaceuticals, pesticides, and in day-to-day household products.
Abstract: Industries are one of the major sources and contributors to the pollution of the environment. The industrial effluents and runoff water from the agriculture fields contain diverse organic and xenobiotic compounds. The usage of aromatics, plasticizers, and pesticides in day-to-day life in cosmetic products, edible fruits, vegetables, etc. are one of the major concerns because of their commercial usage and recognized as potential threats posed to human health and ecosystem. These compounds are toxic, and acts as endocrine disrupter, mutagen, and/or carcinogen. Bioremediation involves the use of microbes and is considered to be the most efficient, cost-effective, and eco-friendly process to remove/eliminate them. Microorganisms produce a battery of enzymes that catalyze the conversion of these pollutants into innocuous products, which can further be metabolized completely. This chapter focuses on the metabolic steps and enzymes involved in the degradation pathway of aromatic compounds that are used in cosmetics, pharmaceuticals, pesticides, and in day-to-day household products.
40 citations
TL;DR: In this paper, the authors investigated the degradation of polyacrylamide by single microbial species as well as mixed populations and suggested some hypothetical pathways for the bacterial degradation, although enzymology of bacterial degradation is largely unknown.
40 citations
TL;DR: In this article, the role of plants and microbes in the microbial degradation of petroleum hydrocarbons in contaminated soil is discussed and some important factors necessary for development of in situ bioremediation strategies for risks mitigation in petroleum hydrocarbon-contaminated soil.
Abstract: Petroleum hydrocarbons contamination of soil, sediments and marine environment associated with the inadvertent discharges of petroleum–derived chemical wastes and petroleum hydrocarbons associated with spillage and other sources into the environment often pose harmful effects on human health and the natural environment, and have negative socio–economic impacts in the oil–producing host communities. In practice, plants and microbes have played a major role in microbial transformation and growth–linked mineralization of petroleum hydrocarbons in contaminated soils and/or sediments over the past years. Bioremediation strategies has been recognized as an environmental friendly and cost–effective alternative in comparison with the traditional physico-chemical approaches for the restoration and reclamation of contaminated sites. The success of any plant–based remediation strategy depends on the interaction of plants with rhizospheric microbial populations in the surrounding soil medium and the organic contaminant. Effective understanding of the fate and behaviour of organic contaminants in the soil can help determine the persistence of the contaminant in the terrestrial environment, promote the success of any bioremediation approach and help develop a high–level of risks mitigation strategies. In this review paper, we provide a clear insight into the role of plants and microbes in the microbial degradation of petroleum hydrocarbons in contaminated soil that have emerged from the growing body of bioremediation research and its applications in practice. In addition, plant–microbe interactions have been discussed with respect to biodegradation of petroleum hydrocarbons and these could provide a better understanding of some important factors necessary for development of in situ bioremediation strategies for risks mitigation in petroleum hydrocarbon–contaminated soil.
39 citations
TL;DR: In this article, a review of microbial degradation of high molecular weight polycyclic aromatic hydrocarbons by pure and mixed culture, including biological aspects of biosurfactants produced during the process for increasing the bioavailability of soil-sorbed or non-aqueous phase pyrene is presented.
37 citations
TL;DR: In this paper, a rice paddy-planted microbial fuel cell with a blue-green algal cathode was designed, which achieved a maximum power density of 29.78mW/m3 and a current density of 610 mA/m 3 during the light phase and 399mV in the dark phase.
Abstract: Microbial fuel cells are used as an alternative source of energy and for microbial degradation of waste and pollutants. Different types of microbial fuel cells include sediment microbial fuel cells, waste treatment microbial fuel cells, constructed wetland microbial fuel cells and plant microbial fuel cells. Plant microbial fuel cells use plant–microbe relationships for producing bioelectricity. For this cell, the development of efficient, low-cost cathode is a key challenge. Here, a plant microbial fuel cell using algal-assisted cathode was designed. This cell uses rhizodeposits of plants as carbon source in the anode chamber and photosynthesis of algae to generate the oxygen that acts as a terminal electron acceptor in the cathode chamber. Results show that a maximum power density of 29.78 mW/m3 and a current density of 610 mA/m3 were recorded from the polarization curve during the light phase. The maximum voltage recorded was 399 mV in the light phase and 390 mV in the dark phase. This is the first design of a rice paddy-planted microbial fuel cell assisted with a blue-green algal cathode, capable of operating in self-sustainable mode using entirely natural processes without any external input of organics or oxidant.
TL;DR: The results of integrated toxicity analysis indicated that the pre-treatment of microbial degradation significantly decreased the integrated toxicity of DBPs formed from AAs, and Proteobacteria may play an important role in controlling DBP precursor.
TL;DR: A better understanding of the soil microbial dynamics in response to surfactant amendments in addition to bioaugmentation of a PAH-degrading microbe is provided, which contributes to successful and efficient surfactants-enhanced bioremediation ofPAH-contaminated soils.
27 Nov 2019
TL;DR: Gene cloning and overexpression indicated that a novel nitrile hydratase with three unusual subunits (AnhD, AnhE, and AnhA) without accessory protein mediated IM-1-2 formation could be used to remediate environments contaminated with acetamiprid.
Abstract: Neonicotinoid insecticide pollution in soil and water poses serious environmental risks. Microbial biodegradation is an important neonicotinoid insecticide degradation pathway in the environment. I...
TL;DR: In this article, the changes of the organic composition of coal-derived compounds and the bulk organic profiling were changed because of the microbial degradation, which indicated that the chemical treatment has produced both labile organic components and compounds that are recalcitrant to microbial degradation.
TL;DR: Proper oxidants of moderate dosages were able to promote microbial bioremediation of persistent organic pollutants in soil and significantly promoted viability of microbial community.
TL;DR: The EstA-associated biodegradation of pyrethroids was determined, which could provide novel insights to facilitate the practical application of B. cereus BCC01 in the microbial detoxification of pyrethroid contamination.
Abstract: Microbial degradation has been considered as a rapid, green, and cost-effective technique to reduce insecticide pollutions in a contaminated environment. However, the instability and low efficacy of non-indigenous microorganisms hampers their further exploitation when being introduced into a real environmental matrix. In order to overcome the restriction that these functional microorganisms are under, we investigated the optimal conditions to improve the pyrethroid-degrading ability of one previously isolated bacterium Bacillus cereus BCC01, where 9.6% of the culture suspension (with cell density adjusted to OD600 = 0.6) was inoculated into 50 mL media and cultivated at pH 8 and 30 °C, and its metabolic pathway was illuminated by analyzing the main metabolites via gas chromatography mass spectrometry (GC-MS). Most importantly, a key pyrethroid-hydrolyzing carboxylesterase gene estA was identified from the genomic library of strain BCC01, and then expressed in Escherichia coli BL21 (DE3). After purification, the recombinant protein EstA remained soluble, displaying high degrading activity against different pyrethroids and favorable stability over a wide range of temperatures (from 15 °C to 50 °C) and pH values (6.5–9). Therefore, the EstA-associated biodegradation of pyrethroids was determined, which could provide novel insights to facilitate the practical application of B. cereus BCC01 in the microbial detoxification of pyrethroid contamination.
TL;DR: To evaluate the contribution of several microbial groups in soil anthracene and benzo[a]pyrene degradation, the analysis of phospholipid fatty acid (PLFA) profiles and machine learning techniques were employed.
TL;DR: In this paper, the authors investigated the biodegradation of pentachlorophenol (PCP), the most toxic among chlorophenols, in solid-liquid two-phase bioreactors to demonstrate the feasibility of this technological platform.
TL;DR: Results showed that the fungus could better capture and adsorb organic compounds in liquid and gas phases, and the adsorption was a physical monolayer Adsorption process.
01 Jan 2019
TL;DR: Cultures of fungi that degrade polycyclic aromatic hydrocarbons may be useful for bioremediation of contaminated soils, sediments, and waters.
Abstract: Polycyclic aromatic hydrocarbons (PAHs) are aromatic hydrocarbons having two or more fused benzene rings. PAH are found in environment from natural as well as anthropogenic sources. They are widely distributed environmental contaminants that have detrimental biological effects, including toxicity, mutagenicity, and carcinogenicity. PAHs are thermodynamically more stable and resistant to microbial degradation due to their hydrophobic nature and their stabilization due to presence of multiple benzene rings and low aqueous solubility. Despite these properties, a variety of bacterial, fungal and algal species are reported for biodegradation. Most of studies involved in PAH microbial degradation is based on enzymes involved in PAH metabolism and their mineralization. Several bacteria have been found to degrade PAH such as Sphingomonas sp., Psedomonas sp., Alcaligens eutrophus, Burkhelderia sp. Mycobacterium, Rhodococcus, Nocardioides, Mycobacterium, Rhodococcus, Nocardioides and Novosphingobium, etc. There are several biochemical pathways and gene reported which are responsible for bacterial degradation of PAHs. Many fungi metabolize polycyclic aromatic hydrocarbons with enzymes that include lignin peroxidase, manganese peroxidase, laccase, cytochrome P450, and epoxide hydrolase. The products include trans-dihydrodiols, phenols, quinones, dihydrodiol epoxides, and tetraols, which may be conjugated to form glucuronides, glucosides, xylosides, and sulfates. The fungal and bacterial metabolites generally are less toxic than the parent hydrocarbons. Cultures of fungi that degrade polycyclic aromatic hydrocarbons may be useful for bioremediation of contaminated soils, sediments, and waters. Microalgae and eukaryotic algae sp. have been also reported for their bioaccumulation, biotransformation and degradation capability of PAH. While mechanism of biodegradation pathways from algae are not very specific and vary from species to species. In case of algal biodegradation of PAH it works more precisely in combination with bacterial co-culture.
TL;DR: The results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.
TL;DR: An incubation study by amendment of iso-C9 as substrates for methanogenic degradation in production water from a high-temperature petroleum reservoir provides some useful information on the potential biodegradation of branched alkanes via methanogenesis and also suggest that brancher alkanes are likely activated via fumarate addition in high-Temperature petroleum reservoirs.
Abstract: Branched alkanes are important constituents of crude oil and are usually regarded as resistant to microbial degradation, resulting in little knowledge of biochemical processes involved in anaerobic branched alkanes biodegradation. Here, we initiated an incubation study by amendment of iso-C9 (2-methyl, 3-methyl, and 4-methyloctane) as substrates for methanogenic degradation in production water from a high-temperature petroleum reservoir. Over an incubation period of 367 days, significant methanogenesis was observed in samples amended with these branched alkanes. The strong methanogenic activity only observed in iso-C9 amendments suggested the presence of microbial transformation from iso-alkanes into methane. GC-MS-based examination of the original production water identified an intermediate tentatively to be iso-C9-like alkylsuccinate, but was not detected in the enrichment cultures, combined with the successful amplification of assA functional gene in inoculating samples, revealing the ability of anaerobic biodegradation of iso-C9 via fumarate addition pathway. Microorganisms affiliated with members of the Firmicutes, Synergistetes, and methanogens of genus Methanothermobacter spp. were highly enriched in samples amended with iso-C9. The co-occurrence of known syntrophic acetate oxidizers Thermoacetogenium spp. and Methanothermobacter spp. (known hydrogenotrophic methanogens) indicates a potential syntrophic acetate oxidation associated with the methanogenic biodegradation of iso-C9. These results provide some useful information on the potential biodegradation of branched alkanes via methanogenesis and also suggest that branched alkanes are likely activated via fumarate addition in high-temperature petroleum reservoirs.
TL;DR: A novel approach using hydrocarbonoclastic self-immobilized deep sea bacterial consortium for eco-friendly bioremediation is demonstrated by FTIR, GC-MS, and 13C NMR spectroscopy analyses.
01 Jan 2019
TL;DR: This work has shown that microbial transformation of hydrocarbon compounds to harmless molecules has been characterized under aerobic and anaerobic conditions, which bodes well for the clean-up of contaminated matrices.
Abstract: Crude oil contamination in soils, freshwater, seawater and sediments may occur during petroleum extraction, transport and processing. Ecosystems are negatively impacted by hydrocarbon pollution. Bioremediation represents an environmentally sustainable and cost effective technology, improving microbial degradation of organic pollutants. Bioremediation strategies can be applied in situ or ex situ. A successful bioremediation process typically requires the application of distinct strategies for a specific contaminated site. Bioaugmentation and biostimulation represent two main bioremediation strategies for the clean-up of contaminated matrices. Bacteria and fungi are involved in hydrocarbon degradation and may accelerate bioremediation processes. Microbial transformation of hydrocarbon compounds to harmless molecules has been characterized under aerobic and anaerobic conditions. Novel strategies to improve bioremediation technologies have been successfully applied in recent years, broadening their applications.
01 Jan 2019
TL;DR: A critical overview of current knowledge around the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is presented in this paper, where diverse types of bacterial, fungal, algal, earthworms, protozoans, plant species and their derived compounds such as biocatalysts, and biosurfactants are used.
Abstract: Polycyclic aromatic hydrocarbons (PAHs) are active members of the group of multi-aromatic organic compounds, considered to be the most ubiquitous environmental pollutants, mainly engendered from partial combustion of wood, coal, oil or other organic materials. Currently, more than 500 PAHs are prevalent in the atmosphere; reactions between PAHs and various chemicals such as ozone, sulfur dioxide and nitrogen oxides lead to the formation of more toxic chemicals such as diones, nitro- and dinitro-PAHs and sulfonic acids. Due to high global concern, studies are being carried out by researchers to remove PAHs in an eco-friendly and cost-effective manner. Biodegradation of PAHs is a widely used strategy in which diverse types of bacterial, fungal, algal, earthworms, protozoans, plant species and their derived compounds such as biocatalysts, and biosurfactants are being used. Though the microbial degradation of PAHs has been extensively explored, it is a quite progressive area with many research findings being added to the literature. This chapter focuses on a critical overview of current knowledge around the biodegradation of PAHs. It also discusses the recent advancement including ‘omics’ approaches in bioremediation techniques to illuminate fundamental challenges and future prospects.
01 Jan 2019
TL;DR: Different types of bacteria and fungi are reported to successfully degrade PCBs, but only a few fungi are possible degraders in the absence of alternative carbon sources.
Abstract: Synthetic chlorinated organic compounds—polychlorinated biphenyls (PCBs)—have been used in several industrial applications for over 50 years and are among the most persistent classes of xenobiotic pollutants. PCBs remain in the environment for a long period due to their low reactivity and stability in harsh environmental conditions. Samples of PCBs can be analysed using chromatographic methods (gas or liquid) coupled with mass spectrometry after various pre-treatment and extraction methods. Hydrophobicity and a chemically stable nature cause them to break down very slowly under natural conditions. Catabolism by microbial enzymes is an efficient route for environmental biodegradation of PCBs, but as chlorination substitution in the biphenyl ring increases, the microbial degradation rate decreases. Different types of microbes are reported to degrade PCBs under anaerobic and/or aerobic conditions by reducing and oxidizing dechlorination mechanisms, respectively. Four main enzymes are reported for the biodegradation pathway of PCBs: biphenyl dioxygenase (bphA), dihydrodiol dehydrogenase (bphB), 2,3-dihydroxybiphenyl dioxygenase (bphC) and 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolase (bphD). Different types of bacteria are reported to successfully degrade PCBs, but only a few fungi are possible degraders in the absence of alternative carbon sources.
TL;DR: In this article, the response surface method designed by Box-Behnken was used to study the effect of temperature, pH value and TPH concentration on the biodegradation of Enterobacter sp. S-1contam...
Abstract: In this research, the response surface method designed by Box-Behnken was used to study the effect of temperature, pH value and TPH concentration on the biodegradation of Enterobacter sp. S-1contam...
TL;DR: In this article, the authors investigated the effect of selected plant secondary metabolites (PSMs) on the removal of structurally similar phenoxy herbicides (PHs): 2,4-dichlorophenoxyacetic acid (2,4D) and 2-methyl-4-chlorophenoxy acetic acid(MCPA), and found that the addition of SA particularly stimulated the occurrence of the total number of tfdA genes, with this presence being higher than that observed in the unamended samples.
Abstract: The removal of contaminants from the environment can be enhanced by interactions between structurally-related plant secondary metabolites (PSMs), selected xenobiotics and microorganisms. The aim of this study was to investigate the effect of selected PSMs (ferulic acid—FA; syringic acid—SA) on the removal of structurally-similar phenoxy herbicides (PHs): 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA). The study also examines the biodegradation potential of soil bacteria, based on the occurrence of functional tdfA-like genes, and the ecotoxicity of the samples against two test species: Sinapis alba L. and Lepidium sativum L. The microbial cultures spiked with the PSMs demonstrated higher phenoxy acid removal: 97–100% in the case of 2,4-D and 99%–100% for MCPA. These values ranged from 5% to 100% for control samples not amended with FA or SA. The higher herbicide removal associated with PSM spiking can be attributed to acceleration of the microbial degradation processes. Our findings showed that the addition of SA particularly stimulated the occurrence of the total number of tfdA genes, with this presence being higher than that observed in the unamended samples. PSM spiking was also found to have a beneficial effect on ecotoxicity mitigation, reflected in high (102%) stimulation of root growth by the test species.