Organic carbon effects on aerobic polychlorinated biphenyl removal and bacterial community composition in soils and sediments

Certain organic compounds, including biphenyl and salicylic acid, stimulate polychlorinated biphenyl (PCB) degradation by microorganisms in some environments. However, the usefulness of these amendments for improving PCB removal by microorganisms from diverse habitats has not been extensively explored. This study evaluated the effects of biphenyl, salicylic acid, and glucose on changes in aerobic PCB removal and bacterial communities from an agricultural soil, a wetland peat soil, a river sediment, and a mixture of these samples. PCB removal patterns were significantly different between soils and sediments amended with carbon compounds: (i) terrestrial soil microorganisms removed more PCBs than river sediment microorganisms, particularly with regard to PCBs with >4 chlorine substituents, (ii) glucose-supplemented, agricultural soil microorganisms removed more hexachlorobiphenyl than unsupplemented samples, (iii) biphenyl-supplemented, river sediment microorganisms removed more di- and tri-chlorobiphenyls than unamended samples. Carbon amendments also caused unique shifts in soil and sediment bacterial communities, as determined by specific changes in bacterial 16S rRNA denaturing gradient gel electrophoresis banding patterns. These results indicate that organic carbon amendments had site-specific effects on bacterial populations and PCB removal. Further work is needed to more accurately characterize PCB degrading communities and functional gene expression in diverse types of environments to better understand how they respond to bioremediation treatments.     

芳香族化合物生物降解代谢及其分子遗传研究

芳香族碳水化合物（烃）是自然环境中普遍存在的。由于这些芳香烃在环境中的化学稳定性高、水溶性低且许多可能是致癌因子，由此引起的环境问题是一个世界性的难题。利用生物工程技术阵解芳香烃是一条较为有效和快速分解的新途径。为此，本文综述了几种芳香烃生物降解途径的多样性、引发生物降解的生化和分子遗传机制及其所涉基因的克隆分析和应用研究进展。     

Impact of composting strategies on the treatment of soils contaminated with organic pollutants

Chemical pollution of the environment has become a major source of concern. Studies on degradation of organic compounds have shown that some microorganisms are extremely versatile at catabolizing recalcitrant molecules. By harnessing this catabolic potential, it is possible to bioremediate some chemically contaminated environmental systems. Composting matrices and composts are rich sources of xenobiotic-degrading microorganisms including bacteria, actinomycetes and lignolytic fungi, which can degrade pollutants to innocuous compounds such as carbon dioxide and water. These microorganisms can also biotransform pollutants into less toxic substances and/or lock up pollutants within the organic matrix, thereby reducing pollutant bioavailability. The success or failure of a composting/compost remediation strategy depends however on a number of factors, the most important of which are pollutant bioavailability and biodegradability. This review discusses the interactions of pollutants with soils; look critically at the clean up of soils contaminated with a variety of pollutants using various composting strategies and assess the feasibility of using composting technologies to bioremediate contaminated soil.     

Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils

In recent years, microbial degradation and bioremediation approaches of polychlorinated biphenyls (PCBs) have been studied extensively considering their toxicity, carcinogenicity and persistency potential in the environment. In this direction, different catabolic enzymes have been identified and reported for biodegradation of different PCB congeners along with optimization of biological processes. A genome analysis of PCB-degrading bacteria has led in an improved understanding of their metabolic potential and adaptation to stressful conditions. However, many stones in this area are left unturned. For example, the role and diversity of uncultivable microbes in PCB degradation are still not fully understood. Improved knowledge and understanding on this front will open up new avenues for improved bioremediation technologies which will bring economic, environmental and societal benefits. This article highlights on recent advances in bioremediation of PCBs in soil. It is demonstrated that bioremediation is the most effective and innovative technology which includes biostimulation, bioaugmentation, phytoremediation and rhizoremediation and acts as a model solution for pollution abatement. More recently, transgenic plants and genetically modified microorganisms have proved to be revolutionary in the bioremediation of PCBs. Additionally, other important aspects such as pretreatment using chemical/physical agents for enhanced biodegradation are also addressed. Efforts have been made to identify challenges, research gaps and necessary approaches which in future, can be harnessed for successful use of bioremediation under field conditions. Emphases have been given on the quality/efficiency of bioremediation technology and its related cost which determines its ultimate acceptability.     

Biodegradation of organic pollutants in saline wastewater by halophilic microorganisms: a review

Agro-food, petroleum, textile, and leather industries generate saline wastewater with a high content of organic pollutants such as aromatic hydrocarbons, phenols, nitroaromatics, and azo dyes. Halophilic microorganisms are of increasing interest in industrial waste treatment, due to their ability to degrade hazardous substances efficiently under high salt conditions. However, their full potential remains unexplored. The isolation and identification of halophilic and halotolerant microorganisms from geographically unrelated and geologically diverse hypersaline sites supports their application in bioremediation processes. Past investigations in this field have mainly focused on the elimination of polycyclic aromatic hydrocarbons and phenols, whereas few studies have investigated N-aromatic compounds, such as nitro-substituted compounds, amines, and azo dyes, in saline wastewater. Information regarding the growth conditions and degradation mechanisms of halophilic microorganisms is also limited. In this review, we discuss recent research on the removal of organic pollutants such as organic matter, in terms of chemical oxygen demand (COD), dyes, hydrocarbons, N-aliphatic and N-aromatic compounds, and phenols, in conditions of high salinity. In addition, some proposal pathways for the degradation of aromatic compounds are presented.     

Detection of dioxygenase genes present in various activated sludge

GOAL, SCOPE AND BACKGROUND: Activated sludge from refineries contains various microorganisms that could utilize aromatics under aerobic conditions due to the oxygenase enzymes. Dioxygenase enzymes are oxygenases, which are involved in the ring cleavage step of aromatic hydrocarbons. In this study, the selected catabolic loci involved in ring cleavage have been monitored in the activated sludge samples at different time intervals. The investigation of the dioxygenase genes in the Effluent Treatment Plants (ETPs) and evaluation of their presence at different time points provides a clue for the aromatic utilizing potential of the inherent microbial flora. METHODS: The catabolic gene loci pheB, xylE, tod-isp, bed and nahG responsible for the enzymes catechol 1,2-dioxygenase, catechol 2,3-dioxygenase, toluene dioxygenase-iron-sulphur protein component, benzene dioxygenase and naphthalene dioxygenase were used respectively. The time dependent change in eubacterial population was demonstrated by the amplification of 16S rDNA product, followed by restriction digestion. The template DNA was obtained from the activated sludge collected from ETPs. The supporting physiological data for the overall performance of sludge was developed using respirometric analysis. The on-site COD and MLSS analysis for ETP was used in final evaluation. The study was carried out with samples collected from three different ETPs and also from a selected ETP at different time intervals. RESULTS AND DISCUSSION: The respirometric studies were carried out with phenol, catechol, toluene, and naphthalene to arrive at the target genotypes for further study by PCR protocol. The respirometric analysis coupled with the COD and MLSS analysis represented the physiological capacity of the various sludges. Initially, the tracking protocol was optimized by using different sludge samples, which were collected from refineries. The selected genotypes were amplified and their presence has been confirmed using Southern analysis. The gene loci tod-isp, bed and xylE were commonly observed at various time intervals of the sludge from the same source. The gene loci pheB and nahG were found to be relatively rare. CONCLUSION: The 16S rDNA PCR products after restriction digestion produced different DNA fingerprint patterns, suggesting that the microbial community composition was diverse in the three sources. Similarly, the presence of the catechol 2,3-dioxygenase, benzene dioxygenase and toluene dioxygenase genes confirmed the aromatic degrading potential in the various sludges. The probes could not pick the nahG and pheB genes. However, the respirometeric assay suggested that the oxidative capacity to use naphthalene as a substrate exists. RECOMMENDATION AND PERSPECTIVE: Our study of the diversity at various time points from the ETP provided an overview of the shifts of the catabolic composition of the sludge. This also depends on the influential parameters like the incoming pollutant level and the environmental conditions that are prevailing and often changing from time to time. The results of direct DNA extraction and PCR amplification do reflect the relative abundance of a particular catabolic genotype, which could be used to monitor the efficiency of treatment.     

单环硝基芳香化合物好氧生物降解及其遗传学研究进展

硝基芳香化合物是环境中难降解的有机污染物之一 ,对环境的污染日益严重 ,利用生物技术对这类有机物进行降解是行之有效的新途径。针对几种单环硝基芳香化合物好氧降解的微生物、降解途径以及降解过程中的主要酶、降解性质粒、基因定位等分子遗传学的研究进展进行了综述     

Anaerobic PAH degradation in soil by a mixed bacterial consortium under denitrifying conditions

Polycyclic aromatic hydrocarbons (PAHs) are one of the main classes of contaminants in the terrestrial environment. Concentrations of biphenyl, fluorene, phenanthrene and pyrene were added to soil samples in order to investigate the anaerobic degradation potential of PAHs under denitrifying conditions. A mixed population of microorganisms obtained from a paddy soil was incubated for 20 days in anaerobic conditions in the presence of soil alone or with nitrate, adding, as electron donors, PAHs and, in some samples, glucose or acetate. At regular time intervals oxidation-reduction potential, PAHs concentration, microbial ATP and nitrate concentration into the solution were measured. Degradation trends for each hydrocarbon are similar under all conditions, indicating that the molecular conformation prevails over other parameters in controlling the degradation. Poor degradation results were obtained when PAHs were the only organic matter available for the inoculum, thus confirming the recalcitrance to degradation of these compounds. Biodegradation was influenced by the addition of other carbon sources. As better degradation results were generally obtained when acetate or glucose were added, the hypothesis of a co-metabolic enhancement of PAH biodegradation seems likely. Thus, anaerobic biodegradation of PAHs studied, biphenyl, fluorene, phenanthrene and pyrene, seems to be possible both through fermentative and respiratory metabolism, provided that low molecular weight co-metabolites and suitable electron acceptors (nitrate) are present.     

Chlorophenols and other related derivatives of environmental concern: properties, distribution and microbial degradation processes

Chlorophenols are chlorinated aromatic compound structures and are commonly found in pesticide preparations as well as industrial wastes. They are recalcitrant to biodegradation and consequently persistent in the environment. A variety of chlorophenols derivatives compounds are highly toxic, mutagenic and carcinogenic for living organisms. Biological transformation by microorganisms is one of the key remediation options that can be exploited to solve environmental pollution problems caused by these notorious compounds. The key enzymes in the microbial degradation of chlorophenols are the oxygenases and dioxygenases. These enzymes can be engineered for enhanced degradation of highly chlorinated aromatic compounds through directed evolution methods. This review underscores the mechanisms of chlorophenols biodegradation with the view to understanding how bioremediation processes can be optimized for cleaning up chloroaromatic contaminated environments.     

Assessment of the emission of PCDD/Fs and dioxin-like PCBs from an industrial area over a nearby town using a selective wind direction sampling device

The development of new sampling devices or strategies to assess the concentration of persistent organic pollutants (POPs) in the environment has increased in the last two decades. In this study, a selective sampling device was used to evaluate the impact of potential local sources of polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/Fs) and dioxin-like polychlorinated biphenyl (dl-PCBs) emissions on the ambient air levels of such compounds in a town near an important industrial estate. Average concentrations of target compounds of up to 2.5 times for PCDD/Fs and 2 times for dl-PCBs were found to come from the industrial state confirming this area as the main responsible for the majority of such compounds reaching the town.This finding was supported by a PCDD/F and dl-PCB sample profile analysis and a principal component analysis (PCA), which established a direct link between the dioxin-like compounds found in the samples collected in the town and their source.     

Biological dehalogenation and halogenation reactions

A large number of halogenated compounds is produced by chemical synthesis. Some of these compounds are very toxic and cause enormous problems to human health and to the environment. Investigations on the degradation of halocompounds by microorganisms have led to the detection of various dehalogenating enzymes catalyzing the removal of halogen atoms under aerobic and anaerobic conditions involving different mechanisms. On the other hand, more than 3500 halocompounds are known to be produced biologically, some of them in great amounts. Until 1997, only haloperoxidases were thought to be responsible for incorporation of halogen atoms into organic compounds. However, recent investigations into the biosynthesis of halogenated metabolites by bacteria have shown that a novel type of halogenating enzymes, FADH(2)-dependent halogenases, are involved in biosyntheses of halogenated metabolites. In every gene cluster coding for the biosynthesis of a halogenated metabolite, isolated so far, one or several genes for FADH(2)-dependent halogenases have been identified.     

Characterization of genes for enzymes involved in the phenanthrene degradation in Nocardioides sp. KP7

The nucleotide sequence of the gene cluster, phdEFABGHCD, encoding enzymes responsible for the transformation of phenanthrene to 1-hydroxy-2-naphthoate in Nocardioides sp. strain KP7 was determined. This gene cluster, which may constitute a single operon, resided at 6.1-kb downstream of the phdIJK gene cluster encoding the enzymes for the transformation of 1-hydroxy-2-naphthoate to o-phthalate. In general, the phd products exhibited moderate degrees of homology with isofunctional enzymes found in pathways for the degradation of other aromatic compounds. Remarkably, the phdC gene product had features of the [3Fe-4S] type ferredoxin, which has not been found so far as a component of the ring-hydroxylating dioxygenase. Escherichia coli carrying the genes for phenanthrene dioxygenase, phdABCD, was capable to oxidize phenanthrene.     

Novel approaches for remediation of pesticide pollutants

The use of synthetic pesticides has become an indispensable tool in agriculture for the control of pests. Therefore, the search for remedies and techniques for decontamination and detoxification of a pesticide-contaminated environment has become an important part of the research. Currently, bioremediation seems to be one of the most environmentally safe and cost-effective methods. In nature, the existence of abundant material resources can be used to degrade the environmental pesticide pollutants. At present, a number of microorganisms, capable of degrading pesticides, have been isolated and characterised. For insects, insecticide resistance-associated esterases have been purified and characterised from several insect species, and a new family of cytochrome P450 apparently associated with insecticide resistance in the tobacco budworm, was discovered. Generally, two bioremediation approaches have been used one directly based on microorganisms, and the other involved in isolated enzymes. For the former, in addition to using natural microorganism strains, with genetic techniques certain desirable biodegradation pathways from different organisms are brought together in a single host. However, because of their own limits, especially problems associated with releasing genetically altered microorganisms into the environment, the strategy based on enzymes seems more feasible. In the long term, collaborations between microbiologists, biochemists, and engineers will become increasingly important to efficiently dispose of the pesticide pollutants.     

Impact of Bioaugmentation with a Consortium of Bacteria on the Remediation of Wastewater-Containing Hydrocarbons (5 pp)

Goals, Scope and Background It has been observed that hydrocarbon treated wastewaters still contain high COD and a number of intermediates. This suggests that the required catabolic gene pool for further degradation might be absent in the system or, that its titer value is not significant enough. By providing the desired catabolic potential, the overall efficiency of the treatment system can be improved. This study aims to demonstrate this concept by bioaugmentation of a lab-scale reactor treating refinery wastewater with a consortium having the capacity to complement the alkB genotype to the available microbial population. Methods Two reactors were set up using activated biomass collected from a refinery treatment plant and operated at a continuous mode for a period of 8 weeks. The feed to both reactors was kept constant. Crude oil was spiked regularly. One reactor was bioaugmented with a consortium previously described for crude oil spill remediation. The efficiency of the bioaugmented reactor was demonstrated by reduced COD. The changes in the microbial population over a period of time were analyzed by RAPD. Catabolic activity of the biomass in both reactors was monitored by PCR. The presence of the catabolic loci was confirmed by Southern Hybridization. Results and Discussion 52.2% removal of COD was observed in the bioaugmented reactor while only 15.1% reduction of COD was observed in the reactor without bioaugmentation. The change in microbial population can be seen from the 4th week, which also corresponds to improved catabolic activity. The presence of the bedA locus was seen in all samples, which indicates the presence of aromatic degraders, but the appearance of the alkB locus, from the 6th week onwards, which was observed only in the samples from the bioaugmented reactor. The results suggest that the gene pool of the bioaugmented reactor has catabolic loci that can degrade accumulated intermediates, thus improving the efficiency of the system. Conclusions In this study, improvement of efficiency of bioremediation was demonstrated by addition of catabolic loci that are responsible for degradation. Bioaugmentation was carried out in biomass that was collected from an ETP (effluent treatment plant) treating hydrocarbon containing wastewater to study the strategies for improvement of the treatment system. Biostimulation, only marginally improved the efficiency, when compared to bioaugmentation. The improved efficiency was demonstrated by COD removal. The presence of the alkB locus suggests the importance of a catabolic gene pool that acts on accumulated intermediates. It is well documented that straight chain aliphatics and intermediates of aromatic compounds after ring cleavage, accumulate in refinery wastewater systems, thereby hindering further degradation of the wastewater. Supplementation of a catabolic gene pool that treats the lower pathway compounds and alkanes will improve the overall efficiency. In this study, results suggest that the alkB locus can also be used to monitor the degradative mode of the activated biomass. Recommendations and Perspective . Pollution from petroleum and petroleum products around the globe are known to have grave consequences on the environment. Bioremediation, using activated sludge, is one option for the treatment of such wastes. Effluent treatment plants are usually unable to completely degrade the wastewater being treated in the biological unit (the aerator chambers). The efficiency of degradation can be improved by biostimulation and bioaugmentation. This study demonstrates the improved efficiency of a treatment system for wastewater containing hydrocarbons by bioaugmentation of a consortium that supports degradation. Further experiments on a pilot scale are recommended to assess the use of bioaugmentation on a large scale. The use of molecular tools, like DNA probes for alkB, to monitor the system also needs to be explored.     

Mycoremediation of hydrocarbons with basidiomycetes—a review

ABSTRACT

The literature on hydrocarbon remediation with basidiomycetes was reviewed. Two ecological groups are considered for bioremediation, the saprotrophic basidiomycetes (white-rot and brown-rot fungi) and the ectomycorrhizal basidiomycetes. A remarkable capacity of basidiomycetes for in vitro degradation of simple and recalcitrant hydrocarbons, such as PAH, persistent organic pollutants (POPs), halogenated HC, aromatic HC and phenols, explosives and dyes was reported for many species. However, there is a need for more studies on the practical feasibility of field applications with basidiomycetes.     

Exposure of ruminants to persistent organic pollutants and potential of decontamination

Human activities are emitting persistent organic pollutants (POPs) to the environment. These compounds have raised concerns about the risk of transfer through the food chain via animal products. They are characterized by a strong persistence in environmental matrices and a lipophilicity which may lead to their accumulation in fat tissues. In EU Regulations (no. 1881/2006, 1259/2011), maximum acceptable levels for polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans (PCDD/Fs), and dioxin-like or nondioxin-like polychlorinated biphenyls (PCBs) in food of animal origin have been set. Transfer rates from contaminated fodder to milk have been established: for PCBs, the rate of transfer varies from 5 to 90 % and for PCDD/Fs from 1 to 40 %. The differential transfer of the compounds towards milk is related to the hydrophobicity of the pollutants and to their metabolic susceptibility. According to numerous authors, soil is the major reservoir for POPs, and its involuntary ingestion by farm animals reared outdoors may be the main cause of animal product contamination (meat, milk, or eggs). Recent studies seem to indicate that soil is a real risk matrix in terms of transfer of pollutants to the food chain. A POP crisis management is extremely difficult, since it impacts many farmers located in the contaminated area. The question arising is to know if livestock contaminated by POPs may be decontaminated and further used for their initial purpose. Recent data demonstrate that the decontamination process appear feasible and depends on initial level of contamination or the physiological status of the animals.     

Dioxin-like activity in environmental and human samples from Greenland and Denmark

Dioxins and dioxin-like (DL) compounds are some of the most toxic chemicals being highly persistent in the environment. The toxicological effects of dioxins are mediated via the aryl hydrocarbon receptor (AhR). Compounds of diverse structure and lipophility can bind and activate AhR. The AhR transactivation bioassay is utilized in an array of projects to study the AhR-mediated activities of individual chemicals and mixtures and for epidemiological purposes.This review summarizes a series of studies regarding the DL-activity of single compounds and complex compound mixtures in the environment and humans.We found that some pesticides, plasticizers and phytoestrogens can activate the AhR, and the combined effect of compounds with no or weak AhR potency cannot be ignored.The significant DL-activity in the wastewater effluent indicates the treatment is not sufficient to prevent contamination of surface waters with dioxins. Our results from human studies suggest that the serum DL-activity reflect the complex mixture of persistent organic pollutants (POPs). Greenlandic Inuit had lower serum DL-activity level compared to Europeans, probably due to long distance from the dioxin sources and UV degradation of the high potent dioxin and/or the inhibitory effect of the high level of non-DL POPs. Selective bioaccumulation of PCBs in the food chain may contribute to the negative correlation between serum POPs and DL-activity observed in Greenlandic Inuit.Hence the AhR transactivation bioassay provides a cost-effective and integrated screening tool for measurement of the DL-activity in human, environmental and commercial samples.     

酶体外定向分子进化技术:环境生物污染治理中的新星

环境生物技术在环境控制与污染治理中的应用主要是利用微生物降解和转换污染物.一些人类合成的化学物质由于具有高毒性,且难以被自然界微生物降解,已经严重威胁生态环境和人类的健康.生物治理以其低成本、完成矿质化和实现原位处理等特点,成为较好的治理技术.体外定向分子进化技术是一种发现新的生物表型和新酶的好方法,DNA改组是重要的体外分子进化技术,成功地改造了许多在医药、工业和环境保护等的商业酶.综述了近年来体外定向分子进化技术在环境生物污染治理中的研究进展和应用.