Nematode-microbe interactions as emerging biological tools in environmental bioremediation

The influence of long-term mixed organic and inorganic contamination on soil microbial activity, community structure and genetic diversity was investigated in soil samples from a coke oven plant located in Upper Silesia, Poland. The tested soils were heavily contaminated with polycyclic aromatic hydrocarbons (PAHs) and heavy metals. The microbial communities were characterized using the phospholipid fatty acid (PLFA) and the denaturing gradient gel electrophoresis (DGGE) methods. Analysis of the PLFA profiles showed that the biomass of Gram-negative bacteria and fungi was affected by heavy metals but not by PAHs. Similar results were obtained for total microbial activity measured as the rate of fluorescein acetate hydrolysis. Statistical analysis of the obtained results revealed that heavy metals rather than PAHs were primarily responsible for the reduction in microbial activity and the differences in the microbial community structure as showed by PLFA. The DGGE analysis showed that the most contaminated soil had a very low biodiversity and richness but a very high evenness index. The correlation analysis revealed that the biodiversity and richness indices were negatively correlated with PAHs but not with heavy metals. However, there was a positive relationship between the evenness index and tested metals as well as the PAH content. The partial 16S rRNA sequence analysis showed that some of the clones were closely related to the genera Pseudomonas, Sphingomonas and Arthrobacter, which are well-known hydrocarbon degraders. Obtained results indicated that a high level of contamination suppress the some bacterial community member giving finally a reduction in the genetic diversity.

Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics

Chapter 44 - Remediation of organic pollutants by Brassica species

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous persistent environmental contaminants generated by natural combustion processes and human activities. PAHs are considered hazardous because of cytotoxic, mutagenic, and carcinogenic effects. Sixteen individual PAH compounds have been identified as priority pollutants by the United States Environmental Protection Agency (U.S. EPA). All substances originated in to the environment by either biogenic or anthropogenic sources. Anthropogenic compounds describe synthetic compounds, and compound classes as well as elements and naturally occurring chemical entities which are mobilized by man’s activities. In the marine environment, the fate of pollutants is largely determined by biogeochemical process. Some of these chemical changes enhance the toxicity of the pollutants. Other chemical changes cause the degradation or immobilization of pollutants and, as a result, act to purify the waters. Possible fates for PAHs, released into the environment, include volatilization, photo-oxidation, chemical oxidation, bioaccumulation and adsorption on soil particles, leaching, and microbial degradation. Elevated concentrations of polycyclic aromatic hydrocarbons (PAHs) have been found in mangrove sediments due to anthropogenic compounds.

Industrial development has enhanced the release into the environment of large quantities of chemical compounds with high toxicity and limited prospects of degradation. The pollution of soil and water with xenobiotic chemicals has become a major ecological issue; therefore, innovative treatment technologies need to be explored. Fungal bioremediation is a promising technology exploiting their metabolic potential to remove or lower the concentrations of xenobiotics. In particular, white rot fungi (WRF) are unique microorganisms that show high capacities to degrade a wide range of toxic xenobiotic compounds such as synthetic dyes, chlorophenols, polychlorinated biphenyls, organophosphate pesticides, explosives and polycyclic aromatic hydrocarbons (PAHs). In this review, we address the main classes of enzymes involved in the fungal degradation of organic pollutants, the main mechanisms used by fungi to degrade these chemicals and the suitability of fungal biomass or extracellular enzymes for bioremediation. We also exemplify the role of several fungi in degrading pollutants such as synthetic dyes, PAHs and emerging pollutants such as pharmaceuticals and perfluoroalkyl/polyfluoroalkyl substances (PFASs). Finally, we discuss the existing current limitations of using WRF for the bioremediation of polluted environments and future strategies to improve biodegradation processes.

The increase of soil and water contamination, caused by oil leakages during transportation and storage of petroleum components, present serious threat to human health and the environment. Total petroleum hydrocarbons (TPH) is a commonly used gross parameter for quantifying environmental contamination that is originated by various petroleum hydrocarbons. The characterization of the petroleum contaminated soils will enable the selection of the most appropriate methods for bioremediation and rehabilitation of theses soils. Qatar's economic boom, based on the hydrocarbon industry, is putting a strain on other scarce resources. Due to the increase of industrial activates; several environmental issues arose in the recent years, putting at risk the natural and cultural resources of Qatar. Soil in Qatar is in general shallow sandy calcareous, overlying rocky bedrock. The available nutrition is poor with salty soil; they are adapted and tolerate different physical and chemical factors. In areas with long history of oil spells, it's important to conduct large-scale study in which oil weathering in the sediments is evaluated in terms of toxicity to the environment. Rehabilitation of lands should be further developed to preserve agricultural soils, and to prevent the spread of harmful molecules and their infiltration into the groundwater and in the food chain. Solvent extraction is a promising technology for degrading polluted soil. Consequently, several solvent has been researched; namely methanol, hexane, dichloromethane and acetone. The solvent mixture [hexane: dichloromethane (50:50)] efficiently extracts the polycyclic aromatic hydrocarbons (PAHs) compounds. The solvent extraction methods are useful to identify the composition of soil contamination which would assist in the treatment and remediation. Accelerated solvent extraction has been applied to extract of wide range of petroleum hydrocarbons, including aliphatic, polycyclic aromatic hydrocarbons (PAHs), phenols, and polychlorinated biphenyls (PCBs), while gas chromatography-mass spectrometry (GC-MS) is used to quantify the hydrocarbon compound in environmental samples. In this study, Total petroleum hydrocarbons was extracted and quantified in several samples collected from aged contaminated sites. The analytical results, indicated that the quantitative determination of the PAH was depended strongly on the sample preparation, and solvents The data collected in this baseline study should be further validated and incorporated with other studies that would guide the future remediation strategies.

Earthworms may promote the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but the mechanism through which they exert such influence is still unknown. To determine if the stimulation of PAH degradation by earthworms is related to changes in microbial communities, a microcosm experiment was conducted consisting of columns with natural uncontaminated soil covered with PAH-contaminated dredge sediment. Columns without and with low and high Eisenia andrei densities were prepared. Organic matter and PAH content, microbial biomass, and dehydrogenase activity (DHA) were measured in soil and sediment over time. Biolog Ecoplate™ and polymerase chain reaction using denaturing gradient gel electrophoresis were used to evaluate changes in metabolic and structural diversity of the microbial community, respectively. Earthworm activity promoted PAH degradation in soil, which was significant for biphenyl, benzo[a]pyrene, and benzo[e]pyrene. Microbial biomass and DHA activity generally did not change over the experiment. Earthworm activity did change microbial community structure, but this did not affect its functioning in terms of carbon substrate consumption. Results suggest no relationship between changes in the microbial community by earthworm activity and increased PAH disappearance. The role of shifts in soil microbial community structure induced by earthworms in PAH removal needs further investigation.

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Bioremediation, involving the strategic use of microorganisms, has proven to be a cost-effective alternative for restoring areas impacted by persistent contaminants such as polycyclic aromatic hydrocarbons (PAHs). In this context, the aim of this study was to explore hydrocarbon-degrading microbial consortia by prospecting native species from soils contaminated with blends of diesel and biodiesel (20% biodiesel/80% diesel). After enrichment in a minimal medium containing diesel oil as the sole carbon source and based on 16S rRNA, Calmodulin and β-tubulin gene sequencing, seven fungi and 12 bacteria were identified. The drop collapse test indicated that all fungal and four bacterial strains were capable of producing biosurfactants with a surface tension reduction of ≥20%. Quantitative analysis of extracellular laccase production revealed superior enzyme activity among the bacterial strains, particularly for Stenotrophomonas maltophilia P05R11. Following antagonistic testing, four compatible consortia were formulated. The degradation analysis of PAHs and TPH (C5-C40) present in diesel oil revealed a significantly higher degradation capacity for the consortia compared to isolated strains. The best results were observed for a mixed bacterial-fungal consortium, composed of Trichoderma koningiopsis P05R2, Serratia marcescens P10R19 and Burkholderia cepacia P05R9, with a degradation spectrum of ≥91% for all eleven PAHs analyzed, removing 93.61% of total PAHs, and 93.52% of TPH (C5-C40). Furthermore, this study presents the first report of T. koningiopsis as a candidate for bioremediation of petroleum hydrocarbons.

Molecular characterization of methanogenic microbial communities for degrading various types of polycyclic aromatic hydrocarbon

Remediation of weathered petroleum hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), dioxins, and polychlorinated biphenyls (PCBs) through monitored natural attenuation, in-situ biostimulation, and/or bioaugmentation was assessed using laboratory-scale microcosms. These contaminants of interest (COIs) have persisted in Santa Susana Field Laboratory (SSFL) soils for over 40 years in some cases. The objective of this United States Department of Energy (DOE)-funded study was to determine the potential of the aforementioned remediation methods to reduce COI concentrations in soil and estimate potential biodegradation rates of COIs in SSFL soils. Several types of soil microcosms were established: one set of microcosms was run without amendments to estimate natural attenuation rates at the site; biostimulation was tested by addition of nitrogen and phosphorus, rice hulls, and biosurfactant (soya lecithin), another set was augmented with the white-rot fungus Phanerochaete chrysosporium, and gamma-irradiated microcosms served as sterilized controls. Soil samples were collected and analyzed for dioxins, PCBs, PAHs, and extractable fuel hydrocarbons (EFH) after 0, 4, and 8 months of incubation. Soil contamination in the microcosms initially consisted of primarily heavily chlorinated dioxins and PCBs, longer petroleum hydrocarbons (21-40 equivalent carbon chain length), and PAHs with 4-6 aromatic rings. Small decreases in PAH, PCB, and dioxin soil concentrations were observed, but these decreases were not statistically significant. EFH concentrations were inflated at the final sampling event, but they appeared to reduce for two of three soils (Soils A and C) tested at the second sampling event. No COI concentration reductions were statistically significantly during 8 months of incubation. Because petroleum hydrocarbons were primarily longer-chain hydrocarbons in the C21 to C40 EFH range, it is likely that lighter hydrocarbons had been preferentially degraded, leaving the more recalcitrant longer-chain hydrocarbons in the soil. Dioxin concentrations appeared to decrease in some cases, but these reductions were not statistically significant at the 95% confidence level. Larger PAHs (4-6 rings) comprise the majority of residual PAH soil contamination. Given that concentrations of these PAHs have not decreased significantly during this 8-month long study, it is likely that these larger PAH contaminants are somewhat recalcitrant and will take a long time to biodegrade. Similarly, little or no PCB biodegradation was observed which is not surprising because the PCBs are heavily chlorinated, and bacterial biodegradation of these highly chlorinated compounds is reported to occur only under anaerobic conditions. The primary dioxin congener present in soils was octachlorodibenzodioxin (OCDD), which is the heaviest-chlorinated dioxin congener. Like

Groundwater pollution by petroleumderived contaminants in coastal semiarid environment

Determination and remediation of pollutants such as polycyclic aromatic hydrocarbons (PAHs) have not being fully regulated in Nigeria; hence contamination of surface water by such pollutant is a major concern. This study was designed to determine the level of selected PAHs in petroleum contaminated water using spectroscopic techniques and the efficacy of activated carbons made from Bambusa vulgaris and Oxytenanthera vabyssinaca. Bambusa vulgaris and Oxytenanthera abyssinaca were carbonized at 350OC and activated with Phosphoric acid (CBV350OC H3PO4) and Potassium chloride (COA 350OC KCl) as dehydrating agent respectively. The adsorbents were then used to remediate PAHs in petroleum contaminated water. Liquid-Liquid extraction procedures were used for extracting selected PAHs from sampled solutions. The batch experiment was performed to study the adsorption capacity of adsorbents at 5hrs contact time. Analysis of PAHs concentration for each sampling day was determined by GC-MS. Total PAHs in simulated wastewater did not show a clear trend, contrary to the expectation that there should be a progressive increase with time due to photolysis or photodecomposition of compounds or PAHs. COA 350OC KCl showed a range of 6.2-19.3% removal efficiency of each selected PAH with a total percentage efficiency of 27.7-70.8 for all days. For CBV350OC H3PO4 removal efficiency ranged from 10.26-19.30% for each selected PAH and a total efficiency of 50.8-100% for all selected PAHs for the 4 days intervals. The experimental result showed that adsorbent made from Bambusa vulgaris and Oxytenanthera abyssinaca and activated with H3PO4 and KCl as dehydrating agentrespectively can efficiently adsorb the selected PAHs in contaminated water. The study also revealed that PAHs in contaminated water increases with time due to photodecomposition, thus necessitating their treatment on time.

Environmental protection from emerging pollutants has become a significant challenge for mankind as an increasing number of contaminants, including synthetic dyes and polycyclic aromatic hydrocarbons (PAHs), represent a serious risk to ecological and environmental balance. Most synthetic dyes have complex aromatic structures and are resistant to degrade by classical approaches, such as physical and chemical processes, including adsorption, chemical coagulation, flocculation, ion exchange, membrane separation, froth flotation, and reverse osmosis. Enzymes-assisted catalytic transformation of pollutants has become a potential alternative to classical methods because of their ability to react with complex compounds, a quick degradation rate, and producing less harmful by-products. Plant peroxidases, and microbial laccase and lignin-degrading peroxidases (manganese and lignin peroxidase) have gained significant attention for treating aromatic waste due to their capability of oxidizing and detoxifying a wide range of recalcitrant xenobiotics, including PAHs and synthetic dyes. Peroxidases being efficient biocatalysts detoxify an array of toxic compounds by simple free-radical mechanism resulting in the formation of oxidized and depolymerized products of significantly reduced toxicity. Moreover, it is an ecofriendly and economically favorable approach towards the biodegradation of recalcitrant and toxic industrial waste. Among microbial and plant peroxidases, bacterial enzymes have broad substrate specificity and can transform a wide range of recalcitrant substrates. Ligninolytic enzymes oxidize the aromatic ring into quinones and acids by producing free hydroxyl radicals instead of dihydrodiols and mineralize aromatic hydrocarbon in combination with cytochrome P450, monooxygenases, and epoxide hydrolases. In the review, an attempt has been made to provide detailed knowledge about the availability of inexpensive peroxidases sources, their mechanism of action, and degradation potential. The present review summarizes the exploitation of peroxidases from plants, bacteria, and fungus (manganese peroxidase, lignin peroxidase, and laccases) for detoxification and degradation of textile dyes as well as PAHs. Conclusively, peroxidases have great potential to react with almost all classes of synthetic dyes and most PAHs due to broad substrate specificity and transformed them into less harmful metabolites.

Phytotoxicity alleviation by bacterial species isolated from polycyclic aromatic hydrocarbons (PAHs) contaminated sites