Chapter 5 - Environmental factors affecting the bioremediation potential of microbes

In the last years, a high number of polluting compounds has been released into the environment because of several industrial and/or agricultural activities. In particular, the rapid industrialization of agriculture, expansions in the chemical industry, and the need to generate cheap forms of energy have all resulted in an ever-increasing reliance on anthropogenic organic chemicals and caused the contamination of a significant number of soil environments by xenobiotic compounds with negative, irreversible effects on environmental quality and health. Polycyclic aromatic hydrocarbons (PAHs) and polychlorinated organic compounds (PCB) are surely the most extensively investigated of the chemical pollutants being toxic to many living organisms, including humans, and extensively used for several industrial activities. Because of their low water solubility, stable aromatic ring system, high chlorine content, these compounds have a high persistence in the environment, and may accumulate in food chains and thus have harmful effects on human health. Bioremediation of contaminated sites relies on the metabolic capacities of living organisms to reduce organic pollutants into harmless or, at least, less dangerous compounds. The process can be realized introducing directly into a contaminated system micro-organisms able to consume selectively the target compound (bioaugmentation) or increasing the microbial indigenous population by addition of nutrients in form of organic and/or inorganic fertilizers such as urea, sawdust, compost, manure and biosolids (biostimulation). The evaluation of the effectiveness of a bioremediation process in contaminated soil, however, should not only look at pollutant removal and/or transformation in non toxic end-products but it should also monitor whether and how soil biological functions are affected by and during the process. Studies were performed on an agricultural soil artificially contaminated with phenanthrene (Phe) or pentachlorophenol (PCP), selected as representative of PAHs and PCBs. In a long-term experiment the efficiency of a phenanthrene-degrading microbial culture, the potentiality of compost and dissolved organic matter in soil decontamination, and the dynamics of the main soil biochemical and biological properties were evaluated. The variations of the major physical and chemical properties were also monitored. The efficiency of the different bioremediating approaches was also evaluated against a Phe-aged (2 years) contaminated soil. The obtained results demonstrated that two complex processes occurred simultaneously in the contaminated soil: natural attenuation and ageing. The investigated soil showed an intrinsic capability of degrading Phe and PCP. The addition of a limited dose of compost, as well as the inoculation with a Phe-degrading bacterial culture strongly stimulated and enhanced the attenuation process. Furthermore, several of the soil properties showed differentiated responses to the presence of the Phe, the compost, and/or the exogenous culture. The results obtained with the soil contaminated with phenanthrene and incubated for 2 years supported the occurrence of the ageing process. The impact of PCP on the properties of the soil was the result of opposite effects. The PCP strongly decreased the levels of some biochemical properties that diminished with increasing the incubation time, thus suggesting a depressing effect on the soil micro flora that not recovered from the initial toxic response towards PCP. Conversely, the presence of the contaminant promoted the development of fungal colonies, contributing to its degradation and consequent production of PCP metabolites, considered more toxic than the parent compound. An ageing phenomenon, also favoured by the presence of the dissolved organic matter and leading to the decrease of the extractable PCP, was also hypothesized. The results obtained in this thesis work suggest that soil biological investigations can give information about the intensity and the kind and duration of the effects of pollutants on the metabolic activity of soil. Although the experiments are limited by the laboratory, controlled conditions adopted, they are well suited for measuring the effects of pollution on soil health and to act as a monitoring tool for the decontamination process of a polluted soil. Furthermore, such investigations may be helpful for further studies aimed at validating and extrapolating the data to natural situations.

Catfish is a freshwater fish that is widely cultivated but overfeeding causes organic pollution. This study aims to evaluate the water quality profile based on physicochemical and plankton as bioindicators in catfish ponds in Gondosuli Village, Tulungagung Regency. This type of research was ex post facto by monitoring the physicochemical parameters of water and the structure of the plankton community in control ponds, ponds with catfish aged <1 month, 2-3 months, and 3-4 months each with three replications. Water samples for each pond were measured on the physicochemical water quality included water temperature, conductivity, pH, water transparency, DO, BOD, and turbidity. Plankton identified and analyzed to determine community structure (Abundance, Frequency, Relative Abundance, Relative Frequency, Important Value Index) and biotic index (H', TDI, and %PTV) for water quality. The results of measurements of each physicochemical parameter between locations were statistically analyzed inferentially using a different test. The interaction between the plankton community structure and the physicochemical of water quality was analyzed using biplots. The results showed that ponds with the age of catfish ready to harvest had an impact on decreasing water quality. This condition was indicated by the high organic matter pollution reflected by the high BOD, high turbidity levels, and low DO values. Catfish pond waters quality based on the H' value of plankton community showed that organic matter pollution had not yet occurred. Based on TDI values, catfish pond waters were categorized as poor status (hyper eutrophic) and based on the %PTV index in ponds with catfish age 2-3 and 3-4 months were classified as high levels of organic matter pollution.

Fluorescence spectroscopy is a rapidly evolving method for determining freshwater organic pollution. Historically, measurement was confined to the laboratory with a coarse temporal resolution. The development of field-deployable sensors has enabled in-situ, multi-peak monitoring - although challenges remain regarding fluctuating environmental conditions (e.g. pH and turbidity) that can impact on fluorometer accuracy and interpretation. This study aimed to use fluorescence spectroscopy (including in-situ sensors) to detect and differentiate sources of organic matter pollution in a predominantly groundwater fed, sewage-impacted, chalk stream.High frequency monitoring (15 min resolution for 12 months) was undertaken at two sites on the River Chess, S. England. Two multi-parameter water quality sondes were installed above and below a Wastewater Treatment Works (WWTW) effluent outflow point in a mixed land use catchment (105 km2). Additional grab sampling was conducted during baseflow and stormflow for laboratory-based nutrient, spectrofluorimetric and bacterial analysis.All sites had low turbidity (

2 - Removal of pollutants from wastewater via biological methods and shifts in microbial community profile during treatment process

Chapter 30 - Vermicomposting—the sustainable solid waste management

21 - Extremophilic yeasts and their potential in bioremediation of polluted environments

The process of Bioremediation uses the microorganisms/their enzymes to aid the degradation and removal of contaminants present in the environment. The microbial metabolic ability is used for degradation and removal of environmental pollutants providing an economically safer alternative compared to the rest of physicochemical methodologies. One of the hazardous organic priority pollutants are the Polyaromatic hydrocarbons (PAHs). There are a lot of public concerns and critical environmental challenges in the world because of being carcinogenically toxic and mutagenic properties, their ubiquitous distribution, recalcitrance and their environmental presence. The understanding about harmful effects of PAHs on ecosystems and human health has resulted in an interest of researchers on their degradation. Many types of microbes like bacteria, fungi, and algae are capable to use PAHs as carbon and energy source under aerobic and anaerobic conditions leading to their degradation or transformation. Microbial genetic makeup having genes conceal catabolic enzymes results in PAH-degradation mechanism. From the past twenty years, PAH- biodegradation mechanism, catabolic gene system encoding catabolic enzymes, and adaptation through genetics and regulations have been investigated in detail. This review is to attain an overview of the present knowledge of the genetically modified organisms in crude oil spills using PAH degradation mechanism.

Bioremediation is a process of degrading the environmental contaminants, that are introduced accidentally or purposely which cause hazardous effect on earth and harm the normal life process. The conversion of these contaminants into less toxic forms is the goal of bioremediation process that can be achieved by the use of microorganisms. The bioremediation approaches have more advantages when compared with the traditional methods, as it can be directly implemented at the targeted contaminant site. Even though some bacteria and fungus were employed to decompose the chemical compounds, but they have only limited ratio to metabolize the hydrocarbons on their own. The genetically modified organisms are applied nowadays in bioremediation process for effective removal of contaminants, where the indigenous microbes cannot degrade. Genetically modified microorganisms (GMOs) play an important role in remediating the industrial waste, reduce the toxicity of some hazardous compounds, and also help in removal of pollution by hydrocarbons and petrol discharges. A variety of molecular tools such as molecular cloning, horizontal transfer of DNA in bacteria, electroporation, protoplast transformation, biolistic transformation, conjugation and transformation of competent cells are available for the successful construction of GMOs. Transfer of gene into the bacteria makes it as a novel strain, for eliminating the hydrocarbon contaminants from the environment in minimal time. Similarly, removal of compounds such as xylene, toluene, octane, naphthalene and salicylate is coded on bacterial plasmids for successful degradation of the environment. This chapter represents the applications of genetically modified organisms in bioremediation processes, molecular tools used for construction of GMOs, pros and cons, ethical issues and laws governing the application of GMOs.

Preface. Contributors. I: Biomass Estimation Techniques. Rapid Detection/Identification of Microbes, Bacterial Spores, Microbial Communities, and Metabolic Activities in Environmental Matrices D.C. White, et al. Comparison of Effective Organisms in Bioremediation Processes: Potential Use of Nucleic Acid Probes to Estimate Cyanide Degradation in situ M. Barclay, et al. Modern Methods for Estimating Soil Microbial Biomass and Diversity: An Integrated Approach J.A. Harris, J. Steer. Part II: Comparison of Effective Organisms in Bioremediation Process. Recent Advances in the Biodegradation of Polycyclic Aromatic Hydrocarbons by Mycobacterium Species C.E. Cerniglia. Toxic Metal Contamination Treatment with Microbes G.M. Gadd. Aerobic Biodegradation of Polychlorinated Biphenyls (PCBs): The Fate, Distribution, Kinetics and Enhancement of PCB Biodegradation Efficacy in the Bacterial Cell Suspension of Pseudomonas stutzeri K. Dercova, et al. Adsorption of Heavy Metals to Microbial Biomass: Use of Biosorption for Removal of Metals from Solutions P. Baldrian, J. Gabriel. Nonenzymic Degradation and Decolorization of Recalcitrant Compounds F. Nerud, et al. The Impact of Sulfonation Pattern on Indigo Degradation by Phanerochaete chrysosporium Ligninolytic Enzymes* H. Podgornik, A. Perdih. Screening of Fungal Strains for Remediation of Water and Soil Contaminated with Synthetic Dyes* C. Novotny, et al. Effect of Countermeasures of Radionuclide Uptake by Agricultural Plants* N. Goncharova, P. Kislushko. Part III: Ecotoxicology and Toxicity Monitoring of Bioremediation Measures. Low-Cost Microbiotests for Toxicity Monitoring during Bioremediation of Contaminated Sites G.Persoone, B. Chial. Application of Bioassays for Site-Specific Risk Assessment A.P. Loibner, et al. Effect of PAH-Contaminated Soil on some Plants and Microorganisms B. Maliszewska-Kordybach, B. Smreczak. Development of immunomicroscopic methods for bioremediation K.C. Ruel, J.-P. Joseleau. Ecotoxicological Evaluation of PAH-Contaminated Soil Using Earthworms* M. Bhatt, et al. Use of Bioassays in Determining the Ecotoxicity of Industrial Soils* M.A.T. Dela Cruz, et al. Genotoxicity Estimation in Soils Contaminated with Polycyclic Aromatic Hydrocarbons after Biodegradation* K. Malachova, et al. Ecotoxicological Hazard Assessment of Solid-Phase Samples* L. Pollumaa, A. Kahru. Monitoring of Polychlorinated Biphenyls in Slovak Freshwater Sediments: Use of Semipermeable Membrane Devices* R. Tandlich, et al. Part IV: Application of Bioremediation to Environmental Problems. Biopiles for Remediation of Petroleum-Contaminated Soil: A Polish Case Study T. Hazen, et al. Why mycoremediations have not yet come into practice V. Sasek. From Laboratory to Industrial Scale: Composting of Polluted Soils from Former Coal Industry and Gas Plants: Future Research Needs H.C. Dubourguier. Plant Biotechnology for the Removal of Organic Pollutants and Toxic Metals from Wastewaters and Contaminated Sites: Phytoremediation T. Vanek, J.-P. Schwitzguebel. Consideration of Plant Based Remediation and Restoration of Contaminated Sites Containing Heavy Metals: The Canadian Experience T. McIntyre. Combined Removal of Oil, Toxic Heavy Metals and Arsenic from Polluted Soil S.N. Groudev. Landfarming Framework for Sustainable Soil Bioremediation R.C. Sims, J.L. Sims. Spent Mushroom Substrate: White Rot Fungi in Aged Creosote-Contaminated Soil* T. Eggen.

Organic Pollution is now being a global environmental problem. Polycyclic aromatic hydrocarbons (PAHs) are one of the widestspread organic compounds containing two or more fused aromatic benzene rings arranged in different configurations. The fate of PAHs is a great environmental and human health concern due to their toxic, mutagenic and carcinogenic properties. They are widely distributed in the environment through various sources such as domestic, industrial, agriculture and natural sources and finally discharge into the soil strata. Various chemical and physical techniques used for soil remediation are incomplete, harmful to the environment and also expensive. Hence, the addition of biostimulating agents such as a surfactant, nutrients, and agricultural compost accelerates the bioremediation process and simultaneously enhances the soil organic matter content and soil fertility. Thus, this is believed to be one of the better cost-effective and eco-friendly methods for removal of PAHs pollutants from soil. However, appropriate implementation of naturally occurring microorganisms for field bioremediation could be significantly enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. PAHs are biodegraded or bio transformed into less complex metabolite through various enzymatic routes as monooxygenase, dioxygenase, and ligninolytic enzymes mostly produced by the indigenous microbial community. The objective of this chapter is to provide a comprehensive overview concerning remediation of PAHs, with a special focus on the treatment effect of simulating agents for field bioremediation. Futuristic road map of chapter is to search novel green and sustainable technology to accelerate remediation process. The study thus opens new avenues for effective bioremediation strategies for PAHs contaminated habitats, which will help policymakers and stakeholders to make a proper direction for implementation.

The membrane biofilm reactor (MBfR) is a novel wastewater treatment technology, garnering attention due to its high gas utilization rate and effective pollutant removal capability. This paper outlines the working mechanism, advantages, and disadvantages of MBfR, and the denitrification pathways, assessing the efficacy of MBfR in removing oxidized pollutants (sulfate (SO4-), perchlorate (ClO4-)), heavy metal ions (chromates (Cr(VI)), selenates (Se(VI))), and organic pollutants (tetracycline (TC), p-chloronitrobenzene (p-CNB)), and delves into the role of related microorganisms. Specifically, through the addition of nitrates (NO3-), this paper analyzes its impact on the removal efficiency of other pollutants and explores the changes in microbial communities. The results of the study show that NO3- inhibits the removal of other pollutants (oxidizing pollutants, heavy metal ions and organic pollutants), etc., in the simultaneous removal of multiple pollutants by MBfR.

Approximately half of the global annual production of wastewater is released untreated into aquatic environments, which results in worldwide organic matter pollution in urban rivers, especially in highly populated developing countries. Nonetheless, information on microbial community assembly and assembly-driving processes in organic matter-polluted urban rivers remains elusive. In this study, a field study based on water and sediment samples collected from 200 organic matter-polluted urban rivers of 82 cities in China and Indonesia is combined with laboratory water-sediment column experiments. Our findings demonstrate a unique microbiome in these urban rivers. Among the community assembly-regulating factors, both organic matter and geographic conditions play major roles in determining prokaryotic and eukaryotic community assemblies, especially regarding the critical role of organic matter in regulating taxonomic composition. Using a dissimilarity-overlap approach, we found universality in the dynamics of water and sediment community assembly in organic matter-polluted urban rivers, which is distinctively different from patterns in eutrophic and oligotrophic waters. The prokaryotic and eukaryotic communities are dominated by deterministic and stochastic processes, respectively. Interestingly, water prokaryotic communities showed a three-phase cyclic succession of the community assembly process before, during, and after organic matter pollution. Our study provides the first large-scale and comprehensive insight into the prokaryotic and eukaryotic community assembly in organic matter-polluted urban rivers and supports their future sustainable management.

In this study, a dual chamber MFC was constructed for simultaneous removal of organic matter and nitrogenous pollutants and bioelectricity generation from synthetic and complex industrial wastewaters and it was operated in batch and continuous mode. When the cell potential was stable after 16 days of batch mode operation, the MFC was converted to continuous mode (from batch mode) and operated for 125 days with different organic loading rates (OLR) and ammonia loading rates (ALR) and fixed hydraulic retention time (HRT) of 40 h. The OLR of 1.49 kg COD m−3 d−1 and ALR of 0.58 kg NH3− m−3 d−1, for anodic and cathodic chambers, respectively, gave the best results. The highest value of cell potential on these OLRs was 310 mV with current density of 85.11 mA m−2, power density of 26.38 mW m−2 and volumetric power density of 192.20 mW m−3. During this period, COD reduction was 78–83% in the anodic chamber and the ammonia reduction was 36–38%. After stable operation with synthetic wastewater one case study was performed with complex industrial wastewater. Continuous mode operation was performed at two different OLR and HRT with a constant ALR. A stable power density and volumetric power density of 23.56 mW m−2 and 112.50 mW m−3, respectively were achieved after 24 days of continuous operation at an OLR of 0.35 kg COD/m3 day with an ALR of 0.43 kg NH3− m−3 day−1 and corresponding HRT of 68 h. A maximum of 89% COD removal and 40% removal of ammonia was obtained after 50 days. A stable voltage of 300 mV was obtained across 1000 Ω resistance. These findings suggest that BMFC can be used for the treatment of industrial wastewater, with carbon removal in anodic chamber and electricity generation.

The persistence of heavy metals in the environment may pollute or contaminate soils and aqueous streams as both natural components or as the result of human activity. Bioremediation process in this regards is an option that offers the possibility to destroy or render harmless various contaminants using plants and microbes. Amongst the various bioremediation processes, phytoremediation and bioremediation by microbes are quite effective. Phytoremediation includes the removal of contaminants with the help of green plants, while the microbial bioremediation includes the removal of heavy metals by microorganisms (bacteria, fungi, yeast and algae) as sorbets. Amongst the various heavy metal contaminants arsenic and lead are recognized as the leading toxicants worldwide and having the various toxic effects on human and animal health as well as on the environment. The aim of this article is to give an overview of the arsenic and lead contaminant in soil and also the mechanism of removal of these toxic metals from the contaminated sources by the potent application of plants and microbes.

The goal of this study was to evaluate the effect of high Tween 80 concentrations on hydrocarbon contaminants and hydrocarbonoclastic microorganisms present in contaminated mining soil during a bioremediation process. The independent variables included Tween 80 concentration and process time. The elected response variables included concentration of total petroleum hydrocarbons (TPH), the chemical composition of contaminants, viable microbial count, and CO2 production. These were measured at various time points during the bioremediation process, which was conducted at room temperature. Higher removal of pollutants occurred at low Tween 80 concentrations. An analysis of the normalized variables shows that the rate of TPH degradation depended on microbial growth rate, which depended on Tween 80 concentration. The addition of Tween 80 changed the concentration and type of the residual hydrocarbon contaminants present, as well as the count and genus of the hydrocarbonoclastic microorganisms that grew during the bioremediation process. Higher concentrations of Tween 80 increased the levels of the chemical compounds present in the bioremediated soil while reducing the viable count and microbial diversity during the bioremediation process. Conversely, low Tween 80 concentrations produced only monoethylhexyl phthalate, which is not a petroleum hydrocarbon derivative. Overall, these results prove that the removal of TPH is dependent on the count and genus of active indigenous hydrocarbonoclastic microorganisms in soil, and these conditions may be controlled by modulating the concentration of Tween 80 that is applied.