Microbial Bioremediation of Non-metals: Current Research | Book
Caister Academic Press
Department of Chemistry University of Ioannina, Ioannina 45110, Greece
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Microbial biodegradation of non-metals pollutants plays a pivotal role in the bioremediation of contaminated soil and groundwater sites. Such pollutants include chloroethenes, steroids, organophosphorus compounds, alkanes, PAHs and PCBs. In this important new book, expert international authors exhaustively review this topic from a biochemical and genetic viewpoint, providing a timely overview of current research.
Topics covered include: enzymatic biodegradation reactions; the impact of bioturbation on hydrocarbon dynamics in marine sediments; the structure, function and biodiversity of ring-hydroxylating dioxygenases involved in PAH biodegradation; strategies to engineer PCB-degrading bacteria; PCB-degrading plant-microbe systems strategies; the structure, regulation and diversity of microbial genes encoding biodegradative enzymes. In addition there are excellent reviews detailing the application of the state-of-the-art molecular technologies to study biodegradative processes. Technologies covered are community fingerprinting, molecular detection of degradative genes, and metagenomics for the analysis and monitoring of microorganisms in situ. These are complemented well by the fascinating reviews of the catabolic plasmids and mobile genetic elements involved in bioremediation, including discussions on the origin and evolution of these catabolic pathways to different genera. In addition the best procedures for the evaluation and design of relevant in situ remediation strategies are examined and classical ex-situ technologies such Landfarming, Composting, Biopiling and Slurry-phase bioremediation are described.
This book is a vital reference resource for research scientists, graduate students, and other specialists interested on microbial bioremediation of organic pollutants and is recommended reading for environmental microbiologists, chemists and engineers.
Table of contents
1. Reductive Dechlorination of Chloroethenes: From the Laboratory to Field Scale Investigations
Federico Aulenta, Mauro Majone, Marco Petrangeli Papini, Simona Rossetti and Valter Tandoi
In situ technologies are cost-effective, expanding technologies for the clean-up of soil and groundwater in contaminated sites. On the other hand, these technologies are knowledge-intensive and their application requires thoroughly understanding of the microbiology, ecology, hydrogeology, and geochemistry of contaminated soils and aquifers, under both natural and enhanced conditions. In this chapter, we summarize current knowledge and future perspectives in the area of microbial anaerobic dechlorination of chlorinated solvents, particularly chloroethenes. Main attention is paid at discussing environmental factors and conditions that influence microbial activity under field conditions. Approaches to stimulate and manipulate the activity of native dechlorinating populations in order to meet target remediation goals are examined. Finally, appropriate characterization procedures for optimal evaluation and design of the in situ remediation strategies are examined with main reference to three tools: a) microbial tools, b) modelling, c) microcosms vs field studies.
2. Bacterial Degradation of Cholesterol and Other Contaminant Steroids
J.L. García, Iria Uhía, Esther García and Beatriz Galán
Cholesterol is a steroid highly abundant in the environment that plays a major role in the global carbon cycle. Many synthetic steroidic compounds like some sexual hormones frequently appear in municipal and industrial wastewaters, acting as environmental pollutants with strong metabolic activities negatively affecting the ecosystems. Since these compounds are common carbon sources for many different microorganisms their aerobic and anaerobic mineralization has been extensively studied. The interest of these studies lies on the biotechnological applications of sterol transforming enzymes for the industrial synthesis of sexual hormones and corticoids. Very recently the catabolism of cholesterol has acquired a high relevance because it is involved in the infectivity of Mycobacterium tuberculosis. This review describes the current knowledge on the catabolism of cholesterol and related steroids in bacteria both at biochemical and genetic levels.
3. Organophosphorus Compounds-degrading Bacteria and Enzymes, and Their Application
Katsumasa Abe, Shouji Takahashi and Yoshio Kera
Organophosphorus compounds are widely used as pesticides, flame retardants and plasticizers. Due to their large-scale use, they have been detected in various environments, including surface and ground water, soil and air in the world. Since many of these compounds are toxic for many organisms including human, their widespread contamination has become a serious problem for various organisms in the environment. Microbial degradation of organophosphorus compounds has received attention, because it is thought to be more environmentally friendly way than chemical methods. Therefore, many microorganisms capable of degrading organophosphorus compounds have been isolated and characterized. In this chapter, we describe organophosphorus compounds-degrading bacteria and enzymes, and also their application for bioremediation purpose.
4. Biodegradation of Hydrocarbons in Bioturbated Marine Sediments
Philippe Cuny, Cristiana Cravo-Laureau, Vincent Grossi, Franck Gilbert and Cécile Militon
Sediments can serve as sinks for hydrocarbon contaminants in marine ecosystems. Once settled, hydrocarbons fate will be dominated by several abiotic and biotic processes that will result in either their partial or total degradation or in a selective preservation when buried within the sediment. Biodegradation of hydrocarbons in marine sediments is mainly due to the existence of prokaryotes harboring specific catabolic genes enabling the degradation of these compounds under oxic, suboxic and anoxic conditions. The interplay of the various factors that govern hydrocarbons biodegradation in marine sediments is highly complex as illustrated by bioturbation processes carried out by macrofaunal organisms. For instance, the redox oscillation regimes generated by macrofaunal organisms, and the efficiency of metabolic coupling between functional groups associated to these specific redox regimes, are probably determinant factors controlling the biodegradation rates of hydrocarbons in marine sediments. From the understanding of how these natural occurring factors may modulate the rates of hydrocarbons biodegradation, innovative bioremediation strategies may emerge.
5. Hydrocarbon-degrading Soil Bacteria: Current Research
Anna-Irini Koukkou and Elpiniki Vandera
Hydrocarbons are the major representatives of non-metal pollutants found in many contaminated soils by natural or industrial and social activities. Their removal from polluted environmental niches depends to a great extent on microbial degradation, which can also be applied on several technological applications. The extended microbial diversity in soil has served as a rich source for the isolation of efficient PAH-degrading strains. Bacterial isolates with the ability to use PAHs as an alternative source of carbon and energy facilitate their mineralisation to harmless products. Culture-based approaches have resulted in the isolation of a range of soil hydrocarbon-degrading bacteria, which primarily are members of different subdivisions of Proteobacteria as well as of the high G+C Gram-positive bacteria. Generally, in polluted-soils Gram-negative bacteria such as Pseudomonas, Burkholderia and Sphingomonas seem to degrade preferentially lower molecular weight PAHs such as naphthalene and phenanthrene, while Gram-positive isolates are more specialized in the degradation of high molecular weight PAHs such as pyrene.
6. Bioremediation of PAH Contaminated Sites: From Pathways to Bioreactors
Maria Pouli and Spiros N. Agathos
Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants found in industrial sites linked with petroleum, gas production or other activities involving incomplete combustion of organic matter. These compounds constitute a priority for treatment of contaminated soils and sediments due to their toxicity and carcinogenicity. Microbial degradation represents an important mechanism of PAH removal and can be used for the treatment of contaminated sites by in situ or ex situ bioremediation. This technology is taking advantage of a few established peripheral catabolic pathways converting different PAHs into a limited number of central intermediates. Peripheral pathways are typically initiated by dioxygenases, oxidizing PAHs into dihydroxylated intermediates, which, in turn, are catabolized further and degraded via central pathways into TCA cycle metabolites. However, both the hydrophobic characteristics of most PAHs as well as the physicochemical properties of soils diminish the bioavailability of these pollutants and thus limit the degradation capacity of naturally occurring microorganisms for bioremediation of contaminated sites. The success of biotreatment interventions can be enhanced by measures promoting bioavailability (e.g. addition of surfactants or solvents) and/or boosting microbial activity (e.g. by biostimulation or bioaugmentation). The same strategies can be further optimized by implementing appropriately designed bioreactors for faster and more complete removal of recalcitrant PAHs from contaminated soils and sediments.
7. Ring-hydroxylating Dioxygenases Involved in PAH Biodegradation: Structure, Function, and Biodiversity
Yves Jouanneau, Florence Martin, Serge Krivobok and John C. Willison
The first step in the biodegradation of PAHs by aerobic bacteria is catalyzed by metalloenzymes known as ring-hydroxylating dioxygenases (RHDs). Because of the hydrophobic nature and chemical resistance of PAHs, their initial attack by RHDs is a difficult reaction, which is critical to the whole degradation process. This chapter gives an overview of the current knowledge on the genetics, structure, catalytic mechanism and diversity of RHDs involved in PAH degradation. In the past decade, the crystal structures of 10 RHDs have been determined, giving insights into the mechanism of substrate recognition and regioselectivity of dioxygenation. The reaction catalyzed by the archetypal naphthalene dioxygenase has been investigated in detail, thus providing a better understanding of the RHD catalytic mechanism. Studies on the catabolic genes responsible for PAH degradation in several bacterial taxa have highlighted the great phylogenetic diversity of RHDs. The implementation of culture-independent methods has afforded means to further explore the environmental diversity of PAH-degrading bacteria and RHDs. Recent advances in this field now allow the in situ identification of bacteria responsible for pollutant removal. Further biotechnological developments based on microarrays and functional metagenomics should lead to the conception of molecular tools useful for the bioremediation of PAH-contaminated ecosystems.
8. Engineering Microbial Enzymes and Plants to Promote PCB Degradation in Soil: Current State of Knowledge
Michel Sylvestre and Jean-Patrick Toussaint
The fate of PCBs in soil and sediments is driven by a combination of interacting processes including several known biological processes. Under anaerobic conditions some bacteria use organohalides (including PCBs) as terminal acceptors. This process is responsible for the depletion of highly chlorinated congeners. Under aerobic conditions, PCBs are oxidized and mineralized by fungi through various pathways involving ligninolytic enzymes and monooxygenases and by bacteria through an initial dioxygenation reaction. Furthermore, several investigations have brought evidence that the rhizosphere provides a remarkable ecological niche to enhance the PCB degradation process by rhizobacteria. In this review, we will briefly summarize our current knowledge regarding the four above-mentioned biological processes involved in PCB degradation. Currently, the biochemistry of the anaerobic PCB-degrading process is still poorly understood. In the case of fungal enzymes, it is not yet clear which of the ligninolytic or monooxygenase systems prevails in PCB degradation. However, the bacterial oxidative enzymes have been investigated extensively. Furthermore, recent studies suggest that designing processes based on plant-microbe association are very promising avenues to remediate PCB-contaminated sites. In this review emphasis will be placed on the current state of knowledge regarding the strategies that are proposed to engineer PCB-degrading bacterial oxidative enzymes and PCB-degrading plant-microbe systems to degrade PCBs.
9. Catabolic Plasmids and Mobile Genetic Elements Involved in The Degradation of Non-Metal Xenobiotic Compounds
Amalia S. Afendra, Maria Parapouli and Constantin Drainas
During the last century, xenobiotic pollutants harmful to environment and health were dramatically increased as a consequence of human activities, such as petroleum industries, agro-industries, household or commercial use. In the polluted areas a large diversity of bacteria with the ability to use these compounds as carbon and/or nitrogen source were developed and proved to be useful for bioremediation applications. Their biodegradation properties are due to genes, which were modified, recombined and improved accordingly over the years helping bacteria to adapt in the new harsh xenobiotic environment. Over time, catabolic genes were evolutionary grouped in clusters, established through genetic rearrangements in transmissible regions of mobile genetic elements, and spread by horizontal gene transfer among bacteria of different genera or taxa coexisting in polluted areas. This chapter focuses on plasmids and other mobile genetic elements which carry genes or gene clusters coding for catabolic enzymes involved in the degradation of a number of industrially important xenobiotic pollutants. These include chlorinated and polychlorinated compounds, phthalates, sulfur compounds and some major groups of pesticides. The origin and evolution of these catabolic pathways to different genera is also reviewed.
10. Microbial biodegradative genes and enzymes in mineralization of non-metal pollutants
Nazia Mojib, Jack T. Trevors and Asim K. Bej
Bioremediation is an attractive, generally low cost, innovative technology that is a fundamental and sustainable approach to clean up non-metal or organic compounds from contaminated environments. These pollutants include hydrocarbons- principal components of petroleum and fossil fuels, polychlorinated biphenyls (PCBs) - broad family of man-made organic chemicals also known as chlorinated hydrocarbons, polyaromatic hydrocarbons (PAHs)- industrial pollutants that are significant byproducts of coal, chemical, petroleum processing and refining and toxic pesticides used in agricultural lands. The principle of bioremediation lies in the diverse metabolism of microorganisms to degrade or transform organic compounds to assimilate energy with the help of enzymes encoded by diverse biodegradative genes. This can lead to the efficient removal of a wide range of pollutants and wastes from the environment. This chapter elucidates the structure, diversity and function of the biodegradative genes and enzymes involved in the biodegradation pathways of different contaminants. Also, the use of modern genetic methodologies and genome-based global techniques to better understand the function of these biodegradative genes are briefly discussed. Since, many degradation pathways, along with the enzymes and their respective genes are known and reactions are well understood, a bioinformatics approach in predicting enzymes and reactions involved in biodegradation of new compounds is also examined.
11. Molecular Technologies for Analysis of Petroleum Bioremediation
Bioremediation is a cost-effective technique for treatment of polluted environments and it involves usage of microorganisms for pollutant degradation. It can be defined as natural attenuation (intrinsic bioremediation), biostimulation (introduction of nutrients and chemicals to stimulate indigenous microorganisms), and bioaugmentation (inoculation with exogenous microorganisms). When carrying out bioremediation, special attention should be paid to its effects on the indigenous microbiota and dispersal and outbreaks of the inoculated organisms. Recent advances in microbial ecology have provided molecular technologies, such as community fingerprinting, molecular detection of degradative genes, and metagenomics, which facilitate the analysis and monitoring of indigenous and inoculated microorganisms in contaminated sites. This chapter outlines these technologies and discusses how they can contribute to bioremediation.
12. Ex-situ Bioremediation of Contaminated Soils: From Biopiles to Slurry Phase Bioreactors
Although in-situ bioremediation technologies for the treatment of contaminated soils are economically attractive, ex-situ approaches are more often used for surface contaminated soils (typical depths less than 5 m) since they allow a much tighter control of the bioremediation process and provide better estimates of the residual contamination at the end of the treatment period. Ex-situ bioremediation is the method of choice for hot spot treatment if they are reasonably accessible. In this chapter, the classical ex-situ technologies (Landfarming, Composting, Biopiling and Slurry-phase bioremediation) are presented with a few examples of innovative modifications that enhance their productivity and/or effectiveness. Ex-situ bioremediation typically refers to the methods applied for the remediation of excavated contaminated soils. Besides slurry-phase bioremediation where the soil is mixed with water and other nutrients in mechanically agitated bioreactors, ex-situ bioremediation includes solid phase bioremediation that covers the techniques of landfarming and the various forms of composting, namely windrows, biopiles and in-vessel composting. In the following sections, the above methods are presented focusing on design principles and on experience gathered from their application.
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(EAN: 9781904455837 Subjects: [bacteriology] [microbiology] [molecular microbiology] [environmental microbiology] )