Comprehensive biotechnology Vol. 6/ principles and practices in industry agriculture medicine and the environment Moo-Young,Murray

6.01. Introduction

6.02. Biodegradation

Glossary

6.02.1. Introduction and Scope

6.02.2. Traditional and Cultural Techniques

6.02.3. Omics and Related Techniques

6.02.4. Summary Example

6.03. Systems Biology Approaches to Bioremediation

Glossary

Acknowledgments

6.03.1. Introduction

6.03.2. Back to the Environment

6.03.3. What Is in a Genome

6.03.4. The Catabolic Gene Landscape: Methods and Abstractions

6.03.5. Categories of Environmental Metabolites

6.03.6. Pan-Enzymes

6.03.7. The Global Biodegradation Network

6.03.8. The Environmental Fate of Chemical Pollutants

6.03.9. Chemical Logic versus Microbiological Sense

6.03.10. Translating Biodegradation Knowledge into Predictive Power

6.03.11. Metabolic Engineering of Biodegradation: From Systems to Synthetic Biology

6.03.12. Conclusion

6.04. Molecular Approaches for the Analysis of Natural Attenuation and Bioremediation

Glossary

6.04.1. Introduction

6.04.2. Detection of Degradative Genes

6.04.3. Community Fingerprinting

6.04.4. Metagenomics

6.04.5. Conclusions

6.05. New Developments and Applications of Microarrays for Microbial Community Analysis in Natural and Impacted Ecosystems

Glossary

Acknowledgments

6.05.1. Introduction

6.05.2. Microarrays for Microbial Analysis

6.05.3. Future Perspectives

6.06. Metagenomics for Bioremediation

Glossary

6.06.1. Introduction: Molecular Tools Used to Study Environmental Communities

6.06.2. Potential of Metagenomics for Bioremediation

6.06.3. Application of Metagenomics to Contaminated Environments

6.06.4. Conclusions – Advancing the Field

6.07. In Situ Bioremediation

Glossary

6.07.1. Introduction

6.07.2. Unsaturated Zone Treatment Methods

6.07.3. Saturated Zone Treatment Methods

6.07.4. Use of Inocula

6.07.5. Monitoring Methods

6.07.6. Conclusions and Future Prospects

6.08. Bioaugmentation as a Strategy for the Treatment of Persistent Pollutants

Glossary

6.08.1. Introduction

6.08.2. Site-Specific Bioaugmentation Strategies

6.08.3. Pros and Cons of Bioaugmentation

6.08.4. Future Directions

6.08.5. Conclusions

6.09. Bioavailability and Bioaccessibility as Key Factors in Bioremediation

Glossary

6.09.1. Introduction: Bioavailability, Bioaccessibility, and Chemical Activity

6.09.2. Bioavailability Processes

6.09.3. Biological Adaptations Improving Bioavailability

6.09.4. Measuring and Predicting Bioavailability and Bioaccessibility

6.09.5. Influencing Bioavailability

6.09.6. Bioavailability and Environmental Regulation

6.10. Biodegradability of Recalcitrant Aromatic Compounds

Glossary

6.10.1. Introduction and Scope

6.10.2. The Nature of Aromatic Compounds and Their Sources

6.10.3. Overview of Microbial Biodegradation Principles and Their Application to Aromatic Hydrocarbons

6.10.4. Interactions between Habitat Characteristics, Microbes, and Aromatic Compounds Determine Their Biodegradability

6.10.5. Summary

6.11. Proteomic Applications to Elucidate Bacterial Aromatic Hydrocarbon Metabolic Pathways

Glossary

Acknowledgments

6.11.1. Introduction

6.11.2. Traditional Approaches to the Study of Aromatic Hydrocarbon Metabolic Pathways

6.11.3. Proteomic Applications to the Study of Bacterial Degradation of Aromatic Hydrocarbons

6.11.4. Monocyclic and Low-Molecular-Weight Aromatic Hydrocarbons

6.11.5. Proteomic Analysis of Samples from HMW PAH Degradation

6.11.6. Conclusions

6.12. Rieske-Type Dioxygenases

Glossary

Acknowledgments

6.12.1. Introduction

6.12.2. Degradation of Toluene, Benzene, and Ethylbenzene

6.12.3. Degradation of Isopropylbenzene (Cumene)

6.12.4. Degradation of Other Alkylbenzenes with Side Chains of Three or More Carbon Atoms

6.12.5. Degradation of Xylenes

6.12.6. Degradation of Styrene

6.12.7. Degradation of Biphenyl

6.12.8. Degradation of Naphthalene

6.12.9. Degradation of PAHs

6.12.10. Concluding Remarks

6.13. Dehalogenation of Polychlorinated Dibenzo-p-Dioxins and Dibenzofurans, Polychlorinated Biphenyls, and Brominated Flame Retardants, and Potential as a Bioremediation Strategy

Glossary

6.13.1. Introduction

6.13.2. Sediment Contamination: Legacy Pollutants and Emerging Challenges

6.13.3. Biodehalogenation and Dehalorespiration of Organohalides

6.13.4. Sediment Bioremediation: Engineering Challenges

6.14. Microbial Degradation of Polychlorinated Biphenyls

Glossary

Acknowledgments

6.14.1. Introduction

6.14.2. Chemistry and Environmental Fate of PCBs

6.14.3. Biodegradation of PCBs by Higher Organisms

6.14.4. Bacterial Transformation of PCBs

6.14.5. Engineered Systems for Bacterial Degradation of PCBs

6.14.6. Genetically Modified Bacteria for PCB Biodegradation

6.14.7. Conclusions

6.15. Biodegradation and Bioremediation of TNT and Other Nitro Explosives

Glossary

6.15.1. Introduction

6.15.2. Nitroaromatic Explosives

6.15.3. Nitramine Explosives

6.15.4. Nitroester and Nitroalkane Explosives

6.15.5. Bioremediation of Environments Contaminated by Nitro Explosives

6.15.6. Conclusion and Perspectives

6.16. Oxidative Fungal Enzymes for Bioremediation

Glossary

Acknowledgments

6.16.1. Introduction

6.16.2. Fungi

6.16.3. Oxidative Fungal Enzymes

6.16.4. Optimizing Bioremediation

6.16.5. Practical Approach

6.16.6. Concluding Remarks

6.17. Biotechnological Strategies Applied to the Decontamination of Soils Polluted with Heavy Metals

Glossary

6.17.1. Soil Contamination

6.17.2. Heavy Metal Contamination

6.17.3. Soil Microorganisms – Structure and Analysis Tools

6.17.4. Microorganisms and the Contamination by Heavy Metals

6.17.5. Biological Methods of Remediation – Bioremediation

6.17.6. Phytoremediation

6.17.7. Metallophyte Plants

6.17.8. Interaction between Microorganisms and Plants

6.17.9. Rhizoremediation

6.17.10. Conclusion and Final Remarks

6.18. Phytofiltration of Heavy Metals

Glossary

6.18.1. Introduction

6.18.2. Selection of the Plant Species Offering the Best Performance

6.18.3. Selection of the Most Appropriate Phytofiltration System

6.18.4. Factors Affecting Metal Uptake by Plants

6.18.5. Treatment and Disposal of Biomass Containing Metals

6.18.6. Concluding Remarks

6.19. Phycoremediation

Glossary

6.19.1. Introduction

6.19.2. Nutrient Removal Utilizing Microalgae Strains with Special Attributes

6.19.3. Removal of Heavy Metals

6.19.4. Biodegradation of Toxic and Persistent Organic Pollutants

6.19.5. Use of Immobilized Microalgae and Cyanobacteria for Nutrient and Heavy Metal Removal

6.19.6. Concluding Remarks

6.20. Transgenic Plants and Associated Bacteria for Phytoremediation of Organic Pollutants

Glossary

Acknowledgments

6.20.1. Introduction

6.20.2. Phytoremediation: Cleaning Up Pollution with Plants and Associated Bacteria

6.20.3. Transgenic Plants and Bacteria for Phytoremediation

6.20.4. Conclusions

6.21. Potential for Enhanced Phytoremediation of Landfills Using Biosolids – A Review

Glossary

6.21.1. Introduction

6.21.2. Environmental Issues of Landfill

6.21.3. Postclosure Treatment

6.21.4. Phytoremediation of Landfills

6.21.5. Use of Biosolids in Landfill Phytoremediation

6.21.6. Conclusion

6.22. Methanotrophs

Glossary

Acknowledgments

6.22.1. Introduction

6.22.2. A Brief Overview of Methanotrophs

6.22.3. Cultivation of Methanotrophs

6.22.4. Potential Applications of Methanotrophs in Environmental Bioengineering

6.22.5. Engineering Challenges in the Use of Methanotrophs in Environmental Biotechnology

6.22.6. Conclusions and Future Prospects

6.23. Petroleum Spill Control with Biological Means

Glossary

6.23.1. Introduction

6.23.2. Fate (Weathering) of Oil Spills

6.23.3. Biostimulation

6.23.4. Bioaugmentation

6.23.5. Bioaugmentation or Biostimulation?

6.24. Biological Wastewater Treatment Systems

Glossary

6.24.1. Introduction

6.24.2. Life and Nutrient Transformation Processes

6.24.3. Microbial Carbon and Phosphorus Processes

6.24.4. Nitrogen Transformation Processes

6.24.5. Reaction Kinetics in Biological Treatment Systems

6.24.6. Biological Wastewater Treatment Systems

6.24.7. WWTPs – The Activated Sludge Process

6.25. Ecological Models

Glossary

Acknowledgments

6.25.1. Introduction

6.25.2. Wastewater Treatment Model Terminology

6.25.3. Wastewater Treatment Model Compartments

6.25.4. Plant-Wide Models

6.25.5. Guidelines for Application of WWTP Models

6.25.6. A General Framework for Application of WWTP Models

6.25.7. Major Limitations of Activated Sludge Models

6.26. Activated Sludge Model-Based Modeling of Membrane Bioreactor Processes

Glossary

Acknowledgements

6.26.1. Introduction

6.26.2. Application of Unmodified ASMs to MBR Processes

6.26.3. Application of Modified ASMs to MBR Processes

6.26.4. Outlook and Future Perspectives

6.26.5. Conclusions

6.27. Biological Nitrogen Removal from Domestic Wastewater

Glossary

6.27.1. Introduction

6.27.2. N-Removal Processes Based on Heterotrophic Denitrification

6.27.3. Advanced N-Removal Processes by Autotrophic Denitrification

6.27.4. Emerging Technologies and New Challenges in Urban WWTP

6.27.5. Conclusions

6.28. Biotechnological Methods for Nutrient Removal from Wastewater with Emphasis on the Denitrifying Phosphorus Removal Process

Glossary

6.28.1. Introduction

6.28.2. Biological–Chemical Phosphorus Removal

6.28.3. Historical Background

6.28.4. Biochemical and Microbiological Aspects

6.28.5. Denitrifying Phosphorus Removal

6.28.6. Future Perspectives

6.28.7. Summary

6.29. Constructed Wetlands for Water Treatment

Glossary

6.29.1. Introduction

6.29.2. Constructed Wetland Design

6.29.3. Constructed Wetland Bioprocesses

6.29.4. Limitations of Wetland Bioprocesses

6.29.5. Models for Constructed Wetland Performance Determination

6.29.6. Conclusions

6.30. Attached Growth Biological Systems in the Treatment of Potable Water and Wastewater

Glossary

6.30.1. Introduction

6.30.2. Water Treatment

6.30.3. Wastewater Treatment

6.30.4. Summary

6.31. Kinetics and Modeling of Anaerobic Treatment and Biotransformation Processes

Glossary

6.31.1. Introduction

6.31.2. Principles of Anaerobic Treatment

6.31.3. Kinetics and Modeling

6.31.4. Anaerobic Biotransformation Processes

6.32. Anaerobic Treatment of Organic Sulfate-Rich Wastewaters

Glossary

6.32.1. Introduction

6.32.2. Anaerobic Treatment of Organic Sulfate-Rich Wastewaters

6.32.3. Two-Phase Anaerobic Treatment

6.32.4. Effect of Low pH on Anaerobic Microbial Conversions

6.32.5. Toxicity

6.32.6. Concluding Remarks

6.33. Biotechnological Aspects of the Use of Methane as Electron Donor for Sulfate Reduction

Glossary

6.33.1. Sulfate-Containing Wastewaters and Biological Sulfate Reduction

6.33.2. Electron Donors for Biological Sulfate Reduction of Wastewaters from Power Plants and Metallurgical Industries

6.33.3. Methane as Electron Donor for Sulfate Reduction

6.33.4. Concluding Remarks

6.34. Sulfate Reduction for Inorganic Waste and Process Water Treatment

Glossary

Acknowledgments

6.34.1. Introduction

6.34.2. Waste and Process Streams with Sulfate

6.34.3. Electron Donor and Carbon Source for Sulfate Reduction

6.34.4. Effect of Process Conditions on Sulfate Reduction

6.34.5. Bioreactor Types Used for Sulfate Reduction

6.34.6. Sulfate-Reducing Applications and Metal Recovery

6.34.7. Future Prospects for Sulfate Reduction

6.35. Anaerobic Biotreatment of Municipal Sewage Sludge

Glossary

6.35.1. Introduction

6.35.2. Sludge Production and Characterization

6.35.3. Theory of Anaerobic Digestion

6.35.4. Process Configurations

6.35.5. Process Benefits

6.35.6. Biosolids Disposal and Reuse

6.36. Anaerobic Digestion of the Organic Fraction of Municipal Solid Waste for Methane Production

Glossary

6.36.1. Background

6.36.2. Waste Characteristics and Collection Strategies

6.36.3. The Importance for AD Design of Having Appropriate Values for B0 and G0

6.36.4. The Attainment of Representative Values for B0

6.36.5. Sorting/Preparation Technologies

6.36.6. AD Technologies and Performances

6.36.7. Carbon Footprint and Global Warming Potential of AD of Biowaste

6.36.8. A Case Study: AD as a Service Technology for the Territory

6.36.9. Conclusions

6.37. Occurrence, Toxicity, and Biodegradation of Selected Emerging Priority Pollutants in Municipal Sewage Sludge

Glossary

6.37.1. Introduction

6.37.2. Phthalic Acid Esters (Phthalates), PAEs

6.37.3. Polycyclic Aromatic Hydrocarbons (PAHs)

6.37.4. Surface-Active Agents (Surfactants)

6.37.5. Conclusions

6.38. Biodegradation of Micropollutants and Prospects for Water and Wastewater Biotreatment

Glossary

Acknowledgments

6.38.1. Introduction

6.38.2. Persistence and Effects of Micropollutants in the Environment

6.38.3. Properties of Micropollutants

6.38.4. Micropollutants in Activated Sludge Systems

6.38.5. Prospects for Water and Wastewater Biotreatment

6.38.6. Conclusions

6.39. Microbial Sensors for Monitoring and Control of Aerobic, Anoxic, and Anaerobic Bioreactors in Wastewater Treatment

Glossary

6.39.1. Introduction

6.39.2. Biosensors for Control of Aerobic Processes

6.39.3. Biosensors for Control of Anaerobic Digestion

6.39.4. Denitrification Control Biosensors

6.39.5. Other Types of Biosensors

6.39.6. Conclusions

6.40. Efficiency and Sustainability of Urban Wastewater Treatment with Maximum Separation of the Solid and Liquid Fraction

Glossary

6.40.1. Introduction

6.40.2. Actual Situation in Wastewater Treatment Plants

6.40.3. Sustainability in Wastewater Treatment

6.40.4. Overall Technology Ranking

6.40.5. Conclusions

6.41. Biotreatment of Drinking Water

Glossary

6.41.1. Introduction: Bacteria and Biofiltration – A Serendipitous Partnership

6.41.2. Biofilms and Oligotrophic Growth

6.41.3. Different Types of Biofilters

6.41.4. Parameters and Methodology for Biofiltration Monitoring

6.41.5. Conclusions, Questions, and Future Perspectives

6.42. Agriculture and Agro-Industrial Wastes, Byproducts, and Wastewaters

Glossary

6.42.1. Introduction

6.42.2. Guidelines for the Valorization of Agriculture and Agro-Industrial Wastes and Wastewaters

6.42.3. Biomass Resources

6.42.4. Wastewaters

6.42.5. Byproducts of the Olive-Oil Extraction Industry: An Emblematic Case

6.42.6. Conclusions

6.43. Production of Fine Chemicals by (Bio)Transformation of Agro-Food Byproducts and Wastes

Glossary

Acknowledgmentss

6.43.1. Introduction

6.43.2. Extraction and Extraction Techniques

6.43.3. Modification of Carbohydrates

6.43.4. Modification of Lipids (Oils and Fats) and Glycerol

6.43.5. Modification of Proteins

6.43.6. Modification of Phenol Derivatives

6.43.7. Production of d-Glucurono-γ-Lactone from Corn Wastes – A Case Study

6.43.8. Conclusions

6.45. Application of White-Rot Fungi in Transformation, Detoxification, or Revalorization of Agriculture Wastes

Glossary

Acknowledgments

6.45.1. Introduction

6.45.2. Fungal Transformation of Hazardous Organic Compounds in the Bioremediation of Polluted Soils and Industrial Wastewaters

6.45.3. Application of White-Rot Fungi and Laccases in the Pulp and Paper Industry

6.45.4. Revalorization of byproducts from Agriculture

6.45.5. The Role of White-Rot Fungi and Their Enzymes on Second-Generation Bioethanol

6.45.6. Concluding Remarks

6.46. A Microbial Perspective on Ethanolic Lignocellulose Fermentation

Glossary

6.46.1. Introduction

6.46.2. Fermenting Microorganisms

6.46.3. Conclusions and Perspectives

6.47. Techno-Economic Aspects of Ethanol Production from Lignocellulosic Agricultural Crops and Residues

Glossary

6.47.1. Introduction

6.47.2. Which Process Steps Can Be Considered Most Important?

6.47.3. Process Modeling

6.47.4. Conclusions

6.48. Biohydrogen Production from Agricultural Agrofood-Based Resources

Glossary

6.48.1. Introduction

6.48.2. Light-Driven Biohydrogen Production

6.48.3. Dark Fermentation

6.48.4. Strategies to Increase Biohydrogen Yields

6.48.5. Conclusions

6.49. Microbial Fuel Cells and Bioelectrochemical Systems

6.49.1. Introduction: BES in the Context of Industrial and Environmental Biotechnology

6.49.2. Fundamentals of Microbial Extracellular Electron-Transfer Processes

6.49.3. Microbial BES Generating Electricity: MFCs

6.49.4. Microbial BES for the Production of Chemicals: Microbial Electrolysis Cells

6.49.5. Microbial BES for Analytical Application: Microbial Biosensors

6.49.6. Microbial BES for Remediation of Contaminated Sites

6.50. Vanillin Production from Agro-Industrial Wastes

Glossary

6.50.1. Introduction

6.50.2. Bioconversion of Ferulic Acid into Vanillin

6.50.3. Corn-Based Processes

6.50.4. Rice-Based Processes

6.50.5. Wheat-Based Processes

6.50.6. Non-Cereal-Based Processes

6.50.7. Conclusions

6.51. Mixed Culture Processes for Polyhydroxyalkanoate Production from Agro-Industrial Surplus/Wastes as Feedstocks

Glossary

6.51.1. What Are Polyhydroxyalkanoates?

6.51.2. How Are PHAs Synthesized by Microbial Cells?

6.51.3. Governing the Selective Pressure for PHA-Storing Organisms in FF Processes

6.51.4. How Can Mixed Culture Processes Convert Organic Byproducts into PHAs?

6.51.5. Concluding Remarks and Future Perspectives

6.52. Biosorption for Industrial Applications

Glossary

6.52.1. Introduction

6.52.2. Biosorption Material Preparation

6.52.3. Biosorbent Material Processing and Formulation

6.52.4. Biosorption Process Principles

6.52.5. Biosorption Process Example

6.52.6. Conclusion

6.53. BT Technology for the Control of Methane Emissions from Permafrost and Natural Gas Hydrates

Glossary

6.53.1. Introduction

6.53.2. Oxic and Anoxic Methane Oxidation

6.53.3. Methane-Oxidizing Consortia and Biofilms

6.53.4. Membrane-Attached Bioreactors

6.53.5. Technical-Scale Methanotrophic Membrane Biofilm Reactors

6.53.6. Concluding Remarks

6.54. Molecular Aspects of Microbial Dissimilatory Reduction of Radionuclides

Glossary

6.54.1. Introduction

6.54.2. Phylogenetic Diversity of Dissimilatory Radionuclide-Reducing Microorganisms

6.54.3. Enzymatic Aspects of Microbial Dissimilatory Reduction of Radionuclides

6.54.4. Genomic Aspects of Microbial Dissimilatory Reduction of Radionuclides

6.54.5. In situ Bioremediation Potential of Dissimilatory Radionuclide-Reducing Microorganisms

6.54.6. Conclusions

6.55. Today’s Wastes, Tomorrow’s Materials for Environmental Protection

Glossary

Acknowledgments

6.55.1. Introduction

6.55.2. Case Histories Illustrating Bioconversion of Wastes into New Materials