Development in Wastewater Treatment Research and Processes: Microbial Ecology, Diversity and Functions of Ammonia Oxidizing Bacteria

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Development in Wastewater Treatment Research and Processes: Microbial Ecology, Diversity, and Functions of Ammonia-Oxidizi ...
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Contents
Contributors
Chapter 1: Anammox process: An innovative approach and a promising technology
	1.1. Introduction
	1.2. Mechanism of anammox process
	1.3. Role of microorganisms in anammox
	1.4. Role of various parameters on anammox
		1.4.1. Ammonium
		1.4.2. Nitrite
		1.4.3. Organic matter
	1.5. The limitations and solutions of the anammox system
	1.6. Conclusion
	Conflict of interest
	References
Chapter 2: Abundance of ammonia-oxidizing bacteria and archaea in industrial wastewater treatment systems
	2.1. Introduction
	2.2. Key enzymes involved
	2.3. Physiology and cellular structure
		2.3.1. Physiology of AOA
			2.3.1.1. Kinetics stoichiometry of ammonia oxidation
		2.3.2. Physiology of AOB
	2.4. Diversity in WWTPs
		2.4.1. Diversity of AOA
		2.4.2. Diversity of AOB
	2.5. Mechanism of action of AOA and AOB
		2.5.1. Mechanism of AOA
		2.5.2. Mechanism of AOB
	2.6. Competition and symbiotic relationships between AOMs
	2.7. AOA at low DO or in special WWTPs
	2.8. Factors influencing AOB abundance and diversity
		2.8.1. Ammonia levels
		2.8.2. FNA and nitrite
		2.8.3. Process conditions and regime
	2.9. Quantification techniques
		2.9.1. DNA extraction
		2.9.2. Quantitative PCR and reverse transcriptional qPCR
		2.9.3. High throughput sequencing
		2.9.4. Phylogenetic analysis
	2.10. Environmental factors affecting AOA and AOB
		2.10.1. Ammonia concentration
		2.10.2. Temperature
		2.10.3. Oxygen and aeration pressure
		2.10.4. Organic loading
		2.10.5. Salinity
		2.10.6. DO
		2.10.7. Sulfide
	2.11. Future perspectives
	2.12. Conclusion
	References
Chapter 3: Autotrophic nitrification in bacteria
	3.1. Introduction
	3.2. Symbiotic nitrogen fixers
		3.2.1. Molecular mechanism of endosymbionts
		3.2.2. Molecular mechanism of nodule formation
		3.2.3. Mechanism of exchange of nutrients and nitrogen
	3.3. Events of nitrogen fixation
		3.3.1. Nitrification
		3.3.2. Nitrate and nitrite synthesis during nitrification
		3.3.3. Hydroxylamine oxidoreductase
		3.3.4. Nitrous oxide production during nitrification
	3.4. Genetic regulation of nitrogen fixation
	3.5. Understanding the balance between Photosynthesis and nitrogen fixation
		3.5.1. Nitrogen fixation by cyanobacteria
		3.5.2. Nitrogen fixation by rhizobia
			3.5.2.1. Nitrogenase and its mode of action
		3.5.3. Role of abiotic factors in BNF
	3.6. Conclusion and future aspect
	References
Chapter 4: Omics: A revolutionary tool to study ammonia-oxidizing bacteria and their application in bioremediation
	4.1. Introduction
	4.2. Chemolitho-autotrophic ammonia oxidation
	4.3. Role of ammonia-oxidizing bacteria in nitrogen cycling
	4.4. Commercial significance and application of ammonia-oxidizing bacteria
	4.5. Difficulties associated with nitrification and ammonia-oxidizing bacteria
	4.6. Isolation of ammonia-oxidizing bacteria from the environment
	4.7. Cultivation of new ammonia oxidizers
	4.8. Genomics and metabolic models
	4.9. Terminology of environmental proteomics
	4.10. Microbial culture proteomic studies techniques
	4.11. Potential applications of environmental proteomics
	4.12. Enzymology of ammonia-oxidation
	4.13. Ammonia-oxidizers in the environment and production of N2O
	4.14. Remediation of recalcitrant pollutants
	4.15. Conclusion
	References
Chapter 5: Diversity of ammonia-oxidizing bacteria
	5.1. Introduction
	5.2. Emission of nitrous oxide
		5.2.1. Potential sources
		5.2.2. Yield
	5.3. Niche differentiation
		5.3.1. Oligotrophy
		5.3.2. pH
	5.4. Conclusion
	References
Chapter 6: Aerobic and anaerobic ammonia oxidizing bacteria
	6.1. Introduction
	6.2. Ammonia-oxidizing bacteria
		6.2.1. Ecology
		6.2.2. Environmental regulators of ammonia oxidation
		6.2.3. Strategic functional, anatomical, and biological differentiations among ammonia oxidizers
	6.3. Anaerobic ammonium oxidation bacteria
		6.3.1. Ecology
			6.3.1.1. Geographical distribution
			6.3.1.2. Geochemical importance and important environmental constituents
		6.3.2. Physiology of anammox bacteria
	6.4. Microbial interactions and their contribution to enhanced nitrogen removal
	6.5. Conclusion
	References
Chapter 7: Recent advances in biological nitrogen removal from wastewater: Special focus on reactor configuration and nan ...
	7.1. Introduction
	7.2. Chemolithotrophs and their diversity
		7.2.1. Obligate chemolithotroph bacteria
		7.2.2. Facultative chemolithotroph bacteria
		7.2.3. Sulfur-oxidizing bacteria
		7.2.4. Ammonium-oxidizing bacteria
		7.2.5. Nitrite-oxidizing bacteria
		7.2.6. Methane-oxidizing bacteria or methanotrophs
		7.2.7. Ferrous-oxidizing bacteria
		7.2.8. Hydrogen-oxidizing bacteria
	7.3. BNR technologies for wastewater treatment
		7.3.1. Nitrification/denitrification
		7.3.2. Nitritation/denitritation
		7.3.3. Sidestream partial nitritation/anammox
		7.3.4. Mainstream partial nitritation/anammox
		7.3.5. Nitrogen recovery
		7.3.6. Phototrophic systems
		7.3.7. Microbial electrochemical cells
	7.4. Advances in the nitrification process
		7.4.1. Sequencing batch reactor
		7.4.2. Activated sludge models
	7.5. Effect of nanomaterials on microbial nitro-transformation
	7.6. Conclusion and future perspective
	References
Chapter 8: Diversity of nitrogen-removing microorganisms
	8.1. Introduction
	8.2. Nitrogen removal by microorganisms that use sulfur compounds as electron donor
		8.2.1. Autotrophic denitrifying sulfur-oxidizing bacteria
		8.2.2. Growth conditions of ADSOB
		8.2.3. Metabolic pathways involved in sulfur compound oxidation
		8.2.4. Molecular tools for assessing microbial diversity in SDAD processes
		8.2.5. Technologies used to carry out the SDAD process to treat wastewaters
		8.2.6. Relevant operating conditions in the SDAD process to treat wastewaters
		8.2.7. Projections of using the SDAD process to remove nitrogen in wastewaters
	8.3. Nitrogen removal by microorganisms that use hydrogen as electron donor: Hydrogenotrophic denitrification
		8.3.1. Nitrate removal pathway and hydrogen as electron donor
		8.3.2. Microorganisms and microbial community involved in the process
		8.3.3. Basis of operational conditions
		8.3.4. Possibilities and available technologies for large-scale application
	8.4. Nitrogen removal by anaerobic nitrate-dependent methanotrophic microorganisms
		8.4.1. Nitrogen removal pathways and ecosystem distribution of the different types of microorganisms
		8.4.2. Activity and factors affecting the enrichment of these microorganisms
		8.4.3. Molecular tools for assessing microbial diversity
		8.4.4. Application possibilities in sewage and industrial wastewater treatment plants-Main operating conditions description
	Acknowledgments
	References
Chapter 9: An overview of the anammox process
	9.1. Introduction
	9.2. The evolution of anammox reaction stoichiometry
	9.3. The existing problems and countermeasures for anammox process application
		9.3.1. The rapid start-up and recovery of anammox-based process
		9.3.2. The retention of anammox sludge in the reactor
		9.3.3. The further improvement of NRE
	9.4. The status of several main anammox-related processes
		9.4.1. Nitritation process
		9.4.2. Pure anammox process
		9.4.3. PNA process
			9.4.3.1. One-stage PNA and two-stage PNA
			9.4.3.2. The comparison of the one-stage and two-stage PNA process
		9.4.4. Simultaneous nitrogen removal and phosphorus recovery process
		9.4.5. Denitratation/anammox process
		9.4.6. DAMO/anammox process
	9.5. Conclusion
	References
Chapter 10: Aerobic and anaerobic ammonia-oxidizing bacteria: A resilient challenger or innate collaborator
	10.1. Introduction
	10.2. Physiology and ecology of ammonia-oxidizing bacteria
		10.2.1. Ecology of ammonia-oxidizing bacteria
		10.2.2. Physiology of ammonia-oxidizing bacteria
		10.2.3. Biodiversity of aerobic and anaerobic oxidizing bacteria
		10.2.4. Species diversity
	10.3. Factors affecting aerobic and anaerobic oxidizing bacteria
		10.3.1. Ammonia levels
		10.3.2. Organic carbon
		10.3.3. Temperature
		10.3.4. Salinity
		10.3.5. DO levels
		10.3.6. pH
		10.3.7. Sulfide levels
		10.3.8. Phosphate
	10.4. Role of aerobic and anaerobic ammonia-oxidizing bacteria in wastewater treatment plants
	10.5. Application of anammox in wastewater treatment
		10.5.1. Advantages
		10.5.2. Disadvantages
	10.6. Ammonia-oxidizing microorganisms: Key players in the promotion of plant growth
		10.6.1. Autotrophic nitrification
		10.6.2. Heterotrophic nitrification
		10.6.3. Diversity of ammonia oxidizers
	10.7. Mechanism of ammonia oxidation by ammonia-oxidizing microorganisms
	10.8. Function and activity of ammonia-oxidizing microbes in different soil types
		10.8.1. pH
		10.8.2. Bioavailability of nutrients
		10.8.3. Temperature
		10.8.4. Soil water content
	10.9. Conclusion
	References
Chapter 11: A technique to boost the nitrogen-rich agricultural ecosystems efficiency by anaerobic ammonium oxidation (an ...
	11.1. Introduction
	11.2. Role of anaerobic ammonium oxidation in nitrogen cycle
	11.3. Diversity and richness of anammox bacteria
	11.4. Uncovering anammox bacteria and its reaction
	11.5. Role of anammox in agricultural soil
		11.5.1. Anammox in paddy soil
		11.5.2. Anammox in arable high grounded soil
		11.5.3. Anammox in special sites
			11.5.3.1. Rhizosphere
			11.5.3.2. Surface soil
	11.6. Factors affecting anammox
		11.6.1. Nitrate, nitrite, and ammonium
		11.6.2. Salinity and pH of the soil
		11.6.3. Rhizosphere effect
	11.7. Outlook for anammox research and concluding remarks
	11.8. Future prospects
	Acknowledgments
	References
Chapter 12: Genomics of ammonia-oxidizing bacteria and denitrification in wastewater treatment plants
	12.1. Introduction
	12.2. Nitrogen cycle
	12.3. Role of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrogen cycle
	12.4. Factors that influence AOM abundance and distribution
	12.5. Other ammonia-oxidizing microorganisms in wastewater treatment
	12.6. Genetic regulation for ammonia oxidation by AOMs
		12.6.1. Genes involved in the oxidation of ammonia to hydroxylamine
		12.6.2. Genes involved in the oxidation of hydroxylamine to nitric oxide and further to nitrite
		12.6.3. Genes involved in the direct oxidation of ammonia to nitrate
	12.7. Gene amoA as a functional marker for AOM
		12.7.1. Evolutionary relation of AMO and pMMO
	12.8. Denitrification
		12.8.1. Nitrate reduction to nitrite
		12.8.2. Nitrite reduction to nitric oxide
		12.8.3. Nitric oxide reduction to nitrous oxide
		12.8.4. Nitrous oxide reduction to molecular nitrogen
	12.9. Nitrifier denitrification
	12.10. Conclusions
	References
Chapter 13: Genomic modules of the nitrifying and denitrifying bacterial population in the aerated wastewater tre
	13.1. Introduction
	13.2. Microbial association and biofilm formation in the aerated bioreactors
	13.3. Mutualism between the microbial communities
	13.4. Factors influencing the microbial shift
		13.4.1. Substrate availability
		13.4.2. Carbon-nitrogen (C/N) ratio
		13.4.3. Dissolved oxygen (DO) concentration
		13.4.4. Temperature
		13.4.5. pH
	13.5. Population dynamics of the bacterial groups
		13.5.1. Functional plasticity and functional redundancy
	13.6. Microbial community in the biofilm
	13.7. Heterotrophic nitrification and aerobic denitrification
	13.8. Functional genomics of the microbial community
		13.8.1. Nitrifiers
		13.8.2. Comammox
		13.8.3. Anammox
		13.8.4. Denitrifiers
	13.9. Molecular approaches and bioinformatics tools-Dynamics of the microbial population
	13.10. Conclusion
	References
Chapter 14: Influence of the different operational strategies on anammox processes for the sustainable ammonium wastew
	14.1. Introduction
	14.2. Microorganisms involved in the anammox process
	14.3. Mechanism of anoxic removal of ammonia
	14.4. Factors affecting Anammox process and operational strategies
		14.4.1. Temperature
		14.4.2. pH
		14.4.3. Dissolved oxygen (DO)
		14.4.4. Nitrogen loading
		14.4.5. Carbon sources
		14.4.6. Organic toxicants
			14.4.6.1. Alcohol and aldehydes
			14.4.6.2. Phenols
			14.4.6.3. Antibiotics
		14.4.7. Effect of toxic metals on anammox process
			14.4.7.1. Copper
			14.4.7.2. Zinc
			14.4.7.3. Cadmium
	14.5. Recent advancement in anammox process
	14.6. Diverse applications of anammox process
	14.7. Future prospectus of anammox process
	14.8. Conclusion
	Acknowledgments
	References
Chapter 15: Anammox processes in marine environment: Deciphering the roles and applications
	15.1. Introduction
	15.2. Overview of the anammox process
	15.3. Anammox bacteria in marine environment
	15.4. Anammox processes in different marine ecosystems
		15.4.1. Marine sediment
		15.4.2. Oxygen minimum zone
		15.4.3. Marine sponges
		15.4.4. Arctic sea ice
	15.5. Role of anammox in marine environment
		15.5.1. Anammox and marine biogeochemical cycles
		15.5.2. Marine nitrogen cycling and anammox: A global perspective
	15.6. Application of anammox process in marine environment and its potential
		15.6.1. Application in marine aquaculture
		15.6.2. Application in wastewater treatment
	15.7. Conclusion
	References
Chapter 16: Diversity and versatility of ammonia-oxidizing bacteria
	16.1. Introduction
	16.2. Evolution and classification of ammonium-oxidizing microorganisms (AOMs)
		16.2.1. AOB and AOA
		16.2.2. Ammonium oxidizer in Comammox
		16.2.3. Anaerobic ammonium oxidizer in anammox
		16.2.4. Heterotrophic nitrifying bacteria (HNB) as ammonium oxidizers
	16.3. Diversity, specificity, and adaptability of AOB
		16.3.1. Diversity of AOB
		16.3.2. Specificity of AOB
			16.3.2.1. pH and Temperature
			16.3.2.2. DO concentration
			16.3.2.3. Hydraulic retention time (HRT) and Sludge residence time (SRT)
		16.3.3. Adaptability in cohabitation with other species
	16.4. Tolerance and inhibition of AOB
		16.4.1. Ammonia
		16.4.2. Carbon
		16.4.3. Other inhibitory substances
	16.5. Recent applications and challenges of AOB
		16.5.1. Novel and Hybrid reactors involving AOBs
		16.5.2. Challenges on employing AOB
	16.6. Future research prospects employing the versatile ammonium oxidizers
	16.7. Conclusions
	References
Chapter 17: Role of ammonia oxidizers in performing simultaneous nitrification and denitrification process in advanced
	17.1. Introduction
	17.2. Theory of SND and practical applications in different WWTPs/technologies
	17.3. Advantages of SND over anammox and other biological nitrogen removal processes
		17.3.1. Nitrification-denitrification
		17.3.2. Nitritation-Denitritation
		17.3.3. Simultaneous nitrification and denitrification (SND) (or aerobic denitrification)
		17.3.4. Nitritation-ANAMMOX
		17.3.5. CANON process
	17.4. Types and characteristics of different ammonia oxidizers and nitrate reducers encouraging SND mechanism prevailing  ...
	17.5. Operational parameters/factors that control the diversity of nitrifiers (ammonia and nitrite oxidizers) and denitri ...
		17.5.1. Carbon source: Readily biodegradable COD, soluble COD, soluble BOD5
		17.5.2. C/N ratio
		17.5.3. Floc size and PHB storage
		17.5.4. Dissolved oxygen control
		17.5.5. ORP
		17.5.6. pH
		17.5.7. Temperature
		17.5.8. HRT and SRT
	17.6. Effect of free ammonia (FA), nitrate concentrations, and some metals on AOBs
	17.7. Conclusion
	References
Chapter 18: Diversity and functional role of ammonia-oxidizing bacteria in soil microcosms
	18.1. Introduction
	18.2. Diversity and distribution of ammonia-oxidizing bacteria in soil
		18.2.1. Diversity of ammonia-oxidizing bacteria in different ecological niches
			18.2.1.1. Agricultural soil
			18.2.1.2. Grassland and forest soil
			18.2.1.3. Cold habitats
		18.2.2. Determination of soil AOB diversity
			18.2.2.1. Culture-dependent method
			18.2.2.2. Culture-independent method
	18.3. Factors affecting ammonia oxidation in soil
		18.3.1. Ammonia concentration
		18.3.2. Soil pH
		18.3.3. Temperature
		18.3.4. Moisture content
		18.3.5. Fertilizers and manures
		18.3.6. Contaminants
		18.3.7. Salinity
	18.4. Molecular biology of ammonia oxidation in bacteria
	18.5. Economic importance of AOBs
	18.6. Conclusion and prospects
	References
Chapter 19: Anaerobic ammonia oxidation: From key physiology to full-scale applications
	19.1. Introduction
	19.2. Anammox bacteria: Diversity and cell biology
	19.3. Physiological parameters and the metabolic pathway involved in anammox
	19.4. Possible reaction mechanism for the anammox process and the factors influencing the reaction
	19.5. Anammox culture in the laboratory
	19.6. Full-scale applications of the anammox process
	19.7. Conclusions
	References
Chapter 20: Ammonification in the oral microbiome with plausible link to diet and health and their systemic role
	20.1. Introduction
	20.2. Ammonification and chemolithotrophs
		20.2.1. Gluconeogenesis
		20.2.2. Role of ammonia-oxidizing bacteria
		20.2.3. Ammonia flux
			20.2.3.1. Measurement of ammonia flux
	20.3. Oral microbiome
		20.3.1. The oral microbiota
		20.3.2. Streptococcus mutans group
		20.3.3. Role of enzymes
		20.3.4. Halitosis
		20.3.5. Impact on daily life
	20.4. Plausible link to diet and health
	20.5. Contemporary scenario and future perception
		20.5.1. Quorum sensing (QS)
		20.5.2. Inhibition mechanism
	20.6. Conclusion
	References
Chapter 21: Nitritation kinetics and its application in wastewater treatment
	21.1. Introduction
	21.2. Factors affecting kinetics of ammonia oxidation microorganisms and nitritation performance
		21.2.1. Aerobic ammonia-oxidizing microorganisms
		21.2.2. Temperature
		21.2.3. Free ammonia, and free nitrous acids and pH
		21.2.4. Aeration control
		21.2.5. DO concentration
	21.3. Unit processes of nitritation
		21.3.1. Suspended growth systems
		21.3.2. Attached growth systems
		21.3.3. Hybrid systems
	21.4. Conclusions and perspectives
	References
Index
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