Note: Front Cover -- Plant Small RNA: Biogenesis, Regulation and Application -- Copyright -- Contents -- Contributors -- Section: 1 Basics -- Chapter 1 Introduction to plant small RNAs -- Introduction -- Discovery history of small RNAs -- Diversity of small RNAs -- miRNAs -- Biogenesis of plant miRNAs -- miRNA turnover -- Mode of action of miRNAs -- miRNA-guided transcript cleavage -- miRNA-mediated translation repression -- miRNAs in plant development -- miRNA-mediated regulation of meristem organization and cell polarity -- miRNA-mediated regulation of flower development -- miRNA-mediated regulation of root architecture -- miRNA-mediated regulation of seed development -- siRNAs -- Biogenesis of siRNAs -- Mode of action of siRNAs -- Biological functions of 24-nt transposable element (TE)-derived siRNAs -- phasiRNAs -- Biogenesis of phasiRNAs -- Biological functions of phasiRNAs -- Movement of small RNAs -- Future perspectives -- Acknowledgment -- References -- Further reading -- Chapter 2 Diversity and types of small RNA -- Small regulatory RNAs: Historical milestones -- Classifying endogenous small RNA in plants -- Hairpin sRNA and microRNA -- Natural antisense transcript siRNA -- Secondary and trans-acting siRNA -- Heterochromatic siRNA -- References -- Chapter 3 Biogenesis of small RNA: Molecular pathways and regulatory mechanisms -- DNA-dependent RNA polymerase -- RNA-dependent RNA polymerase -- Dicer -- Argonaute proteins in plants -- Ago1 -- Ago10 -- Ago5 -- Ago7 -- AGO2 and AGO3 -- Ago4 -- Ago6 -- AGO8 and AGO9 -- Determinants for AGO-sRNA sorting and biological function -- Small RNA in transgenerational epigenetic inheritance -- Interrelationship between sRNA pathways -- Analyzing sRNA: Computational challenges from the "dry lab" -- References. , Chapter 4 Transcriptome-based identification of small RNA in plants: The need for robust prediction algorithms -- Introduction -- The need for small RNA Seq in plants -- Types of RNA Seq strategies -- dUTP-based strand-specific RNA Seq -- Bulked segregant analysis (BSA) using RNA Seq -- Double-stranded RNA Seq -- Differential RNA Seq -- Elements of RNA Seq data and analyses -- Raw read -- Read alignment -- Quantification -- Transcript identification -- Alignment -- Differential gene expression analyses -- Alternative splicing identification -- Identifying gene fusions -- Challenges and solutions for annotating small RNAs in plants -- Empirical toolkits and databases -- Fastx -- miRCat -- SiloCo -- miRBASE -- TAPIR [ http://bioinformatics.psb.ugent.be/webtools/tapir/ ] -- Emerging algorithms -- Validation of expression using time course data -- Normalization and log ratio transformation method -- Tools and databases available according to the basic steps of RNA Seq data analyses -- Quality control -- Trimming and adapters removal -- Error correction -- Bias correction -- Other tasks/preprocessing data -- Alignment tools -- De novo splice aligners -- Normalization, quantitative analysis, and differential expression -- Open (free) source solutions -- Alternative splicing analysis -- Differential isoform/transcript usage -- Fusion genes/chimeras/translocation finders/structural variations -- Single-cell RNA Seq -- Integrated packages -- Genome-guided assemblers [88, 89] -- Co-expression networks -- Visualization tools -- Functional, network, and pathway analysis tools -- Links to databases used for analysis of plant transcriptome data -- A case study: Transcriptome analyses from Vigna mungo and identification of miRNAs -- Background of the work -- Sample preparation and sequencing -- Screening and identification of miRNAs from sequenced data. , Identification of established and novel miRNA sequences -- miRNA target prediction, gene ontology classification, and quantification of target genes -- Quantification of miRNAs in different tissues to study their tissue-specific expression -- Expression patterns of miRNAs from both mock control (MC) and MYMIV-inoculated (MI) datasets -- qPCR validation of miRNA targets in MYMIV-susceptible and -resistant background -- References -- Further reading -- Section: 2 Expression and regulation mechanism of small RNA -- Chapter 5 Role of RNA interference in seed germination -- Introduction -- Mechanism of seed germination -- Phases in seed germination -- Factors regulating seed germination -- The phenomenon of RNA silencing -- Mechanism of RNA silencing -- miRNAs -- Tasi-RNAs -- Role of small RNAs in seed germination -- miRNA serve as convergence regulatory nodes -- Conclusion -- Acknowledgment -- References -- Chapter 6 Importance of small RNA in plant seed germination -- Brief introduction of seed germination -- miRNAs related to seed germination in Arabidopsis -- miRNAs related to seed germination in crops -- siRNAs related to seed germination -- References -- Further reading -- Chapter 7 Importance of small RNA in plant metabolism -- Introduction -- Major types of plant sRNA -- Biogenesis of small RNA in plants: microRNA and small interference RNA -- Diverse functions of sRNA in controlling plant metabolism during stress condition -- Role of miRNAs in ABA-mediated stress responses -- miRNA-mediated adaptive response to drought and salt stress conditions -- Regulation of cold and heat stress tolerance by miRNAs expression -- miRNAs expression to hypoxia and oxidative stress -- miRNA in response to nutrient homeostasis -- Regulating plant metabolism: Role of sRNAs -- miRNA-mediated regulation plant phytohormone signaling. , miRNA: Transcription factors in regulating plant metabolism -- Functional role of miRNA in plant secondary metabolism biosynthesis -- Regulatory role of siRNAs in plant stress responses -- Conclusion and future prospectus -- References -- Further reading -- Chapter 8 Small RNA in tolerating various biotic stresses -- Small RNA: Discovery, classifications, and biogenesis -- Classification -- MicroRNAs and isomiRs -- Ta-siRNAs -- Nat siRNA -- Heterochromatic-siRNA -- Pathogen-derived sRNAs and miRNA-like molecules -- Biogenesis -- Methodologies applied for sRNA research -- Parameters applied for sRNA prediction -- Plant miRNAs and pathogen milRs -- Plant ta-siRNAs -- Plant isomiRs -- Databases available for sRNAs -- SRNA-mediated biotic stress responses in plants -- SRNA-mediated responses against insects -- SRNA-mediated responses against fungi -- SRNA-mediated responses against virus -- SRNA-mediated responses against bacteria -- SRNA-mediated responses against abiotic stress -- SRNAs and agricultural improvement -- Small RNA as a spray -- Conclusion -- References -- Further reading -- Chapter 9 Role of small RNA in regulating plant viral pathogenesis -- Introduction -- Illustrations of siRNA-mediated and miRNA-mediated antivirus pathway mechanisms -- Role of miRNA in plant antiviral defense -- Application of siRNA against plant antiviral defense -- Regulation of siRNA for plant viral pathogenesis -- siRNA response against bacterial diseases -- Role of siRNA to prevent fungal disease -- References -- Chapter 10 Salt stress tolerance and small RNA -- Introduction -- Plant sRNAs: Types and biogenesis -- miRNA -- siRNA -- Trans-acting siRNAs (ta-siRNAs) -- Natural antisense siRNAs (nat-siRNAs) -- Heterochromatic siRNAs (hec-siRNAs) -- Role of sRNAs in salt stress response -- Conclusion and future perspective -- Acknowledgment -- References. , Further reading -- Chapter 11 Small RNAs and cold stress tolerance -- Introduction -- Cold stress sensing and second messengers -- Mechanism of cold acclimatization -- Small RNAs and cold stress tolerance -- Biogenesis of miRNAs and siRNAs -- Role of miRNAs in cold stress tolerance -- Role of siRNAs in cold stress tolerance -- Genes involved in cold stress -- Conclusion -- References -- Further reading -- Chapter 12 Toward elucidating the functions of miRNAs in drought stress tolerance -- Introduction -- Drought and drought tolerance mechanisms -- Drought escape -- Drought avoidance -- Drought tolerance -- Physiological and biochemical mechanisms of drought tolerance -- Stomatal aperture regulation -- Reactive oxygen species accumulation -- Metabolism maintenance -- Molecular basis of drought tolerance -- Transcription factors -- MiRNAs -- Discovery of miRNAs -- Biogenesis of miRNAs -- Functional modes of miRNAs -- MiRNA responses to drought stress -- Targets of drought-responsive miRNAs -- Contribution of miRNAs to drought stress tolerance -- Conclusion and future perspectives -- References -- Chapter 13 Regulation of photosynthesis and vegetative growth of plants by small RNAs -- Introduction -- Roles of small RNAs in vegetative growth -- Regulation of shoot apical meristem genes -- Abaxial-adaxial polarity -- Morphology and size of leaves -- Guard cell patterning -- Leaf senescence -- Vegetative phase transition -- Regulation of root traits -- Roles of small RNAs in photosynthesis -- Possible applications of small RNAs in modulating photosynthesis and vegetative growth -- Rice -- Tobacco -- Potato -- Maize -- Legume -- Wheat -- Poplar -- Tomato -- Conclusion -- References -- Chapter 14 Heat stress tolerance through small RNA -- Introduction -- Biogenesis -- How do miRNAs regulate stress response? -- Heat-responsive miRNAs in plants. , MiRNA families in cereal crops and their regulatory pathways.

Note: Intro -- Preface -- Acknowledgments -- Contents -- About the Editors -- Part I: Bioremediation and Biodegradation -- 1: Bioremediation and Functional Metagenomics: Advances, Challenges, and Opportunities -- 1.1 Introduction -- 1.2 Bioremediation -- 1.3 History of Bioremediation -- 1.4 Bioremediation Successes -- 1.5 Mechanism of Bioremediation -- 1.6 Microorganisms Used in Bioremediation -- 1.6.1 Fungi -- 1.6.1.1 Phanerochaete Chrysosporium -- 1.7 Factors Affecting Bioremediation -- 1.7.1 Biotic Factors -- 1.7.1.1 The Availability of Bacteria That Degrade Hydrocarbons -- 1.7.1.2 Competition and Cooperation Among Bacteria -- 1.7.1.3 Exogenous and Indigenous Hydrocarbon-Degrading Bacteria -- 1.7.1.4 Number of Hydrocarbon-Degrading Bacteria -- 1.7.1.5 Redox Potential of the Bacteria -- 1.7.1.6 Effect of Biosurfactants -- 1.7.2 Abiotic Factors -- 1.7.2.1 Contaminant Physical and Chemical Properties -- 1.7.2.2 Hydrocarbon Concentration -- 1.7.2.3 Nutrient Availability -- 1.7.2.4 Oxygen Availability -- 1.7.2.5 Moisture Availability -- 1.7.2.6 Bioavailability -- 1.8 Bioremediation Types -- 1.8.1 Ex Situ Bioremediation -- 1.8.1.1 Treatment in the Solid Phase -- 1.8.1.2 Slurry-Phase Bioremediation -- 1.8.2 In Situ Bioremediation -- 1.9 Bioremediation Approaches for Environmental Clean-Up -- 1.9.1 Ex Situ Bioremediation Approaches -- 1.9.1.1 Biopile -- 1.9.1.2 Biofilter -- 1.9.1.3 Land Farming -- 1.9.1.3.1 Composting -- 1.9.1.4 Bioreactor -- 1.9.2 In Situ Bioremediation Approaches -- 1.9.2.1 Bioventing -- 1.9.2.2 Biosparging -- 1.9.2.3 Bioslurping -- 1.10 Metagenomics -- 1.11 Metagenomics in Bioremediation Process -- 1.12 Metagenomics Research in a Contaminated Environment -- 1.12.1 Sampling from Contaminated Site -- 1.12.2 Extracting the DNA from Contaminated Samples -- 1.12.3 Metagenome Analysis -- 1.12.3.1 Targeted Metagenomics Using a Library. , 1.12.3.1.1 Creating a Metagenomics Library -- 1.12.3.1.2 Screening of Metagenomic Clones -- 1.12.3.1.2.1 Screening Based on a Sequence -- 1.12.3.1.2.2 Function-Driven Sequence -- 1.12.4 Direct Sequencing of Metagenomics -- 1.12.5 Next-Generation Sequencing -- 1.12.6 Bioinformatics Analysis -- 1.12.7 Assembly -- 1.12.8 Binning -- 1.12.9 Annotation -- 1.13 Metagenomics in Bioremediation: Current Challenges and Future -- 1.14 Conclusion -- References -- 2: Bioremediation: Gaining Insights Through Metabolomics -- 2.1 Introduction -- 2.2 Impact of Metabolomics on Bioremediation -- 2.3 Application of Computer in Metabolomic Study -- 2.4 Application of Metabolomics in Space Bioremediation -- 2.5 Future Advancement -- 2.6 Conclusion -- References -- 3: Metagenomics, Microbial Diversity, and Environmental Cleanup -- 3.1 Introduction -- 3.2 Conventional Methods of Gene Sequencing -- 3.2.1 Polymerase Chain Reaction (PCR) -- 3.2.2 Fluorescence In Situ Hybridization (FISH) -- 3.2.3 Amplified Ribosomal DNA Restriction Analysis -- 3.2.4 Ribosomal Intergenic Spacer Analysis -- 3.2.5 DNA Microarrays -- 3.2.6 Randomly Amplified Polymorphic DNA (RAPD) Analysis -- 3.3 Next-Generation Sequencing Techniques -- 3.3.1 Pyrosequencing Technology -- 3.3.2 Roche 454 (GS FLX Plus) -- 3.3.3 Reverse Terminator Technology -- 3.3.3.1 Illumina Solexa -- 3.3.3.2 Ion Torrent -- 3.3.3.3 Sequencing by Ligation Technology -- 3.3.3.4 ABI SOLiD -- 3.4 Metagenomics Sequencing and Its Framework -- 3.5 Tools for Metagenomic Data Analysis -- 3.6 Bioinformatics Tools for Functional Analysis of Metagenome -- 3.7 Application of Metagenomics -- 3.7.1 Food Industries -- 3.7.2 Novel Bioactive Discovery -- 3.7.3 Novel Antimicrobials Discovery -- 3.7.4 Xenobiotic Degradation -- 3.8 Importance of Metagenomics in Bioremediation of Pollutants -- 3.9 Conclusion and Future Perspectives -- References. , 4: Plant-Microbe Associations in Remediation of Contaminants for Environmental Sustainability -- 4.1 Introduction -- 4.2 Plant-Microbe Interaction -- 4.2.1 Endophytic Microbiome -- 4.2.2 Plant Growth-Promoting Rhizobacteria -- 4.2.3 Plant-Released Signals -- 4.2.4 Microbial Signals -- 4.2.5 Quorum Sensing -- 4.3 Remediation of Contaminants by Plant-Microbe Combination -- 4.3.1 Removal of Pollutants from Aquatic Environments -- 4.3.2 Removal of Pollutants from Terrestrial Environment -- 4.3.3 Removal of Pollutants from Atmosphere -- 4.4 Examples of Bacterial-Assisted Phytoremediation -- 4.5 Microbial-Assisted Phytoextraction -- 4.6 Microbial-Assisted Phytostabilisation -- 4.7 Microbial-Assisted Phytovolatilisation -- 4.8 Rhizoremediation -- 4.9 Phytostimulation -- 4.10 Microbial-Assisted Phytodegradation -- 4.11 Challenges Faced During Remediation by Plant-Microbe Associations -- 4.12 Conclusion -- References -- 5: Recent Trends in Bioremediation of Heavy Metals: Challenges and Perspectives -- 5.1 Introduction -- 5.2 Heavy Metal Pollution -- 5.3 Bioremediation of Heavy Metals: Principles, Mechanisms and Factors -- 5.3.1 Principles of Bioremediation -- 5.3.2 Mechanisms of Bioremediation -- 5.3.3 Factors Affecting Bioremediation -- 5.4 Techniques for Detection and Assessment of Heavy Metals in the Environment -- 5.5 Techniques of Bioremediation -- 5.5.1 In Situ Techniques -- 5.5.2 Ex Situ Techniques -- 5.6 Plant-Mediated Heavy Metal Removal -- 5.7 Role of Microbes in Heavy Metal Removal -- 5.8 Recent Advancement in Heavy Metal Removal Techniques -- 5.9 Advantages and Limitations -- 5.10 Application and Future Prospects of Bioremediation -- 5.11 Conclusions -- References -- 6: Enzyme Technology for Remediation of Contaminants in the Environment -- 6.1 Introduction -- 6.2 Enzyme as Contaminant Sterilizing Agent -- 6.3 Pollutants. , 6.3.1 Organic Pollutants -- 6.3.1.1 Nitro Compounds -- 6.3.1.2 Dyes -- 6.3.1.3 Organophosphorus Hydrolase -- 6.3.1.4 Cytochrome P450 Monooxygenase -- 6.3.1.5 Peroxidase from Horseradish -- 6.3.2 Inorganic Pollutants -- 6.3.2.1 Arsenic -- 6.3.2.2 Chromium -- 6.3.2.3 Mercury -- 6.3.2.4 Lead -- 6.4 Microbial Enzymes in Bioremediation -- 6.4.1 Microbial Oxidoreductase -- 6.4.2 Microbial Laccases -- 6.4.3 Microbial Oxygenases -- 6.4.3.1 Monooxygenases -- 6.4.3.2 Microbial Dioxygenases -- 6.5 Strategies for Overcoming Difficulties Associated with the Enzyme Technology -- 6.6 Plants and their Associated Enzymes: A Agents for Decontamination -- 6.7 Conclusion -- References -- Part II: Environmental Pollution and Wastewater Treatment -- 7: Environmental Toxicity, Health Hazards, and Bioremediation Strategies for Removal of Microplastics from Wastewater -- 7.1 Introduction -- 7.2 Sources of Microplastics in Wastewater -- 7.3 Properties of Microplastics -- 7.4 Ecotoxicity and Health Hazards of Microplastics -- 7.5 Factors Affecting Toxicity of Microplastics -- 7.6 Techniques for Characterization of Microplastics in Wastewater -- 7.7 Bioremediation Strategies for Microplastics -- 7.7.1 Bacterial Degradation of Microplastics -- 7.7.2 Fungal Degradation of Microplastics -- 7.7.3 Microalgal Degradation of Microplastics -- 7.7.4 Microbial Consortia in Microplastics Degradation -- 7.7.5 Microbial Biofilm in Microplastics Degradation -- 7.7.6 Bioreactor Systems for Microplastic Removal from Wastewater -- 7.8 Challenges and Future Perspectives -- 7.9 Conclusion and Recommendations -- References -- 8: Microbial Community Composition and Functions in Activated Sludge Treatment System -- 8.1 Introduction -- 8.2 Characteristics of Activated Sludge -- 8.3 Microbial Diversity in Activated Sludge. , 8.4 Enzyme Activity and Associated Physiological Function of Microbiome in Activated Sludge -- 8.5 Antibiotic Resistance Genes of Activated Sludge -- 8.6 Future Challenges and Opportunities -- 8.7 Conclusion -- References -- 9: Decontamination and Management of Industrial Wastewater Using Microorganisms Under Aerobic Condition -- 9.1 Introduction -- 9.2 Physical and Chemical Attributes of Wastewater -- 9.3 Biological Parameters of Wastewater -- 9.4 Aerobic Treatment of Wastewater -- 9.5 Advanced Biological Wastewater Treatment Technologies -- 9.6 Treatment of Sludge After Treatment of Wastewater -- 9.7 Management and Regulation for Quality Control and Quality Assurance of WTPs -- 9.8 Conclusions -- References -- 10: Omics in Industrial Wastewater Treatment -- 10.1 Introduction -- 10.2 The Composition of Industrial Wastewater -- 10.2.1 Food and Dairy Industry -- 10.2.2 Paper and Pulp Industry -- 10.2.3 Textile Industry -- 10.2.4 Mining and Quarry Industry -- 10.2.5 Chemical Industry -- 10.2.6 Leather and Tannery Industry -- 10.3 Industrial Wastewater Treatment Methods -- 10.3.1 Physical Wastewater Treatment Processes -- 10.3.2 Chemical Wastewater Treatment Processes -- 10.3.3 Biological Treatment of Wastewater -- 10.3.3.1 Aerobic Treatment -- 10.3.3.2 Anaerobic Treatment -- 10.4 Application of Omics in Biological Treatment -- 10.4.1 Omics Approaches in Wastewater Treatment -- 10.4.2 Omics in Remediation of Organic Pollutants -- 10.4.3 Omics for the Remediation of Metal Species -- 10.4.4 Genomic Information for Industrial Wastewater Treatment -- 10.5 Challenges, Limitations, and Futuristic Approaches -- References -- 11: Microalgae in Wastewater Treatment and Biofuel Production: Recent Advances, Challenges, and Future Prospects -- 11.1 Introduction -- 11.2 Benefits of Using Microalgae for Environmental Applications. , 11.3 Techniques for Microalgae Culture.