Nguồn ngoài

ESC4103 - Environmental Microbiology

Biology

Tác giả: Noor Hafizah Mohd Pushiri
Nhà xuất bản: Universiti Putra Malaysia
Nguồn: LibreTexts
Ngôn ngữ: EN
Danh mục: Khoa học cơ bản

Đọc trực tuyến Tải PDF (nguồn mở)

Mục lục· 240 mục

01: Main concepts and history
1.01: Defining Microbes
1.02: History of Microbiology - Hooke van Leeuwenhoek and Cohn
1.03: Pasteur and Spontaneous Generation
1.04: Koch and Pure Culture
02: Types and habitats
2.01: 1.2A Types of Microorganisms
2.02: Classification of Microorganisms
2.03: Microbes and the Origin of Life on Earth
2.04: Environmental Diversity of Microbes
03: Microbial Ecology
3.01: Microbial Ecology
3.1A: Microbes and Ecosystem Niches
3.1B: Organization of Ecosystems
3.1C: Role of Microbes in Biogeochemical Cycling
3.1D: Microbial Environments and Microenvironments
3.02: Soil and Plant Microbiology
3.2A: Soil Composition
3.2B: Physical Properties of Soil
3.2C: Mycorrhiza
3.2D: Wetland Soils
3.2E: Endophytes and Plants
3.2F: Mycorrhizae- The Symbiotic Relationship between Fungi and Roots
3.2F: Plant Pathogens
3.2G: Nitrogen Fixation- Root and Bacteria Interactions
3.03: Aquatic Microbiology
3.3A: Marine Habitats
3.3B: Planktonic Communities
3.3C: Planktonic Food Webs
3.3D: Ocean Floor
3.3E: Cold-Seep Ecosystems
3.3F: The Deep Sea and Barophilism
3.3G: Sea Coral and Sea Anemone Zooxanthellae
3.3H: Sponge Communities
3.3I: Freshwater Environments
3.04: Nutrient Cycles
3.4A: Sources and Sinks of Essential Elements
3.4B: The Carbon Cycle
3.4C: Syntrophy and Methanogenesis
3.4D: The Phosphorus Cycle
3.4E: The Nitrogen Cycle
3.4F: The Sulfur Cycle
3.4G: The Iron Cycle
3.05: Microbial Symbioses
3.5A: Mutualism vs. Symbiosis
3.5B: The Rumen and Ruminant Animals
3.5C: Hydrothermal Vent Microbial Ecosystems
3.5D: Squid-Aliivibrio Symbiosis
3.5E: Mutualistic Relationships with Fungi and Fungivores
3.5F: Agrobacterium and Crown Gall Disease
3.5G: The Legume-Root Nodule Symbiosis
04: Microbial Metabolism
4.01: Types of Metabolism
4.1A: Photoautotrophs and Photohetrotrophs
4.1B: Chemoautotrophs and Chemohetrotrophs
4.02: Energy Production
4.2A: Control of Catabolic Pathways
4.2B: Transforming Chemical Energy
4.2C: Connecting Other Sugars to Glucose Metabolism
4.03: Catabolism
4.3A: Types of Catabolism
4.3B: Pyruvic Acid and Metabolism
4.04: Glycolysis
4.4A: Importance of Glycolysis
4.4B: Electron Donors and Acceptors
4.4C: ATP Yield
4.4D: Respiration and Proton Motive Force
4.05: Respiratory ETS and ATP Synthase
4.5A: Cofactors and Energy Transitions
4.5B: Oxidoreductase Protein Complexes
4.5C: F10 ATP Synthase
4.5D: Sodium Pumps as an Alternative to Proton Pump
4.06: The Citric Acid (Krebs) Cycle
4.6A: Citric Acid Cycle
4.6B: Breakdown of Pyruvate
4.6C: Acetyl CoA and the Citric Acid Cycle
4.07: Alternatives to Glycolysis
4.7A: The Entner-Doudoroff Pathway
4.7B: Aerobic Hydrocarbon Oxidation
4.7C: The Pentose Phosphate Shunt
4.7D: Organic Acid Metabolism
4.7E: Lipid Metabolism
4.7F: Connecting Proteins to Glucose Metabolism
4.7G: Methylotrophy and Methanotrophy
4.08: Fermentation
4.8A: Anaerobic Cellular Respiration
4.8B: Clostridial and Propionic Acid Fermentation
4.8C: Fermentation Without Substrate-Level Phosphorylation
4.8C: Syntrophy
4.09: Anaerobic Respiration
4.9A: Electron Donors and Acceptors in Anaerobic Respiration
4.9B: Nitrate Reduction and Denitrification
4.9C: Sulfate and Sulfur Reduction
4.9D: Methanogenesis
4.9E: Proton Reduction
4.9F: Anoxic Hydrocarbon Oxidation
4.10: Chemolithotrophy
4.10A: The Energetics of Chemolithotrophy
4.10B: Hydrogen Oxidation
4.10C: Oxidation of Reduced Sulfur Compounds
4.10D: Iron Oxidation
4.10E: Nitrification
4.10F: Anammox
4.10G: Benzoate Catabolism
4.10H: Polycyclic Aromatic Hydrocarbons
4.11: Phototrophy
4.11A: The Purpose and Process of Photosynthesis
4.11B: Main Structures and Summary of Photosynthesis
4.11C: The Two Parts of Photosynthesis
4.11D: Bacteriorhodopsin
4.11E: Carotenoids and Phycobilins
4.11F: Facultative Phototrophy
4.11G: Oxygenic Photosynthesis
4.11H: Anoxygenic Photosynthesis
4.12: Biosynthesis
4.12A: Substrates for Biosysnthesis
4.12B: Biosynthesis and Energy
4.12C: The Calvin Cycle
4.12D: Intermediates Produced During the Calvin Cycle
4.12E: Regulation of the Calvin Cycle
4.12F: The Reverse TCA Cycle
4.12G: The Acetyl-CoA Pathway
4.12H: The 3-Hydroxypropionate Cycle
4.13: Anabolism
4.13A: Polysaccharide Biosynthesis
4.13B: Lipid Biosynthesis
4.13C: Regulation by Biosynthetic Enzymes
4.13D: Bacterial Polyesters
4.13E: Polyketide Antibiotics
4.14: Amino Acids and Nucleotide Biosynthesis
4.14A: Amino Acid Synthesis
4.14B: Purine and Pyrimidine Synthesis
4.14C: Nonribosomal Peptide Antibiotics
4.14D: Biosynthesis of Tetrapyrroles
4.15: Nitrogen Fixation
4.15A: Nitrogenase and Nitrogen Fixation
4.15B: Early Discoveries in Nitrogen Fixation
4.15C: Nitrogen Fixation Mechanism
4.15D: Anaerobiosis and N Fixation
4.15E: Genetics and Regulation of N Fixation
05: Microbial Genetics
5.01: Genes
5.1A: Bacterial Genomes
5.1B: DNA Replication in Prokaryotes
5.1C: Gene Inversion
5.1D: Slipped-Strand Mispairing
5.02: Prokaryotic Genomes
5.2A: Bacterial Chromosomes in the Nucleoid
5.2B: Supercoiling
5.2C: Size Variation and ORF Contents in Genomes
5.2D: Bioinformatic Analyses and Gene Distributions
5.03: DNA Replication
5.3A: Basics of DNA Replication
5.3B: DNA Replication in Eukaryotes
5.04: Plasmids
5.4A: Introduction to Plasmids
5.4B: Types of Plasmids and Their Biological Significance
5.05: RNA Synthesis - Transcription
5.5A: Elongation and Termination in Eukaryotes
5.5B: The Promoter and the Transcription Machinery
5.06: Translation- Protein Synthesis
5.6A: Processing of tRNAs and rRNAs
5.6B: The Protein Synthesis Machinery
5.6C: Prokaryotic Transcription and Translation Are Coupled
5.6D: The Incorporation of Nonstandard Amino Acids
5.6E: Unsticking Stuck Ribosomes
5.07: Protein Modification Folding Secretion and Degradation
5.7A: mRNA Processing
5.7B: Denaturation and Protein Folding
5.7C: Protein Folding Modification and Targeting
5.7D: Regulating Protein Activity and Longevity
5.08: Archaeal Genetics
5.8A: Chromosomes and DNA Replication in the Archaea
5.8B: Shared Features of Bacteria and Archaea
5.8C: Shared Features of Archaea and Eukaryotes
5.09: Eukaryotic Genetics
5.9A: The Role of the Cell Cycle
5.9B: The Relationship Between Genes and Proteins
5.10: Genetic Transfer in Prokaryotes
5.10A: Generalized Recombination and RecA
5.10B: Bacterial Transformation
5.10C: Bacterial Transduction
5.10D: Prokaryotic Reproduction
5.10E: Complementation
5.10F: Gene Transfer in Archaea
5.11: Genomics and Proteomics
5.11A: Microarrays and the Transcriptome
5.11B: Proteomics
5.11C: Metabolomics
5.12: Mutation
5.12A: DNA Repair
5.13: Genome Evolution
5.13A: Gene Families
5.13B: Genomics and Biofuels
5.13C: Genome Reduction
5.13D: Pathogenicity Islands
06: Microbial biotechnology
6.01: Tools of Genetic Engineering
6.1A: Recombinant DNA Technology
6.1B: Selection
6.1C: Mutation
6.1D: Reproductive Cloning
6.1E: Basic Techniques to Manipulate Genetic Material (DNA and RNA)
6.1F: Molecular and Cellular Cloning
6.1G: Plasmids as Cloning Vectors
6.02: Cloning Techniques
6.2A: Putting Foreign DNA into Cells
6.2B: Obtaining DNA
6.2C: Hosts for Cloning Vectors
6.2D: Shuttle Vectors and Expression Vectors
6.2E: Bacteriophage Lambda as a Cloning Vector
6.2F: Vectors for Genomic Cloning and Sequencing
6.03: Bioinformatics
6.3A: Strategies Used in Sequencing Projects
6.3B: Annotating Genomes
6.3C: Homologs Orthologs and Paralogs
6.3D: Synthesizing DNA
6.3E: Amplifying DNA - The Polymerase Chain Reaction
6.3F: DNA Sequencing Based on Sanger Dideoxynucleotides
6.3G: Metagenomics
6.3H: Reporter Fusions
6.04: Environmental Genomics
6.4A: Environmental Metagenomics
6.4B: Detecting Uncultured Microorganisms
6.4C: Viral Genomes in Nature
07: Environmental application
7.01: Genomics and Biofuels
7.02: Microbial Bioremediation
7.2A: Microbial Ore Leaching
7.2B: Petroleum Biodegradation
7.2C: The Degradation of Synthetic Chemicals in Soils and Water
08: Environmental Microbiomes
8.01: Environmental Nutrient Cycling and Human Health
8.02: The Ocean Microbiome and Marine Life
8.03: Soil Microbiomes
8.04: Plant Microbiomes
8.05: Pollution and Bioremediation
8.06: Forensic Microbiomes
09: Case study
9.01: Case Study - Environment