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ESC4103 - Environmental Microbiology

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ESC4103 - Environmental Microbiology

Biology
Author
Noor Hafizah Mohd Pushiri
Publisher
Universiti Putra Malaysia
Source
LibreTexts
Language
EN
Category
Basic Sciences
Read online Download PDF (open licence)
Contents· 240 sections
  1. 01: Main concepts and history
  2. 1.01: Defining Microbes
  3. 1.02: History of Microbiology - Hooke van Leeuwenhoek and Cohn
  4. 1.03: Pasteur and Spontaneous Generation
  5. 1.04: Koch and Pure Culture
  6. 02: Types and habitats
  7. 2.01: 1.2A Types of Microorganisms
  8. 2.02: Classification of Microorganisms
  9. 2.03: Microbes and the Origin of Life on Earth
  10. 2.04: Environmental Diversity of Microbes
  11. 03: Microbial Ecology
  12. 3.01: Microbial Ecology
  13. 3.1A: Microbes and Ecosystem Niches
  14. 3.1B: Organization of Ecosystems
  15. 3.1C: Role of Microbes in Biogeochemical Cycling
  16. 3.1D: Microbial Environments and Microenvironments
  17. 3.02: Soil and Plant Microbiology
  18. 3.2A: Soil Composition
  19. 3.2B: Physical Properties of Soil
  20. 3.2C: Mycorrhiza
  21. 3.2D: Wetland Soils
  22. 3.2E: Endophytes and Plants
  23. 3.2F: Mycorrhizae- The Symbiotic Relationship between Fungi and Roots
  24. 3.2F: Plant Pathogens
  25. 3.2G: Nitrogen Fixation- Root and Bacteria Interactions
  26. 3.03: Aquatic Microbiology
  27. 3.3A: Marine Habitats
  28. 3.3B: Planktonic Communities
  29. 3.3C: Planktonic Food Webs
  30. 3.3D: Ocean Floor
  31. 3.3E: Cold-Seep Ecosystems
  32. 3.3F: The Deep Sea and Barophilism
  33. 3.3G: Sea Coral and Sea Anemone Zooxanthellae
  34. 3.3H: Sponge Communities
  35. 3.3I: Freshwater Environments
  36. 3.04: Nutrient Cycles
  37. 3.4A: Sources and Sinks of Essential Elements
  38. 3.4B: The Carbon Cycle
  39. 3.4C: Syntrophy and Methanogenesis
  40. 3.4D: The Phosphorus Cycle
  41. 3.4E: The Nitrogen Cycle
  42. 3.4F: The Sulfur Cycle
  43. 3.4G: The Iron Cycle
  44. 3.05: Microbial Symbioses
  45. 3.5A: Mutualism vs. Symbiosis
  46. 3.5B: The Rumen and Ruminant Animals
  47. 3.5C: Hydrothermal Vent Microbial Ecosystems
  48. 3.5D: Squid-Aliivibrio Symbiosis
  49. 3.5E: Mutualistic Relationships with Fungi and Fungivores
  50. 3.5F: Agrobacterium and Crown Gall Disease
  51. 3.5G: The Legume-Root Nodule Symbiosis
  52. 04: Microbial Metabolism
  53. 4.01: Types of Metabolism
  54. 4.1A: Photoautotrophs and Photohetrotrophs
  55. 4.1B: Chemoautotrophs and Chemohetrotrophs
  56. 4.02: Energy Production
  57. 4.2A: Control of Catabolic Pathways
  58. 4.2B: Transforming Chemical Energy
  59. 4.2C: Connecting Other Sugars to Glucose Metabolism
  60. 4.03: Catabolism
  61. 4.3A: Types of Catabolism
  62. 4.3B: Pyruvic Acid and Metabolism
  63. 4.04: Glycolysis
  64. 4.4A: Importance of Glycolysis
  65. 4.4B: Electron Donors and Acceptors
  66. 4.4C: ATP Yield
  67. 4.4D: Respiration and Proton Motive Force
  68. 4.05: Respiratory ETS and ATP Synthase
  69. 4.5A: Cofactors and Energy Transitions
  70. 4.5B: Oxidoreductase Protein Complexes
  71. 4.5C: F10 ATP Synthase
  72. 4.5D: Sodium Pumps as an Alternative to Proton Pump
  73. 4.06: The Citric Acid (Krebs) Cycle
  74. 4.6A: Citric Acid Cycle
  75. 4.6B: Breakdown of Pyruvate
  76. 4.6C: Acetyl CoA and the Citric Acid Cycle
  77. 4.07: Alternatives to Glycolysis
  78. 4.7A: The Entner-Doudoroff Pathway
  79. 4.7B: Aerobic Hydrocarbon Oxidation
  80. 4.7C: The Pentose Phosphate Shunt
  81. 4.7D: Organic Acid Metabolism
  82. 4.7E: Lipid Metabolism
  83. 4.7F: Connecting Proteins to Glucose Metabolism
  84. 4.7G: Methylotrophy and Methanotrophy
  85. 4.08: Fermentation
  86. 4.8A: Anaerobic Cellular Respiration
  87. 4.8B: Clostridial and Propionic Acid Fermentation
  88. 4.8C: Fermentation Without Substrate-Level Phosphorylation
  89. 4.8C: Syntrophy
  90. 4.09: Anaerobic Respiration
  91. 4.9A: Electron Donors and Acceptors in Anaerobic Respiration
  92. 4.9B: Nitrate Reduction and Denitrification
  93. 4.9C: Sulfate and Sulfur Reduction
  94. 4.9D: Methanogenesis
  95. 4.9E: Proton Reduction
  96. 4.9F: Anoxic Hydrocarbon Oxidation
  97. 4.10: Chemolithotrophy
  98. 4.10A: The Energetics of Chemolithotrophy
  99. 4.10B: Hydrogen Oxidation
  100. 4.10C: Oxidation of Reduced Sulfur Compounds
  101. 4.10D: Iron Oxidation
  102. 4.10E: Nitrification
  103. 4.10F: Anammox
  104. 4.10G: Benzoate Catabolism
  105. 4.10H: Polycyclic Aromatic Hydrocarbons
  106. 4.11: Phototrophy
  107. 4.11A: The Purpose and Process of Photosynthesis
  108. 4.11B: Main Structures and Summary of Photosynthesis
  109. 4.11C: The Two Parts of Photosynthesis
  110. 4.11D: Bacteriorhodopsin
  111. 4.11E: Carotenoids and Phycobilins
  112. 4.11F: Facultative Phototrophy
  113. 4.11G: Oxygenic Photosynthesis
  114. 4.11H: Anoxygenic Photosynthesis
  115. 4.12: Biosynthesis
  116. 4.12A: Substrates for Biosysnthesis
  117. 4.12B: Biosynthesis and Energy
  118. 4.12C: The Calvin Cycle
  119. 4.12D: Intermediates Produced During the Calvin Cycle
  120. 4.12E: Regulation of the Calvin Cycle
  121. 4.12F: The Reverse TCA Cycle
  122. 4.12G: The Acetyl-CoA Pathway
  123. 4.12H: The 3-Hydroxypropionate Cycle
  124. 4.13: Anabolism
  125. 4.13A: Polysaccharide Biosynthesis
  126. 4.13B: Lipid Biosynthesis
  127. 4.13C: Regulation by Biosynthetic Enzymes
  128. 4.13D: Bacterial Polyesters
  129. 4.13E: Polyketide Antibiotics
  130. 4.14: Amino Acids and Nucleotide Biosynthesis
  131. 4.14A: Amino Acid Synthesis
  132. 4.14B: Purine and Pyrimidine Synthesis
  133. 4.14C: Nonribosomal Peptide Antibiotics
  134. 4.14D: Biosynthesis of Tetrapyrroles
  135. 4.15: Nitrogen Fixation
  136. 4.15A: Nitrogenase and Nitrogen Fixation
  137. 4.15B: Early Discoveries in Nitrogen Fixation
  138. 4.15C: Nitrogen Fixation Mechanism
  139. 4.15D: Anaerobiosis and N Fixation
  140. 4.15E: Genetics and Regulation of N Fixation
  141. 05: Microbial Genetics
  142. 5.01: Genes
  143. 5.1A: Bacterial Genomes
  144. 5.1B: DNA Replication in Prokaryotes
  145. 5.1C: Gene Inversion
  146. 5.1D: Slipped-Strand Mispairing
  147. 5.02: Prokaryotic Genomes
  148. 5.2A: Bacterial Chromosomes in the Nucleoid
  149. 5.2B: Supercoiling
  150. 5.2C: Size Variation and ORF Contents in Genomes
  151. 5.2D: Bioinformatic Analyses and Gene Distributions
  152. 5.03: DNA Replication
  153. 5.3A: Basics of DNA Replication
  154. 5.3B: DNA Replication in Eukaryotes
  155. 5.04: Plasmids
  156. 5.4A: Introduction to Plasmids
  157. 5.4B: Types of Plasmids and Their Biological Significance
  158. 5.05: RNA Synthesis - Transcription
  159. 5.5A: Elongation and Termination in Eukaryotes
  160. 5.5B: The Promoter and the Transcription Machinery
  161. 5.06: Translation- Protein Synthesis
  162. 5.6A: Processing of tRNAs and rRNAs
  163. 5.6B: The Protein Synthesis Machinery
  164. 5.6C: Prokaryotic Transcription and Translation Are Coupled
  165. 5.6D: The Incorporation of Nonstandard Amino Acids
  166. 5.6E: Unsticking Stuck Ribosomes
  167. 5.07: Protein Modification Folding Secretion and Degradation
  168. 5.7A: mRNA Processing
  169. 5.7B: Denaturation and Protein Folding
  170. 5.7C: Protein Folding Modification and Targeting
  171. 5.7D: Regulating Protein Activity and Longevity
  172. 5.08: Archaeal Genetics
  173. 5.8A: Chromosomes and DNA Replication in the Archaea
  174. 5.8B: Shared Features of Bacteria and Archaea
  175. 5.8C: Shared Features of Archaea and Eukaryotes
  176. 5.09: Eukaryotic Genetics
  177. 5.9A: The Role of the Cell Cycle
  178. 5.9B: The Relationship Between Genes and Proteins
  179. 5.10: Genetic Transfer in Prokaryotes
  180. 5.10A: Generalized Recombination and RecA
  181. 5.10B: Bacterial Transformation
  182. 5.10C: Bacterial Transduction
  183. 5.10D: Prokaryotic Reproduction
  184. 5.10E: Complementation
  185. 5.10F: Gene Transfer in Archaea
  186. 5.11: Genomics and Proteomics
  187. 5.11A: Microarrays and the Transcriptome
  188. 5.11B: Proteomics
  189. 5.11C: Metabolomics
  190. 5.12: Mutation
  191. 5.12A: DNA Repair
  192. 5.13: Genome Evolution
  193. 5.13A: Gene Families
  194. 5.13B: Genomics and Biofuels
  195. 5.13C: Genome Reduction
  196. 5.13D: Pathogenicity Islands
  197. 06: Microbial biotechnology
  198. 6.01: Tools of Genetic Engineering
  199. 6.1A: Recombinant DNA Technology
  200. 6.1B: Selection
  201. 6.1C: Mutation
  202. 6.1D: Reproductive Cloning
  203. 6.1E: Basic Techniques to Manipulate Genetic Material (DNA and RNA)
  204. 6.1F: Molecular and Cellular Cloning
  205. 6.1G: Plasmids as Cloning Vectors
  206. 6.02: Cloning Techniques
  207. 6.2A: Putting Foreign DNA into Cells
  208. 6.2B: Obtaining DNA
  209. 6.2C: Hosts for Cloning Vectors
  210. 6.2D: Shuttle Vectors and Expression Vectors
  211. 6.2E: Bacteriophage Lambda as a Cloning Vector
  212. 6.2F: Vectors for Genomic Cloning and Sequencing
  213. 6.03: Bioinformatics
  214. 6.3A: Strategies Used in Sequencing Projects
  215. 6.3B: Annotating Genomes
  216. 6.3C: Homologs Orthologs and Paralogs
  217. 6.3D: Synthesizing DNA
  218. 6.3E: Amplifying DNA - The Polymerase Chain Reaction
  219. 6.3F: DNA Sequencing Based on Sanger Dideoxynucleotides
  220. 6.3G: Metagenomics
  221. 6.3H: Reporter Fusions
  222. 6.04: Environmental Genomics
  223. 6.4A: Environmental Metagenomics
  224. 6.4B: Detecting Uncultured Microorganisms
  225. 6.4C: Viral Genomes in Nature
  226. 07: Environmental application
  227. 7.01: Genomics and Biofuels
  228. 7.02: Microbial Bioremediation
  229. 7.2A: Microbial Ore Leaching
  230. 7.2B: Petroleum Biodegradation
  231. 7.2C: The Degradation of Synthetic Chemicals in Soils and Water
  232. 08: Environmental Microbiomes
  233. 8.01: Environmental Nutrient Cycling and Human Health
  234. 8.02: The Ocean Microbiome and Marine Life
  235. 8.03: Soil Microbiomes
  236. 8.04: Plant Microbiomes
  237. 8.05: Pollution and Bioremediation
  238. 8.06: Forensic Microbiomes
  239. 09: Case study
  240. 9.01: Case Study - Environment