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Microbiology for Earth Scientists

Nguồn ngoài

Microbiology for Earth Scientists

Microorganisms are the most abundant form of life on Earth and in recent decades it has become increasingly clear that their collective activities are one of the dominant forces shaping the Earth. This book is specifically designed for earth science students and can provide a helpful free resource for students in Geomicrobiology courses. However, portions of the book can also have value for students and professionals from any field who are interested in environmental microbiology.

MicrobiologyBiology
Tác giả
Matthew F Kirk
Nhà xuất bản
Kansas State University
Nguồn
LibreTexts
Giấy phép
CC BY-SA
Ngôn ngữ
EN
Danh mục
Khoa học cơ bản
Đọc trực tuyến Tải PDF (nguồn mở)
Mục lục· 181 mục
  1. 01: Earths Microbiome
  2. 1.01: Some key features of Earths Microbiome
  3. 1.02: Interactions with their environments
  4. 1.03: Structure of this book
  5. 1.04: Defining geomicrobiology
  6. 1.05: Concept Check Questions
  7. 1.06: References
  8. 02: Classification and Phylogeny
  9. 2.01: Three domains of cellular life
  10. 2.02: Evaluating phylogeny
  11. 2.03: What is taxonomy
  12. 2.04: Analyzing microbial populations using 16S rRNA genes
  13. 2.05: Example analysis
  14. 2.06: Viruses
  15. 2.07: Concept Check Questions
  16. 2.08: References
  17. 03: Properties of Microorganisms
  18. 3.01: Components of cells
  19. 3.02: Cell morphology and size
  20. 3.03: Gram-positive and gram-negative bacteria
  21. 3.04: Bacterial sporulation
  22. 3.05: Biofilms
  23. 3.06: Cell growth
  24. 3.07: Virions
  25. 3.08: Concept Check Questions
  26. 3.09: References
  27. 04: Redox and Mechanism
  28. 4.01: Redox basics
  29. 4.02: Balancing redox reactions
  30. 4.03: Metabolism
  31. 4.04: Chemotrophy
  32. 4.05: Phototrophy
  33. 4.06: Answers to Practice Problems
  34. 4.07: Concept Check Questions
  35. 4.08: References
  36. 05: Global Biogeochemical Cycles
  37. 5.01: Carbon cycle
  38. 5.1.01: Organic matter
  39. 5.1.02: Aerobic and anaerobic respiration
  40. 5.1.03: Fermentation and syntrophy
  41. 5.1.04: Methanogenesis
  42. 5.1.05: Acetogenesis
  43. 5.1.06: Methanotrophy
  44. 5.02: Nitrogen cycle
  45. 5.2.01: Nitrogen fixation
  46. 5.2.02: Ammonification
  47. 5.2.03: Nitrification
  48. 5.2.04: Anaerobic ammonia oxidation (anammox)
  49. 5.2.05: Denitrification
  50. 5.2.06: Dissimilatory nitrate reduction to ammonia (DNRA)
  51. 5.03: Iron cycle
  52. 5.3.01: Ferric iron reduction
  53. 5.3.02: Ferrous iron oxidation
  54. 5.04: Sulfur cycle
  55. 5.4.01: Sulfate reduction
  56. 5.4.02: Desulfurylation
  57. 5.4.03: Oxidation of sulfide and intermediate sulfur compounds
  58. 5.4.04: Reduction of intermediate sulfur compounds
  59. 5.4.05: Sulfur disproportionation
  60. 5.05: Concept Check Questions
  61. 5.06: References
  62. 06: Basic Environmental Controls
  63. 6.01: Categories of controls
  64. 6.02: Basic properties of the environment
  65. 6.2.01: Temperature
  66. 6.2.02: Pressure
  67. 6.2.03: Oxygen
  68. 6.2.04: pH
  69. 6.2.05: Water availability
  70. 6.03: Transport processes
  71. 6.04: Environment stability
  72. 6.05: Dispersal mechanisms and barriers
  73. 6.06: Interactions between controls
  74. 6.07: Concept Check Questions
  75. 6.08: References
  76. 07: Nutrient and Energy Resources
  77. 7.01: Nutrients
  78. 7.02: Extracellular enzymes
  79. 7.03: Nutrient stoichiometry
  80. 7.04: Energy sources for phototrophs
  81. 7.05: Energy sources for chemotrophs
  82. 7.5.01: Organic matter
  83. 7.5.02: Reduced inorganic components of minerals
  84. 7.5.03: Mantle degassing
  85. 7.5.04: Serpentinization
  86. 7.5.05: Radiolysis of water
  87. 7.5.06: Silica radical-based reactions
  88. 7.5.07: Trace atmospheric gases
  89. 7.06: Electroactive organisms
  90. 7.07: Concept Check Questions
  91. 7.08: References
  92. 08: Thermodynamic Controls
  93. 8.01: Mass action
  94. 8.02: Gibbs free energy
  95. 8.03: Impacts of changes in product and reactant activities
  96. 8.04: Available captured and usable energy
  97. 8.05: Redox zonation
  98. 8.06: Characterizing redox processes in aqueous systems
  99. 8.07: Answers to practice problems
  100. 8.08: Concept Check Questions
  101. 8.09: References
  102. 09: Kinetic Controls
  103. 9.01: Role of enzymes
  104. 9.02: Influence of pH and temperature on enzyme activity
  105. 9.03: Influence of substrate concentrations
  106. 9.04: Kinetic rate laws
  107. 9.05: Thermodynamic constraints on rates
  108. 9.06: Kinetic constraints on competition between sulfate reducers and methanogens
  109. 9.07: External controls on microbial reaction rates
  110. 9.08: Answers to practice problems
  111. 9.09: Concept Check Questions
  112. 9.10: References
  113. 10: Biological Environment
  114. 10.01: Microbial interactions
  115. 10.02: Example interactions
  116. 10.2.01: Viral predation parasitism of bacteria
  117. 10.2.02: Mutualisms between plants and soil microorganisms
  118. 10.2.03: Interactions of anammox microorganisms with other nitrogen cycles
  119. 10.2.04: Interactions among iron and sulfur cycling microorganisms
  120. 10.2.05: Interactions among iron reducers methanogens and methanotrophs
  121. 10.03: Spatial scales of interactions
  122. 10.04: Concept Check Questions
  123. 10.05: References
  124. 11: Mechanisms of Microbial Impacts
  125. 11.01: Catalyzing reactions
  126. 11.1.01: Direct impacts
  127. 11.1.02: Indirect impacts
  128. 11.1.03: Practice
  129. 11.02: Generating biomass
  130. 11.03: Forming minerals
  131. 11.04: Dissolving minerals
  132. 11.4.01: Redox mechanism
  133. 11.4.02: Acid mechanism
  134. 11.4.03: Chelation mechanism
  135. 11.05: Answers to practice problems
  136. 11.06: Concept Check Questions
  137. 11.07: References
  138. 12: Impacts to the Lithosphere
  139. 12.01: Examples of biomineralization
  140. 12.1.01: Carbonates
  141. 12.1.02: Amorphous silica
  142. 12.1.03: Iron (oxyhydr)oxides
  143. 12.1.04: Sulfides
  144. 12.1.05: Clay minerals
  145. 12.02: Microbial influence on marine sediments
  146. 12.03: Microbial influences on tectonic activity
  147. 12.04: Mineral evolution
  148. 12.05: Concept Check Questions
  149. 12.06: 12.6 References
  150. 13: Impacts to the Atmosphere
  151. 13.01: Oxygen
  152. 13.02: Trends in greenhouse gases
  153. 13.03: Carbon dioxide
  154. 13.04: Methane
  155. 13.05: Nitrous oxide
  156. 13.06: Responses of microorganisms to climate change
  157. 13.07: Managing greenhouse gas emissions
  158. 13.08: Answers to practice problems
  159. 13.09: Concept Check Questions
  160. 13.10: References
  161. 14: Impacts to the Hydrosphere
  162. 14.01: Pathogens
  163. 14.02: Groundwater quality
  164. 14.2.01: Chemical evolution of groundwater
  165. 14.2.02: Middendorf aquifer
  166. 14.03: Surface water quality
  167. 14.3.01: Connections to groundwater
  168. 14.3.02: Algal blooms
  169. 14.04: Examples of microbial impacts to chemical contaminants
  170. 14.4.01: Nitrate
  171. 14.4.02: Arsenic
  172. 14.4.03: Acid mine drainage
  173. 14.4.04: Chlorinated solvents
  174. 14.4.05: Petroleum hydrocarbons
  175. 14.05: Applying microbiology to remediate contaminated water
  176. 14.06: Concept Check Questions
  177. 14.07: References
  178. 15: Appendix A- Thermodynamic Data for Select Reactions
  179. 15.01: Redox Reactions
  180. 15.02: Gas Solubility Reactions
  181. 15.03: Mineral Reactions