Microbiology for Earth Scientists

by Matthew F Kirk

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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.

Description from LibreTexts.

Publisher
Kansas State University
Subjects
Biology, Microbiology
Licence
CC BY-SA 4.0, as LibreTexts states it
Who can read
Tweens profiles and older, judged from its title and subjects

Contents

LibreTexts writes equations in TeX, and here they show as TeX; the PDF has them typeset.

  1. Front Matter
  2. TitlePage
  3. InfoPage
  4. Table of Contents
  5. Licensing
  6. Preface
  7. Table of Figures
  8. 1: Earth’s Microbiome
  9. 1.1: Some key features of Earth’s Microbiome
  10. 1.2: Interactions with their environments
  11. 1.3: Structure of this book
  12. 1.4: Defining ‘geomicrobiology’
  13. 1.5: Concept Check Questions
  14. 1.6: References
  15. 2: Classification and Phylogeny
  16. 2.1: Three domains of cellular life
  17. 2.2: Evaluating phylogeny
  18. 2.3: What is taxonomy?
  19. 2.4: Analyzing microbial populations using 16S rRNA genes
  20. 2.5: Example analysis
  21. 2.6: Viruses
  22. 2.7: Concept Check Questions
  23. 2.8: References
  24. 3: Properties of Microorganisms
  25. 3.1: Components of cells
  26. 3.2: Cell morphology and size
  27. 3.3: Gram-positive and gram-negative bacteria
  28. 3.4: Bacterial sporulation
  29. 3.5: Biofilms
  30. 3.6: Cell growth
  31. 3.7: Virions
  32. 3.8: Concept Check Questions
  33. 3.9: References
  34. 4: Redox and Mechanism
  35. 4.1: Redox basics
  36. 4.2: Balancing redox reactions
  37. 4.3: Metabolism
  38. 4.4: Chemotrophy
  39. 4.5: Phototrophy
  40. 4.6: Answers to Practice Problems
  41. 4.7: Concept Check Questions
  42. 4.8: References
  43. 5: Global Biogeochemical Cycles
  44. 5.1: Carbon cycle
  45. 5.1.1: Organic matter
  46. 5.1.2: Aerobic and anaerobic respiration
  47. 5.1.3: Fermentation and syntrophy
  48. 5.1.4: Methanogenesis
  49. 5.1.5: Acetogenesis
  50. 5.1.6: Methanotrophy
  51. 5.2: Nitrogen cycle
  52. 5.2.1: Nitrogen fixation
  53. 5.2.2: Ammonification
  54. 5.2.3: Nitrification
  55. 5.2.4: Anaerobic ammonia oxidation (anammox)
  56. 5.2.5: Denitrification
  57. 5.2.6: Dissimilatory nitrate reduction to ammonia (DNRA)
  58. 5.3: Iron cycle
  59. 5.3.1: Ferric iron reduction
  60. 5.3.2: Ferrous iron oxidation
  61. 5.4: Sulfur cycle
  62. 5.4.1: Sulfate reduction
  63. 5.4.2: Desulfurylation
  64. 5.4.3: Oxidation of sulfide and intermediate sulfur compounds
  65. 5.4.4: Reduction of intermediate sulfur compounds
  66. 5.4.5: Sulfur disproportionation
  67. 5.5: Concept Check Questions
  68. 5.6: References
  69. 6: Basic Environmental Controls
  70. 6.1: Categories of controls
  71. 6.2: Basic properties of the environment
  72. 6.2.1: Temperature
  73. 6.2.2: Pressure
  74. 6.2.3: Oxygen
  75. 6.2.4: pH
  76. 6.2.5: Water availability
  77. 6.3: Transport processes
  78. 6.4: Environment stability
  79. 6.5: Dispersal mechanisms and barriers
  80. 6.6: Interactions between controls
  81. 6.7: Concept Check Questions
  82. 6.8: References
  83. 7: Nutrient and Energy Resources
  84. 7.1: Nutrients
  85. 7.2: Extracellular enzymes
  86. 7.3: Nutrient stoichiometry
  87. 7.4: Energy sources for phototrophs
  88. 7.5: Energy sources for chemotrophs
  89. 7.5.1: Organic matter
  90. 7.5.2: Reduced inorganic components of minerals
  91. 7.5.3: Mantle degassing
  92. 7.5.4: Serpentinization
  93. 7.5.5: Radiolysis of water
  94. 7.5.6: Silica radical-based reactions
  95. 7.5.7: Trace atmospheric gases
  96. 7.6: Electroactive organisms
  97. 7.7: Concept Check Questions
  98. 7.8: References
  99. 8: Thermodynamic Controls
  100. 8.1: Mass action
  101. 8.2: Gibbs free energy
  102. 8.3: Impacts of changes in product and reactant activities
  103. 8.4: Available, captured, and usable energy
  104. 8.5: Redox zonation
  105. 8.6: Characterizing redox processes in aqueous systems
  106. 8.7: Answers to practice problems
  107. 8.8: Concept Check Questions
  108. 8.9: References
  109. 9: Kinetic Controls
  110. 9.1: Role of enzymes
  111. 9.2: Influence of pH and temperature on enzyme activity
  112. 9.3: Influence of substrate concentrations
  113. 9.4: Kinetic rate laws
  114. 9.5: Thermodynamic constraints on rates
  115. 9.6: Kinetic constraints on competition between sulfate reducers and methanogens
  116. 9.7: External controls on microbial reaction rates
  117. 9.8: Answers to practice problems
  118. 9.9: Concept Check Questions
  119. 9.10: References
  120. 10: Biological Environment
  121. 10.1: Microbial interactions
  122. 10.2: Example interactions
  123. 10.2.1: Viral predation/parasitism of bacteria
  124. 10.2.2: Mutualisms between plants and soil microorganisms
  125. 10.2.3: Interactions of anammox microorganisms with other nitrogen cycles
  126. 10.2.4: Interactions among iron and sulfur cycling microorganisms
  127. 10.2.5: Interactions among iron reducers, methanogens, and methanotrophs
  128. 10.3: Spatial scales of interactions
  129. 10.4: Concept Check Questions
  130. 10.5: References
  131. 11: Mechanisms of Microbial Impacts
  132. 11.1: Catalyzing reactions
  133. 11.1.1: Direct impacts
  134. 11.1.2: Indirect impacts
  135. 11.1.3: Practice
  136. 11.2: Generating biomass
  137. 11.3: Forming minerals
  138. 11.4: Dissolving minerals
  139. 11.4.1: Redox mechanism
  140. 11.4.2: Acid mechanism
  141. 11.4.3: Chelation mechanism
  142. 11.5: Answers to practice problems
  143. 11.6: Concept Check Questions
  144. 11.7: References
  145. 12: Impacts to the Lithosphere
  146. 12.1: Examples of biomineralization
  147. 12.1.1: Carbonates
  148. 12.1.2: Amorphous silica
  149. 12.1.3: Iron (oxyhydr)oxides
  150. 12.1.4: Sulfides
  151. 12.1.5: Clay minerals
  152. 12.2: Microbial influence on marine sediments
  153. 12.3: Microbial influences on tectonic activity
  154. 12.4: Mineral evolution
  155. 12.5: Concept Check Questions
  156. 12.6: 12.6 References
  157. 13: Impacts to the Atmosphere
  158. 13.1: Oxygen
  159. 13.2: Trends in greenhouse gases
  160. 13.3: Carbon dioxide
  161. 13.4: Methane
  162. 13.5: Nitrous oxide
  163. 13.6: Responses of microorganisms to climate change
  164. 13.7: Managing greenhouse gas emissions
  165. 13.8: Answers to practice problems
  166. 13.9: Concept Check Questions
  167. 13.10: References
  168. 14: Impacts to the Hydrosphere
  169. 14.1: Pathogens
  170. 14.2: Groundwater quality
  171. 14.2.1: Chemical evolution of groundwater
  172. 14.2.2: Middendorf aquifer
  173. 14.3: Surface water quality
  174. 14.3.1: Connections to groundwater
  175. 14.3.2: Algal blooms
  176. 14.4: Examples of microbial impacts to chemical contaminants
  177. 14.4.1: Nitrate
  178. 14.4.2: Arsenic
  179. 14.4.3: Acid mine drainage
  180. 14.4.4: Chlorinated solvents
  181. 14.4.5: Petroleum hydrocarbons
  182. 14.5: Applying microbiology to remediate contaminated water
  183. 14.6: Concept Check Questions
  184. 14.7: References
  185. 15: Appendix A- Thermodynamic Data for Select Reactions
  186. 15.1: Redox Reactions
  187. 15.2: Gas Solubility Reactions
  188. 15.3: Mineral Reactions
  189. Back Matter
  190. Glossary
  191. Detailed Licensing