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Lessons in Environmental
Microbiology
Lessons in Environmental
Microbiology

Authored by
Roger Tim Haug
CRC Press
Taylor & Francis Group
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© 2020 by Taylor & Francis Group, LLC

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Title: Lessons in environmental microbiology / Roger Tim Haug.
Description: Boca Raton : Taylor & Francis, 2019. | Includes bibliographical references and index.
Identifiers: LCCN 2019003192 | ISBN 9781138336582 (hardback : alk. paper)
Subjects: LCSH: Microbial ecology.
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 To Peggy
My patient wife of 50 years
So looking forward to our next 50 years together
To our sons David and James
So proud to be your father

To Family
Contents

Preface.......................................................................................................................................... xxiii
Author........................................................................................................................................... xxv

1 Introduction to Environmental Microbiology...................................................................1

What Is Microbiology?.............................................................................................................1
Why Should I Study Microbiology?....................................................................................... 2
The Roster of Microbes............................................................................................................ 3
The Branches of Microbiology................................................................................................ 4
Environmental Microbiology.................................................................................................. 7

2 Oxidation and Reduction: The Energy Reactions of Life...............................................9

Introduction...............................................................................................................................9
Electrons and Life................................................................................................................9
Oxidation and Reduction – The Transfer of Electrons................................................. 10
The Atomic Nature of Things............................................................................................... 10
What Is an Electron?.......................................................................................................... 10
The Black Body Problem................................................................................................... 11
The Gold Leaf Experiment............................................................................................... 11
Absorption and Emission Spectra................................................................................... 12
The Double Slit Experiment............................................................................................. 12
The Periodic Table of Elements............................................................................................. 14
Electron Shells and Orbitals.................................................................................................. 16
Who Has the Electrons?......................................................................................................... 17
The Outermost Valence Electrons................................................................................... 17
Ionic and Pure Covalent Bonds........................................................................................ 18
Polar Covalent Bonds........................................................................................................ 19
Electronegativity................................................................................................................ 19
Oxidation States and Numbers........................................................................................ 20
Electron Donors and Acceptors............................................................................................ 23
The Common Electron Donors........................................................................................ 23
The Common Terminal Electron Acceptors................................................................... 23
Approaches to Balancing Redox Reactions......................................................................... 24
Balancing the Whole Reaction, the Eight Step Plan...................................................... 24
Balancing with Half-Cell Reactions................................................................................30
Electrons and COD/BOD....................................................................................................... 31
Summary.................................................................................................................................. 32

3 The Chemistry of Carbon (for the Non-Chemist in All of Us).................................... 35

Introduction............................................................................................................................. 35
Organic vs Inorganic.............................................................................................................. 35
Carbon, the Enchanted Element........................................................................................... 36
Water, the Wondrous Molecule............................................................................................. 38
Kekulé Structures................................................................................................................... 40

vii
viii Contents

Overview of Carbon Compounds........................................................................................42

Carbon Bonded with Hydrogen...........................................................................................43
Saturated with Hydrogen.................................................................................................43
Unsaturated with Hydrogen............................................................................................44
Conjugate Double Bonds – Life Gets Colorful...............................................................44
The Triple Bond.................................................................................................................. 46
Hydrocarbon Rings........................................................................................................... 46
Functional Groups with Oxygen.......................................................................................... 47
Alcohols............................................................................................................................... 47
Aldehydes and Ketones..................................................................................................... 49
Acids (Carboxylic Acids)................................................................................................... 50
Esters and Ethers................................................................................................................ 51
Combinations..................................................................................................................... 52
Stereoisomerism...................................................................................................................... 52
Functional Groups with Sulfur.............................................................................................54
Functional Groups with Nitrogen........................................................................................ 55
Amines................................................................................................................................ 55
Amides................................................................................................................................. 55
Amino Acids and the Peptide Bond................................................................................ 56
Nitro and Nitrate Compounds......................................................................................... 59
Functional Groups with Phosphorus................................................................................... 60
The Aromatics......................................................................................................................... 61
The Benzene Ring.............................................................................................................. 61
Substituted Benzenes........................................................................................................ 61
Polynuclear Aromatics......................................................................................................63
Heterocyclic Compounds......................................................................................................65
Natural Products and Foodstuffs......................................................................................... 68
Proteins................................................................................................................................ 68
Lipids, Waxes, and Membranes....................................................................................... 70
Fats and Oils.................................................................................................................. 70
Waxes and Paraffin....................................................................................................... 73
Phospholipids and the Membrane Bilayer................................................................ 73
Archaea and the Membrane Monolayer.................................................................... 74
The Steroids and Sterols............................................................................................... 75
Carbohydrates (the Sugars)............................................................................................... 76
Soaps and Detergents.............................................................................................................80
Synthetic Compounds............................................................................................................ 81
A Second Look at Hydrogen Bonding.................................................................................84
Summary.................................................................................................................................. 86

4 Life and Energy: The Principles of Chemical and Photo Thermodynamics............. 89

What Is Thermodynamics?................................................................................................... 89
The Laws of Thermodynamics.............................................................................................90
The Equivalence of Heat and Work.................................................................................90
Quantifying Heat Flow..................................................................................................... 92
The First Law...................................................................................................................... 93
The Concept of Enthalpy.................................................................................................. 95
Standard States and Standard Conditions..................................................................... 96
Determining the Enthalpy of Formation........................................................................ 97
Contents ix

Enthalpy Is a Property...................................................................................................... 99
Entropy and the Second Law......................................................................................... 101
Open and Closed Systems.............................................................................................. 103
The Third Law.................................................................................................................. 104
The Gibbs Free Energy......................................................................................................... 104
The Effect of Entropy....................................................................................................... 104
The Free Energy of Formation....................................................................................... 106
The Direction of Reaction............................................................................................... 106
Adjusting to Actual Concentrations.............................................................................. 109
Activity versus Concentration....................................................................................... 110
Gibbs Free Energy and the Equilibrium Constant...................................................... 113
The Effect of Temperature on Equilibrium.................................................................. 114
Coupled Reactions........................................................................................................... 114
The Equilibrium Constant for Dissolved Gases.......................................................... 114
Storing Gibbs Free Energy in Ion Gradients..................................................................... 117
The Thermodynamics of Light........................................................................................... 123
What Is Light?................................................................................................................... 123
The Electromagnetic Spectrum...................................................................................... 124
Enter Quantum Physics.................................................................................................. 126
Wave–Particle Duality and Spacetime.......................................................................... 129
A Definition of Light?...................................................................................................... 130
The Solar Constant........................................................................................................... 131
The Solar Spectrum......................................................................................................... 132
Photosynthetically Active Radiation (PAR)................................................................. 133
Photosynthetic Photon Flux Density (PPFD)............................................................... 133
The Laws of Microbes.......................................................................................................... 136
The First Law of Microbes.............................................................................................. 136
The Second Law of Microbes......................................................................................... 136
Summary................................................................................................................................ 137

5 Metabolic and Nutritional Classifications..................................................................... 139

Introduction........................................................................................................................... 139
Relationship to Oxygen........................................................................................................ 139
Aerobic Metabolism (Sometimes Called Oxic)............................................................ 139
Anoxic Metabolism (Sometimes Called Anaerobic Respiration).............................. 140
Anaerobic Metabolism (Also Called Fermentation)................................................... 143
Relationship to Environmental Factors............................................................................. 144
Temperature...................................................................................................................... 144
Hydrogen Ion and pH..................................................................................................... 147
Osmotic Pressure (Salinity)............................................................................................ 149
Barometric Pressure......................................................................................................... 150
Other Relationships......................................................................................................... 150
Nutritional Categories.......................................................................................................... 150
Energy, Electrons, and Carbon....................................................................................... 150
Chemolithoautotrophs.................................................................................................... 151
Chemoorganoheterotrophs............................................................................................ 155
Photolithoautotrophs....................................................................................................... 155
Photoorganoheterotrophs............................................................................................... 158
Other Minor Categories.................................................................................................. 159
x Contents

Chemolithoheterotrophs............................................................................................ 159
Photolithoheterotrophs............................................................................................... 159
Categories That Simply Don’t Exist............................................................................... 159
Case Studies........................................................................................................................... 160
The Extremophiles of Yellowstone and Rotorua......................................................... 160
Extreme Halophiles of the Great Salt Lake.................................................................. 164
The White Water Incident............................................................................................... 166
Summary................................................................................................................................ 168

6 The Synthesis Reactions of Microbial Life.................................................................... 171

Introduction........................................................................................................................... 171
Composition of a Microbial Cell......................................................................................... 171
Sources of Cell Carbon......................................................................................................... 172
Developing the Synthesis Reaction.................................................................................... 173
Using the Cell Formula C5H7O2N.................................................................................. 173
Using Organics for Cell Carbon..................................................................................... 174
Nitrogen Assimilation and Fixation.............................................................................. 176
Using CO2 for Cell Carbon.............................................................................................. 180
Thermodynamics of the Synthesis Reactions................................................................... 183
The Free Energy of Cell Formation............................................................................... 183
Free Energy Requirements Using Organics for Synthesis......................................... 185
Free Energy Requirements Using CO2 for Synthesis.................................................. 186
Summary................................................................................................................................ 189

7 Thermodynamics and Cell Yield...................................................................................... 191

Introduction........................................................................................................................... 191
The Cell Yield Coefficient, Y................................................................................................ 191
Cell Yield from Organic Redox Reactions......................................................................... 192
Organic Usage.................................................................................................................. 192
Energy Capture................................................................................................................ 193
Energy Required for Synthesis...................................................................................... 194
Energy Required for Nitrogen Reduction.................................................................... 194
Combined Equation......................................................................................................... 195
The Yield Coefficient....................................................................................................... 195
Calculation Procedures................................................................................................... 195
A Few Things to Note..................................................................................................... 199
Cell Yield from Inorganic Redox Reactions...................................................................... 200
Cell Yield Using Light Energy for Growth....................................................................... 205
Energy Captured from Photosynthesis........................................................................ 206
Energy Required for Synthesis...................................................................................... 207
Combined Equation......................................................................................................... 207
Photosynthetic Efficiency................................................................................................ 208
Photosynthetic Yield and Specific Growth Rate.......................................................... 209
Combining Energy and Synthesis Reactions.................................................................... 210
Problem Type 1: Using Calculated Y Values................................................................ 211
Problem Type 2: Using Assumed Y Values.................................................................. 212
Final Thoughts...................................................................................................................... 217
Summary................................................................................................................................ 217
Contents xi

8 Historic Moments in Microbiology and Public Health............................................... 219

The Microscope and the Kingdom Protista...................................................................... 219
The Binomial Naming System............................................................................................ 220
Spontaneous Generation and Vital Force.......................................................................... 221
Sterilization and Pasteurization......................................................................................... 224
Culturing Techniques...........................................................................................................225
The Germ Theory of Disease.............................................................................................. 227
Staining.................................................................................................................................. 228
Aseptic Surgical Practices.................................................................................................... 230
Immunology and Serology.................................................................................................. 231
Variolation and Smallpox............................................................................................... 231
Pasteur and Rabies........................................................................................................... 232
Serums for Diphtheria..................................................................................................... 232
The Story of Polio............................................................................................................. 233
Microbial Ecology (Soil Microbiology).............................................................................. 235
Chemotherapy (from Salvarsan to Sulfa to Penicillin).................................................... 236
Ehrlich and Salvarsan...................................................................................................... 236
Domagk and Sulfa........................................................................................................... 236
Penicillin and the Age of Antibiotics............................................................................ 238
Antibiotic Resistance....................................................................................................... 240
Probiotics................................................................................................................................ 241
The Discovery of Viruses..................................................................................................... 242
Disinfection Theory.............................................................................................................. 242
Molecular Biology................................................................................................................. 243
Epidemics and Pandemics................................................................................................... 244
London and Cholera, the Blue Death............................................................................ 245
Chicago and Typhoid Fever............................................................................................ 249
Los Angeles and Sewage Farming................................................................................ 251
The Great Sanitary Awakening.......................................................................................... 251
The Modern Era Begins....................................................................................................... 253

9 The World of Microbes (And a Few Related Friends).................................................. 257

Taxonomy and Phylogeny................................................................................................... 257
Prokaryotic and Eukaryotic Cell Types............................................................................. 257
Early Classification Schemes............................................................................................... 259
RNA Sequencing Leads to Domains and Beyond........................................................... 260
Prokaryotic Cell Structure................................................................................................... 262
Eukaryotic Cell Structure.................................................................................................... 264
The Bacteria........................................................................................................................... 265
The Eubacteria.................................................................................................................. 265
The Archaea...................................................................................................................... 267
Representative Phyla of Eubacteria............................................................................... 268
Proteobacteria (Mostly Gram-Negative Rods and Cocci)...................................... 268
Firmicutes (the Gram-Positive, Low G+C Bacteria)................................................ 271
Actinobacteria (the Gram-Positive, High G+C Bacteria)....................................... 272
Cyanobacteria.............................................................................................................. 273
Chlorobi and Chloroflexi........................................................................................... 274
Chlamydiae.................................................................................................................. 274
xii Contents

Spirochaetes................................................................................................................. 274
Bacteroidetes................................................................................................................ 274
Aquificae and Thermotogae...................................................................................... 275
Deinococcus-Thermus................................................................................................ 275
Phyla of the Archaea........................................................................................................ 275
Crenarchaeota.............................................................................................................. 275
Euryarchaeota.............................................................................................................. 276
Bacterial Strains................................................................................................................ 277
The Protista (the Protoctista)............................................................................................... 277
The “Animal-Like” Protozoa.......................................................................................... 278
The Photosynthetic Microalgae..................................................................................... 280
The Fungi............................................................................................................................... 282
The Molds.......................................................................................................................... 283
The Yeasts.......................................................................................................................... 287
The Fungi and Lignin...................................................................................................... 288
Some Important Metazoa.................................................................................................... 289
The Rotifers....................................................................................................................... 289
Tardigrades (Water Bears)............................................................................................... 289
Helminths......................................................................................................................... 291
Resistant Forms..................................................................................................................... 291
Acellular Infectious Agents (Akaryotic)............................................................................ 292
The Viruses....................................................................................................................... 292
Viroids............................................................................................................................... 294
Protein Infectious Particle (Prion)................................................................................. 294
Indicator Organisms............................................................................................................. 295
The Tree of Life..................................................................................................................... 296
Summary................................................................................................................................ 297

10 Infectious Diseases Important to Public Health and Sanitary Practice................... 301

Introduction........................................................................................................................... 301
Viral Diseases........................................................................................................................ 302
Poliomyelitis (Infantile Paralysis).................................................................................. 302
Hepatitis Type A (Infectious Hepatitis)........................................................................ 303
Influenza............................................................................................................................ 303
Gastroenteritis..................................................................................................................304
Smallpox............................................................................................................................304
Acquired Immune Deficiency Syndrome (AIDS)........................................................305
West Nile Fever.................................................................................................................305
Ebola (a Form of Hemorrhagic Fever)...........................................................................306
Bacterial Diseases.................................................................................................................306
Cholera...............................................................................................................................306
Salmonellosis.................................................................................................................... 307
Typhoid Fever................................................................................................................... 307
Dysentery..........................................................................................................................308
Escherichia coli O157:H7....................................................................................................308
Legionnaires’ Disease (Legionellosis)........................................................................... 310
Tuberculosis (TB), the White Death or Consumption................................................. 310
Contents xiii

Lyme Disease.................................................................................................................... 311

Anthrax.............................................................................................................................. 311
Trachoma........................................................................................................................... 311
Stomach Ulcers and Gastritis......................................................................................... 312
Bubonic Plague, the Black Death................................................................................... 312
Protozoan Diseases............................................................................................................... 313
Amoebic Dysentery or Amebiasis (Montezuma’s Revenge)...................................... 313
Giardiasis (Backpacker’s Diarrhea)............................................................................... 313
Cryptosporidiosis (Crypto)............................................................................................. 314
Malaria............................................................................................................................... 316
Trypanosomiasis.............................................................................................................. 316
Toxoplasmosis................................................................................................................... 317
Amoebic Brain Infection................................................................................................. 317
Fungal Diseases.................................................................................................................... 318
Aspergillosis..................................................................................................................... 318
Coccidioidomycosis (Valley Fever, San Joaquin Fever).............................................. 319
Farmer’s Lung................................................................................................................... 320
Candidiasis....................................................................................................................... 320
Histoplasmosis................................................................................................................. 320
Sporotrichosis................................................................................................................... 320
Helminth Diseases (Intestinal Worms and Flukes)......................................................... 320
Roundworms (Nematodes)............................................................................................. 321
The Flatworm Tapeworms (Cestodes).......................................................................... 325
The Flatworm Flukes (Trematodes).............................................................................. 326
Microbial Control by Heat Inactivation............................................................................. 327
Sterilization....................................................................................................................... 327
Pasteurization................................................................................................................... 328
Milk Pasteurization..................................................................................................... 328
Biosolids Pasteurization............................................................................................. 329
Bacterial Regrowth.......................................................................................................... 331
Summary................................................................................................................................ 332

11 Biochemistry and Bioenergetics (The Molecules of Life)........................................... 335

Introduction........................................................................................................................... 335
Tools of the Trade.................................................................................................................. 336
Building With Glucose......................................................................................................... 337
Using Glucose for Energy Storage................................................................................. 337
Using Glucose for Structure........................................................................................... 339
Using Glucose as a Tough Outer Hide.......................................................................... 341
Other Energy Storage Molecules........................................................................................ 341
Nucleotide Bases...................................................................................................................342
The Carriers of Energy and Electrons...............................................................................344
The ATP–ADP Energy System.......................................................................................344
The Electron Carrier Systems.........................................................................................346
Enzymes (Speeding Things Up).........................................................................................348
The Porphyrin Ring.............................................................................................................. 351
The Porphyrin Ring and Heme...................................................................................... 351
xiv Contents

The Porphyrin Ring and Chlorophyll........................................................................... 352

Peptidoglycan........................................................................................................................ 353
Oxygen and Nitrate as Electron Acceptors....................................................................... 356
Oxygen Free Radicals...................................................................................................... 356
Nitrate Reduction............................................................................................................. 357
Nitrogen Assimilation.......................................................................................................... 358
Assimilatory Nitrate Reduction..................................................................................... 358
Nitrogen Fixation............................................................................................................. 359
The Concept of the Common Intermediate...................................................................... 360
Biochemical Pathways in Heterotrophic Metabolism..................................................... 361
Glycolysis........................................................................................................................... 362
Fermentation Pathways................................................................................................... 363
The Kreb’s Cycle...............................................................................................................364
The Respiratory Chain and the Terminal Electron Acceptor.................................... 366
Chemiosmosis and the Proton Motive Force............................................................... 368
Other Metabolic Pathways.............................................................................................. 370
Hydrolysis.................................................................................................................... 370
General Oxidation....................................................................................................... 370
Beta Oxidation (β-Oxidation).................................................................................... 371
Protein Metabolism..................................................................................................... 372
Overall Metabolic Flow................................................................................................... 372
Metabolic Pathways of Photosynthesis.............................................................................. 373
The “Light” Reactions (Light-Driven Electron Flow)................................................. 373
The Bacterial One-Center System............................................................................. 373
The Two-Center or Tandem System......................................................................... 376
The “Dark” Reactions...................................................................................................... 378
The Calvin Cycle......................................................................................................... 378
The Problem of RuBisCo............................................................................................ 380
Carbon Concentrating Mechanisms......................................................................... 380
Combining the Light and Dark Reactions.................................................................... 381
Organization of the Light Absorbing Pigments.......................................................... 381
Energy Flow in the Cell....................................................................................................... 382
Information Macromolecules.............................................................................................. 383
Deoxyribonucleic Acid (DNA)....................................................................................... 383
Ribonucleic Acid (RNA).................................................................................................. 387
Messenger RNA (mRNA)........................................................................................... 387
Transfer RNA (tRNA) (Also Known as Soluble RNA or sRNA).......................... 387
Ribosomal RNA (rRNA)............................................................................................. 388
The Genetic Code............................................................................................................. 389
Final Overview...................................................................................................................... 391
Summary................................................................................................................................ 392

12 A Brief History of Life........................................................................................................ 395

Introduction........................................................................................................................... 395
What Is Life?.......................................................................................................................... 396
The Journey Starts with a Bang.......................................................................................... 396
Deep Time.............................................................................................................................. 398
Contents xv

The Earth Forms a Primordial Soup?................................................................................ 399

Prebiotic Chemistry on Earth......................................................................................... 399
Prebiotic Chemistry in the Cosmos............................................................................... 401
Was the Primordial Soup Enough?............................................................................... 402
Deep Sea Hydrothermal Vents – The Black Smokers?.................................................... 403
Deep Sea Hydrothermal Vents – The Lost City?..............................................................404
First Life.................................................................................................................................405
Stromatolites..................................................................................................................... 406
Banded Iron Formations.................................................................................................408
Ancient Graphite Layers................................................................................................. 410
Microfossils....................................................................................................................... 411
From Soup to the First Cell?................................................................................................ 411
Key Events in the Story of Life............................................................................................ 413
Is There Life Out There?......................................................................................................425
Seeking Intelligent Life................................................................................................... 426
Searching for Microbial Life........................................................................................... 427
Searching for Biomarkers............................................................................................... 427
Mirror Life on Earth?....................................................................................................... 428
Summary................................................................................................................................ 429

13 Kinetics and Biodegradability.......................................................................................... 431

Kinetics and Thermodynamics........................................................................................... 431
Catalysts and Enzymes........................................................................................................ 431
Mathematical Functions to Describe Reaction Rates...................................................... 433
Zero-Order Reactions...................................................................................................... 433
First-Order Reactions......................................................................................................434
Second-Order Reactions.................................................................................................. 435
Enzyme Kinetics................................................................................................................... 435
Single Enzyme–Substrate Model................................................................................... 436
Determining k and K M..................................................................................................... 439
Environmental Effects on Enzyme and Microbial Activity...........................................440
Effect of pH.......................................................................................................................440
Effect of Temperature......................................................................................................440
Enzyme Inhibition...........................................................................................................440
Microbial Reaction Rates..................................................................................................... 441
Effect of Temperature on Reaction Rates..........................................................................442
Substrate Biodegradability..................................................................................................443
A Question of Kinetics....................................................................................................443
Proteins, Lipids, and Sugars...........................................................................................444
Lignocellulosic Matter.....................................................................................................444
Respirometry.........................................................................................................................448
BOD and COD Testing....................................................................................................448
Constant Volume, Aerobic Respirometers.................................................................... 453
Constant Pressure, Aerobic Respirometers..................................................................454
Constant Pressure, Anaerobic Respirometers............................................................. 455
Case Study......................................................................................................................... 456
Complex Substrate Characteristics..................................................................................... 459
Summary................................................................................................................................ 461
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