Environmental microbiology of aquatic and waste systems

Part I Introduction 1 Nature, Properties, and Distribution of Water........................................ 3 1.1 Physical and Chemical Properties of Water and Their Consequences...................................................................................... 3 1.1.1 Molecular Structure of Water and Its Strong Surface Tension....................................................................... 3 1.1.2 The High Surface Tension of Water and Capillarity in Plants................................................................................... 4 1.1.3 The Three Physical States of Water, and the Floatation of Ice.......................................................... 4 1.1.4 The Thermal Properties of Water and Their Effect on Climate.................................................... 5 1.1.5 The Change in the Nature of Water at Different Temperatures and Lake Temperatures..................................... 5 1.1.6 The Low Electrical Conductivity of Pure Water..................... 6 1.1.7 The High Chemical Reactiveness of Water............................. 7 1.1.8 The pH of Water...................................................................... 7 1.1.9 The High Solvent Power of Water.......................................... 7 1.2 Importance and Uses of Water............................................................ 7 1.2.1 Composition of Biological Objects......................................... 7 1.2.2 Drinking by Man and Animals and Domestic Use................. 7 1.2.3 Irrigation and Aquaculture...................................................... 8 1.2.4 Power Generation.................................................................... 8 1.2.5 Transportation......................................................................... 8 1.2.6 Recreation............................................................................... 8 1.2.7 Human Affairs......................................................................... 8 1.3 The Hydrologic Cycle......................................................................... 8 1.4 Classification of Waters....................................................................... 9 1.4.1 Natural Waters......................................................................... 9 1.4.2 Artificial Waters...................................................................... 10 1.5 Global Distribution of Water on Earth and Its Study.......................... 10 References.................................................................................................... 12 2 Peculiarities of Water as an Environmental Habitat for Microorganisms.................................................................................... 15 2.1 The Peculiar Nature of Water as an Environment for Microbial Habitation..................................................................... 152.2 Ecological Habitats of Microorganisms in Aquatic Environments...................................................................................... 17 2.3 Foreign Versus Indigenous Aquatic Bacteria...................................... 17 2.4 Challenges of Aquatic Life: Factors Affecting the Microbial Population in Natural Waters.............................................................. 18 2.5 Methods for the Enumeration of Microorganisms in the Aquatic Environment........................................................................................ 20 2.5.1 Cultural Methods..................................................................... 20 2.5.2 Direct Methods........................................................................ 22 2.5.2.1 Light Microscopy..................................................... 22 2.5.2.2 Electron Microscopy................................................ 27 2.5.2.3 Flow Cytometry........................................................ 27 2.5.3 Determination of Bacterial Mass............................................ 29 2.5.3.1 Direct Methods......................................................... 29 2.5.3.2 Indirect Methods...................................................... 29 References.................................................................................................... 29 Part II Biological Aspects of Microorganisms in Aquatic Environments 3 Aspects of the Molecular Biology of Microorganisms of Relevance to the Aquatic Environment............................................... 33 3.1 Protein Synthesis................................................................................. 33 3.1.1 Transcription........................................................................... 35 3.1.2 Translation............................................................................... 35 3.2 The Polymerase Chain Reaction......................................................... 37 3.2.1 Some Applications of PCR in Environmental Biotechnology......................................................................... 38 3.3 Microarrays......................................................................................... 38 3.3.1 Applications of Microarray Technology................................. 40 3.4 Sequencing of DNA............................................................................ 41 3.4.1 Sequencing of Short DNA Fragments..................................... 41 3.4.2 Sequencing of Genomes or Large DNA Fragments................ 42 3.4.2.1 Use of Bacterial Artificial Chromosomes................ 42 3.4.2.2 Use of the Shotgun Approach.................................. 42 3.5 The Open Reading Frame and the Identification of Genes................. 42 3.6 Metagenomics..................................................................................... 44 References.................................................................................................... 45 4 Taxonomy, Physiology, and Ecology of Aquatic Microorganisms......... 47 4.1 Taxonomy of Microorganisms in Aquatic Environments................. 47 4.1.1 Nature of Modern Taxonomy............................................. 47 4.1.2 Evolution of the Classification of Living Things................ 48 4.1.3 Determining Taxonomic Groups Within Domains............. 48 4.1.3.1 Definition of Species............................................ 50 4.1.3.2 Nomenclature of Biological Objects................... 51 4.1.3.3 Criteria and Methods for the Identification and Classification of Bacteria and Archae: Morphological, Physiological, Nucleic Acid, and Chemical Properties................ 514.1.4 Bacteria............................................................................... 57 4.1.4.1 Taxonomic Groups Among Bacteria................... 57 4.1.4.2 Aspects of the Physiology and Ecology of Microorganisms in the Aquatic Environment................................. 65 4.1.5 Archae................................................................................. 75 4.1.5.1 General Properties of Archaea............................. 75 4.1.5.2 Taxonomic Groups Among Archeae................... 76 4.1.6 Microbial Taxonomic Groups Among Eucharia................. 78 4.1.6.1 Protozoa............................................................... 78 4.1.6.2 Fungi.................................................................... 80 4.1.6.3 Algae.................................................................... 82 4.1.7 Viruses................................................................................ 84 4.1.7.1 Viral Taxonomy and Nomenclature..................... 86 4.1.7.2 The Viral Groups................................................. 87 4.1.7.3 Bacteriophages in the Aquatic Environment....... 90 4.1.8 Small Multicellular Macroorganisms in Aquatic Systems............................................................. 97 4.1.8.1 Crustaceans (Including Rotifers)......................... 104 4.1.8.2 Nematodes........................................................... 104 References.................................................................................................... 106 Part III The Ecology of Microorganisms in Natural Waters 5 Ecology of Microorganisms in Freshwater.............................................. 111 5.1 Microbial Ecology of Atmospheric Waters...................................... 111 5.2 Microbial Ecology of Surface Waters............................................... 112 5.2.1 Rivers and Streams............................................................. 112 5.2.2 Lakes and Ponds................................................................. 112 5.2.3 Wetlands.............................................................................. 112 5.3 Ground Waters.................................................................................. 114 5.4 Some Microorganisms Usually Encountered in Fresh Water........... 116 5.4.1 Bacteria............................................................................... 116 5.4.1.1 New Data Regarding Freshwater Bacteria........... 116 5.4.1.2 Some Bacteria in Freshwater............................... 118 5.4.2 Fungi................................................................................... 118 5.4.3 Algae................................................................................... 119 5.4.4 Protozoa.............................................................................. 119 5.5 Succession of Organisms in the Breakdown Materials Added to Aquatic Systems............................................... 119 5.5.1 The Physiological Basis of Aquatic Microbial Ecology.............................................................. 119 5.6 Microbial Loop and the Food Web in a Freshwater System............. 121 References.................................................................................................... 122 6 Ecology of Microorganisms in Saline Waters (Seas and Oceans).......... 123 6.1 The Ocean Environment................................................................... 123 6.2 Some Properties of Sea Water.......................................................... 127 6.2.1 Salinity................................................................................ 127 6.2.2 Temperature........................................................................ 128xii Contents 6.2.3 Light.................................................................................... 129 6.2.4 Nutrients............................................................................. 130 6.2.5 Oxygen and CO2 in the Marine Environment..................... 130 6.2.6 Sea Sediments..................................................................... 130 6.3 Microbial Ecology of the Seas and Oceans...................................... 130 6.3.1 Bacteria............................................................................... 130 6.3.2 Archae................................................................................. 133 6.3.3 Fungi................................................................................... 133 6.3.4 Algae................................................................................... 133 6.3.5 Protozoa.............................................................................. 135 6.3.6 Viruses................................................................................ 136 6.3.7 Plankton.............................................................................. 136 6.4 Unique Aspects of the Existence of Microorganisms in the Marine Environment............................................................... 137 6.4.1 Low Temperature................................................................ 137 6.4.2 High Pressure...................................................................... 138 6.4.3 Oxygen................................................................................ 138 6.4.4 Food/Nutrients.................................................................... 138 6.4.5 Light.................................................................................... 138 6.4.6 High Temperature............................................................... 139 6.4.7 Size in Marine Microorganisms.......................................... 139 6.5 The Place of Microorganisms in the Food Chains of the Oceans and Seas..................................................................... 139 6.6 Marine Microorganisms and Their Influence on Global Climate and Global Nutrient Recycling......................................................... 141 6.6.1 The Influence of Marine Microorganisms on Global Climate and Global Nutrient Recycling............. 141 6.6.1.1 Global Marine Algal Sulfur Recycling, Dimethylsulfoniopropionate, Dimethyl Sulfide and Climate Change.............................................. 142 6.6.1.2 Carbon Recycling by Marine Algae and Reduction of Global Warming............................. 144 6.6.1.3 Marine Microorganisms and the Nitrogen Economy of Seas and Oceans.............................. 145 6.6.1.4 The Global C:N:P Marine Ratio and Its Maintenance Through Microbial Activity: The Redfield Ratio............................................... 147 References.................................................................................................... 148 Part IV Pollution and Purification of, and Disease Transmission in, Water 7 Pollution of Aquatic Systems: Pollution Through Eutrophication, Fecal Materials, and Oil Spills.................................................................. 151 7.1 Nature of Pollution........................................................................... 151 7.1.1 The Concept of the Self-purification of Water as Basis for the Understanding of Pollution....................... 152 7.1.2 Definition of Pollution........................................................ 153 7.1.3 Kinds of Pollutants............................................................. 1547.1.4 Pollution by Eutrophication................................................ 154 7.1.4.1 “Algal Blooms” and Eutrophication.................... 155 7.1.5 Biological Indicators of Pollution by Eutrophication......... 156 7.2 Pollution of Water with Reference to Human Health: Bacterial Indicators of Fecal Pollution............................................. 157 7.2.1 Microbiological Examination of Water for Fecal Contamination..................................................... 157 7.2.1.1 Principle of Indicator Organisms......................... 158 7.2.1.2 Procedure for the Determination of Fecal Contamination........................................ 159 7.2.1.3 Methods Used in the Enumeration of Indicator Organisms in Water.......................... 160 7.2.1.4 Standard Water Analysis...................................... 165 7.2.1.5 Total Maximum Daily Loads and Microbial Source Tracking in Water Pollution.................................................... 165 7.3 Pollution by Petroleum in Oceans and Seas: Role of Microorganisms in Oil Degradation and Remediation................... 173 7.3.1 Composition of Crude Oil.................................................. 173 7.3.1.1 Categorization of Crude Petroleum..................... 173 7.3.2 Oil Spills............................................................................. 177 7.3.2.1 Behavior of Oil in an Oil Spill............................. 178 7.3.2.2 Remediation of Oil Spills.................................... 183 References.................................................................................................... 186 8 Disease Transmission in Water................................................................. 189 8.1 Disease Transmission Through Drinking Water............................... 189 8.1.1 Communicable Diseases Transmitted Through Drinking Water..................................................... 190 8.1.2 Disease Outbreaks in Drinking Water Due to the Presence of Chemicals, and Biotoxins...................... 193 8.1.2.1 Brief Notes on Some Water-Borne Diseases....... 193 8.2 Disease Transmission in Recreational Waters.................................. 200 8.2.1 Disease Transmission in Recreational Waters Through Fecal Material...................................................... 201 8.2.1.1 Fecal Bacteria Which Have Caused Disease Outbreaks in Recreational Waters........................ 201 8.2.1.2 Fecal Protozoa Which Have Caused Disease Outbreaks in Recreational Waters........................ 201 8.2.1.3 Fecal Viruses Which Have Caused Disease Outbreaks in Recreational Waters........................ 202 8.2.2 Disease Transmission in Recreational Water Through Non-fecal Material............................................... 202 8.2.2.1 Disease Transmission by Bacteria in Recreational Water Through Non-fecal Material................................................................ 202 8.2.2.2 Disease Transmission by Viruses in Recreational Water Through Non-fecal Material............................................... 206Contents 8.2.2.3 Disease Transmission by Protozoa in Recreational Water Through Non-fecal Material............................................... 207 8.2.2.4 Disease Transmission by Fungi in Recreational Water Through Non-fecal Material: Trichophyton spp. and Epidermophyton floccosum............................................................. 208 8.3 Disease Transmission Through Shellfish Growing in Fecally Contaminated Water......................................................................... 208 8.3.1 Description of Shellfish...................................................... 208 8.3.2 Monitoring the Aquatic Environment of Shellfish Growth............................................................. 209 8.3.2.1 Procedure for Monitoring Shellfish Growing Areas in the US.................................................... 210 8.4 Recent Developments Regarding Knowledge of Pathogens in Drinking Water............................................................................. 211 References.................................................................................................... 213 9 Municipal Purification of Water............................................................... 215 9.1 The Need for Water Purification....................................................... 215 9.2 The Quality of the Raw Water to Be Purified................................... 216 9.3 Processes for the Municipal Purification of Water........................... 217 9.3.1 Pretreatments...................................................................... 217 9.3.2 Storage and Sedimentation Without Coagulation............... 218 9.3.3 Aeration.............................................................................. 218 9.3.4 Coagulation and Flocculation............................................. 219 9.3.5 Sedimentation..................................................................... 220 9.3.6 Filtration............................................................................. 220 9.3.7 Chlorination (and Other Methods of) Disinfection............ 221 9.3.7.1 Reactions of Chlorine with Chemicals Found in Water..................................................... 222 9.3.7.2 The Present Practice of Water Chlorination........ 224 9.3.7.3 Mode of Action of Chlorine Disinfection............ 225 9.3.7.4 Factors Affecting the Efficacy of Disinfection in Water by Chlorine (and the other halogens)... 225 9.3.7.5 Tests for Chlorine in Water.................................. 226 9.3.7.6 Alternative Methods of Disinfection Besides Chlorine and Other Halogens.............................. 227 9.3.7.7 Ozone................................................................... 227 9.3.8 Ultraviolet Light................................................................. 229 9.3.8.1 Mode of Action and Use of UV........................... 229 9.3.9 Iron and Manganese Control.............................................. 229 9.3.10 Softening of Water.............................................................. 230 9.3.11 Fluoridation......................................................................... 230 9.3.12 Algae Control (and Control of Taste and Odors)................ 231 9.3.12.1 Methods for the Control of Algae and Taste and Odor............................................................. 231 9.3.13 Color and Turbidity Removal............................................. 2319.3.14 Miscellaneous Treatments Water Purification.................... 231 9.3.14.1 Plumbosolvency Removal................................. 231 9.3.14.2 Radium (Radioactivity) Removal...................... 232 9.3.14.3 Reverse Osmosis................................................ 232 9.3.14.4 Ion Exchange..................................................... 232 9.3.14.5 Electrodeionization............................................ 232 9.4 Purification of Bottled Water............................................................ 233 9.5 Standards Required of Water............................................................ 233 9.5.1 Standards Required for Drinking Water............................. 233 9.5.1.1 The Microbiological Standards......................... 235 9.5.1.2 Turbidity............................................................ 235 9.5.1.3 Chemical Standards........................................... 243 9.5.2 Standards Required for Recreational Waters...................... 243 9.5.3 Standards Required for Shellfish Harvesting Waters............................................................... 244 References.................................................................................................... 245 Part V Waste Disposal in Aquatic and Solid Media 10 Waste Disposal in the Aqueous Medium: Sewage Disposal................... 249 10.1 Nature of Wastes............................................................................... 249 10.2 Methods for the Determination of Organic Matter Content in Sewage and Wastewaters.............................................................. 250 10.2.1 Determination of Dissolved Oxygen.................................. 250 10.2.1.1 The Biological or Biochemical Oxygen Demand Test...................................................... 250 10.2.1.2 Permanganate Value Test................................... 253 10.2.1.3 Chemical Oxygen Demand................................ 253 10.2.1.4 Total Organic Carbon........................................ 254 10.2.1.5 Total Suspended Solids...................................... 254 10.2.1.6 Volatile Suspended Solids................................. 254 10.3 Systems for the Treatment of Sewage.............................................. 254 10.3.1 Aerobic Breakdown of Raw Waste Waters......................... 254 10.3.1.1 The Activated Sludge System............................ 255 10.3.1.2 The Trickling Filter........................................... 259 10.3.1.3 Rotating Discs................................................... 261 10.3.1.4 Oxidation Ponds................................................ 262 10.3.2 Anaerobic Sewage Systems................................................ 264 10.3.2.1 Treatment of the Sludge from Aerobic Sewage Treatment Systems: Anaerobic Breakdown of Sludge....................... 264 10.3.2.2 The Septic Tank................................................. 265 10.3.2.3 The Imhoff Tank................................................ 267 10.3.2.4 Cesspools........................................................... 267 10.4 Advanced Wastewater Treatment..................................................... 268 10.4.1 Methods Used in Advanced Wastewater Treatment........... 269 References.................................................................................................... 27311 The Disposal of Municipal Solid Wastes.................................................. 275 11.1 The Nature of Wastes in General...................................................... 275 11.2 The World-Wide Development of Interest in the Environment........ 276 11.2.1 The Stockholm Conference, 1972: Beginning of World-Wide Interest in the Protection of the Environment ........................................................... 276 11.2.2 Environmental Regulation in the European Union............. 281 11.2.3 Environmental Regulations in Japan.................................. 281 11.2.4 Governmental Regulation of the Environment in Ghana.... 281 11.2.5 Egypt’s Environmental Affairs Agency.............................. 282 11.3 Nature of Municipal Solid Wastes.................................................... 282 11.3.1 Integrated Solid Waste Management.................................. 283 11.3.1.1 Source Reduction............................................... 284 11.3.1.2 Recycling........................................................... 284 11.3.1.3 Incineration with Energy Recovery................... 285 11.3.1.4 Composting........................................................ 290 11.3.1.5 Landfills Used in the Disposal of MSW............ 292 11.4 Anaerobic Breakdown of Organic Matter in Landfills (and Aquatic Sediments)................................................................... 298 11.4.1 Some Properties of Methanogens....................................... 298 11.4.2 Landfill Gas........................................................................ 299 11.4.2.1 Landfill Methane Capture Technology.............. 301 11.5 Options for Municipal Solid Wastes Management........................... 301 References.................................................................................................... 302 Index.................................................................................................................... 305