Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment

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1. Verfasser: Sigee, David C. (VerfasserIn)
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Sprache:English
Veröffentlicht: Hoboken, NJ Wiley 2005
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650 4 |a aFresh Water  |a xmicrobiology 
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Datensatz im Suchindex

DE-BY-TUM_call_number 1002 BIO 250f 2006 B 1898
DE-BY-TUM_katkey 1531399
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DE-BY-TUM_media_number 040090224450
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adam_text FRESHWATER MICROBIOLOGY BIODIVERSITY AND DYNAMIC INTERACTIONS OF MICROORGANISMS IN THE AQUATIC ENVIRONMENT DAVID C. SIGEE UNIVERSITY OF MANCHESTER, UK JOHN WILEY SONS, LTD CONTENTS PREFACE COPYRIGHT ACKNOWLEDGEMENTS 1 MICROBIAL DIVERSITY AND FRESHWATER ECOSYSTEMS 1.1 GENERAL INTRODUCTION 1.1.1 THE AQUATIC EXISTENCE 1.1.2 1.1.3 1.1.4 THE GLOBAL WATER SUPPLY - LIMNOLOGY AND OCEANOGRAPHY FRESHWATER SYSTEMS: SOME TERMS AND DEFINITIONS THE BIOLOGY OF FRESHWATER MICROORGANISMS A. BIOLOGICAL DIVERSITY IN THE FRESHWATER ENVIRONMENT 1.2 BIODIVERSITY OF MICROORGANISMS 1.2.1 DOMAINS OF LIFE 1.2.2 SIZE RANGE 1.2.3 AUTOTROPHS AND HETEROTROPHS 1.2.4 PLANKTONIC AND BENTHIC MICROORGANISMS 1.2.5 METABOLICALLY ACTIVE AND INACTIVE STATES 1.2.6 EVOLUTIONARY STRATEGIES: R-SELECTED AND K-SELECTED ORGANISMS BIODIVERSITY IN ECOSYSTEMS, COMMUNITIES, AND SPECIES POPULATIONS 1.3.1 MAIN ECOSYSTEMS 1.3.2 DIVERSITY WITHIN SUBSIDIARY COMMUNITIES 1.3.3 BIODIVERSITY WITHIN SINGLE-SPECIES POPULATIONS 1.3 B. ECOSYSTEMS 1.4 1.5 1.6 THE BIOFILM COMMUNITY: A SMALL-SCALE FRESHWATER ECOSYSTEM 1.4.1 INTERACTIONS BETWEEN MICROORGANISMS 1.4.2 BIOMASS FORMATION AND TRANSFER 1.4.3 1.4.4 THE PELAGIC ECOSYSTEM: A LARGE-SCALE UNIT WITHIN THE LAKE ENVIRONMENT 1.5.1 INTERACTIONS BETWEEN ORGANISMS 1.5.2 1.5.3 1.5.4 HOMEOSTASIS AND ECOSYSTEM STABILITY 1.6.1 STRESS FACTORS 1.6.2 1.6.3 MAINTENANCE OF THE INTERNAL ENVIRONMENT INTERACTIONS WITH THE EXTERNAL ENVIRONMENT TROPHIC CONNECTIONS AND BIOMASS TRANSFER MAINTENANCE OF THE INTERNAL ENVIRONMENT INTERACTIONS WITH THE EXTERNAL ENVIRONMENT GENERAL THEORETICAL PREDICTIONS: THE COMMUNITY RESPONSE OBSERVED STRESS RESPONSES: FROM MOLECULES TO COMMUNITIES 1 1 1 1 3 4 4 4 4 6 10 11 12 15 15 16 16 17 18 19 20 20 21 21 21 23 28 28 29 30 30 31 CONTENTS 1.6.4 ASSESSMENT OF ECOSYSTEM STABILITY 1.6.5 1.6.6 BIOLOGICAL RESPONSE SIGNATURES FOOD WEBS IN LENTIC AND LOTIC SYSTEMS ECOSYSTEM STABILITY AND COMMUNITY STRUCTURE C. 1.7 PELAGIC FOOD WEBS CASE STUDY 1.1 CASE STUDY 1.2 MICROBIAL FOOD WEB ASSOCIATED WITH AN ALGAL BLOOM GENERAL FOOD WEB IN THE WATER COLUMN OF LAKE BAIKAL (RUSSIA) 1.8 COMMUNITIES AND FOOD WEBS OF RUNNING WATERS 1.8.1 1.8.2 PELAGIC AND BENTHIC COMMUNITIES 1.8.3 THE MICROBIAL FOOD WEB ALLOCHTHONOUS CARBON: DISSOLVED AND PARTICULATE MATTER IN RIVER SYSTEMS 2 FRESHWATER ENVIRONMENTS: THE INFLUENCE OF PHYSICO-CHEMICAL CONDITIONS ON MICROBIAL COMMUNITIES A. INTRODUCTION 2.1 THE AQUATIC MEDIUM: WATER, DISSOLVED AND PARTICULATE COMPONENTS 2.1.1 PARTICULATE MATTER 2.1.2 AQUATIC MATRIX 2.2 FRESHWATER ENVIRONMENTS B. LAKES 2.3 LAKE MORPHOLOGY AND HYDROLOGY 2.3.1 LAKE MORPHOLOGY 2.3.2 2.4 LAKES AS ISOLATED ENVIRONMENTS 2.4.1 ISOLATED DEVELOPMENT 2.4.2 2.5 CLIMATIC INFLUENCES ON LAKES 2.5.1 2.5.2 BIOLOGICAL SIGNIFICANCE OF STRATIFICATION 2.5.3 TROPICAL LAKES POLAR AND SUB-POLAR LAKES LAKE HYDROLOGY AND THE SURROUNDING TERRESTRIAL ENVIRONMENT LAKE BAIKAL: AN ANCIENT LAKE WITH A DIVERSE AND UNIQUE FAUNA AND FLORA TEMPERATE LAKES - SEASONAL VARIATIONS AND LAKE STRATIFICATION C. WETLANDS 2.6 GENERAL CHARACTERISTICS 2.6.1 2.6.2 UNIFYING FEATURES OF WETLANDS 2.6.3 CASE STUDIES ON WETLAND AREAS CASE STUDY 2.1 TREBON BASIN BIOSPHERE RESERVE WETLAND DIVERSITY AND GLOBAL SCALE THE ROLE OF WETLANDS IN ENERGY AND MATERIAL FLOW 2.7 WETLAND HABITATS AND COMMUNITIES 2.8 D. STREAMS AND RIVERS 2.9 2.10 COMPARISON OF LOTIC AND LENTIC SYSTEMS RIVER FLOW AND THE BENTHIC COMMUNITY 2.10.1 2.10.2 FLOW CHARACTERISTICS OF LOTIC SYSTEMS INFLUENCE OF WATER FLOW ON BENTHIC MICROORGANISMS 2.1 1 RIVER HYDROLOGY E. ESTUARIES 2.12 RIVER INFLOW: WATER MIXING, ESTUARINE PRODUCTIVITY, AND EUTROPHICATION OF COASTAL AREAS 31 32 34 34 34 34 36 40 40 42 43 47 47 47 47 48 52 53 53 53 57 60 60 62 63 65 66 67 68 68 68 68 69 69 70 71 72 72 73 73 75 78 79 80 CONTENTS 2.12.1 2.12.2 2.12.3 2.13 HABITATS AND COMMUNITIES 2.13.1 PELAGIC ZONE 2.13.2 SEDIMENTS AND MUDFLATS MIXING OF FRESH AND SALTWATERS HIGH PRODUCTIVITY OF ESTUARINE SYSTEMS EUTROPHICATION OF SURROUNDING COASTAL AREAS F. ADVERSE AND EXTREME CONDITIONS IN FRESHWATER ENVIRONMENTS 2.14 ADVERSE CONDITIONS AS PART OF THE ENVIRONMENTAL CONTINUUM 2.14.1 VARIATIONS IN OXYGEN CONCENTRATION 2.14.2 NUTRIENT AVAILABILITY 2.14.3 SOLAR RADIATION 2.15 EXTREME ENVIRONMENTAL CONDITIONS TEMPERATURE 2.15.2 PH 2.15.3 2.15.5 VARIATIONS IN HYDROSTATIC PRESSURE 2.15.6 ORGANIC AND INORGANIC POLLUTION A POTENTIALLY EXTREME MICROENVIRONMENT: THE AI-WATER SURFACE 2.16.1 CHEMICAL COMPOSITION OF THE SURFACE MICROLAYER 2.16.2 PHYSICAL PROCESSES AND TRANSFORMATIONS IN THE SURFACE BIOFILM 2.1 6.3 MICROBIAL COMMUNITY AT THE AIR-WATER INTERFACE MICROBIAL COMMUNITIES OF SNOW AND ICE: LIFE IN THE FROZEN STATE 2.17.1 SNOW AND ICE AS AN EXTREME ENVIRONMENT 2.17.2 REQUIREMENT FOR WATER IN THE LIQUID STATE 2.17.3 SNOW ECOSYSTEMS 2.17.4 THE PHYSICAL PROPERTIES OF SNOW 2.17.5 SNOW AND ICE MICROORGANISMS CONDITIONS OF LOW WATER AVAILABILITY: SALINE ENVIRONMENTS CONDITIONS OF LOW WATER AVAILABILITY: ICE AND SNOW ENVIRONMENTS 2.16 2.17 3 ALGAE: THE MAJOR MICROBIAL BIOMASS IN FRESHWATER SYSTEMS A. TAXONOMIC AND MOLECULAR CHARACTERIZATION 3.1 MAJOR TAXONOMIC DIVISIONS OF FRESHWATER ALGAE 3.1.1 3.1.2 BIOCHEMICAL AND CYTOLOGICAL CHARACTERISTICS 3.1.3 ALGAL SPECIES: TAXONOMY AND INTRASPECIFIC VARIATION 3.2.1 TAXONOMY OF ALGAL SPECIES 3.2.2 CHEMICAL DIVERSITY WITHIN SPECIES - ENZYME ANALYSIS, MOLECULAR GROUPS. AND ELEMENTAL COMPOSITION MOLECULAR CHARACTERIZATION AND IDENTIFICATION OF ALGAE INVESTIGATION OF GENE FUNCTION IN FRESHWATER ALGAE MICROSCOPICAL APPEARANCE, MOTILITY AND ECOLOGICAL FEATURES GENERAL SUMMARY OF THE DIFFERENT GROUPS 3.2 3.3 MOLECULAR ANALYSIS 3.3.1 3.3.2 B. SIZE, SHAPE, AND SURFACE MUCILAGE 3.4 PHYTOPLANKTON SIZE AND SHAPE. 3.4.1 CELL COUNTS AND BIOVOLUME 3.4.2 FROM PICOPLANKTON TO MACROPLANKTON 3.4.3 3.4.4 3.5.1 CHEMICAL COMPOSITION OF MUCILAGE BIOLOGICAL SIGNIFICANCE OF SIZE AND SHAPE VARIATION IN SIZE AND SHAPE WITHIN PHYTOPLANKTON POPULATIONS 3.5 MUCILAGINOUS AND NON-MUCILAGINOUS ALGAE 80 81 82 82 82 82 84 85 85 85 86 86 86 89 91 92 93 93 95 95 96 98 99 99 99 99 100 102 107 107 107 110 112 114 114 115 116 116 119 123 123 123 123 124 128 130 131 CONTENTS 3.5.2 3.5.3 ROLE OF MUCILAGE IN PHYTOPLANKTON ACTIVITIES ENVIRONMENTAL IMPACT AND BIOGEOCHEMICAL CYCLES C. ACTIVITIES WITHIN THE FRESHWATER ENVIRONMENT 3.6 3.7 3.8 3.9 BENTHIC ALGAE: INTERACTIONS WITH PLANKTONIC ALGAE AND ECOLOGICAL SIGNIFICANCE 3.6.1 PLANKTONIC AND BENTHIC ALGAE 3.6.2 LAKE PERIPHYTON 3.6.3 BENTHIC ALGAE IN FLOWING WATERS 3.6.4 ECOLOGICAL ROLE OF BENTHIC ALGAE TEMPORAL ACTIVITIES OF FRESHWATER ALGAE 3.7.1 SHORT-TERM CHANGES: MOLECULAR AND CELLULAR PROCESSES 3.7.2 MEDIUM-TERM CHANGES: ALGAL SUCCESSION 3.7.3 LONG-TERM CHANGES: VARIATIONS OVER A NUMBER OF YEARS PHYTOPLANKTON DISTRIBUTION WITHIN THE WATER COLUMN CASE STUDY 3.1 ACTIVE MIGRATION OF ALGAE 3.8.2 FRESHWATER ALGAE AND NUTRIENT STATUS OF THE ENVIRONMENT 3.9.1 3.9.2 VERTICAL ZONATION OF PHYTOPLANKTON IN A STRATIFIED LAKE PASSIVE MOVEMENT OF ALGAE WITHIN THE WATER COLUMN PHYTOPLANKTON SPECIES COMPOSITION AND LAKE NUTRIENT STATUS NUTRIENT STATUS OF RIVER ENVIRONMENTS - EFFECT ON BENTHIC ALGAL BIOFILMS D. STRATEGIES FOR SURVIVAL 3.10 STRATEGIES FOR SURVIVAL: THE PLANKTONIC ENVIRONMENT 3.10.1 MEROPLANKTONIC ALGAE 3.10.2 HETEROTROPHIC NUTRITION IN FRESHWATER ALGAE 3.1 1.1 ORGANOTROPHY 3.1 1.2 PHAGOTROPHY SURVIVAL IN SNOW AND ICE: ADAPTATIONS OF CRYOPHILIC ALGAE 3.12.1 3.12.2 3.12.3 STRATEGIES FOR UNSTABLE AND STABLE ENVIRONMENTS: R-SELECTED AND K-SELECTED ALGAE 3.11 3.12 MAJOR GROUPS OF CRYOPHILIC ALGAE LIFE CYCLES OF SNOW ALGAE PHYSIOLOGICAL ADAPTATIONS OF SNOW ALGAE BIODIVERSITY IN THE ALGAL COMMUNITY VARIETY OF FRESHWATER ALGAE: INDICES OF SPECIES DIVERSITY 3.13.1 THE PARADOX OF PHYTOPLANKTON DIVERSITY 3.13.2 BIODIVERSITY INDICES 3.13.3 NUMERICAL COMPARISON OF PHYTOPLANKTON POPULATIONS 3.13.4 BIODIVERSITY AND ECOSYSTEM FUNCTION E. 3.13 4 COMPETITION FOR LIGHT 4.1 THE LIGHT ENVIRONMENT 4.1.1 4.1.2 4.1.3 4.1.4 PHOTOSYNTHETIC PROCESSES IN THE FRESHWATER ENVIRONMENT 4.2.1 LIGHT AND DARK REACTIONS 4.2.2 PHOTOSYNTHETIC MICROORGANISMS 4.2.3 MEASUREMENT OF PHOTOSYNTHESIS 4.2.4 LIGHT AS A GROWTH RESOURCE 4.3.1 4.3.2 PHYSICAL PROPERTIES OF LIGHT: TERMS AND UNITS OF MEASUREMENT LIGHT THRESHOLDS FOR BIOLOGICAL ACTIVITIES LIGHT UNDER WATER: REFRACTION, ABSORPTION, AND SCATTERING LIGHT ENERGY CONVERSION: FROM LAKE SURFACE TO ALGAL BIOMASS 4.2 PHOTOSYNTHETIC RESPONSE TO VARYING LIGHT INTENSITY STRATEGIES FOR LIGHT UPTAKE AND UTILIZATION LIGHT-PHOTOSYNTHETIC RESPONSE IN DIFFERENT ALGAE 4.3 131 133 133 133 133 136 138 139 140 142 146 148 148 149 156 157 157 160 161 161 162 164 165 167 168 171 171 173 174 177 177 177 178 179 180 181 182 182 183 184 186 188 188 189 189 190 192 192 193 CONTENTS 4.4 4.5 4.6 4.7 4.8 4.9 4.3.3 CONSERVATION OF ENERGY 4.3.4 ALGAL GROWTH AND PRODUCTIVITY 4.4.1 4.4.2 4.4.3 PHOTOSYNTHETIC BACTERIA 4.5.1 MAJOR GROUPS 4.5.2 PHOTOSYNTHETIC PIGMENTS 4.5.3 BACTERIAL PRIMARY PRODUCTIVITY PHOTOADAPTATION: RESPONSES OF AQUATIC ALGAE TO LIMITED SUPPLIES OF LIGHT ENERGY 4.6.1 DIFFERENT ASPECTS OF LIGHT LIMITATION 4.6.2 VARIABLE LIGHT INTENSITY: LIGHT-RESPONSIVE GENE EXPRESSION 4.6.3 PHOTOSYNTHETIC RESPONSES TO LOW LIGHT INTENSITY 4.6.4 SPECTRAL COMPOSITION OF LIGHT: CHANGES IN PIGMENT COMPOSITION CARBON UPTAKE AND EXCRETION BY ALGAL CELLS CHANGES IN ENVIRONMENTAL AND PH 4.7.2 EXCRETION OF DISSOLVED ORGANIC CARBON BY PHYTOPLANKTON CELLS COMPETITION FOR LIGHT AND CARBON DIOXIDE BETWEEN ALGAE AND HIGHER PLANTS 4.8.1 THE BALANCE BETWEEN ALGAE AND MACROPHYTES IN DIFFERENT AQUATIC ENVIRONMENTS LAKES OF THE TREBON WETLANDS 4.8.2 DAMAGING EFFECTS OF HIGH LEVELS OF SOLAR RADIATION: PHOTOINHIBITION 4.9.1 SPECIFIC MECHANISMS OF PHOTOINHIBITION 4.9.2 GENERAL EFFECTS OF PHOTOINHIBITION 4.9.3 4.9.4 PHOTOINHIBITION AND CELL SIZE 4.9.5 4.9.6 DIVERSITY IN SMALL MOLECULAR WEIGHT SOLUTES AND OSMOREGULATION PRIMARY PRODUCTION: CONCEPTS AND TERMS PRIMARY PRODUCTION AND ALGAL BIOMASS FIELD MEASUREMENTS OF PRIMARY PRODUCTIVITY CASE STUDY 4.1 COMPETITION BETWEEN ALGAE AND MACROPHYTES IN SHALLOW PHYSIOLOGICAL AND ENVIRONMENTAL ADAPTATIONS IN THE COMPETITION BETWEEN ALGAE AND MACROPHYTES STRATEGIES FOR THE AVOIDANCE OF PHOTOINHIBITION LACK OF PHOTOINHIBITION IN BENTHIC COMMUNITIES PHOTOINHIBITION IN EXTREME HIGH-LIGHT ENVIRONMENTS 4.10 PERIODIC EFFECTS OF LIGHT ON SEASONAL AND DIURNAL ACTIVITIES OF FRESHWATER BIOTA 4.10.1 SEASONAL PERIODICITY 4.10.2 DIURNAL CHANGES 4.10.3 4.10.4 CIRCADIAN RHYTHMS IN DINOFLAGELLATES CIRCADIAN RHYTHMS IN BLUE-GREEN ALGAE 5 INORGANIC NUTRIENTS: UPTAKE AND CYCLING IN FRESHWATER SYSTEMS 5.1 CHEMICAL COMPOSITION OF NATURAL WATERS 5.1.1 5.1.2 AERIAL DEPOSITION OF NUTRIENTS 5.1.3 5.1.4 5.1.5 NUTRIENT UPTAKE AND GROWTH KINETICS 5.2.1 5.2.2 5.2.3 5.2.4 A. NITROGEN SOLUBLE INORGANIC MATTER IN LAKES AND RIVERS NUTRIENT INFLOW FROM TERRESTRIAL SOURCES CHEMICAL REQUIREMENTS AND COMPOSITION OF FRESHWATER BIOTA NUTRIENT AVAILABILITY AND CYCLING IN AQUATIC SYSTEMS EMPIRICAL MODELS FOR ALGAL NUTRIENT KINETICS COMPETITION AND GROWTH IN THE AQUATIC ENVIRONMENT NUTRIENT AVAILABILITY AND WATER MOVEMENT ACUTE NUTRIENT DEPRIVATION AS AN ENVIRONMENTAL STRESS FACTOR CASE STUDY 5.1 ELEMENTAL COMPOSITION OF CERATIUM HIRUNDINELLA 5.2 5.3 BIOLOGICAL AVAILABILITY OF NITROGEN IN FRESHWATER ENVIRONMENTS 5.3.1 SOLUBLE NITROGENOUS COMPOUNDS 194 195 196 196 197 197 199 200 200 20 1 202 203 204 205 209 210 210 21 1 215 215 216 218 22 1 22 1 224 225 227 228 228 230 230 23 1 232 234 235 235 235 237 237 238 240 243 246 246 248 250 25 1 25 1 25 1 25 1 CONTENTS 5.4 THE NITROGEN CYCLE 5.4.1 5.4.2 UPTAKE OF NITRATE AND AMMONIUM IONS BY ALGAE BIOCHEMICAL PROCESSES 5.5.2 5.6.1 5.6.3 5.6.4 ANAEROBIC ENVIRONMENT: NITROGEN-FIXING BACTERIA NITRATE ENTRY AND UPTAKE (SOLUBLE INORGANIC TO INSOLUBLE ORGANIC NITROGEN) COMPLEX ORGANIC NITROGEN (BIOMASS) TRANSFORMATIONS (SUCCESSIVE STATES OF INSOLUBLE ORGANIC NITROGEN) REMINERALIZATION (INSOLUBLE ORGANIC TO SOLUBLE INORGANIC NITROGEN) NITRIFICATION/DENITRIFICATION (OXIDATION/REDUCTION OF SOLUBLE INORGANIC COMPOUNDS) 5.5 SPECIES VARIATIONS IN NITRATE UPTAKE ENVIRONMENTAL REGULATION OF NITRATE ASSIMILATION NITROGEN UPTAKE, ASSIMILATION, AND PHOTOSYNTHESIS ECOLOGICAL SIGNIFICANCE OF NITROGEN FIXATION THE NITROGENASE ENZYME AND STRATEGIES OF FIXATION HETEROCYSTS: NITROGEN FIXATION BY COLONIAL BLUE-GREEN ALGAE DIURNAL CONTROL OF NITROGEN FIXATION: UNICELLULAR BLUE-GREEN ALGAE 5.6 NITROGEN FIXATION B. PHOSPHORUS 5.7 OCCURRENCE AND BIOLOGICAL AVAILABILITY OF PHOSPHORUS 5.7.1 PHOSPHORUS AVAILABILITY AND LIMITATION 5.7.2 THE PHOSPHORUS CYCLE ADAPTATIONS OF FRESHWATER MICROORGANISMS TO LOW PHOSPHORUS CONCENTRATIONS KINETICS OF PHOSPHORUS UPTAKE LUXURY CONSUMPTION OF PHOSPHATE SECRETION OF ALKALINE PHOSPHATASE 5.8 C. SILICON: A WIDELY-AVAILABLE ELEMENT OF LIMITED METABOLIC IMPORTANCE 5.9 THE SILICON CYCLE 5.10 SILICON AND DIATOMS 5.10.1 5.10.2 SI UPTAKE AND PHYTOPLANKTON SUCCESSION SI UPTAKE AND CELL-WALL FORMATION D. TRACE ELEMENTS 5.1 1 BIOLOGICAL ROLE OF TRACE ELEMENTS 5.1 1.1 5.1 1.2 CYCLING OF IRON AND OTHER TRACE METALS IN THE AQUATIC ENVIRONMENT 5.12.1 THE IRON CYCLE 5.12.2 THE MANGANESE CYCLE ENVIRONMENTAL UPTAKE OF TRACE ELEMENTS STIMULATION OF GROWTH IN AQUATIC ENVIRONMENTS IMPORTANCE OF TRACE METALS IN THE CULTURE OF AQUATIC ALGAE BIOCHEMICAL ROLES OF TRACE ELEMENTS 5.12 6 BACTERIA: THE MAIN HETEROTROPHIC MICROORGANISMS IN FRESHWATER SYSTEMS A. GENERAL DIVERSITY WITHIN THE ENVIRONMENT 6.1. GENERAL DIVERSITY, HABITAT PREFERENCES, AND ECOLOGICAL SIGNIFICANCE OF FRESHWATER BACTERIA 6.1.1 GENERAL DIVERSITY 6.1.2 HABITAT PREFERENCES 6.1.3 TAXONOMIC, BIOCHEMICAL, AND MOLECULAR CHARACTERIZATION OF FRESHWATER BACTERIA 6.2.1 SPECIES IDENTIFICATION ENVIRONMENTAL SIGNIFICANCE OF FRESHWATER BACTERIA 6.2 254 254 255 255 255 257 257 258 258 259 260 260 260 26 262 263 265 265 265 266 269 269 269 27 1 272 272 274 274 275 279 280 280 28 1 28 1 282 283 283 286 287 287 287 287 288 290 29 1 29 1 CONTENTS 6.2.2 6.2.3 CASE STUDY 6.1 A RESPONSE TO VARIATIONS IN THE SUPPLY OF DISSOLVED ORGANIC MATERIAL (DOM) GENETIC MARKERS: DETECTION OF PARTICULAR STRAINS IN THE AQUATIC ENVIRONMENT BIOCHEMICAL CHARACTERIZATION OF BACTERIAL COMMUNITIES CHANGES IN BACTERIAL COMMUNITY FUNCTION AND COMPOSITION AS B. GENETIC INTERACTIONS 6.3 GENETIC DIVERSITY 6.3.1 CHROMOSOMAL AND ACCESSORY DNA 6.3.2 6.3.3 MECHANISMS FOR GENE TRANSFER IN FRESHWATER SYSTEMS 6.4.1 6.4.2 6.4.3 EVIDENCE FOR GENE TRANSFER IN THE AQUATIC ENVIRONMENT 6.5.1 RETROSPECTIVE ANALYSIS CASE STUDY 6.2 6.5.2 CASE STUDY 6.3 6.5.3 THE ECOLOGICAL IMPORTANCE OF GENE TRANSFER IN FRESHWATER SYSTEMS TOTAL GENETIC DIVERSITY: THE *COMMUNITY GENOME* TRANSFORMATION: UPTAKE OF EXOGENOUS DNA TRANSDUCTION: GENE TRANSFER BETWEEN BACTERIA VIA BACTERIOPHAGES CONJUGATION: TRANSFER OF PLASMID DNA BY DIRECT CELL CONTACT 6.4 6.5 PLASMID-BORNE RESISTANCE IN AQUATIC BACTERIA PLASMID TRANSFER IN PSEUDOMONAS AERUGINOSA LABORATORY (IN VITRO) STUDIES ON PLASMID TRANSFER FIELD (IN SITU) STUDIES ON BACTERIAL GENE TRANSFER C. METABOLIC ACTIVITIES 6.6 METABOLIC DIVERSITY OF FRESHWATER BACTERIA 6.6.1 KEY METABOLIC PARAMETERS 6.6.2 CO2 FIXATION 6.6.4 6.7 PHOTOSYNTHETIC BACTERIA 6.7.1 GENERAL CHARACTERISTICS 6.7.2 MOTILITY 6.7.3 ECOLOGY 6.8.1 BREAKDOWN OF ORGANIC MATTER IN AEROBIC AND ANAEROBIC ENVIRONMENTS BACTERIAL ADAPTATIONS TO LOW-NUTRIENT ENVIRONMENTS 6.8 BACTERIA AND INORGANIC CYCLES BACTERIAL METABOLISM AND THE SULPHUR CYCLE D. BACTERIAL POPULATIONS AND PRODUCTIVITY 6.9 6.10 BACTERIAL POPULATIONS 6.9.1 6.9.2 BACTERIAL PRODUCTIVITY 6.10.1 MEASUREMENT OF PRODUCTIVITY 6.10.2 6.10.3 6.10.4 6.10.5 TECHNIQUES FOR COUNTING BACTERIAL POPULATIONS BIOLOGICAL SIGNIFICANCE OF TOTAL AND VIABLE COUNTS REGULATION OF BACTERIAL POPULATIONS AND BIOMASS PRIMARY AND SECONDARY PRODUCTIVITY: CORRELATION BETWEEN BACTERIAL AND ALGAL POPULATIONS PRIMARY AND SECONDARY PRODUCTIVITY: THE ROLE OF DISSOLVED ORGANIC CARBON BACTERIAL PRODUCTIVITY AND AQUATIC FOOD WEBS E. BACTERIAL COMMUNITIES IN THE LOTIC ENVIRONMENT 6.11 BACTERIAL BIOFILMS 6.1 1.1 6.1 1.2 CASE STUDY 6.4 THE DEVELOPMENT OF BIOFILMS DYNAMIC INTERACTIONS IN THE ESTABLISHMENT OF BIOFILMS: THE ROLE OF BACTERIAL CO-AGGREGATION SPECIFIC RECOGNITION AND ADHESION AMONGST AQUATIC BIOFILM BACTERIA E BACTERIAL INTERACTIONS WITH PHYTOPLANKTON INTERACTIONS BETWEEN PHYTOPLANKTON AND PLANKTONIC BACTERIA 6.12.1 COMPETITION FOR INORGANIC NUTRIENTS 6.12.2 6.12 ANTAGONISTIC INTERACTIONS BETWEEN BACTERIA AND ALGAE 292 293 293 294 294 294 295 296 297 297 300 300 300 300 301 301 302 303 304 304 304 304 305 310 312 312 3 12 314 314 3 15 316 316 316 317 318 318 319 320 321 323 324 324 324 326 326 328 328 328 329 CONTENTS 6.13 EPIPHYTIC ASSOCIATIONS OF BACTERIA WITH PHYTOPLANKTON 6.13.1 BACTERIA WITHIN THE PHYCOSPHERE 6.13.2 OBSERVATION AND ENUMERATION OF EPIPHYTIC BACTERIA SPECIFIC ASSOCIATIONS BETWEEN BACTERIA AND BLUE-GREEN ALGAE 7 VIRUSES: MAJOR PARASITES IN THE FRESHWATER ENVIRONMENT 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 VIRUSES AS FRESHWATER BIOTA 7.1.1 GENERAL ROLE IN THE FRESHWATER ENVIRONMENT 7.1.2 MAJOR GROUPS AND TAXONOMY OF FRESHWATER VIRUSES THE VIRUS LIFE CYCLE: INTRACELLULAR AND FREE VIRAL STATES 7.2.1 SIGNIFICANCE OF THE LYSOGENIC STATE DETECTION AND QUANTITATION OF FRESHWATER VIRUSES 7.3.1 FREE PARTICULATE VIRUSES 7.3.2 INFECTED HOST CELLS THE GROWTH AND CONTROL OF VIRAL POPULATIONS 7.4.1 VIRUS PRODUCTIVITY 7.4.2 REGULATION OF VIRAL ABUNDANCE CONTROL OF HOST POPULATIONS BY AQUATIC VIRUSES: IMPACT ON THE MICROBIAL FOOD WEB 7.5 METABOLIC EFFECTS OF VIRUSES: REDUCTION OF ALGAL PRIMARY PRODUCTIVITY 7.5.2 DESTRUCTION OF ALGAL AND BACTERIAL POPULATIONS 7.5.3 VIRUSES AND THE MICROBIAL LOOP CYANOPHAGES: VIRUSES OF BLUE-GREEN ALGAE 7.6.1 CLASSIFICATION AND TAXONOMIC CHARACTERISTICS 7.6.2 INFECTION OF HOST CELLS PHYCOVIRUSES: PARASITES OF EUKARYOTE ALGAE 7.7.1 GENERAL CHARACTERISTICS 7.7.2 HOST CELL INFECTION CASE STUDY 7.1 7.7.3 ECOLOGICAL IMPACT OF PHYCOVIRUSES VIRUS INFECTION OF FRESHWATER BACTERIA 7.8.2 7.8.3 7.8.4 INCIDENCE OF BACTERIAL INFECTION 7.8.5 7.8.6 CASE STUDY 7.2 7.8.7 CASE STUDY 7.3 PSEUDOMONAS AERUGINOSA THE INFECTIVE LIFE CYCLE OF CHLOROVIRUS GENERAL ROLE OF BACTERIOPHAGES IN THE BIOLOGY OF FRESHWATER BACTERIA BACTERIOPHAGES IN PELAGIC AND BENTHIC SYSTEMS OCCURRENCE OF FREE BACTERIOPHAGES IN AQUATIC SYSTEMS TEMPERATE/VIRULENT PHAGE EQUILIBRIUM AND BACTERIAL SURVIVAL BACTERIOPHAGE CONTROL OF PLANKTONIC BACTERIAL POPULATIONS VIRAL LYSIS OF BACTERIA IN A EUTROPHIC LAKE TRANSDUCTION: BACTERIOPHAGE-MEDIATED GENE TRANSFER BETWEEN FRESHWATER BACTERIA TRANSDUCTION OF PLASMID AND CHROMOSOMAL DNA IN 8 FUNGI AND FUNGAL-LIKE ORGANISMS: AQUATIC BIOTA WITH A MYCELIAL GROWTH FORM A. ACTINOMYCETES, OOMYCETES, AND TRUE FUNGI 8.1 FUNGI AND FUNGAL-LIKE ORGANISMS: THE MYCELIAL GROWTH HABIT 8.2 ACTINOMYCETES 8.2.1 TAXONOMIC CHARACTERISTICS 8.2.2 HABITAT 8.2.3 NUTRITION 8.2.4 COMPETITION WITH OTHER MICROORGANISMS 8.3.1 OOMYCETES AND TRUE FUNGI 8.3 OOMYCETES 332 333 334 336 339 339 339 340 340 34 342 342 345 345 345 346 349 349 350 350 35 1 351 352 354 354 356 356 359 360 360 360 36 1 36 1 363 365 365 367 368 371 37 1 37 1 372 372 373 374 374 374 375 CONTENTS 8.3.2 TAXONOMIC DIVERSITY 8.4 TRUE FUNGI 8.4.1 OLD AND NEW TERMINOLOGY 8.4.2 TAXONOMIC DIVERSITY WITHIN THE TRUE FUNGI B. FUNGI AS SAPROPHYTES AND PARASITES 8.5 8.6 8.7 SAPROPHYTIC ACTIVITY OF FUNGI 8.5.1 8.5.2 BREAKDOWN OF LEAF LITTER 8.5.3 PARASITIC ACTIVITIES OF AQUATIC FUNGI 8.6.1 8.6.2 FUNGAL EPIDEMICS IN THE CONTROL OF PHYTOPLANKTON POPULATIONS 8.7.1 ECOLOGICAL SIGNIFICANCE COLONIZATION, GROWTH, AND FUNGAL SUCCESSION SAPROPHYTIC FUNGI - CHYTRIDS AND DEUTEROMYCETES PARASITIC AND PREDATORY DEUTEROMYCETES: FUNGI THAT ATTACK SMALL ANIMALS PARASITIC CHYTRIDS: HIGHLY SPECIALIZED PARASITES OF FRESHWATER ORGANISMS CASE STUDY 8.1 AUTUMN DIATOM BLOOM CHYTRID INFECTION OF THE ASTERIONELLA DURING AN 8.7.2 8.7.3 NET EFFECT OF INFECTED AND NON-INFECTED HOST CELLS FACTORS AFFECTING THE DEVELOPMENT OF FUNGAL INFECTION 9 GRAZING ACTIVITIES IN THE FRESHWATER ENVIRONMENT: THE ROLE OF PROTOZOA AND INVERTEBRATES A. PROTOZOA 9.1 9.2 9.3 9.4 9.5 9.6 INTRODUCTION 9.1.1 9.1.2 ECOLOGICAL ROLE OF PROTOZOA PROTOZOA, ALGAE, AND INDETERMINATE GROUPS TAXONOMIC DIVERSITY OF PROTOZOA IN THE FRESHWATER ENVIRONMENT 9.3.1 CILIATES 9.3.2 FLAGELLATE PROTOZOA 9.3.3 AMOEBOID PROTOZOA ECOLOGICAL IMPACT OF PROTOZOA: THE PELAGIC ENVIRONMENT 9.4.1 POSITIONING WITHIN THE WATER COLUMN 9.4.2 TROPHIC INTERACTIONS IN THE WATER COLUMN HETEROTROPHIC NANOFLAGELLATES: AN INTEGRAL COMPONENT OF PLANKTONIC COMMUNITIES 9.5.1 ENUMERATION OF NANOFLAGELLATE POPULATIONS IN AQUATIC SAMPLES 9.5.2 TAXONOMIC COMPOSITION OF HNF COMMUNITIES ABUNDANCE AND CONTROL OF FLAGELLATE POPULATIONS 9.5.4 NANOFLAGELLATE GRAZING RATES AND CONTROL OF BACTERIAL POPULATIONS 9.5.5 CO-DISTRIBUTION OF BACTERIA AND PROTOZOA WITHIN THE WATER COLUMN ECOLOGICAL IMPACT OF PROTOZOA: THE BENTHIC ENVIRONMENT 9.6.1 BENTHIC MICROENVIRONMENTS 9.6.2 SEASONAL CHANGES 9.6.3 ORGANIC POLLUTION 9.6.4 SEWAGE-TREATMENT PLANTS: ACTIVATED SLUDGE RELATIVE IMPORTANCE OF PROTOZOANS, ROTIFERS, AND CRUSTACEANS IN PELAGIC COMMUNITIES B. GRAZING OF MICROBIAL POPULATIONS BY ZOOPLANKTON 9.7 GENERAL FEATURES OF ZOOPLANKTON: ROTIFERS, CLADOCERANS AND COPEPODS 9.7.1 MORPHOLOGY AND SIZE 9.7.2 REPRODUCTION AND GENERATION TIMES 9.7.3 PREDATION OF ZOOPLANKTON GRAZING ACTIVITY AND PREY SELECTION 9.8.1 9.8 SEASONAL SUCCESSION IN ZOOPLANKTON FEEDING 376 377 377 378 381 381 382 383 386 388 388 389 392 392 392 394 395 40 1 401 40 1 402 402 403 403 407 409 412 412 413 413 414 415 415 416 418 419 419 42 1 42 422 423 423 423 426 426 427 421 CONTENTS 9.8.2 METHOD OF FEEDING 9.9 GRAZING RATES OF ZOOPLANKTON 9.9.1 MEASUREMENT 9.9.2 FACTORS AFFECTING GRAZING RATES 9.9.3 EFFECTS OF ALGAL TOXINS ON ZOOPLANKTON BIOMASS RELATIONSHIPS BETWEEN PHYTOPLANKTON AND ZOOPLANKTON POPULATIONS 9.1 1.1 9.1 1.2 BIOMASS TRANSFER SELECTION OF FOOD BY ZOOPLANKTON DIURNAL VARIATIONS IN GRAZING ACTIVITY 9.10 9.1 1 CONTROL OF ZOOPLANKTON POPULATIONS C. GRAZING OF BENTHIC MICROORGANISMS COMPARISON OF PELAGIC AND BENTHIC SYSTEMS ROLE OF INVERTEBRATES IN CONSUMING RIVER MICROORGANISMS 9.13.1 GRAZING OF PERIPHYTON BIOMASS 9.13.2 9.12 9.13 EFFECTS OF GRAZING ON PERIPHYTON COMMUNITY STRUCTURE 10 EUTROPHICATION: THE MICROBIAL RESPONSE TO HIGH NUTRIENT LEVELS A. ORIGINS OF EUTROPHICATION 10.1 NUTRIENT STATUS OF FRESHWATER ENVIRONMENTS: FROM OLIGOTROPHIC TO EUTROPHIC SYSTEMS 10.1.1 10.1.2 10.1.3 10.1.4 EUTROPHIC AND OLIGOTROPHIC LAKES: DEFINITION OF TERMS DETERMINANTS OF TROPHIC STATUS: LOCATION, MORPHOLOGY AND HYDROLOGY ARTIFICIAL EUTROPHICATION: THE IMPACT OF HUMAN ACTIVITIES EUTROPHICATION OF RIVERS AND STREAMS B. ECOLOGICAL EFFECTS OF EUTROPHICATION IN STANDING WATERS 10.2 GENERAL BIOLOGICAL CHANGES 10.2.1 10.2.2 10.2.3 BIOLOGICAL ASSESSMENT OF WATER QUALITY 10.3.1 ALGAL INDICATOR GROUPS CASE STUDY 10.1 EUTROPHICATION IN LAKE TAHOE (USA) 10.3.2 INDICES OF SPECIES DIVERSITY PROBLEMS WITH INTENTIONAL EUTROPHICATION: DESTABILIZATION OF FISHPOND ECOSYSTEMS 10.4.1 10.4.2 THE PROGRESSION FROM OLIGOTROPHIC TO EUTROPHIC WATERS EFFECTS OF EUTROPHICATION ON THE WATER COLUMN OF STRATIFIED LAKES MAJOR CHANGES IN ECOLOGICAL BALANCE: THE BREAKDOWN OF HOMEOSTASIS 10.3 USING THE A/C (ARAPHID PENNATE/CENTRIC) DIATOM RATIO TO ASSESS 10.4 PROMOTION OF HIGH PRODUCTIVITY IN FISHPONDS DESTABILIZATION AND RESTORATION OF THE ECOSYSTEM C. THE GROWTH AND IMPACT OF ALGAL BLOOMS 10.5 ALGAL BLOOMS AND EUTROPHICATION 10.6 FORMATION OF COLONIAL BLUE-GREEN ALGAL BLOOMS 10.6.1 10.6.2 COMPETITION WITH OTHER ALGAE CASE STUDY 10.2 BLUE-GREEN DOMINANCE ENVIRONMENTAL EFFECTS OF BLUE-GREEN BLOOMS 10.7.1 GENERAL ENVIRONMENTAL CHANGES 10.7.2 10.7.3 PRODUCTION OF TOXINS GENERAL REQUIREMENTS FOR BLOOM FORMATION USE OF ENCLOSURE EXPERIMENTS TO STUDY FACTORS AFFECTING 10.7 SPECIFIC EFFECTS ON WATER QUALITY 429 429 432 432 433 434 435 437 437 437 438 43 8 440 440 44 1 444 444 444 445 446 446 448 448 448 452 452 45 3 45 3 454 455 455 455 456 451 451 459 459 459 46 1 46 1 46 1 462 462 CONTENTS D. CONTROL OF BLUE-GREEN ALGAE 10.8 10.9 STRATEGIES FOR THE CONTROL OF BLUE-GREEN ALGAE NUTRIENT LIMITATION (BOTTOM-UP CONTROL) CASE STUDY 10.3 10.8.2 DIRECT ERADICATION 10.8.3 CASE STUDY 10.4 THE BROADS WETLAND AREA (UK) BIOLOGICAL CONTROL OF BLUE-GREEN ALGAE 10.9.1 BIOLOGICAL CONTROL AGENTS 10.9.2 CASE STUDY 10.5 10.9.3 RESTORATION OF WATER QUALITY IN LAKE WASHINGTON, NORTH WEST USA TOP-DOWN CONTROL OF BLUE-GREEN ALGAE: THE USE OF BIOMANIPULATION TOP-DOWN AND BOTTOM-UP CONTROL OF ALGAL POPULATIONS IN PROTOCOL FOR THE DEVELOPMENT OF BIOLOGICAL CONTROL AGENTS APPLICATION OF PLANT LITTER TO CONTROL BLUE-GREEN ALGAE POTENTIAL PROTOZOON CONTROL AGENTS 10.10 STRATEGIES FOR THE CONTROL OF BLUE-GREEN ALGAE IN DIFFERENT WATER BODIES 10.10.1 INTEGRATED MANAGEMENT POLICY CASE STUDY 10.6 GREATER MANCHESTER (UK) 10.10.2 SPECIFIC REMEDIAL MEASURES IN DIFFERENT FRESHWATER SYSTEMS ENVIRONMENTAL MONITORING AT HOLLINGWORTH LAKE, GLOSSARY REFERENCES INDEX 464 464 465 466 466 467 467 47 1 472 474 475 475 477 477 479 48 1 483 495 517
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spellingShingle Sigee, David C.
Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment
Microbiologie d'eau douce
aFreshwater microbiology
aFresh Water xmicrobiology
Mikrobiologie (DE-588)4316357-9 gnd
Süßwasser (DE-588)4058507-4 gnd
subject_GND (DE-588)4316357-9
(DE-588)4058507-4
title Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment
title_auth Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment
title_exact_search Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment
title_full Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment David C. Sigee
title_fullStr Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment David C. Sigee
title_full_unstemmed Freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment David C. Sigee
title_short Freshwater microbiology
title_sort freshwater microbiology biodiversity and dynamic interactions of microorganisms in the aquatic environment
title_sub biodiversity and dynamic interactions of microorganisms in the aquatic environment
topic Microbiologie d'eau douce
aFreshwater microbiology
aFresh Water xmicrobiology
Mikrobiologie (DE-588)4316357-9 gnd
Süßwasser (DE-588)4058507-4 gnd
topic_facet Microbiologie d'eau douce
aFreshwater microbiology
aFresh Water xmicrobiology
Mikrobiologie
Süßwasser
url http://www.loc.gov/catdir/toc/ecip051/2004021738.html
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