Freshwater Microbiology: Biodiversity and Dynamic Interactions of Microorganisms in the Aquatic Environment

541 Pages·2005·8.05 MB·English

by  David Sigee

Freshwater Microbiology
Biodiversity and Dynamic Interactions of
Microorganisms in the Aquatic Environment
David C. Sigee
University of Manchester, UK
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LibraryofCongressCataloging-in-PublicationData
Sigee,D.C.
Freshwatermicrobiology:biodiversityanddynamicinteractionsofmicroorganismsinthefreshwater
environment/DavidC.Sigee.
p. ; cm.
Includesbibliographicalreferencesandindex.
ISBN0-471-48528-4(cloth:alk.paper)–ISBN0-471-48529-2(pbk. :alk.paper) 1.Freshwater
microbiology.
[DNLM: 1.FreshWater–microbiology. QW80S574f2004] I.Title.
QR105.5.S545 2004
5790.176–dc22 2004021738
BritishLibraryCataloguinginPublicationData
AcataloguerecordforthisbookisavailablefromtheBritishLibrary
ISBN0471485284hardback
ISBN0471485292paperback
Typesetin10/12ptTimesbyThomsonPress,NewDelhi,India
PrintedandboundinGreatBritainbyAntonyRowe,Ltd,Chippenham,Wiltshire
Thisbookisprintedonacid-freepaperresponsiblymanufacturedfromsustainableforestry
inwhichatleasttwotreesareplantedforeachoneusedforpaperproduction.
Contents
Preface xvii
Copyright acknowledgements xix
1 Microbial diversity and freshwater ecosystems 1
1.1 General introduction 1
1.1.1 Theaquaticexistence 1
1.1.2 Theglobalwatersupply–limnologyandoceanography 1
1.1.3 Freshwatersystems:sometermsanddefinitions 3
1.1.4 Thebiologyoffreshwatermicroorganisms 4
A. BIOLOGICAL DIVERSITY IN THE FRESHWATER ENVIRONMENT 4
1.2 Biodiversityofmicroorganisms 4
1.2.1 Domainsoflife 4
1.2.2 Sizerange 6
1.2.3 Autotrophsandheterotrophs 7
1.2.4 Planktonicandbenthicmicroorganisms 10
1.2.5 Metabolicallyactiveandinactivestates 11
1.2.6 Evolutionarystrategies:r-selectedandK-selectedorganisms 12
1.3 Biodiversityinecosystems,communities,andspeciespopulations 15
1.3.1 Mainecosystems 15
1.3.2 Diversitywithinsubsidiarycommunities 16
1.3.3 Biodiversitywithinsingle-speciespopulations 16
B. ECOSYSTEMS 17
1.4 Thebiofilmcommunity:asmall-scale freshwater ecosystem 18
1.4.1 Interactionsbetweenmicroorganisms 19
1.4.2 Biomassformationandtransfer 20
1.4.3 Maintenanceoftheinternalenvironment 20
1.4.4 Interactionswiththeexternalenvironment 21
1.5 Thepelagicecosystem:alarge-scale unitwithin thelake environment 21
1.5.1 Interactionsbetweenorganisms 21
1.5.2 Trophicconnectionsandbiomasstransfer 23
1.5.3 Maintenanceoftheinternalenvironment 28
1.5.4 Interactionswiththeexternalenvironment 28
1.6 Homeostasisandecosystem stability 29
1.6.1 Stressfactors 30
1.6.2 Generaltheoreticalpredictions:thecommunityresponse 30
1.6.3 Observedstressresponses:frommoleculestocommunities 31
vi CONTENTS
1.6.4 Assessmentofecosystemstability 31
1.6.5 Ecosystemstabilityandcommunitystructure 32
1.6.6 Biologicalresponsesignatures 34
C. FOODWEBS IN LENTIC AND LOTIC SYSTEMS 34
1.7 Pelagicfoodwebs 34
CASESTUDY1.1 MICROBIALFOODWEBASSOCIATEDWITHANALGALBLOOM 34
CASESTUDY1.2 GENERALFOODWEBINTHEWATERCOLUMNOFLAKEBAIKAL(RUSSIA) 36
1.8 Communitiesand foodwebsofrunningwaters 40
1.8.1 Allochthonouscarbon:dissolvedandparticulatematterinriversystems 40
1.8.2 Pelagicandbenthiccommunities 42
1.8.3 Themicrobialfoodweb 43
2 Freshwater environments: the influence of physico-chemical
conditions on microbial communities 47
A. INTRODUCTION 47
2.1 The aquaticmedium: water,dissolvedandparticulate components 47
2.1.1 Particulatematter 47
2.1.2 Aquaticmatrix 48
2.2 Freshwater environments 52
B. LAKES 53
2.3 Lakemorphologyandhydrology 53
2.3.1 Lakemorphology 53
2.3.2 Lakehydrologyandthesurroundingterrestrialenvironment 57
2.4 Lakesasisolated environments 60
2.4.1 Isolateddevelopment 60
2.4.2 LakeBaikal:anancientlakewithadiverseanduniquefaunaandflora 60
2.5 Climatic influences onlakes 62
2.5.1 Temperatelakes–seasonalvariationsandlakestratification 63
2.5.2 Biologicalsignificanceofstratification 65
2.5.3 Tropicallakes 66
2.5.4 Polarandsub-polarlakes 67
C. WETLANDS 68
2.6 General characteristics 68
2.6.1 Wetlanddiversityandglobalscale 68
2.6.2 Unifyingfeaturesofwetlands 68
2.6.3 Theroleofwetlandsinenergyandmaterialflow 69
2.7 Wetlandhabitatsandcommunities 69
2.8 Case studiesonwetlandareas 70
CASESTUDY2.1 TRˇEBONˇ BASINBIOSPHERERESERVE 71
D. STREAMS AND RIVERS 72
2.9 Comparison ofloticandlentic systems 72
2.10 Riverflowandthebenthiccommunity 73
2.10.1 Flowcharacteristicsofloticsystems 73
2.10.2 Influenceofwaterflowonbenthicmicroorganisms 75
2.11 Riverhydrology 78
E. ESTUARIES 79
2.12 Riverinflow:water mixing,estuarine productivity,andeutrophication ofcoastalareas 80
CONTENTS vii
2.12.1 Mixingoffreshandsaltwaters 80
2.12.2 Highproductivityofestuarinesystems 81
2.12.3 Eutrophicationofsurroundingcoastalareas 82
2.13 Habitatsandcommunities 82
2.13.1 Pelagiczone 82
2.13.2 Sedimentsandmudflats 82
F. ADVERSE AND EXTREME CONDITIONS IN FRESHWATER ENVIRONMENTS 84
2.14 Adverseconditionsaspart oftheenvironmentalcontinuum 85
2.14.1 Variationsinoxygenconcentration 85
2.14.2 Nutrientavailability 85
2.14.3 Solarradiation 86
2.15 Extremeenvironmentalconditions 86
2.15.1 Temperature 86
2.15.2 pH 89
2.15.3 Conditionsoflowwateravailability:salineenvironments 91
2.15.4 Conditionsoflowwateravailability:iceandsnowenvironments 92
2.15.5 Variationsinhydrostaticpressure 93
2.15.6 Organicandinorganicpollution 93
2.16 Apotentiallyextrememicroenvironment:theair–watersurface 95
2.16.1 Chemicalcompositionofthesurfacemicrolayer 95
2.16.2 Physicalprocessesandtransformationsinthesurfacebiofilm 96
2.16.3 Microbialcommunityattheair–waterinterface 98
2.17 Microbialcommunities ofsnowandice:lifeinthefrozenstate 99
2.17.1 Snowandiceasanextremeenvironment 99
2.17.2 Requirementforwaterintheliquidstate 99
2.17.3 Snowecosystems 99
2.17.4 Thephysicalpropertiesofsnow 100
2.17.5 Snowandicemicroorganisms 102
3 Algae: the major microbial biomass in freshwater systems 105
A. TAXONOMIC AND MOLECULAR CHARACTERIZATION 107
3.1 Majortaxonomicdivisionsoffreshwater algae 107
3.1.1 Microscopicalappearance,motilityandecologicalfeatures 107
3.1.2 Biochemicalandcytologicalcharacteristics 110
3.1.3 Generalsummaryofthedifferentgroups 112
3.2 Algalspecies:taxonomy andintraspecificvariation 114
3.2.1 Taxonomyofalgalspecies 114
3.2.2 Chemicaldiversitywithinspecies–enzymeanalysis,moleculargroups,
andelementalcomposition 115
3.3 Molecularanalysis 116
3.3.1 Molecularcharacterizationandidentificationofalgae 116
3.3.2 Investigationofgenefunctioninfreshwateralgae 119
B. SIZE, SHAPE, AND SURFACE MUCILAGE 123
3.4 Phytoplanktonsizeand shape 123
3.4.1 Cellcountsandbiovolume 123
3.4.2 Frompicoplanktontomacroplankton 123
3.4.3 Biologicalsignificanceofsizeandshape 124
3.4.4 Variationinsizeandshapewithinphytoplanktonpopulations 128
3.5 Mucilaginousand non-mucilaginousalgae 130
3.5.1 Chemicalcompositionofmucilage 131
viii CONTENTS
3.5.2 Roleofmucilageinphytoplanktonactivities 131
3.5.3 Environmentalimpactandbiogeochemicalcycles 133
C. ACTIVITIES WITHIN THE FRESHWATER ENVIRONMENT 133
3.6 Benthic algae:interactions withplanktonicalgaeand ecologicalsignificance 133
3.6.1 Planktonicandbenthicalgae 133
3.6.2 Lakeperiphyton 136
3.6.3 Benthicalgaeinflowingwaters 138
3.6.4 Ecologicalroleofbenthicalgae 138
3.7 Temporalactivitiesoffreshwater algae 139
3.7.1 Short-termchanges:molecularandcellularprocesses 140
3.7.2 Medium-termchanges:algalsuccession 142
3.7.3 Long-termchanges:variationsoveranumberofyears 146
3.8 Phytoplankton distributionwithinthewater column 148
CASESTUDY3.1 VERTICALZONATIONOFPHYTOPLANKTONINASTRATIFIEDLAKE 148
3.8.1 Activemigrationofalgae 149
3.8.2 Passivemovementofalgaewithinthewatercolumn 156
3.9 Freshwater algaeandnutrient statusoftheenvironment 157
3.9.1 Phytoplanktonspeciescompositionandlakenutrientstatus 157
3.9.2 Nutrientstatusofriverenvironments–effectonbenthicalgalbiofilms 160
D. STRATEGIES FOR SURVIVAL 161
3.10 Strategiesforsurvival:theplanktonicenvironment 161
3.10.1 Meroplanktonicalgae 162
3.10.2 Strategiesforunstableandstableenvironments:r-selectedandK-selectedalgae 164
3.11 Heterotrophic nutritioninfreshwater algae 165
3.11.1 Organotrophy 167
3.11.2 Phagotrophy 168
3.12 Survivalinsnowandice:adaptations ofcryophilic algae 171
3.12.1 Majorgroupsofcryophilicalgae 171
3.12.2 Lifecyclesofsnowalgae 173
3.12.3 Physiologicaladaptationsofsnowalgae 174
E. BIODIVERSITY IN THE ALGAL COMMUNITY 177
3.13 Varietyoffreshwater algae:indicesofspeciesdiversity 177
3.13.1 Theparadoxofphytoplanktondiversity 177
3.13.2 Biodiversityindices 178
3.13.3 Numericalcomparisonofphytoplanktonpopulations 179
3.13.4 Biodiversityandecosystemfunction 180
4 Competition for light 181
4.1 The lightenvironment 182
4.1.1 Physicalpropertiesoflight:termsandunitsofmeasurement 182
4.1.2 Lightthresholdsforbiologicalactivities 183
4.1.3 Lightunderwater:refraction,absorption,andscattering 184
4.1.4 Lightenergyconversion:fromlakesurfacetoalgalbiomass 186
4.2 Photosynthetic processesinthefreshwater environment 188
4.2.1 Lightanddarkreactions 188
4.2.2 Photosyntheticmicroorganisms 189
4.2.3 Measurementofphotosynthesis 189
4.2.4 Photosyntheticresponsetovaryinglightintensity 190
4.3 Lightasagrowth resource 192
4.3.1 Strategiesforlightuptakeandutilization 192
4.3.2 Light–photosyntheticresponseindifferentalgae 193
CONTENTS ix
4.3.3 Conservationofenergy 194
4.3.4 Diversityinsmallmolecularweightsolutesandosmoregulation 195
4.4 Algalgrowth andproductivity 196
4.4.1 Primaryproduction:conceptsandterms 196
4.4.2 Primaryproductionandalgalbiomass 197
4.4.3 Fieldmeasurementsofprimaryproductivity 197
4.5 Photosyntheticbacteria 199
4.5.1 Majorgroups 200
4.5.2 Photosyntheticpigments 200
4.5.3 Bacterialprimaryproductivity 201
4.6 Photoadaptation:responsesofaquaticalgaetolimitedsupplies oflightenergy 202
4.6.1 Differentaspectsoflightlimitation 203
4.6.2 Variablelightintensity:light-responsivegeneexpression 204
4.6.3 Photosyntheticresponsestolowlightintensity 205
4.6.4 Spectralcompositionoflight:changesinpigmentcomposition 209
4.7 Carbonuptake andexcretionbyalgalcells 210
4.7.1 ChangesinenvironmentalCO andpH 210
2
4.7.2 Excretionofdissolvedorganiccarbonbyphytoplanktoncells 211
4.8 Competitionforlightand carbondioxide betweenalgaeandhigherplants 215
4.8.1 Thebalancebetweenalgaeandmacrophytesindifferentaquaticenvironments 215
CASESTUDY4.1 COMPETITIONBETWEENALGAEANDMACROPHYTESINSHALLOW
LAKESOFTHETRˇEBONˇ WETLANDS 216
4.8.2 Physiologicalandenvironmentaladaptationsinthecompetitionbetween
algaeandmacrophytes 218
4.9 Damagingeffectsofhighlevels ofsolar radiation:photoinhibition 221
4.9.1 Specificmechanismsofphotoinhibition 221
4.9.2 Generaleffectsofphotoinhibition 224
4.9.3 Strategiesfortheavoidanceofphotoinhibition 225
4.9.4 Photoinhibitionandcellsize 227
4.9.5 Lackofphotoinhibitioninbenthiccommunities 228
4.9.6 Photoinhibitioninextremehigh-lightenvironments 228
4.10 Periodiceffectsoflightonseasonalanddiurnalactivitiesoffreshwater biota 230
4.10.1 Seasonalperiodicity 230
4.10.2 Diurnalchanges 231
4.10.3 Circadianrhythmsinblue-greenalgae 232
4.10.4 Circadianrhythmsindinoflagellates 234
5 Inorganic nutrients: uptake and cycling in freshwater systems 235
5.1 Chemical compositionofnaturalwaters 235
5.1.1 Solubleinorganicmatterinlakesandrivers 235
5.1.2 Aerialdepositionofnutrients 237
5.1.3 Nutrientinflowfromterrestrialsources 237
5.1.4 Chemicalrequirementsandcompositionoffreshwaterbiota 238
CASESTUDY5.1 ELEMENTALCOMPOSITIONOFCERATIUMHIRUNDINELLA 240
5.1.5 Nutrientavailabilityandcyclinginaquaticsystems 243
5.2 Nutrientuptakeand growthkinetics 246
5.2.1 Empiricalmodelsforalgalnutrientkinetics 246
5.2.2 Competitionandgrowthintheaquaticenvironment 248
5.2.3 Nutrientavailabilityandwatermovement 250
5.2.4 Acutenutrientdeprivationasanenvironmentalstressfactor 251
A. NITROGEN 251
5.3 Biologicalavailabilityofnitrogeninfreshwater environments 251
5.3.1 Solublenitrogenouscompounds 251
x CONTENTS
5.4 The nitrogencycle 254
5.4.1 Nitrateentryanduptake(solubleinorganictoinsolubleorganicnitrogen) 254
5.4.2 Complexorganicnitrogen(biomass)transformations
(successivestatesofinsolubleorganicnitrogen) 255
5.4.3 Remineralization(insolubleorganictosolubleinorganicnitrogen) 255
5.4.4 Nitrification/denitrification(oxidation/reductionofsolubleinorganiccompounds) 255
5.5 Uptakeofnitrateand ammoniumionsbyalgae 257
5.5.1 Biochemicalprocesses 257
5.5.2 Speciesvariationsinnitrateuptake 258
5.5.3 Environmentalregulationofnitrateassimilation 258
5.5.4 Nitrogenuptake,CO assimilation,andphotosynthesis 259
2
5.6 Nitrogen fixation 260
5.6.1 Ecologicalsignificanceofnitrogenfixation 260
5.6.2 Thenitrogenaseenzymeandstrategiesoffixation 260
5.6.3 Heterocysts:nitrogenfixationbycolonialblue-greenalgae 261
5.6.4 Diurnalcontrolofnitrogenfixation:unicellularblue-greenalgae 262
5.6.5 Anaerobicenvironment:nitrogen-fixingbacteria 263
B. PHOSPHORUS 265
5.7 Occurrence andbiologicalavailabilityofphosphorus 265
5.7.1 Phosphorusavailabilityandlimitation 265
5.7.2 Thephosphoruscycle 266
5.8 Adaptationsoffreshwater microorganismstolowphosphorusconcentrations 269
5.8.1 Kineticsofphosphorusuptake 269
5.8.2 Luxuryconsumptionofphosphate 269
5.8.3 Secretionofalkalinephosphatase 271
C. SILICON: AWIDELY-AVAILABLE ELEMENT OF LIMITED
METABOLIC IMPORTANCE 272
5.9 The siliconcycle 272
5.10 Siliconanddiatoms 274
5.10.1 Siuptakeandphytoplanktonsuccession 274
5.10.2 Siuptakeandcell-wallformation 275
D. TRACE ELEMENTS 279
5.11 Biological roleoftraceelements 280
5.11.1 Environmentaluptakeoftraceelements 280
5.11.2 Stimulationofgrowthinaquaticenvironments 281
5.11.3 Importanceoftracemetalsinthecultureofaquaticalgae 281
5.11.4 Biochemicalrolesoftraceelements 282
5.12 Cyclingofironandothertracemetalsintheaquaticenvironment 283
5.12.1 Theironcycle 283
5.12.2 Themanganesecycle 286
6 Bacteria: the main heterotrophic microorganisms in freshwater systems 287
A. GENERAL DIVERSITY WITHIN THE ENVIRONMENT 287
6.1. Generaldiversity,habitat preferences, andecologicalsignificanceoffreshwater bacteria 287
6.1.1 Generaldiversity 287
6.1.2 Habitatpreferences 288
6.1.3 Environmentalsignificanceoffreshwaterbacteria 290
6.2 Taxonomic,biochemical,andmolecularcharacterizationoffreshwater bacteria 291
6.2.1 Speciesidentification 291
CONTENTS xi
6.2.2 Geneticmarkers:detectionofparticularstrainsintheaquaticenvironment 292
6.2.3 Biochemicalcharacterizationofbacterialcommunities 293
CASESTUDY6.1 CHANGESINBACTERIALCOMMUNITYFUNCTIONANDCOMPOSITIONAS
ARESPONSETOVARIATIONSINTHESUPPLYOFDISSOLVEDORGANICMATERIAL(DOM) 293
B. GENETIC INTERACTIONS 294
6.3 Geneticdiversity 294
6.3.1 ChromosomalandaccessoryDNA 294
6.3.2 Theecologicalimportanceofgenetransferinfreshwatersystems 295
6.3.3 Totalgeneticdiversity:the‘communitygenome’ 296
6.4 Mechanisms forgenetransferinfreshwater systems 297
6.4.1 Transformation:uptakeofexogenousDNA 297
6.4.2 Transduction:genetransferbetweenbacteriaviabacteriophages 300
6.4.3 Conjugation:transferofplasmidDNAbydirectcellcontact 300
6.5 Evidenceforgenetransfer intheaquaticenvironment 300
6.5.1 Retrospectiveanalysis 300
CASESTUDY6.2 PLASMID-BORNERESISTANCEINAQUATICBACTERIA 301
6.5.2 Laboratory(invitro)studiesonplasmidtransfer 301
CASESTUDY6.3 PLASMIDTRANSFERINPSEUDOMONASAERUGINOSA 302
6.5.3 Field(insitu)studiesonbacterialgenetransfer 303
C. METABOLIC ACTIVITIES 304
6.6 Metabolicdiversityoffreshwater bacteria 304
6.6.1 Keymetabolicparameters 304
6.6.2 CO fixation 304
2
6.6.3 Breakdownoforganicmatterinaerobicandanaerobicenvironments 305
6.6.4 Bacterialadaptationstolow-nutrientenvironments 310
6.7 Photosyntheticbacteria 312
6.7.1 Generalcharacteristics 312
6.7.2 Motility 312
6.7.3 Ecology 314
6.8 Bacteria andinorganic cycles 314
6.8.1 Bacterialmetabolismandthesulphurcycle 315
D. BACTERIAL POPULATIONS AND PRODUCTIVITY 316
6.9 Bacterialpopulations 316
6.9.1 Techniquesforcountingbacterialpopulations 316
6.9.2 Biologicalsignificanceoftotalandviablecounts 317
6.10 Bacterialproductivity 318
6.10.1 Measurementofproductivity 318
6.10.2 Regulationofbacterialpopulationsandbiomass 319
6.10.3 Primaryandsecondaryproductivity:correlationbetweenbacterialandalgalpopulations 320
6.10.4 Primaryandsecondaryproductivity:theroleofdissolvedorganiccarbon 321
6.10.5 Bacterialproductivityandaquaticfoodwebs 323
E. BACTERIAL COMMUNITIES IN THE LOTIC ENVIRONMENT 324
6.11 BacterialBiofilms 324
6.11.1 Thedevelopmentofbiofilms 324
6.11.2 Dynamicinteractionsintheestablishmentofbiofilms:theroleofbacterialco-aggregation 326
CASESTUDY6.4 SPECIFICRECOGNITIONANDADHESIONAMONGSTAQUATICBIOFILMBACTERIA 326
F. BACTERIAL INTERACTIONS WITH PHYTOPLANKTON 328
6.12 Interactions betweenphytoplanktonandplanktonicbacteria 328
6.12.1 Competitionforinorganicnutrients 328
6.12.2 Antagonisticinteractionsbetweenbacteriaandalgae 329