Freshwater Microbiology Biodiversity and Dynamic Interactions of Microorganisms in the Aquatic Environment
David C. Sigee University of Manchester, UK
Copyright # 2005
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Contents Preface
xvii
Copyright acknowledgements
xix
1
Microbial diversity and freshwater ecosystems 1.1
General introduction
1
1.1.1 1.1.2 1.1.3 1.1.4
1 1 3 4
The aquatic existence 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 1.2.2 1.2.3 1.2.4 1.2.5 1.2.6
1.3
B.
1.5
1.6
4 4
Domains of life Size range Autotrophs and heterotrophs Planktonic and benthic microorganisms Metabolically active and inactive states Evolutionary strategies: r-selected and K-selected organisms
4 6 7 10 11 12
Biodiversity in ecosystems, communities, and species populations
15
1.3.1 1.3.2 1.3.3
15 16 16
Main ecosystems Diversity within subsidiary communities Biodiversity within single-species populations
ECOSYSTEMS 1.4
1
17
The biofilm community: a small-scale freshwater ecosystem
18
1.4.1 1.4.2 1.4.3 1.4.4
19 20 20 21
Interactions between microorganisms Biomass formation and transfer Maintenance of the internal environment Interactions with the external environment
The pelagic ecosystem: a large-scale unit within the lake environment
21
1.5.1 1.5.2 1.5.3 1.5.4
21 23 28 28
Interactions between organisms Trophic connections and biomass transfer Maintenance of the internal environment Interactions with the external environment
Homeostasis and ecosystem stability
29
1.6.1 1.6.2 1.6.3
30 30 31
Stress factors General theoretical predictions: the community response Observed stress responses: from molecules to communities
vi
CONTENTS 1.6.4 1.6.5 1.6.6
C.
FOOD WEBS IN LENTIC AND LOTIC SYSTEMS 1.7
1.8
2 A.
34
CASE STUDY 1.1 MICROBIAL FOOD WEB ASSOCIATED WITH AN ALGAL BLOOM CASE STUDY 1.2 GENERAL FOOD WEB IN THE WATER COLUMN OF LAKE BAIKAL (RUSSIA)
34 36
Communities and food webs of running waters
40
1.8.1 1.8.2 1.8.3
40 42 43
Allochthonous carbon: dissolved and particulate matter in river systems Pelagic and benthic communities The microbial food web
INTRODUCTION
47
The aquatic medium: water, dissolved and particulate components
47
2.1.1 2.1.2
Particulate matter Aquatic matrix
47 48
Freshwater environments
52
LAKES 2.3
2.4
2.5
53 Lake morphology and hydrology
53
2.3.1 2.3.2
53 57
Lake morphology Lake hydrology and the surrounding terrestrial environment
Lakes as isolated environments
60
2.4.1 2.4.2
60 60
Isolated development Lake Baikal: an ancient lake with a diverse and unique fauna and flora
Climatic influences on lakes
62
2.5.1 2.5.2 2.5.3 2.5.4
63 65 66 67
Temperate lakes – seasonal variations and lake stratification Biological significance of stratification Tropical lakes Polar and sub-polar lakes
WETLANDS 2.6
2.7 2.8
D.
34
Pelagic food webs
47
2.2
C.
31 32 34
Freshwater environments: the influence of physico-chemical conditions on microbial communities
2.1
B.
Assessment of ecosystem stability Ecosystem stability and community structure Biological response signatures
68
General characteristics
68
2.6.1 2.6.2 2.6.3
68 68 69
Wetland diversity and global scale Unifying features of wetlands The role of wetlands in energy and material flow
Wetland habitats and communities Case studies on wetland areas
69 70
ˇ BASIN BIOSPHERE RESERVE CASE STUDY 2.1 TRˇ EBON
71
STREAMS AND RIVERS 2.9 2.10
2.11
72
Comparison of lotic and lentic systems River flow and the benthic community
72 73
2.10.1 2.10.2
73 75
Flow characteristics of lotic systems Influence of water flow on benthic microorganisms
River hydrology
78
E. ESTUARIES
79
2.12
80
River inflow: water mixing, estuarine productivity, and eutrophication of coastal areas
CONTENTS 2.12.1 2.12.2 2.12.3
2.13
Mixing of fresh and saltwaters High productivity of estuarine systems Eutrophication of surrounding coastal areas
2.15
2.16
2.17
Habitats and communities
82 82 82
Pelagic zone Sediments and mudflats
85
2.14.1 2.14.2 2.14.3
85 85 86
Variations in oxygen concentration Nutrient availability Solar radiation
Extreme environmental conditions
86
2.15.1 2.15.2 2.15.3 2.15.4 2.15.5 2.15.6
86 89 91 92 93 93
Temperature pH Conditions of low water availability: saline environments Conditions of low water availability: ice and snow environments Variations in hydrostatic pressure Organic and inorganic pollution
A potentially extreme microenvironment: the air–water surface
95
2.16.1 2.16.2 2.16.3
95 96 98
Chemical composition of the surface microlayer Physical processes and transformations in the surface biofilm Microbial community at the air–water interface
Microbial communities of snow and ice: life in the frozen state Snow and ice as an extreme environment Requirement for water in the liquid state Snow ecosystems The physical properties of snow Snow and ice microorganisms
Algae: the major microbial biomass in freshwater systems
A. TAXONOMIC AND MOLECULAR CHARACTERIZATION 3.1
3.2
3.3
B.
3.5
99 99 99 99 100 102
105 107
Major taxonomic divisions of freshwater algae
107
3.1.1 3.1.2 3.1.3
107 110 112
Microscopical appearance, motility and ecological features Biochemical and cytological characteristics General summary of the different groups
Algal species: taxonomy and intraspecific variation
114
3.2.1 3.2.2
114
Taxonomy of algal species Chemical diversity within species – enzyme analysis, molecular groups, and elemental composition
115
Molecular analysis
116
3.3.1 3.3.2
116 119
Molecular characterization and identification of algae Investigation of gene function in freshwater algae
SIZE, SHAPE, AND SURFACE MUCILAGE 3.4
84
Adverse conditions as part of the environmental continuum
2.17.1 2.17.2 2.17.3 2.17.4 2.17.5
3
80 81 82
2.13.1 2.13.2
F. ADVERSE AND EXTREME CONDITIONS IN FRESHWATER ENVIRONMENTS 2.14
vii
123
Phytoplankton size and shape
123
3.4.1 3.4.2 3.4.3 3.4.4
123 123 124 128
Cell counts and biovolume From picoplankton to macroplankton Biological significance of size and shape Variation in size and shape within phytoplankton populations
Mucilaginous and non-mucilaginous algae
130
3.5.1
131
Chemical composition of mucilage
viii
CONTENTS 3.5.2 3.5.3
C.
ACTIVITIES WITHIN THE FRESHWATER ENVIRONMENT 3.6
3.7
3.8
3.9
D.
Role of mucilage in phytoplankton activities Environmental impact and biogeochemical cycles
3.11
3.12
133
3.6.1 3.6.2 3.6.3 3.6.4
Planktonic and benthic algae Lake periphyton Benthic algae in flowing waters Ecological role of benthic algae
133 136 138 138
Temporal activities of freshwater algae
139
3.7.1 3.7.2 3.7.3
140 142 146
Short-term changes: molecular and cellular processes Medium-term changes: algal succession Long-term changes: variations over a number of years
Phytoplankton distribution within the water column
4
148
3.8.1 3.8.2
149 156
Active migration of algae Passive movement of algae within the water column
Freshwater algae and nutrient status of the environment
157
3.9.1 3.9.2
157 160
Phytoplankton species composition and lake nutrient status Nutrient status of river environments – effect on benthic algal biofilms
4.2
4.3
161
Strategies for survival: the planktonic environment
161
3.10.1 3.10.2
162 164
Meroplanktonic algae Strategies for unstable and stable environments: r-selected and K-selected algae
Heterotrophic nutrition in freshwater algae
165
3.11.1 3.11.2
167 168
Organotrophy Phagotrophy
Survival in snow and ice: adaptations of cryophilic algae
171
3.12.1 3.12.2 3.12.3
171 173 174
Major groups of cryophilic algae Life cycles of snow algae Physiological adaptations of snow algae
177
Variety of freshwater algae: indices of species diversity
177
3.13.1 3.13.2 3.13.3 3.13.4
177 178 179 180
The paradox of phytoplankton diversity Biodiversity indices Numerical comparison of phytoplankton populations Biodiversity and ecosystem function
Competition for light 4.1
148
CASE STUDY 3.1 VERTICAL ZONATION OF PHYTOPLANKTON IN A STRATIFIED LAKE
E. BIODIVERSITY IN THE ALGAL COMMUNITY 3.13
133
Benthic algae: interactions with planktonic algae and ecological significance
STRATEGIES FOR SURVIVAL 3.10
131 133
181
The light environment
182
4.1.1 4.1.2 4.1.3 4.1.4
182 183 184 186
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
Photosynthetic processes in the freshwater environment
188
4.2.1 4.2.2 4.2.3 4.2.4
188 189 189 190
Light and dark reactions Photosynthetic microorganisms Measurement of photosynthesis Photosynthetic response to varying light intensity
Light as a growth resource
192
4.3.1 4.3.2
192 193
Strategies for light uptake and utilization Light–photosynthetic response in different algae
CONTENTS 4.3.3 4.3.4
4.4
4.5
4.6
4.7
4.8
Conservation of energy Diversity in small molecular weight solutes and osmoregulation
Algal growth and productivity
196 196 197 197
Primary production: concepts and terms Primary production and algal biomass Field measurements of primary productivity
Photosynthetic bacteria
199
4.5.1 4.5.2 4.5.3
200 200 201
Major groups Photosynthetic pigments Bacterial primary productivity
Photoadaptation: responses of aquatic algae to limited supplies of light energy
202
4.6.1 4.6.2 4.6.3 4.6.4
203 204 205 209
Different aspects of light limitation Variable light intensity: light-responsive gene expression Photosynthetic responses to low light intensity Spectral composition of light: changes in pigment composition
Carbon uptake and excretion by algal cells
210
4.7.1 4.7.2
Changes in environmental CO2 and pH Excretion of dissolved organic carbon by phytoplankton cells
210 211
Competition for light and carbon dioxide between algae and higher plants
215
4.8.1
215
4.8.2
4.10
5
The balance between algae and macrophytes in different aquatic environments
Physiological and environmental adaptations in the competition between algae and macrophytes
4.9.1 4.9.2 4.9.3 4.9.4 4.9.5 4.9.6
221 224 225 227 228 228
Specific mechanisms of photoinhibition General effects of photoinhibition Strategies for the avoidance of photoinhibition Photoinhibition and cell size Lack of photoinhibition in benthic communities Photoinhibition in extreme high-light environments
Periodic effects of light on seasonal and diurnal activities of freshwater biota
230
4.10.1 4.10.2 4.10.3 4.10.4
230 231 232 234
Seasonal periodicity Diurnal changes Circadian rhythms in blue-green algae Circadian rhythms in dinoflagellates
235
Chemical composition of natural waters
235
5.1.1 5.1.2 5.1.3 5.1.4
235 237 237 238
5.1.5
Soluble inorganic matter in lakes and rivers Aerial deposition of nutrients Nutrient inflow from terrestrial sources Chemical requirements and composition of freshwater biota ELEMENTAL COMPOSITION OF CERATIUM HIRUNDINELLA
Nutrient availability and cycling in aquatic systems
240
243
Nutrient uptake and growth kinetics
246
5.2.1 5.2.2 5.2.3 5.2.4
246 248 250 251
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
A. NITROGEN 5.3
218
221
CASE STUDY 5.1
5.2
216
Damaging effects of high levels of solar radiation: photoinhibition
Inorganic nutrients: uptake and cycling in freshwater systems 5.1
194 195
4.4.1 4.4.2 4.4.3
CASE STUDY 4.1 COMPETITION BETWEEN ALGAE AND MACROPHYTES IN SHALLOW ˇ WETLANDS LAKES OF THE TRˇ EBON
4.9
ix
251
Biological availability of nitrogen in freshwater environments
251
5.3.1
251
Soluble nitrogenous compounds
x
CONTENTS
5.4
The nitrogen cycle
254
5.4.1 5.4.2
254
5.4.3 5.4.4
5.5
5.6
B.
5.8
Uptake of nitrate and ammonium ions by algae
257 257 258 258 259
Biochemical processes Species variations in nitrate uptake Environmental regulation of nitrate assimilation Nitrogen uptake, CO2 assimilation, and photosynthesis
Nitrogen fixation
260
5.6.1 5.6.2 5.6.3 5.6.4 5.6.5
260 260 261 262 263
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 Anaerobic environment: nitrogen-fixing bacteria
265
Occurrence and biological availability of phosphorus
265
5.7.1 5.7.2
265 266
Phosphorus availability and limitation The phosphorus cycle
Adaptations of freshwater microorganisms to low phosphorus concentrations
269
5.8.1 5.8.2 5.8.3
Kinetics of phosphorus uptake Luxury consumption of phosphate Secretion of alkaline phosphatase
269 269 271
SILICON: A WIDELY-AVAILABLE ELEMENT OF LIMITED METABOLIC IMPORTANCE
272
5.9 5.10
D.
255 255 255
5.5.1 5.5.2 5.5.3 5.5.4
PHOSPHORUS 5.7
C.
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)
The silicon cycle Silicon and diatoms
272 274
5.10.1 5.10.2
274 275
Si uptake and phytoplankton succession Si uptake and cell-wall formation
TRACE ELEMENTS 5.11
5.12
279
Biological role of trace elements
280
5.11.1 5.11.2 5.11.3 5.11.4
280 281 281 282
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
Cycling of iron and other trace metals in the aquatic environment
283
5.12.1 5.12.2
283 286
The iron cycle The manganese cycle
6
Bacteria: the main heterotrophic microorganisms in freshwater systems
287
A.
GENERAL DIVERSITY WITHIN THE ENVIRONMENT
287
6.1.
General diversity, habitat preferences, and ecological significance of freshwater bacteria 6.1.1 6.1.2 6.1.3
6.2
General diversity Habitat preferences Environmental significance of freshwater bacteria
287 287 288 290
Taxonomic, biochemical, and molecular characterization of freshwater bacteria
291
6.2.1
291
Species identification
CONTENTS 6.2.2 6.2.3
Genetic markers: detection of particular strains in the aquatic environment Biochemical characterization of bacterial communities
CASE STUDY 6.1 CHANGES IN BACTERIAL COMMUNITY FUNCTION AND COMPOSITION AS A RESPONSE TO VARIATIONS IN THE SUPPLY OF DISSOLVED ORGANIC MATERIAL (DOM)
B.
GENETIC INTERACTIONS 6.3
6.4
6.5
294 295 296
Mechanisms for gene transfer in freshwater systems
297
6.4.1 6.4.2 6.4.3
297 300 300
Transformation: uptake of exogenous DNA Transduction: gene transfer between bacteria via bacteriophages Conjugation: transfer of plasmid DNA by direct cell contact
Evidence for gene transfer in the aquatic environment
300
6.5.1
300
6.5.3
Retrospective analysis PLASMID-BORNE RESISTANCE IN AQUATIC BACTERIA
Laboratory (in vitro) studies on plasmid transfer PLASMID TRANSFER IN PSEUDOMONAS AERUGINOSA
Field (in situ) studies on bacterial gene transfer
METABOLIC ACTIVITIES
6.8
6.10
304 304 304 304 305 310
Key metabolic parameters CO2 fixation Breakdown of organic matter in aerobic and anaerobic environments Bacterial adaptations to low-nutrient environments
Photosynthetic bacteria
312
6.7.1 6.7.2 6.7.3
General characteristics Motility Ecology
312 312 314
Bacteria and inorganic cycles
314
6.8.1
315
Bacterial metabolism and the sulphur cycle
316
Bacterial populations
316
6.9.1 6.9.2
316 317
Techniques for counting bacterial populations Biological significance of total and viable counts
Bacterial productivity
318
6.10.1 6.10.2 6.10.3 6.10.4 6.10.5
318 319 320 321 323
Measurement of productivity 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
324
Bacterial Biofilms
324
6.11.1 6.11.2
324 326
The development of biofilms Dynamic interactions in the establishment of biofilms: the role of bacterial co-aggregation
CASE STUDY 6.4
SPECIFIC RECOGNITION AND ADHESION AMONGST AQUATIC BIOFILM BACTERIA
F. BACTERIAL INTERACTIONS WITH PHYTOPLANKTON 6.12
302
303
6.6.1 6.6.2 6.6.3 6.6.4
E. BACTERIAL COMMUNITIES IN THE LOTIC ENVIRONMENT 6.11
301
301
Metabolic diversity of freshwater bacteria
D. BACTERIAL POPULATIONS AND PRODUCTIVITY 6.9
294 294
Chromosomal and accessory DNA The ecological importance of gene transfer in freshwater systems Total genetic diversity: the ‘community genome’
CASE STUDY 6.3
6.7
293
6.3.1 6.3.2 6.3.3
6.5.2
6.6
292 293
Genetic diversity
CASE STUDY 6.2
C.
xi
326
328
Interactions between phytoplankton and planktonic bacteria
328
6.12.1 6.12.2
328 329
Competition for inorganic nutrients Antagonistic interactions between bacteria and algae
xii
CONTENTS
6.13
7
Epiphytic associations of bacteria with phytoplankton
332
6.13.1 6.13.2 6.13.3
333 334 336
Bacteria within the phycosphere Observation and enumeration of epiphytic bacteria Specific associations between bacteria and blue-green algae
Viruses: major parasites in the freshwater environment 7.1
7.2
Viruses as freshwater biota
339
7.1.1 7.1.2
339 340
7.4
7.5
7.6
7.7
7.8
General role in the freshwater environment Major groups and taxonomy of freshwater viruses
The virus life cycle: intracellular and free viral states 7.2.1
7.3
339
340
Significance of the lysogenic state
341
Detection and quantitation of freshwater viruses
342
7.3.1 7.3.2
342 345
Free particulate viruses Infected host cells
The growth and control of viral populations
345
7.4.1 7.4.2
345 346
Virus productivity Regulation of viral abundance
Control of host populations by aquatic viruses: impact on the microbial food web
349
7.5.1 7.5.2 7.5.3
349 350 350
Metabolic effects of viruses: reduction of algal primary productivity Destruction of algal and bacterial populations Viruses and the microbial loop
Cyanophages: viruses of blue-green algae
351
7.6.1 7.6.2
351 352
Classification and taxonomic characteristics Infection of host cells
Phycoviruses: parasites of eukaryote algae
354
7.7.1 7.7.2
354 356
General characteristics Host cell infection
CASE STUDY 7.1 THE INFECTIVE LIFE CYCLE OF CHLOROVIRUS
356
7.7.3
359
Ecological impact of phycoviruses
Virus infection of freshwater bacteria
360
7.8.1 7.8.2 7.8.3 7.8.4 7.8.5 7.8.6
360 360 361 361 363 365
General role of bacteriophages in the biology of freshwater bacteria Bacteriophages in pelagic and benthic systems Occurrence of free bacteriophages in aquatic systems Incidence of bacterial infection Temperate/virulent phage equilibrium and bacterial survival Bacteriophage control of planktonic bacterial populations
CASE STUDY 7.2 VIRAL LYSIS OF BACTERIA IN A EUTROPHIC LAKE
365
7.8.7
367
Transduction: bacteriophage-mediated gene transfer between freshwater bacteria
CASE STUDY 7.3 TRANSDUCTION OF PLASMID AND CHROMOSOMAL DNA IN PSEUDOMONAS AERUGINOSA
368
8
Fungi and fungal-like organisms: aquatic biota with a mycelial growth form
371
A.
ACTINOMYCETES, OOMYCETES, AND TRUE FUNGI
371
8.1 8.2
8.3
Fungi and fungal-like organisms: the mycelial growth habit Actinomycetes
371 372
8.2.1 8.2.2 8.2.3 8.2.4
372 373 374 374
Taxonomic characteristics Habitat Nutrition Competition with other microorganisms
Oomycetes
374
8.3.1
375
Oomycetes and true fungi
CONTENTS 8.3.2
8.4
B.
8.6
8.7
377
8.4.1 8.4.2
377 378
Old and new terminology Taxonomic diversity within the true fungi
381
8.5.1 8.5.2 8.5.3
382 383 386
Colonization, growth, and fungal succession Breakdown of leaf litter Saprophytic fungi – chytrids and deuteromycetes
Parasitic activities of aquatic fungi
388
8.6.1 8.6.2
388 389
Parasitic and predatory deuteromycetes: fungi that attack small animals Parasitic chytrids: highly specialized parasites of freshwater organisms
Fungal epidemics in the control of phytoplankton populations
392
8.7.1
392
Ecological significance
CASE STUDY 8.1 CHYTRID INFECTION OF THE ASTERIONELLA DURING AN AUTUMN DIATOM BLOOM
392
8.7.2 8.7.3
394 395
Net effect of infected and non-infected host cells Factors affecting the development of fungal infection
A. PROTOZOA
9.2 9.3
9.4
9.5
9.6
B.
381
Saprophytic activity of fungi
Grazing activities in the freshwater environment: the role of protozoa and invertebrates
9.1
376
True fungi
FUNGI AS SAPROPHYTES AND PARASITES 8.5
9
Taxonomic diversity
xiii
401 401
Introduction
401
9.1.1 9.1.2
401 402
Relative importance of protozoans, rotifers, and crustaceans in pelagic communities Ecological role of protozoa
Protozoa, algae, and indeterminate groups Taxonomic diversity of protozoa in the freshwater environment
402 403
9.3.1 9.3.2 9.3.3
403 407 409
Ciliates Flagellate protozoa Amoeboid protozoa
Ecological impact of protozoa: the pelagic environment
412
9.4.1 9.4.2
412 413
Positioning within the water column Trophic interactions in the water column
Heterotrophic nanoflagellates: an integral component of planktonic communities
413
9.5.1 9.5.2 9.5.3 9.5.4 9.5.5
414 415 415 416 418
Enumeration of nanoflagellate populations in aquatic samples Taxonomic composition of HNF communities Abundance and control of flagellate populations Nanoflagellate grazing rates and control of bacterial populations Co-distribution of bacteria and protozoa within the water column
Ecological impact of protozoa: the benthic environment
419
9.6.1 9.6.2 9.6.3 9.6.4
Benthic microenvironments Seasonal changes Organic pollution Sewage-treatment plants: activated sludge
419 421 421 422
GRAZING OF MICROBIAL POPULATIONS BY ZOOPLANKTON
423
9.7
9.8
General features of zooplankton: rotifers, cladocerans and copepods
423
9.7.1 9.7.2 9.7.3
423 426 426
Morphology and size Reproduction and generation times Predation of zooplankton
Grazing activity and prey selection
427
9.8.1
427
Seasonal succession in zooplankton feeding
xiv
CONTENTS 9.8.2 9.8.3
9.9
9.10 9.11
C.
Method of feeding Selection of food by zooplankton
Grazing rates of zooplankton
432
9.9.1 9.9.2 9.9.3
432 433 434
Measurement Factors affecting grazing rates Diurnal variations in grazing activity
Effects of algal toxins on zooplankton Biomass relationships between phytoplankton and zooplankton populations
435 437
9.11.1 9.11.2
437 437
Control of zooplankton populations Biomass transfer
GRAZING OF BENTHIC MICROORGANISMS 9.12 9.13
429 429
438
Comparison of pelagic and benthic systems Role of invertebrates in consuming river microorganisms
438 440
9.13.1 9.13.2
440 441
Grazing of periphyton biomass Effects of grazing on periphyton community structure
10 Eutrophication: the microbial response to high nutrient levels
443
A.
444
ORIGINS OF EUTROPHICATION 10.1
B.
444
10.1.1 10.1.2 10.1.3 10.1.4
444 445 446 446
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
ECOLOGICAL EFFECTS OF EUTROPHICATION IN STANDING WATERS 10.2
10.3
10.4
C.
Nutrient status of freshwater environments: from oligotrophic to eutrophic systems
448
10.2.1 10.2.2 10.2.3
448 452 452
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
Biological assessment of water quality
453
10.3.1
453
Algal indicator groups
CASE STUDY 10.1 USING THE A/C (ARAPHID PENNATE/CENTRIC) DIATOM RATIO TO ASSESS EUTROPHICATION IN LAKE TAHOE (USA)
454
10.3.2
455
Indices of species diversity
Problems with intentional eutrophication: destabilization of fishpond ecosystems
455
10.4.1 10.4.2
455 456
Promotion of high productivity in fishponds Destabilization and restoration of the ecosystem
THE GROWTH AND IMPACT OF ALGAL BLOOMS 10.5 10.6
10.7
448
General biological changes
457
Algal blooms and eutrophication Formation of colonial blue-green algal blooms
457 459
10.6.1 10.6.2
459 459
General requirements for bloom formation Competition with other algae
CASE STUDY 10.2 USE OF ENCLOSURE EXPERIMENTS TO STUDY FACTORS AFFECTING BLUE-GREEN DOMINANCE
461
Environmental effects of blue-green blooms
461
10.7.1 10.7.2 10.7.3
461 462 462
General environmental changes Specific effects on water quality Production of toxins
CONTENTS
D. CONTROL OF BLUE-GREEN ALGAE 10.8
464
Strategies for the control of blue-green algae
464
10.8.1
465
Nutrient limitation (bottom-up control)
CASE STUDY 10.3
10.8.2 10.8.3
RESTORATION OF WATER QUALITY IN LAKE WASHINGTON, NORTH WEST USA
Direct eradication Top-down control of blue-green algae: the use of biomanipulation
CASE STUDY 10.4 TOP-DOWN AND BOTTOM-UP CONTROL OF ALGAL POPULATIONS IN THE BROADS WETLAND AREA (UK)
10.9
xv
466
466 467 467
Biological control of blue-green algae
471
10.9.1 10.9.2
472 474
Biological control agents Protocol for the development of biological control agents
CASE STUDY 10.5
10.9.3
POTENTIAL PROTOZOON CONTROL AGENTS
Application of plant litter to control blue-green algae
10.10 Strategies for the control of blue-green algae in different water bodies 10.10.1 Integrated management policy
475
475
477 477
CASE STUDY 10.6 ENVIRONMENTAL MONITORING AT HOLLINGWORTH LAKE, GREATER MANCHESTER (UK)
479
10.10.2 Specific remedial measures in different freshwater systems
481
Glossary
483
References
495
Index
517
Preface Although freshwater microorganisms are not as readily apparent as macroscopic fauna (invertebrates, fish) and flora (higher plants, large algae), they are universally present within aquatic habitats and their ecological impact is of fundamental importance. This book examines the diversity and dynamic activities of freshwater microbes including micro-algae, bacteria, viruses, actinomycetes, fungi, and protozoa. On an environmental scale, the activities of these organisms range from the microlevel (e.g., localized adsorption of nutrients, surface secretion of exoenzymes) through community dynamics (interactions within planktonic and benthic populations) to large-scale environmental effects. These include major changes in inorganic nutrient concentrations, formation of anaerobic hypolimnia, and stabilization of mudflats. Thus, although freshwater microorganisms are strongly influenced by their physical and chemical environment, they can in turn exert their own effects on their surroundings. In a temporal dimension, the biology of these biota embraces activities which range from femtoseconds (e.g., light receptor parameters) to seconds (light responsive gene activity), diurnal oscillations, seasonal changes (phytoplankton succession), and transitions over decades and centuries (e.g., long-term response to acidification and nutrient changes). The study of freshwater microorganisms involves all major disciplines within biology, and I have
attempted to bring together aspects of taxonomy, molecular biology, biochemistry, structural biology, and classical ecology within this volume. A complete study of freshwater microorganisms must also clearly relate to other freshwater biota, and I have emphasized links in relation to general food webs – plus specific interactions such as zooplankton grazing, algal/higher plant competition, and the role of fish and macrophytes in the biomanipulation of algal populations. In addition to being an area of intrinsic biological interest, freshwater microbiology has increasing practical relevance in relation to human activities, population increase, and our use of environmental resources. In this respect microorganisms play a key role in the deterioration of freshwater environments that results from eutrophication, and management of aquatic systems requires a good understanding of the principles of freshwater microbiology. The biology of these biota is also important in relation to other applied aspects such as the breakdown of organic pollutants, the spread of human pathogens, and the environmental impact of genetically-engineered microorganisms. Inevitably, a book of this type relies heavily on previously published work, and I would like to thank holders of copyright (see separate listing) for granting permission to publish original diagrams and figures. I am also grateful to colleagues (particularly Professor A.P.J. Trinci and Dr R.D. Butler) for commenting on sections of the manuscript, and
xiv
PREFACE
for the helpful, detailed comments of anonymous reviewers. Finally, my thanks are due to the numerous research colleagues who I have worked with over the years, including Jo Abraham, Martin Andrews, Ed Bellinger, Karen Booth, Ron Butler, Sue Clay, Andrew Dean, Ebtesam El-
Bestawy, Robert Glenn, Harry Epton, Larry Kearns, Vlad Krivtsov, Eugenia Levado, Christina Tien, and Keith White. David Sigee Manchester, 2004.
Copyright acknowledgements I am very grateful to the following individuals for allowing me to use previously unpublished material – Drs Nina Bondarenko, Andrew Dean, Harry Epton, Robert Glenn, Eugenia Levado, Ms Elishka Rigney, Mr Richard Sigee, Mrs Rosemary Sigee, Dr Christina Tien, Professor James Van Etten and Dr Keith White. I also thank the following copyright holders for giving me permission to use previously published
material – The American Society for Microbiology, Biopress Ltd., Blackwell Publishing Ltd., Cambridge University Press, Elsevier Science, European Journal of Phycology, Interresearch Science, John Wiley & Sons, Parthenon Publishing, Kluwer Academic Publishers, The Linnean Society of London, NRC Research Press, Scanning Microscopy Inc. and SpringerVerlag.
1 Microbial diversity and freshwater ecosystems 1.1
General introduction
This book explores the diversity, interactions and activities of microbes (microorganisms) within freshwater environments. These form an important part of the biosphere, which also includes oceans, terrestrial environments and the earth’s atmosphere.
1.1.1
The aquatic existence
It is now generally accepted that life originated between 3.5 and 4 billion years ago in the aquatic environment, initially as self-replicating molecules (Alberts et al., 1962). The subsequent evolution of prokaryotes, followed by eukaryotes, led to the existence of microorganisms which are highly adapted to aquatic systems. The biological importance of the physical properties of water is discussed in Section 2.1.2. Life in the aquatic environment (freshwater and marine) has numerous potential advantages over terrestrial existence. These include physical support (buoyancy), accessibility of three-dimensional space, passive movement by water currents, dispersal of motile gametes in a liquid medium, minimal loss of water (freshwater systems), lower extremes of temperature and solar radiation, and ready availability of soluble organic and inorganic nutrients.
Potential disadvantages of aquatic environments include osmotic differences between the organism and the surrounding aquatic medium (leading to endosmosis or exosmosis) and a high degree of physical disturbance in many aquatic systems. In undisturbed aquatic systems such as lakes, photosynthetic organisms have to maintain their position at the top of the water column for light availability. In many water bodies (e.g., lake water column), physical and chemical parameters show a continuum – with few distinct microhabitats. In these situations, species compete in relation to different growth and reproductive strategies rather than specific adaptations to localized environmental conditions.
1.1.2
The global water supply – limnology and oceanography
Water covers seven tenths of the Earth’s surface and occupies an estimated total volume of 1.38 109 km3 (Table 1.1). Most of this water occurs between continents, where it is present as oceans (96.1 per cent of global water) plus a major part of the atmospheric water. The remaining 3.9 per cent of water (Table 1.1 shaded boxes), present within continental boundaries (including polar ice-caps), occurs mainly as polar ice and ground water. The latter is present as freely exchangeable (i.e., not
Freshwater Microbiology: Biodiversity and Dynamic Interactions of Microorganisms in the Aquatic Environment David C. Sigee # 2005 John Wiley & Sons, Ltd ISBNs: 0-471-48529-2 (pbk) 0-471-48528-4 (hbk)
2
MICROBIAL DIVERSITY AND FRESHWATER ECOSYSTEMS
Table 1.1
Global distribution of water (adapted from Horne and Goldman, 1994)
Site
Volume (km3)
% of water within continents
Oceans Polar ice caps and glaciers Exchangeable ground water Freshwater lakes Saline lakes and inland seas Soil and subsoil water Atmospheric vapour Rivers and streams
1 322 000 000 29 200 000 24 000 000 125 000 104 000 65 000 14 000 1 200
54.57 44.85 0.23 0.19 0.12 0.026 0.022
Annual inputs Surface runoff to ocean Ground water to sea Precipitation Rainfall on ocean Rainfall on land and lakes
37 000 1 600 412 000 000 108 000 000
chemically-bound) water in subterranean regions such as aquifers at varying depths within the Earth’s crust. Non-polar surface freshwaters, including soil water, lakes, rivers and streams occupy approximately 0.0013 per cent of the global water, or 0.37 per cent of water occurring within continental boundaries. The volume of saline lakewater approximately equals that of freshwater lakes. The largest uncertainty is the estimation of ground water volume. Annual inputs by precipitation are estimated at 5:2 108 km3, with a resulting flow from continental (freshwater) systems to oceans of about 38 600 km3. The distinction between oceans and continental water bodies leads to the two main disciplines of aquatic biology – oceanography and limnology. Oceanography is the study of aquatic systems between continents. It mainly involves saltwater, with major impact on global parameters such as temperature change, the carbon cycle and water circulation. Limnology is the study of aquatic systems contained within continental boundaries, including freshwater and saltwater sites.
The study of freshwater biology is thus part of limnology. Although freshwater systems do not have the global impact of oceans, they are of major importance to biology. They are important ecological features within continental boundaries, have distinctive groups of organisms, and show close links with terrestrial ecosystems. The two main sites (over 99 per cent by volume) of continental water – the polar ice-caps and exchangeable ground water – are extreme environments which have received relatively little microbiological attention until recent years. Although most limnological studies have been carried out on lakes, rivers, and wetlands the importance of other water bodies – particularly the vast frozen environments of the polar regions (see below) – should not be overlooked. Microbiological aspects of snow and ice environments are discussed in Sections 2.17 and 3.12, and the metabolic activities of bacteria in ground water in Section 2.14.2. Although there are many differences between limnological (inland) and oceanic (intercontinental) systems, there are also some close similarities. The biology of planktonic organisms in lakes, for example, shows many similarities to that of oceans – and much of our understanding of freshwater biota (e.g.,
GENERAL INTRODUCTION
the biology of aquatic viruses (Chapter 7) comes from studies on marine systems.
1.1.3
Freshwater systems: some terms and definitions
Freshwater microorganisms Microorganisms may be defined as those organisms that are not readily visible to the naked eye, requiring a microscope for detailed observation. These biota have a size range (maximum linear dimension) up to 200 mm, and vary from viruses, through bacteria and archea, to micro-algae, fungi and protozoa. Higher plants, macro-algae, invertebrates and vertebrates do not fall in this category and are not considered in detail, except where they relate to microbial activities. These include photosynthetic competition between higher plants and micro-algae (Section 4.8) and the role of zooplankton as grazers of algae and bacteria (Section 9.8).
Freshwater environments: water in the liquid and frozen state Freshwater environments are considered to include all those sites where freshwater occurs as the main external medium, either in the liquid or frozen state. Although frozen aquatic environments have long been thought of as microbiological deserts, recent studies have shown this not to be the case. The Antarctic sub-continent, for example, is now known to be rich in microorganisms (Vincent, 1988), with protozoa, fungi, bacteria, and microalgae often locally abundant and interacting to form highlystructured communities. New microorganisms, including freeze-tolerant phototrophs and heterotrophs, have been discovered and include a number of endemic organisms. New biotic environments have also been discovered within this apparently hostile environment – which includes extensive snow-fields, tidal lakes, ice-shelf pools, rock crystal pools, hypersaline soils, fellfield microhabitats, and glacial melt-water streams. Many of these polar environments are saline, and the aquatic microbiology
3
of these regions is considered here mainly in terms of freshwater snow-fields in relation to extreme aquatic environments (Section 2.17) and the cryophilic adaptations of micro-algae (Section 3.12). This book deals with aquatic systems where water is present in the liquid state for at least part of the year. In most situations (temperate lakes, rivers, and wetlands) water is frozen for only a limited time, but in polar regions the reverse is true. Some regions of the ice-caps are permanently frozen, but other areas have occasional or periodic melting. In many snow-fields, the short-term presence of water in the liquid state during the annual melt results in a burst of metabolic activity and is important for the limited growth and dispersal of snow microorganisms and for the completion of microbial life cycles (Section 3.12).
Freshwater and saline environments Within inland waters, aquatic sites show a gradation from water with a low ionic content (freshwater) to environments with a high ionic content (saline) – typically dominated by sodium and chlorine ions. Saline waters include estuaries (Sections 2.12 and 2.13), saline lakes (Section 2.15.3) and extensive regions of the polar ice-caps (Vincent, 1988). The high ionic concentrations of these sites can also be recorded in terms of high electrical conductivity (specific conductance) and high osmotic potential. The physiological demands of saline and freshwater conditions are so different that aquatic organisms are normally adapted to one set of conditions but not the other, so they occur in either saline or freshwater conditions. The importance of salinity in determining the species composition of the aquatic microbial community was demonstrated in a recent survey of Australian saline lakes (Gell and Gasse, 1990), where distinct assemblages of diatoms were present in low salinity (oligosaline) and high salinity (hypersaline) waters. Some diatom species, however, were present over the whole range of saline conditions, indicating the ability of some microorganisms to be completely independent of salt concentration and ionic ratios. Long-term adaptability to different saline conditions is also indicated
4
MICROBIAL DIVERSITY AND FRESHWATER ECOSYSTEMS
by the ability of some organisms to migrate from saltwater to freshwater sites, and establish themselves in their new conditions. This appears to be the case for various littoral red algae of freshwater lakes (Section 3.1.3), which were originally derived from marine environments (Lin and Blum, 1977). Differences between freshwater/saltwater environments and their microbial communities, are particularly significant in global terms (Chapter 2), where the dominance of saline conditions is clear in terms of area coverage, total biomass, and overall contribution to carbon cycling.
Lentic and lotic freshwater systems Freshwater environments show wide variations in terms of their physical and chemical characteristics, and the influence these parameters have on the microbial communities they contain. These aspects are considered in Chapter 2, but one important distinction needs to be made at this stage – between lentic and lotic systems. Freshwater environments can be grouped into standing waters (lentic systems – including ponds, lakes, marshes and other enclosed water bodies) and flowing waters (lotic systems – rivers, estuaries and canals). The distinction between lentic and lotic systems is not absolute, and almost all water bodies have some element of through-flow. Key differences between lentic and lotic systems in terms of carbon availability and food webs are considered in Section 1.8.
A. 1.2 1.2.1
1.1.4
The biology of freshwater microorganisms
In this book the biology of freshwater microorganisms is considered from five major aspects: Microbial diversity and interactions within ecosystems (Chapter 1); these interactions include temporal changes in succession and feeding (trophic) interactions. Variations between different environmental systems, including lakes, rivers, and wetlands (Chapter 2). Each system has its own mixture of microbial communities, and its own set of physical and biological characteristics. Characteristics and activities of the five major groups of microbial organisms – algae (Chapter 3), bacteria (Chapter 6), viruses (Chapter 7), fungi (Chapter 8), and protozoa (Chapter 9). The requirement of freshwater microorganisms for two major environmental resources – light (Chapter 4) and inorganic nutrients (Chapter 5). These are considered immediately after the section on algae, since these organisms are the major consumers of both commodities. The microbial response to eutrophication. Environmental problems associated with nutrient increase are of increasing importance and reflect both a microbial response to environmental change and a microbial effect on environmental conditions.
BIOLOGICAL DIVERSITY IN THE FRESHWATER ENVIRONMENT
Biodiversity of microorganisms Domains of life
With the exception of viruses (which constitute a distinct group of non-freeliving organisms) the most fundamental element of taxonomic diversity within the freshwater environment lies in the separation of biota into three major domains – the Bacteria,
Archaea, and Eukarya. Organisms within these domains can be distinguished in terms of a number of key fine-structural, biochemical, and physiological characteristics (Table 1.2). Cell organization is a key feature, with the absence of a nuclear membrane defining the Bacteria (Figure 3.2) and Archaea as prokaryotes. These prokaryote domains also lack complex systems of membrane-enclosed organelles, have
BIODIVERSITY OF MICROORGANISMS
5
Table 1.2 The three domains of life in freshwater environments (adapted from Purves et al., 1997 – shaded areas: distinctive prokaryote/eukaryote features). The four major kingdoms within the Domain Eukarya simply group organisms with broadly similar features, and do not imply any phyllogenetic interrelationships. The Protista (protozoa, algae, sline moulds) and Fungi are particularly heterogeneous assemblages, containing organisms that have arisen via diverse evolutionary routes (polyphyletic) Domains Characteristic
Bacteria
Archaea
Eukarya
Kingdoms
Eubacteria
Archaebacteria
Level of cellular organisation Membrane-enclosed nucleus Membrane-enclosed organelles Ribosomes Peptidoglycan cell wall Membrane lipids
prokaryote Absent Absent 70s Present Ester-linked Unbranched Formyl-methionine Yes Yes One Yes
prokaryote Absent Absent 70s Absent Ether-linked Branched Methionine Yes Yes Several No
Fungi Protista Plantae Animalia eukaryote Present Present 80s Absent Ester-linked Unbranched Methionine No Rare Three No
No
Yes
Yes
No Yes Yes
Yes Yes No
No No Yes
Initiator tRNA Operons Plasmids RNA polymerases Sensitive to chloramphenicol & streptomycin Ribosomes sensitive to diphtheria toxin Some are methanogens Some fix nitrogen Some conduct chlorophyll – based photosynthesis
Excluding viruses, which are not free-living organisms.
70s ribosomes and have genetic systems which include plasmids and function by operons. Prokaryote features also include a unicellular or colonial (but not multicellular) organization, and a small cell size (0.2 mm) ranges from finely dispersed material (including bacteria) to large particulate matter such as leaf litter and other plant debris. Much of this material is directly deposited into the flowing water from surrounding vegetation. Large particulate matter such as leaf litter is an important carbon source for the microbial food web, serving as a substrate for fungal (Section 8.5.2) and bacterial growth and as a source of DOC. On entering a stream or river, leaf litter releases an initial pulse of rapidly leachable, water soluble material, followed by a slow release of DOC due to microbial degradation (Meyer, 1994). The breakdown and release of organic material from leaf litter is accelerated by the feeding activities of invertebrates.
COMMUNITIES AND FOOD WEBS OF RUNNING WATERS
Changes in the concentrations of dissolved and particulate carbon during the seasonal cycle Concentrations of dissolved and particulate carbon show wide fluctuations in many streams and rivers during the annual cycle, with recorded DOC values generally in the range 1–10 mg l1, but reaching much higher levels in some rivers (Burney, 1994). In most cases, this annual variation reflects the allochthonous derivation of these compounds and the seasonal fluctuations of entry into the river system. The large rivers of Southern Asia, for example, have large changes in DOC concentration, with close correlations between seasonal flow patterns and the timing of DOC maxima and minima (Table 1.8). The dissolved organic carbon levels in the Indus and Ganges–Brahmaputra Rivers reach a maximum near the end of rising water levels, due to overflow and entrainment from highly productive flood plains. The pulse of DOC then rapidly declines as water levels recede due to mixing, metabolic removal, and dilution. In the upper Mississippi River (USA), the very high autumn allochthonous
41
DOC levels are derived not from soil, but from leaching of leaf litter. Although many rivers show elevated allochthonous DOC concentrations at times of flood and terrestrial runoff (summarized in Burney, 1994), wide differences in seasonal patterns can occur. The Shetucket River (USA), for example, is unusual in showing minimal DOC levels during high inflow winter months, but maximum levels during the lowflow summer period (Klotz and Matson, 1978). The summer maximum was attributed to the generation of autochthonous carbon by secretion and senescence of benthic algae. In winter, the allochthonous DOC input was overridden and diluted by high discharge due to ice melt and heavy rain. Seasonal patterns in some rivers are at least in part driven by in situ planktonic primary production. In the Gambia River (West Africa), allochthonous DOC concentrations reach a maximum at the time of maximum discharge into the system, but accumulation of autochthonous DOC occurs during the low-flow period. This was linked to phytoplankton production and was associated with elevated river water pH levels (Lesack et al., 1984).
Table 1.8 Varying importance of allochthonous and autochthonous dissolved organic carbon (DOC) in different river systems (taken from Burney, 1994) River
Maximum concentration (mg l1)
Minimum concentration (mg l1)
Allochthonous input Ganges (Bangladesh) Brahmaputra (Bangladesh) Mississippi (USA)
9.3 (July) 6.5 (July) 21 (November)
1.3 (June) 1.3–2.6 (rest of year) 6 (March)
Autochthonous input Shetucket (USA) Gambia (West Africa)
6.2–10 (May and September) 3.7 (September)
2–4 (January–April) 1.3 (December)
DOC origin Rising water from flood plains
Leaching of leaf litter in autumn
Production by benthic algae during low-flow period Mainly allochthonous but some low-water production by phytoplankton
Although DOC in flowing waters is principally derived from external (allochthonous) origin, internal (autochthonous) sourcing may be important in rivers such as the Shetucket (USA) and Gambia (West Africa). In each case the peak in DOC concentration corresponds to the timing and origin of carbon input.
42
1.8.2
MICROBIAL DIVERSITY AND FRESHWATER ECOSYSTEMS
Pelagic and benthic communities
Lotic systems differ considerably in the extent to which pelagic and benthic communities are able to develop. This depends particularly on size and flow, with a major distinction between large, slowflowing rivers and small, turbulent streams.
Large rivers: the development of a phytoplankton community In most lotic systems, phytoplankton are simply displaced by the current, and are not able to form standing populations. Because of this continuous displacement, net production within a defined section can only occur when local growth rates exceed downstream losses. Phytoplankton growth in lotic systems tends to be limited by ambient light intensity (overhanging foliage), turbidity, and circulation within the water column (no stratification), while downstream loss is largely a function of current velocity. Phytoplankton production in riverine systems, and the development of a pelagic community, is thus largely regulated by light availability in combination with hydrological processes. Recent studies by Sellers and Bukaveckas (2003) have demonstrated that phytoplankton production may be significant in large rivers. Local biomass accumulation occurs particularly in shallow reaches during peaks of low discharge and turbidity, when phytoplankton experiences prolonged exposure to favourable light conditions. Observations on a large navigational pool in the Ohio River (USA), for example, showed that at times of high discharge, phytoplankton productivity within the pool was 1 (taken from Meyer, 1994) Assimilation of bacterial carbon
Taxonomic group
Species or family
Insect larvae
Stoneflies (Peltoperlidae) Craneflies (Tipula) Mayflies (Stenonema) Black flies (Simulium) Lirceus Harpacticoid (Atthyella) Ciliates Flagellates
Isopod crustacea Copepod crustacea Protozoa
1.2 104 5 104 2 16–267 0.7–6 103 1–36 6 102 2.8 101
Measured as mg Bacterial C per mg animal per day.
tant basis for the bacterial food chain. Some insect larvae (e.g., stoneflies and craneflies) ingest bacteria simply as part of the litter that they collect, resulting in relatively low bacterial assimilation rates (about 104 mg mg1 d1). Other larvae have specialized bacterial collection strategies, including filtration (black fly) and surface scraping (mayfly), resulting in much higher bacterial assimilation rates (Table 1.10).
Meiofauna These are animals inhabiting the bottom of a lake or river that are just visible to the namost important ked eye and include copepods, nematodes and rotifers. These are generally regarded as the most important bacterial predators in lotic systems, and include both filter feeders and biofilm grazers. Their bacterial carbon assimilation rates are typically 1–4 orders of magnitude greater than that of other bacterial consumers (Meyer, 1994). The microbial loop in running waters is part of a more complex food web that also involves photosynthetic carbon production by algae and higher plants, saprophytic and parasitic activites of fungi and viruses and important roles for the large invertebrate and vertebrate predators (Figure 1.19). Primary production by benthic algae (periphyton) varies in importance in different systems (Table 1.8), depending partly on the depth of the water column
and light penetration to the substratum. The development of periphyton communities is discussed in Section 3.7.2, and the lack of photoinhibition in Section 4.9.5. Light is also important in the water column in relation to degradation of non-assimilable (refractory) DOC. UV-irradiation, in particular, has been shown to have a major effect in converting humic acids to more labile forms of DOC (DeHaan, 1993). The ecological importance of bacteria, protozoa, and fungi in lotic food webs has been mentioned in relation to the microbial loop (Figure 1.18). Further information is subsequently given in relation to the breakdown of organic matter by benthic bacteria (Section 6.6.3), saprophytic activities of benthic fungi (Section 8.5), and the role of protozoa in the ingestion of both living and non-living particulate matter (Section 9.6). The transfer of biomass from microbes to top carnivores does not have such a defined route as pelagic foodwebs, and the domination of herbivorous activities in the water column by crustaceans (zooplankton) does not occur in the lotic food web. Herbivory in running waters occurs mainly at the sediment surface and involves the ingestion of either unattached or attached microorganisms. The consumption of microorganisms in lotic communities is discussed further in Section 9.13 and involves ingestion of:
free-moving biota such as bacteria and protozoa, present as localized populations around
46
MICROBIAL DIVERSITY AND FRESHWATER ECOSYSTEMS
organic debris, by meiofauna and protozoa (Figure 9.7); microorganisms, particularly fungi and bacteria, that are present within organic debris such as leaf litter – this is carried out by invertebrate shredders, gougers, and collector gatherers, prominent amongst which are insect larvae (Table 1.10); biofilm and other microorganisms that are attached to solid substratum – this is carried
out by shredding, scraping and rasping (Figure 9.17).
The fragmentation and ingestion of leaf litter by invertebrates requires partial breakdown of this material by fungal activity (Section 8.5.2). The substrate colonization, invasion, and macerating activity of these organisms thus promotes their own ingestion during the final stages of leaf processing (Figure 8.4).
2 Freshwater environments: the influence of physico-chemical conditions on microbial communities This chapter considers the range and diversity of freshwater environments, emphasizing the influence of physical and chemical conditions on the composition and activities of the microbial communities that they contain. More detailed aspects
of the importance of light (Chapter 4) and inorganic nutrients (Chapter 5) are considered later, and the environmental implications of eutrophication (nutrient enrichment) are discussed in Chapter 10.
A. INTRODUCTION 2.1
The aquatic medium: water, dissolved and particulate components
At the micro level, the aquatic medium surrounding freshwater biota is a heterogeneous mixture of three main constituents – particulate material, soluble components, and water matrix. Soluble constituents are discussed in Sections 5.1 (inorganic components) and 4.7.2 (dissolved organic carbon – DOC).
2.1.1
Particulate Matter
Particulate matter is normally defined as comprising all solid material with a diameter (longest axis) greater than 0.2 mm, and can be further divided into coarse particulate matter (diameter >1 mm) and fine particulate matter (0.2 mm–1 mm). This particulate
material includes both inorganic and organic components, with further separation of the latter into living (e.g., planktonic organisms) and non-living (e.g., leaf debris, dead planktonic organisms) groups (Table 2.1). The arbitrary designation of dissolved organic matter (DOM) as including all material with a size 1 mm
Fine particulate organic material (FPOM) Dissolved organic material (DOM)*
0.2 mm–1 mm
*
300 (Chlorophyta) to 200
Dinoflagellates
7
47
233
Diatoms
6
84
86
21
211
>250
Green
synthesis of low MW compounds for physiological activities (e.g., osmoregulation) and complex macromolecules for growth (anabolic processes). These aspects have evolved in various ways within the different groups of algae, leading to clear distinctions in terms of their ability to grow at different minimum and maximum light levels (Table 4.3), their energy requirements in relation to cell wall synthesis and motility (Table 4.4) and their use of different small MW compounds in osmoregulation (Table 4.5).
4.3.2
Light–photosynthetic response in different algae
Differences in light-response between different algae, and the importance of environmental conditions, can be seen by comparison of the photosynthesis – irradiance (P – I) curves for blue-green algae and diatoms at different temperatures. This is illustrated in Figure 4.8, where PI curves are shown for two commonly-occurring members of the lake phytoplankton community – Microcystis (blue-green alga) and Aulacoseira (diatom). Microcystis (and other blue-greens) showed a general increase in the rate of photosynthesis with temperature (up to 30 C), but the diatom did not respond to increases
Seasonal adaptations Adapted to late summer bloom formation – high Ip , low Imax Adapted to late summer bloom formation – high Ip , low Imax Adapted to early seasonal growth, moderate Imax , low Ip Adapted to rapid growth during early to mid summer
above 20 C. In both cases, the rate of photosynthesis increased with photon flux density up to levels of 210–550 mmol photons m2 s1 (about 10–25 per cent full sunlight), above which photoinhibition was observed in Microcystis but not Aulacoseira (Coles and Jones, 2000). Athough considerable variation exists in P–I curves between individual algae and in relation to environmental parameters, each major group of algae has its own characteristics. The advantage displayed by Microcystis over Aulacoseira at high temperatures, for example, by having higher values for Pmax and under these conditions, is typical of other members within the blue-greens and diatoms. The general response of different algal groups (blue-green algae, dinoflagellates, diatoms, and green algae) have been summarized by Horne and Goldman (1994) in relation to light requirements for minimum photosynthesis ðIc Þ, maximum photosynthesis ðImax Þ and the onset of photoinhibition ðIp Þ – as shown in Table 4.3. The data indicate that: the range of light intensities over which algae grow varies considerably; for most algae, photosynthesis commences at light intensities of around 5–7 mmol m2 s1 – the
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COMPETITION FOR LIGHT
threshold for green algae is substantially higher at 21 mmol m2 s1; the light intensity at which maximum photosynthesis occurs is also higher for green algae compared with blue-greens, dinoflagellates, and diatoms; photoinhibition occurs at much lower light levels in diatoms (86 mmol m2 s1) compared with other algal groups (>200 mmol m2 s1). The differences in light response exhibited by the different algal groups represent varying strategies in their adaptation to environmental light conditions. This is shown in the seasonal succession of algae, where periods of major dominance broadly coincide with appropriate light conditions (Table 4.3). In the case of diatoms, for example, the range of light that is most readily used fits the spring bloom period where light levels are generally low due to circulation of water prior to stratification and to ambient seasonal conditions. In polymictic lakes of temperate regions, continued mixing and circulation of water may lead to reduced average light exposure and domination by diatoms over much of the year. Green algae tend to dominate in the summer, particularly during the clear-water phase, when light intensities are high. Although these algae can use up to 211 mmol m2 s1, this exceeds the light intensity normally available in the epilimnion.
4.3.3
Conservation of energy
Algae show adaptations in terms of conservation or optimal use of the energy that has been transformed by photosynthesis. A major part of this energy is used in the synthesis of macromolecules for growth, of which cell wall materials represent a major investment. Comparison of different algae shows that the energy required for cell wall construction varies considerably (Table 4.4). The silica cell wall of diatoms requires about 12 times less energy for construction compared with the cellulose and peptidoglycan cell walls of other algae, giving these organisms the potential to
Table 4.4 Energy requirements for molecular synthesis and cell processes by freshwater algae (modified from Raven, 1984; Werner, 1977) Process Synthesis of cell wall material, proteins and lipids (per atom C or Si) Cellulose (most algae) Peptidoglycan (blue-greens) Silica (diatoms) Protein (gas vacuoles) Lipid (cell membrane) Activities in the freshwater environment Contractile vacuole activity Cell motion by flagella (50 mm s1)
Energy required (pW)
2.5 3.4 0.11 4.8 6.0
3.4 0.00024
out-compete other algae on an energy basis. This may contribute to the evolutionary success of these organisms and the fact that diatoms are by far the most common algae in both fresh and saline waters. The saving of energy by diatoms does have a tradeoff, however, in terms of silicon requirement and high mass. The need for silicon means that growth of diatom populations may become suddenly limited when supplies of the element become depleted. The high mass of diatom cell walls confers a high specific gravity and sedimentation rate, so that many species require turbulent water conditions to stay in suspension, and may be restricted to particular types of lake or particular times of year. Complete absence of a cell wall saves on energy of construction, but the naked cell requires considerable expenditure of energy in using a contractile vacuole to maintain its osmotic balance so this strategy saves little energy in the freshwater environment. Optimal use of energy is also important in movement within the water column. Active swimming of motile organisms such as cryptophytes and dinoflagellates involves continuous expenditure of energy. Organisms such as blue-green algae that use buoyancy to regulate their position within the
LIGHT AS A GROWTH RESOURCE
water column require energy to synthesize the gas vacuole proteins, but once these have become established regulation is by the deposition and removal of carbohydrate ballast (Section 3.8.1, Figure 3.20). This is a normal part of the diurnal activities of these organisms, so the diurnal migration in the water column requires little extra energy. The formation of ballast at the lake surface under conditions of high light will also sink the cells out of the zone of photoinhibition, so depth regulation in relation to short-term changes in light intensity will also require little energy. The lack of any buoyancy or active motility mechanism in diatoms means that they have no direct energy expenditure in terms of maintaining their position within the water column, but does impose reliance on water turbulence. In temperate lakes, the relative success of these different strategies during the annual cycle depends on the physico/chemical environment and on competition with other algae. Diatoms are clearly adapted to turbulent water conditions from autumn to spring, but tend to be replaced by organisms with buoyancy regulation or active motility during the more static conditions of the stratified water column in summer. Although actively motile organisms such as dinoflagellates require high energy expenditure to migrate in the water column, their ability for nocturnal movement from a nutrient-depleted epilimnion down to lower parts of the hypolimnion for nutrient uptake gives them a competitive advantage in late summer. Blue-green algae are also able to migrate into the hypolimnion, but their buoyancy Table 4.5
Blue-green algae
Brown algaee
mechanism requires active photosynthesis for ballast formation. This may become limited in autumn due to conditions of reduced light, leading to later dominance by dinoflagellates.
4.3.4
Diversity in small molecular weight solutes and osmoregulation
Photosynthesis is closely linked to the generation of low molecular weight organic solutes (Figure 4.6) that are involved in osmoregulation. The formation of simple sugars, in particular, results in the formation of a range of osmotically-active compounds which are diagnostic for particular algal groups (Table 4.5). These compounds are important in the osmotic balance within freshwater environments, where algal cells are surrounded by a hypotonic medium. In such conditions the tendency for water to enter by endosmosis is either counterbalanced by cell wall pressure, or (in naked algae) requires continuous expulsion of water by contractile vacuole activity. In conditions of increasing salinity, where the external medium becomes hypertonic, higher intracellular concentrations of osmoticallyactive solutes are required to balance the elevated external molarity. The importance of light in the osmoregulatory process is illustrated by the diatom Cyclindrotheca fusiformis, where photosynthesis is responsible for maintaining the free internal mannose concentration at an adequate level to balance outside osmolarity (Paul, 1979). In the dark, free mannose can be
Some examples of osmotically-active low molecular weight organic solutes in different algal groups
Algal group
Green algaeb Diatomsc Red algaed
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a
Environmental groups
Low MW solute
Freshwater environments Estuaries Hypersaline lakes Euryhaline species, e.g., Dunaliella Euryhaline species, e.g., Cylindrotheca Members present in ion-rich waters, e.g., Bangia atropurpurea Some species present in varying salinity (estuaries and saltmarshes)
Glucosyl-glycerol Sucrose or trehalose Quaternary ammonium compounds Glycerol Mannose Floridoside D-mannitol
References: aWarr et al. (1987); bGinzburg and Ginzburg (1981); cPaul (1979); dReed (1985); eReed et al. (1985)
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COMPETITION FOR LIGHT
generated from its polymer, polymannose. Under light conditions, a decrease in external molarity (hypotonic conditions) results in a conversion of free mannose to polymannose. If the external molarity is raised, polymannose synthesis is inhibited and free mannose is synthesized directly through CO2 fixation. Some algae such as Dunaliella are euryhaline, able to grow over a wide range of salt concentrations. This alga exists as two varieties able to grow at NaCl concentrations of >0.5 M (halotolerant cells)) and >2 M (halophilic cells) respectively (Ginzburg and Ginzburg, 1981). The halotolerant strain has large red cells which contain high concentrations of glycerol, and is able to grow in environments of high salinity such as the Great Salt Lake of Utah (USA), where it forms dense populations colouring the water red or green. Blue-green algae form a particularly interesting group in terms of osmoregulation, with different small MW molecules being involved in different environmental situations (Warr et al., 1987) as follows. In environments with little variation in salinity, blue-green algae respond to increases in salinity by the formation of glucosyl-glycerol. This is formed relatively slowly, but is adequate to adjust to small changes in salinity. In estuarine environments, where salinity changes occur rapidly as the tide goes in and out, bluegreen algae produce sucrose or trehalose as the major osmoregulant. This production occurs over a short time period, allowing a rapid response to environmental change. In hypersaline environments, such as the Great Salt Lake of Utah (USA), blue-green algae make long-term adjustment to high salinity by the continuous production of osmotically-active quaternary ammonium compounds glycine, betaine, and glutamate betaine. In addition to the production of small MW organic compounds, internal molarity may also be controlled via the internal concentration of inorganic ions such as Kþ. This is particularly important
in blue-green algae, where diurnal fluctuations in photosynthetically-mediated Kþ uptake result in fluctuations in internal pressure (turgor) and the periodic formation and loss of gas vesicles (Section 3.8.2, Figure 3.20).
4.4
Algal growth and productivity
The photosynthetic conversion of light (kinetic) energy into chemical (potential) energy, with the formation of reduced carbon compounds, is the key process which generates biomass within aquatic systems. The rate of synthesis of biological material (primary production) is important in relation to the net increase in biomass and in the development of algal populations.
4.4.1
Primary production: concepts and terms
Algal growth requires the synthesis of a wide range of cellular material and photosynthetic production of organic carbon compounds is clearly only part of this process. The rate of synthesis of algal biomass is an important parameter since it determines the increase in algal population, and is referred to as the ‘gross primary production’. Although this term is widely used, there is no generally accepted definition. Different workers have variously defined gross primary production as follows. The rate of conversion of light energy into chemical energy (Platt et al., 1980). This reflects the view held by theoretical ecologists and plant biophysicists, who consider primary production in terms of energy transformations during the initial steps of photosynthesis. The rate of organic carbon production resulting from photosynthetic activity (Williams, 1993). This definition considers production in terms of carbon flow and reflects the viewpoint of the community ecologist and plant physiologist. The rate of assimilation of inorganic carbon and nutrients into organic and inorganic matter by
ALGAL GROWTH AND PRODUCTIVITY
autotrophs (modified from Underwood and Kromkamp, 1999). This definition considers primary production in terms of the overall production of biomass (including inorganic material such as silica cell walls), and follows the approach of workers such as biogeochemists who are interested in the full range of nutrients within the environment.
4.4.2
Primary production and algal biomass
Gross primary production does not directly translate into algal biomass since the synthetic increase in biomaterials is countered by a range of loss process, including respiration. Net primary production is normally defined as gross primary production minus autotrophic respiration. Other loss processes are also important, including excretion of materials (e.g., enzymes and dissolved organic carbon), cell lysis, and activities of other freshwater biota (e.g., zooplankton grazing, fungal and viral parasitism). In the case of phytoplankton, loss of dead cells from the euphotic zone by sedimentation, and exchange of living cells between the water column and sediments are also important. The growth of phytoplankton can be expressed mathematically: B=t ¼ ðP R EÞB GP S BE
ð4:2Þ
where: B=t ¼ increase in biomass with time, P ¼ rate of gross primary production, R ¼ rate of respiration, E ¼ excretion and cell lysis, B ¼ existing biomass, GP ¼ loss by grazing or parasitism, S ¼ loss by sedimention of dead cells, and BE ¼ exchange of biomass between sediments and water column.
Seasonal relationship between growth and photosynthesis Investigations of the factors that determine seasonal changes in phytoplankton populations often focus on photosynthetic and growth responses of phytoplankton. Because growth of a population of algal cells primarily depends on the increase in protein
197
biomass, which directly relates to carbon assimilation and photosynthesis, the relationship between specific growth rate ( ) and environmental conditions (light, temperature) might be expected to reflect the photosynthetic rate P. The increase in protein and carbon biomass (growth rate) depends on a balance of factors, however (Figure 4.5), and although photosynthesis, growth rate, and population increase are often closely coupled (Coles and Jones, 2000), this is not always so. The relationship between photosynthesis and population increase may vary because of a range of imbalances in cellular processes as follows. Respiration rate does not change in direct proportion to photosynthesis at different light and temperature levels. Cell division rates may peak at lower temperatures than photosynthetic rates. Extracellular release of DOC (loss of biomass) may be less than 5 per cent at optimum light and temperature but can increase to nearly 40 per cent under conditions of low light and high temperature. DOC release under conditions of high light (causing photoinhibition) may also be excessive. Net photosynthesis and carbon assimilation are restricted to the illuminated part of the day, while protein synthesis may continue in the dark.
4.4.3
Field measurements of primary productivity
Most measurements of algal productivity involve determination of photosynthetic activity, either in terms of CO2 fixation or O2 evolution. The 14CO2 uptake method developed by Steemann Nielson (1952) has been extensively used to estimate primary production, which is expressed as fixed carbon mass per unit area per unit time. Productivity may also be considered in terms of long-term development of biomass (algal production). This may be expressed as units of chlorophyll-a
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COMPETITION FOR LIGHT
Table 4.6 Algal type Epipelon
Epiphyton
Metaphyton Phytoplankton
Algal production in wetland communities (data taken from Goldsborough and Robinson, 1996) Biomass (chlorophyll-a concentration)
Wetland a
Freshwater marsh (sediment surface) Freshwater marsh (core sample)b Salt marsh (core sample) Freshwater marsh (attachment surface)c Freshwater marsh (sediment surface)d Peat bog Freshwater marshe Freshwater marshf
2
0–5 mg m 10–400 mg m2 20–150 mg m2 0–4 mg cm2 7–650 mg m2 2–240 mg m2 0–80 mg m2 (dry weight) 5–100 mg l2 (5–100 mg m2)
Carbon fixation rate 0.2–0.5 mg cm2 h1 1.5–6.0 mg cm2 h1 0.2–0.5 mg cm2 h1
1.4–114 mg cm2 y1 3–16 mg l2 h1 (3–16 mg m2 h1)
This table indicates typical values for the range of algal production (expressed as total biomass and rate of carbon fixation) that different workers have measured for epipelon, epiphyton, metaphyton, and phytoplankton in different wetland environments. These data should be interpreted cautiously due to variation arising from geographic and seasonal factors, differences in analytical methods, and differences in the way that data are expressed. a Biomass taken from sediment surface; bbiomass in core sample; c biomass per unit surface to which the algae are attached; dbiomass per wetland surface area; e biomass expressed as dry weight rather than chlorophyll-a mass; fbiomass expressed per litre and per wetland surface area, assuming a depth of 1 m
per unit area (benthic algae) or per unit volume of water (phytoplankton). Measurements of algal production as biomass are particularly useful in complex aquatic environments (e.g., wetlands, Table 4.6) where carbon fixation by different algal groups may be difficult to determine. Assessment of primary productivity varies with complexity of the ecosystem, ranging from relatively simple planktonic populations in lakes to more complex communities in wetlands.
Primary productivity of lake phytoplankton Primary productivity varies considerably in relation to the nutrient status of the lake, environmental conditions and type of algae present. In some cases, productivity occurs mainly via the picoplankton. Measurement of photosynthetic uptake of 14 C-bicarbonate during the summer growth phase of Lake Baikal (Russia), for example, indicated total productivity values of 36 mg C l1 day1, with over 80 per cent being carried out by unicellular blue-green algal picoplankton and nanoplankton (Nagata et al., 1994).
Primary productivity in wetland communities Measurement of algal productivity in wetland systems is complicated in two main ways. The algae being monitored occur as a diverse assemblage of attached and free-floating forms, and can be divided into four main types on the basis of their life style and microhabitat – epipelic algae (present on mud surfaces), epiphytic algae (attached to higher plant and macroalgal surfaces), metaphyton (surface or benthic floating masses of filamentous green algae), and phytoplankton (free-floating cells and colonies entrained in the water column). Because of their different microhabitats, measurements of biomass and carbon fixation tend to use different units in terms of the environmental parameter, making comparability difficult. Thus the biomass of epipelic algae is typically expressed per unit area of wetland, epiphytic algae per unit area of attachment substrate (e.g., higher plant surface), and phytoplankton per unit volume of water.
PHOTOSYNTHETIC BACTERIA
Figure 4.9 Light and algal productivity in a wetland system: diagram showing complexity of algal productivity in a wetland system, with four main groups of algae contributing to carbon fixation – epiphytic algae (epy) on macrophytes, bundles of filamentous metaphyton (m), phytoplankton (ph), and epipelic algae (epl) on fine sediments. Competition for light affects the population growth and productivity of these different groups (not drawn to scale)
The complexities of light availability, algal types, and productivity are illustrated in Figure 4.9. Epipelon biomass can be measured in two main ways. Most studies of freshwater systems involve the collection of an algal sample by placement of lens paper onto the exposed sediment surface. Estimates of epipelic algae by this method tend to give quite low biomass values (
