Preface of the editor V

Preface of the authors V

1. The habitat of aquatic bacteria 1

1.1 Principles of classification of lakes according to their trophic status 1

2. General characteristics of aquatic microflora 2

2.1 Main types of metabolism in micro-organisms 2

2.2 Basic approaches to the study of aquatic microflora 3
2.3 Total numbers of bacteria in waters of different type 6
2.31 Vertical distribution of bacteria in the water mass 6
2.32 Changes in bacterial numbers in an annual cycle in the aerobic zone 7

3. The ecology of micro-organisms participating in the cycle of organic
matter in bodies of water 9

3.1 The aerobic ecological zone 11
3.11 Physico-chemical characteristics 11
3.12 General characteristics of the microflora of the aerobic zone in
different types of lakes 12
3.121 Filamentous bacteria 17
3.122 Morphological characteristics of aquatic microflora, not obtained in
pure cultures 18
3.13 Ecological niches of the aerobic zone in different types of lakes 19

3.131 The ecological niche of the surface film of the water 19
3.132 Ecological niches of the water mass 22
3.132.1The ecological niche of photosynthesis 22
3.132.2 The ecological niches of production of the biomass of heterotrophic
bacteria 28
3.132.3 The ecological niches of organic matter production by
chemolithoautotrophs 31
3.132.4 The ecological niches of organic matter destruction 34
3.133 The ecological niche of the thermocline in the aerobic zone 38

3.2 The microaerophilic zone 40
3.21 The ecological niche of hydrogen-oxidizing bacteria 41
3.22 The ecological niche of methane-oxidizing bacteria 43
3.221 Main representatives 43
3.222 The intensity of methane oxidation 44

3.3 The anaerobic zone 49

3.31 Physico-chemical characteristics 49

3.32 General characteristics of microflora in the anaerobic zone 49

3.4 The ecological zone of mud sediments 50

3.41 Physico-chemical characteristics 50

3.42 The microbiological characteristics of mud sediments 54

3.421 Microzonality of structure of mud sediments and microflora
distributions 54

3.422 General characteristics of the microflora of mud sediments 55

3.43 The ecological niches of mud sediments in lakes of different types 58

3.431 The ecological niches in muds of oligotrophic lakes 58

3.432 The ecological niches in dimictic mesotrophic and eutrophic lakes 59

3.432.1 The ecological niche of the surface layer of the mud 0-2 cm 60

3.432.2 The ecological niche of sulphate-reducing and methane-producing
bacteria 61

3.5 Conclusions 64

4. Species composition and ecology of micro-organisms taking part in the
nitrogen cycle 66

4.1 General characteristics of nitrogen cycle bacteria 66
4.11 Bacteria fixing free nitrogen 66
4.12 Micro-organisms involved in the mineralisation of organic nitrogen 68
4.13 Nitrifying bacteria 69
4.131 Oxidation of ammonia by heterotrophic organisms 71
4.14 Denitrifying bacteria 72

4.2 The ecology of the nitrogen cycle bacteria 74

4.21 Oligotrophicbodiesofwater 74
4.211 The ecological niche of surface layers of mud sediments 75
4.212 The ecological niches in lake littoral 76
4.22 Mesotrophic and eutrophic waters 77
4.221 Physico-chemical characteristics of the habitat 77
4.222 The ecology of nitrogen-fixing bacteria 78
4.223 The rates of free nitrogen fixation 80
4.223.1 Nitrogen fixation by blue-green algae (cyanobacteria) 80
4.223.2 Bacterial nitrogen fixation 83
4.224 The ecology of ammonifying bacteria 87
4.224.1 The intensity of ammonification processes 88
4.225 The ecology of nitrifying bacteria 90
4.225.1 The ecological niches of Vitrification processes 90
4.225.2 The potential capacity for Vitrification 91
4.226 The ecology of denitrifying bacteria 92
4.226.1 The nature of denitrification and the distribution of bacteria
in ecological niches 92
4.226.2 The intensity of denitrification processes 93
4.227 Liberation of molecular nitrogen from mud sediments 95

5. Micro-organisms reducing and oxidizing sulphur compounds 97

5.1 Characteristics of micro-organisms of the sulphur cycle 98
5.11 Micro-organisms taking part in the liberation of sulphur from
organic compounds 98
5.12 The dissimilatory reduction of sulphates 99
5.13 Thiobacteria 102
5.14 Colourless sulphur bacteria 104
5.15 Photosynthetic bacteria 105

5.2 The ecology of micro-organisms of the sulphur cycle 117
5.21 The ecology of sulphate-reducing bacteria 119
5.22 The ecology of micro-organisms oxidising reduced compounds of
sulphur 123
5.221 The characteristics of development of sulphur bacteria in shallow
waters 126

5.221.1 Micro-organisms which change from the benthic to the planktonic way
of life 126
5.221.2 Benthic unicellular non-motile forms, tolerant to oxygen 127
5.221.3 Benthic non-motile forms, strict anaerobes 127
5.221.4 Benthic filamentous forms, which move by gliding over the substrate 127
5.222 Development of phototrophic and colourless sulphur bacteria in
saline waters 127
5.222.1 Physico-chemical parameters in water and mud sediments of saline
shallow waters 128
5.222.2 The structure of the benthic community 129
5.222.3 Limiting factors 131
5.223 Development of sulphur bacteria in shallow freshwaters sub jected
to mixing 131
5.224 The role of some environmental factors in the distribution and
species composition of sulphur bacteria 134
5.224.1 Salinity 134
5.224.2 Light regime 135
5.224.3 Hydrogen sulphide, oxygen and oxidation-reduction potential 135
5.224.4 pH of the environment 136
5.224.5 Temperature 136
5.225 The development of photosynthetic, thionic and colourless
sulphur bacteria in tratified waters containing hydrogen sulphide in
the water layer 137
5.225.1 Oligotrophic meromictic lakes 137
5.225.2 Dimictic mesotrophic and eutrophic freshwater lakes 139
5.225.3 Dystrophic lakes of South Karelia 145
5.225.4 Mesotrophic meromictic lakes 146
5.225.5 EutrophiCfreshwatermeromicticlakes 152
5.225.6 Mesotrophic meromictic lakes with access to the sea 154
5.225.7 Eutrophic meromicticsaltlakes 157
5.225.8 Acidicvolcaniclakes 160
5.226 The role of physico-chemical factors in the distribution of
phototrophic, thionic
and colourless sulphur bacteria in the water mass of lakes 162

6. Species composition and ecology of micro-organisms oxidising iron and
manganese 167

6.1 General characteristics of iron bacteria 167

6.11 The pathways of iron and manganese oxidation by micro-organisms 168
6.12 The physiological role of iron and manganese oxidation processes 170
6.13 The taxonomy of the iron bacteria group 170

6.2 The ecology of iron bacteria 181
6.21 Conditions for the development of iron bacteria in different
types of waters 181
6.211 Oligotrophic dimictic lakes 181
6.212 Oligotrophic meromictic lakes 185
6.213 Mesotrophic dimictic lakes 187
6.214 Mesotrophic meromictic lakes 189
6.215 Mesotrophic lakes with the accumulation of iron-manganese lake-ore 191
6.216 Dimictic eutrophic lakes 198
6.217 Meromictic eutrophic lakes 203
6.218 Dystrophicdimicticlakesandbogs 203
6.219 Iron-rich ("siderotrophic") acidic lakes 208
6.22 The effect of physico-chemical factors on the development of iron
bacteria 210
6.23 The characteristics of the ecological niches of iron bacteria 217
6.24 The ecological forms of iron bacteria 219
6.25 The role of iron bacteria in oxidation and sedimentation of iron
and manganese 221

7. Conclusion 223

References 225
Species Index 245
Subject Index 250