Psychrophiles: From Biodiversity to Biotechnology (eBook)

Preface 5
Contents 7
Contributors 10
Boundary Conditions for Microbial Life at Low Temperatures 15
The Climate of Snow and Ice as Boundary Condition for Microbial Life 16
1.1 The source of energy: solar radiation 16
1.2 Distribution of energy: the energy balance of snow and ice 18
1.3 Air temperature: effects of altitude and latitude 19
1.4 Atmospheric humidity and precipitation 21
1.5 The cryosphere: a matrix for life 22
1.6 Liquid water in the cryosphere 24
1.7 Hot spots in the ice 26
1.8 Conclusions 27
References 27
Limits for Microbial Life at Subzero Temperatures 29
2.1 Introduction 29
2.2 Physical chemical effects of low temperatures 30
2.2.1 Liquid water 30
2.2.2 Reaction rates 32
2.2.3 Molecular stability 33
2.3 Activity of microorganisms at subzero temperatures 34
2.4 Conclusions 37
References 38
Microbial Diversity in Cold Ecosystems 41
Bacteria in Snow and Glacier Ice 42
3.1 Introduction 42
3.2 Characteristics of snow and glacier ice as microbial habitats 43
3.3 History of detection of microorganisms in glacier ice and snow 45
3.4 Trapped and dormant or actively metabolizing? 45
3.5 Methods for microbial analysis of snow and glacier ice 3.5.1 Sampling and decontamination methods 46
3.5.2 Methods for enumeration and morphological characterization 46
3.5.3 Culture independent methods 47
3.5.4 Cultivation methods 48
3.6 Diversity of bacteria in glacier ice 49
3.6.1 Morphological diversity and size of glacier ice bacteria 49
3.6.2 Bacterial diversity detected by culture independent methods 51
3.6.3 Recovery and characteristics of bacterial isolates from glacier ice 51
3.7 How different are bacteria in glacier ice and cryoconite holes? 53
3.8 Diversity of bacteria in snow 54
3.9 Novel bacterial isolates from glacier ice and snow 55
3.10 Functional diversity and microbial activity in glacier ice and snow 56
3.11 Conclusions 58
References 58
Bacteria in Subglacial Environments 62
4.1 Introduction 62
4.2 Liquid water in subglacial environments 4.2.1 Water and life 63
4.2.2 Liquid water in Arctic and Alpine subglacial environments 64
4.2.3 Discovery of subglacial water beneath Antarctica’s ice sheets 64
4.2.4 Liquid water under the Greenland ice sheet 65
4.3 Subglacial lakes 4.3.1 Antarctic subglacial lakes 65
4.3.2 Subglacial Lake Vostok 66
4.3.3 Sampling Antarctic subglacial lakes 67
4.3.4 Subglacial caldera lakes 71
4.4 Adaptations, bioenergetics, and cosmopolitan genera in subglacial environments 4.4.1 Molecular adaptations for survival in icy environments 72
4.4.2 Resistance to high oxygen concentrations 73
4.4.3 Survival under oligotrophic conditions 73
4.4.4 Chemolithotrophy in subglacial environments 76
4.4.5 Do subglacial environments harbor endemic microbial species? 76
4.5 Conclusions 78
References 79
Bacteria in the Deep Sea: Psychropiezophiles 83
5.1 Introduction 83
5.2 The deep-sea psychropiezophiles 85
5.3 Taxonomy of the psychropiezophiles 85
5.3.1 The genus Shewanella 86
5.3.2 The genus Photobacterium 87
5.3.3 The genus Colwellia 87
5.3.4 The genus Moritella 88
5.3.5 The genus Psychromonas 88
5.4 The fatty acid composition of psychropiezophiles 89
5.5 Conclusions 90
References 90
Bacteria in Permafrost 93
6.1 Introduction 93
6.2 Soil cover 95
6.3 Permafrost 99
6.3.1 Bacterial biodiversity 99
6.3.2 Cyanobacteria 100
6.3.3 Anaerobic bacteria 103
6.3.4 Resistance of permafrost bacteria to antibiotics and heavy metals 105
6.3.5 Resistance of permafrost bacteria to radiation 106
6.3.6 Resistance of permafrost bacteria to freezing- thawing stress 107
6.4 Conclusions 109
References 109
Anaerobic Bacteria and Archaea in Cold Ecosystems 113
7.1 Introduction 113
7.2 Bacteria 7.2.1 The genus Clostridium 114
7.2.2 Sulfate-reducing bacteria 116
7.2.3 Sulfur- and iron-reducing bacteria 120
7.2.4 Acetogenic bacteria 121
7.2.5 Anoxygenic phototrophic bacteria 122
7.2.6 Miscellaneous 122
7.3 Archaea 123
7.4 Conclusions 124
References 125
Cyanobacteria in Cold Ecosystems 130
8.1 Introduction 130
8.2 Taxonomy and diversity 131
8.3 General characteristics 132
8.4 Antarctic habitats 133
8.4.1 Ice-based habitats 133
8.4.2 Soils and rock 134
8.4.3 Ponds, lakes, rivers and streams 135
8.4.4 Marine ecosystems 135
8.5 Arctic habitats 135
8.5.1 Ice-based habitats 136
8.5.2 Lakes, streams and ponds 136
8.5.3 Soils and rock 136
8.5.4 Marine ecosystems 137
8.6 Alpine habitats 8.6.1 Streams and lakes 137
8.6.2 Rocks and soils 137
8.7 Ecophysiology 8.7.1 Coping with the cold 138
8.7.2 Osmotic stress 138
8.7.3 High and low irradiance 138
8.8 Biogeography 139
8.9 Conclusions 140
References 141
Fungi in Cold Ecosystems 145
9.1 Introduction 145
9.2 Methods for recovering psychrotolerant and psychrophilic species 147
9.3 Protection and survival of cold ecosystem fungi 148
9.4 Different ecosystems 9.4.1 Fungi in soil and permafrost 148
9.4.2 Fungi in caves 149
9.4.3 Fungi on rocks 149
9.4.4 Fungi on dung 149
9.4.5 Fungi on plants, mosses and lichens 150
9.4.6 Fungi on grass: snow moulds 150
9.4.7 Fungi in glaciers, ice and freshwater 150
9.4.8 Fungi in chilled and frozen foods 151
9.5 Different fungal taxa from cold ecosystems 9.5.1 Fungal genera and cold ecosystems 151
9.5.2 Yeasts 152
9.5.3 Ascomycetes 152
9.5.4 Penicillium 153
9.5.5 Cladosporium 154
9.5.6 Zygomycetes 154
9.5.7 Basidiomycetes 156
9.5.8 Lichens 156
9.6 Conclusions 157
References 157
Cold-Active Viruses 165
10.1 Introduction 165
10.2 Characterization of cold-active viruses and their hosts 10.2.1 Cold- active phages isolated from sewage or food 166
10.2.2 Cold-active phages from marine environments 170
10.2.3 Physico-chemical characteristics of cold-active phages 173
10.3 Molecular and genomic studies of cold-active viruses 174
10.4 Conclusions 179
References 179
Molecular Adaptations to Cold Habitats 182
Membrane Components and Cold Sensing 183
11.1 Introduction 183
11.2 Phylogeny of membrane lipid cold-dependent changes 184
11.3 Thermal (cold) control of membrane lipid changes 184
11.3.1 Desaturases 185
11.3.2 Anaerobic mechanisms of unsaturated fatty acid synthesis 186
11.3.3 Branched-chain fatty acids 187
11.3.4 Fatty acid chain length 188
11.3.5 Some fatty acid thermal “red herrings” 188
11.3.6 Sterols and hopanoids 189
11.4 Do psychrophiles have specific “cold” fatty acid compositions? 189
11.5 Capacity for cold adaptation: psychrophiles versus psychrotolerants 190
11.6 Rate of lipid cold adaptation 191
11.7 Lipid phase behavior and cold adaptation 192
11.8 How do microorganisms sense the cold? 193
11.9 Conclusions 194
References 194
Cold-Shock Proteins 197
12.1 Introduction 197
12.2 Cellular response to cold shock 198
12.3 CspA family of cold-shock proteins 12.3.1 Functional redundancy 200
12.3.2 Regulation of cold-shock induction 200
12.3.3 Structure 200
12.3.4 Function 201
12.3.5 Biotechnological applications 202
12.4 Molecular chaperones 206
12.4.1 Caseinolytic proteases 206
12.4.2 Trigger factor 207
12.5 Desaturases 208
12.5.1 Desaturases from cyanobacteria 208
12.5.2 Desaturases from Bacillus 209
12.5.3 Biotechnological potential 209
12.6 Trehalose synthesis machinery 210
12.6.1 Biotechnological potential 210
12.7 Conclusions 211
References 211
Fundamentals of Cold-Adapted Enzymes 216
13.1 Introduction 216
13.2 The low temperature challenge 217
13.3 Activity 219
13.4 Stability 222
13.4.1 Reversible and irreversible unfolding 222
13.4.2 Global versus local stability 225
13.5 Flexibility 225
13.6 Structural adaptations 227
13.7 Conclusions 228
References 229
Cryoprotectants and Ice-Binding Proteins 233
14.1 Introduction 233
14.2 Cryoprotection in cold-adapted microorganisms 14.2.1 Cryoprotectants of low molecular mass 235
14.2.2 Cryoprotective proteins and cold chaperones from ice- nucleating bacteria 237
14.3 Ice crystal-controlling proteins 14.3.1 Structure and function of ice- nucleation proteins 238
14.3.2 Structure and function of anti-nucleating proteins 242
14.3.3 Structure and function of bacterial antifreeze protein 244
14.4 Conclusions 247
References 247
The Role of Exopolymers in Microbial Adaptation to Sea Ice 251
15.1 Introduction 251
15.1.1 What are exopolymeric substances? 252
15.1.2 Exopolymers in the environment 252
15.2 Exopolymers in sea ice 15.2.1 General concepts 254
15.2.2 Small-scale physics and chemistry of freezing 256
15.2.3 Influence of exopolymers on small-scale processes 258
15.3 Conclusions 263
References 264
Genomic Analysis of Psychrophilic Prokaryotes 269
16.1 Introduction 269
16.2 Genome features and cold temperature adaptations 274
16.2.1 Protein amino acid composition and link with evolution 274
16.2.2 Membrane fluidity 276
16.2.3 Nutrient and energy reserves 278
16.2.4 Compatible solutes 279
16.2.5 Extracellular compounds 281
16.3 The environment molds the genomic traits of organisms 283
16.4 Conclusions 285
References 285
Microalgae in Polar Regions: Linking Functional Genomics and Physiology with Environmental Conditions 289
17.1 Introduction 289
17.2 Environmental conditions 17.2.1 Light 290
17.2.2 Seawater 292
17.2.3 Sea ice 293
17.2.4 Snow 299
17.2.5 Rock surfaces 299
17.2.6 Permanently ice covered lakes 300
17.3 Adaptation of microalgae at high latitudes 17.3.1 Diatoms ( Bacillariophyceae) 301
17.3.2 Green algae (Chlorophyceae) 307
17.4 Conclusions 311
References 312
Metagenomics: Microbial Community Genomes Revealed 317
18.1 Introduction 317
18.2 Tapping into hidden diversity 318
18.3 Approaches in metagenomic analysis 18.3.1 Functional screening 319
18.3.2 Sequence-based screening 321
18.4 Metagenomics: for what purposes? 322
18.4.1 Assessing phylogenetic diversity and population structure 322
18.4.2 Linking novel functional roles to phylogeny 323
18.4.3 Assessing metabolic pathways, ecology and evolution 323
18.4.4 Sequencing whole genomes of communities 324
18.4.5 Bioprospecting 325
18.5 Metagenomics of low temperature environments 325
18.6 Novel applications 18.6.1 Comparative community genomics and pyrosequencing 327
18.6.2 Metatranscriptomics and metaproteomics 329
18.7 Dealing with high volumes of metagenomic sequencing 329
18.8 Conclusions 330
References 331
Proteomic Studies of Psychrophilic Microorganisms 337
19.1 Introduction 337
19.2 Global identification of proteins produced at low temperatures 338
19.2.1 Identification of cold-inducible proteins without whole genome sequence information 338
19.2.2 Methanococcoides burtonii 339
19.2.3 Bacillus psychrosaccharolyticus 339
19.2.4 Psychrobacter cryohalolentis K5 344
19.2.5 Psychrobacter articus 273-4 345
19.2.6 Shewanella livingstonensis Ac10 346
19.3 Conclusions 347
References 347
Biotechnological Aspects 349
Biotechnological Aspects of Cold-Adapted Enzymes 350
20.1 Introduction 350
20.1.1 Mining the cold biosphere for biomolecules of biotechnological interest 351
20.1.2 Cold-adapted enzymes 352
20.2 Industrial enzymes: history and recent advances 355
20.3 Industrial potential of cold-adapted enzymes 356
20.3.1 Enzymes for detergents and personal care 357
20.3.2 Food, pharmaceutical and cosmetic industries 357
20.3.3 Biofuels 359
20.3.4 Molecular biology 360
20.3.5 Enzyme nanobiotechnology 361
20.4 Conclusions 363
References 363
Heterologous Protein Expression in Psychrophilic Hosts 367
21.1 Introduction 367
21.2 The genetic system 369
21.2.1 The psychrophilic host: Pseudoalteromonas haloplanktis TAC125 369
21.2.2 The psychrophilic gene-expression vector 370
21.2.3 Molecular signals for protein addressing 373
21.3 Examples of heterologous protein expression in psychrophilic bacteria 375
21.3.1 P. haloplanktis TAE79 375
galactosidase 375
and Saccharomyces cerevisiae 375
glucosidase production 375
21.3.2 hb- NGF Production 376
21.3.3 Secretion of several heterologous proteins 377
21.4 Conclusions 378
References 379
Cold-Adapted Fungi as a Source for Valuable Metabolites 382
22.2 Extrolites from cold-adapted fungi 383
22.3 Secondary metabolites from cold-adapted fungi 384
22.4 Conclusions 385
References 385
Natural and Stimulated Biodegradation of Petroleum in Cold Marine Environments 389
23.1 Introduction 389
23.2 Oil discharges in cold seawater 390
23.2.1 Petroleum characteristics and weathering 390
23.2.2 Surface oil spills 391
23.2.3 Sediment processes 391
23.2.4 Deepwater oil spills 392
23.3 Hydrocarbon-degrading microorganisms 392
23.3.1 Hydrocarbon-degraders in cold marine environments 392
23.3.2 Hydrocarbon metabolism at low temperatures 394
23.4 Modelling of hydrocarbon degradation 23.4.1 Biodegradation rates 396
23.4.2 Temperature 397
23.5 Oil bioremediation in cold marine environments 397
23.5.1 Biostimulation 398
23.5.2 Bioaugmentation 401
23.6 Conclusions 401
References 402
Microbial Adaptation to Boreal Saturated Subsurface: Implications in Bioremediation of Polychlorophenols 408
24.1 Introduction 408
24.2 Physicochemical properties of chlorophenols 409
24.3 Polychlorophenol degradation is controlled by redox conditions 410
24.4 The Kärkölä case: long-term monitoring of the chlorophenol- contaminated groundwater and on site bioremediation 410
24.5 In situ bioremediation of groundwater polychlorophenols 412
24.6 Distribution and origin of polychlorophenol degraders 24.6.1 Diversity of culturable polychlorophenol degraders 413
24.6.2 Natural evolution of polychlorophenol degradation 415
24.7 Microbial responses to low temperatures 416
24.8 Microbial adaptation to oligotrophic conditions 417
24.9 Biodegradation of polychlorophenols under microaerophilic conditions 418
24.10 Competition for oxygen by iron and chlorophenol oxidation 419
24.11 Competition for oxygen by polychlorophenol, iron and natural organic matter oxidation 420
24.12 Conclusions 420
References 421
Biological Iron Oxidation and Sulfate Reduction in the Treatment of Acid Mine Drainage at Low Temperatures 427
25.1 Introduction 427
25.2 Biological oxidation of iron and sulfur at low temperatures 429
25.3 Biological reduction of sulfate at low temperatures 432
25.4 Passive treatment of AMD 25.4.1 Constructed wetlands 436
25.4.2 In situ remediation 437
25.5 Active treatment of AMD 25.5.1 Application of Fe2+ oxidation 442
25.5.2 Application of sulfate reduction 443
25.6 Conclusions 447
References 448
Index 453