Psychrophiles: from Biodiversity to Biotechnology

Psychrophiles - From Biodiversity to Biotechnology......Page 1
Preface......Page 5
Contents......Page 7
Contributors......Page 10
1.1 The source of energy: solar radiation......Page 15
1.2 Distribution of energy: the energy balance of snow and ice......Page 17
1.3 Air temperature: effects of altitude and latitude......Page 18
1.4 Atmospheric humidity and precipitation......Page 20
1.5 The cryosphere: a matrix for life......Page 21
1.6 Liquid water in the cryosphere......Page 23
1.7 Hot spots in the ice......Page 25
References......Page 26
2.1 Introduction......Page 28
2.2.1 Liquid water......Page 29
2.2.2 Reaction rates......Page 31
2.2.3 Molecular stability......Page 32
2.3 Activity of microorganisms at subzero temperatures......Page 33
2.4 Conclusions......Page 36
References......Page 37
3.1 Introduction......Page 40
3.2 Characteristics of snow and glacier ice as microbial habitats......Page 41
3.4 Trapped and dormant or actively metabolizing?......Page 43
3.5.2 Methods for enumeration and morphological characterization......Page 44
3.5.3 Culture independent methods......Page 45
3.5.4 Cultivation methods......Page 46
3.6.1 Morphological diversity and size of glacier ice bacteria......Page 47
3.6.3 Recovery and characteristics of bacterial isolates from glacier ice......Page 49
3.7 How different are bacteria in glacier ice and cryoconite holes?......Page 51
3.8 Diversity of bacteria in snow......Page 52
3.9 Novel bacterial isolates from glacier ice and snow......Page 53
3.10 Functional diversity and microbial activity in glacier ice and snow......Page 54
References......Page 56
4.1 Introduction......Page 60
4.2.1 Water and life......Page 61
4.2.3 Discovery of subglacial water beneath Antarctica’s ice sheets......Page 62
4.3.1 Antarctic subglacial lakes......Page 63
4.3.2 Subglacial Lake Vostok......Page 64
4.3.3 Sampling Antarctic subglacial lakes......Page 65
4.3.4 Subglacial caldera lakes......Page 69
4.4.1 Molecular adaptations for survival in icy environments......Page 70
4.4.3 Survival under oligotrophic conditions......Page 71
4.4.5 Do subglacial environments harbor endemic microbial species?......Page 74
4.5 Conclusions......Page 76
References......Page 77
5.1 Introduction......Page 81
5.3 Taxonomy of the psychropiezophiles......Page 83
5.3.1 The genus Shewanella......Page 84
5.3.3 The genus Colwellia......Page 85
5.3.4 The genus Moritella......Page 86
5.4 The fatty acid composition of psychropiezophiles......Page 87
References......Page 88
6.1 Introduction......Page 91
6.2 Soil cover......Page 93
6.3.1 Bacterial biodiversity......Page 97
6.3.2 Cyanobacteria......Page 98
6.3.3 Anaerobic bacteria......Page 101
6.3.4 Resistance of permafrost bacteria to antibiotics and heavy metals......Page 103
6.3.5 Resistance of permafrost bacteria to radiation......Page 104
6.3.6 Resistance of permafrost bacteria to freezing-thawing stress......Page 105
References......Page 107
7.1 Introduction......Page 111
7.2.1.1 Psychrophilic clostridia......Page 112
7.2.1.2 Psychrotolerant clostridia......Page 113
7.2.2.1 Psychrophilic sulfate-reducing bacteria......Page 114
7.2.2.2 Psychrotolerant sulfate-reducing bacteria......Page 117
7.2.3 Sulfur- and iron-reducing bacteria......Page 118
7.2.4 Acetogenic bacteria......Page 119
7.2.6 Miscellaneous......Page 120
7.3 Archaea......Page 121
7.4 Conclusions......Page 122
References......Page 123
8.1 Introduction......Page 128
8.2 Taxonomy and diversity......Page 129
8.3 General characteristics......Page 130
8.4.1 Ice-based habitats......Page 131
8.4.2 Soils and rock......Page 132
8.5 Arctic habitats......Page 133
8.5.3 Soils and rock......Page 134
8.6.2 Rocks and soils......Page 135
8.7.3 High and low irradiance......Page 136
8.8 Biogeography......Page 137
8.9 Conclusions......Page 138
References......Page 139
9.1 Introduction......Page 143
9.2 Methods for recovering psychrotolerant and psychrophilic species......Page 145
9.4.1 Fungi in soil and permafrost......Page 146
9.4.4 Fungi on dung......Page 147
9.4.7 Fungi in glaciers, ice and freshwater......Page 148
9.5.1 Fungal genera and cold ecosystems......Page 149
9.5.3 Ascomycetes......Page 150
9.5.4 Penicillium......Page 151
9.5.6 Zygomycetes......Page 152
9.5.8 Lichens......Page 154
References......Page 155
10.1 Introduction......Page 163
10.2.1 Cold-active phages isolated from sewage or food......Page 164
10.2.2.1 Marine surface waters......Page 168
10.2.2.2 Other marine water and sedimentary environments......Page 169
10.2.2.3 Sea ice......Page 170
10.2.3 Physico-chemical characteristics of cold-active phages......Page 171
10.3 Molecular and genomic studies of cold-active viruses......Page 172
References......Page 177
11.1 Introduction......Page 180
11.3 Thermal (cold) control of membrane lipid changes......Page 181
11.3.1 Desaturases......Page 182
11.3.2 Anaerobic mechanisms of unsaturated fatty acid synthesis......Page 183
11.3.3 Branched-chain fatty acids......Page 184
11.3.5 Some fatty acid thermal “red herrings”......Page 185
11.4 Do psychrophiles have specific “cold” fatty acid compositions?......Page 186
11.5 Capacity for cold adaptation: psychrophiles versus psychrotolerants......Page 187
11.6 Rate of lipid cold adaptation......Page 188
11.7 Lipid phase behavior and cold adaptation......Page 189
11.8 How do microorganisms sense the cold?......Page 190
References......Page 191
12.1 Introduction......Page 194
12.2 Cellular response to cold shock......Page 195
12.3.3 Structure......Page 197
12.3.4 Function......Page 198
12.3.5.1 Cold-shock vectors......Page 199
12.3.5.2 Single protein production (SPP) system......Page 201
12.3.5.3 Use of RNA chaperone activity of CspA homologues......Page 202
12.4.1 Caseinolytic proteases......Page 203
12.4.2.2 Biotechnological potential......Page 204
12.5.1 Desaturases from cyanobacteria......Page 205
12.5.3 Biotechnological potential......Page 206
12.6.1 Biotechnological potential......Page 207
References......Page 208
13.1 Introduction......Page 213
13.2 The low temperature challenge......Page 214
13.3 Activity......Page 216
13.4.1 Reversible and irreversible unfolding......Page 219
13.5 Flexibility......Page 222
13.6 Structural adaptations......Page 224
13.7 Conclusions......Page 225
References......Page 226
14.1 Introduction......Page 230
14.2.1 Cryoprotectants of low molecular mass......Page 232
14.2.2 Cryoprotective proteins and cold chaperones from ice-nucleating bacteria......Page 234
14.3.1 Structure and function of ice-nucleation proteins......Page 235
14.3.2 Structure and function of anti-nucleating proteins......Page 239
14.3.3 Structure and function of bacterial antifreeze protein......Page 241
References......Page 244
15.1 Introduction......Page 248
15.1.2.1 General occurrence......Page 249
15.1.2.2 Cold-specific occurrence......Page 250
15.2.1.1 Intracellular and extracellular cryoprotection......Page 251
15.2.1.2 Multi-phase dynamics......Page 252
15.2.2.2 Supercooling and ice nucleation......Page 253
15.2.2.4 Dehydration......Page 254
15.2.3.1 Diffusion......Page 255
15.2.3.3 Solute segregation and selectivity......Page 257
15.2.3.5 Secondary ice nucleation and recrystallization......Page 258
15.2.3.6 Glass transition......Page 259
15.3 Conclusions......Page 260
References......Page 261
16.1 Introduction......Page 266
16.2.1 Protein amino acid composition and link with evolution......Page 271
16.2.2 Membrane fluidity......Page 273
16.2.3 Nutrient and energy reserves......Page 275
16.2.4 Compatible solutes......Page 276
16.2.5 Extracellular compounds......Page 278
16.3 The environment molds the genomic traits of organisms......Page 280
References......Page 282
17.1 Introduction......Page 286
17.2.1 Light......Page 287
17.2.2 Seawater......Page 289
17.2.3 Sea ice......Page 290
17.2.5 Rock surfaces......Page 296
17.2.6 Permanently ice covered lakes......Page 297
17.3.1 Diatoms (Bacillariophyceae)......Page 298
17.3.1.1 Functional genomics......Page 299
17.3.1.2 Molecular physiology......Page 302
17.3.2 Green algae (Chlorophyceae)......Page 304
17.3.2.1 Molecular physiology......Page 305
17.4 Conclusions......Page 308
References......Page 309
18.1 Introduction......Page 314
18.2 Tapping into hidden diversity......Page 315
18.3.1 Functional screening......Page 316
18.3.2 Sequence-based screening......Page 318
18.4.1 Assessing phylogenetic diversity and population structure......Page 319
18.4.3 Assessing metabolic pathways, ecology and evolution......Page 320
18.4.4 Sequencing whole genomes of communities......Page 321
18.5 Metagenomics of low temperature environments......Page 322
18.6.1 Comparative community genomics and pyrosequencing......Page 324
18.7 Dealing with high volumes of metagenomic sequencing......Page 326
18.8 Conclusions......Page 327
References......Page 328
19.1 Introduction......Page 334
19.2.1 Identification of cold-inducible proteins without whole genome sequence information......Page 335
19.2.3 Bacillus psychrosaccharolyticus......Page 336
19.2.4 Psychrobacter cryohalolentis K5......Page 341
19.2.5 Psychrobacter articus 273-4......Page 342
19.2.6 Shewanella livingstonensis Ac10......Page 343
References......Page 344
20.1 Introduction......Page 346
20.1.1 Mining the cold biosphere for biomolecules of biotechnological interest......Page 347
20.1.2 Cold-adapted enzymes......Page 348
20.2 Industrial enzymes: history and recent advances......Page 351
20.3 Industrial potential of cold-adapted enzymes......Page 352
20.3.2 Food, pharmaceutical and cosmetic industries......Page 353
20.3.3 Biofuels......Page 355
20.3.4 Molecular biology......Page 356
20.3.5 Enzyme nanobiotechnology......Page 357
References......Page 359
21.1 Introduction......Page 363
21.2.1 The psychrophilic host: Pseudoalteromonas haloplanktis TAC125......Page 365
21.2.2 The psychrophilic gene-expression vector......Page 366
21.2.2.1 Psychrophilic origin of replication......Page 367
21.2.2.2 Psychrophilic transcription initiation signals......Page 368
21.2.3 Molecular signals for protein addressing......Page 369
21.3.1 P. haloplanktis TAE79 b-galactosidase and Saccharomyces cerevisiae a-glucosidase production......Page 371
21.3.2 hb-NGF Production......Page 372
21.3.3 Secretion of several heterologous proteins......Page 373
21.4 Conclusions......Page 374
References......Page 375
22.1 Introduction......Page 378
22.2 Extrolites from cold-adapted fungi......Page 379
22.3 Secondary metabolites from cold-adapted fungi......Page 380
References......Page 381
23.1 Introduction......Page 385
23.2.1 Petroleum characteristics and weathering......Page 386
23.2.3 Sediment processes......Page 387
23.3.1.1 Arctic and Antarctic seawater, sediments and sea ice......Page 388
23.3.1.2 Deep water......Page 389
23.3.2.1 Aerobic degradation......Page 390
23.3.2.3 Microbial metabolism in sea ice......Page 391
23.4.1 Biodegradation rates......Page 392
23.5 Oil bioremediation in cold marine environments......Page 393
23.5.1.1 Shoreline sediments......Page 394
23.5.1.2 Seawater......Page 395
23.5.1.3 Sea ice......Page 396
23.6 Conclusions......Page 397
References......Page 398
24.1 Introduction......Page 404
24.2 Physicochemical properties of chlorophenols......Page 405
24.4 The Kärkölä case: long-term monitoring of the chlorophenol-contaminated groundwater and on site bioremediation......Page 406
24.5 In situ bioremediation of groundwater polychlorophenols......Page 408
24.6.1 Diversity of culturable polychlorophenol degraders......Page 409
24.6.2 Natural evolution of polychlorophenol degradation......Page 411
24.7 Microbial responses to low temperatures......Page 412
24.8 Microbial adaptation to oligotrophic conditions......Page 413
24.9 Biodegradation of polychlorophenols under microaerophilic conditions......Page 414
24.10 Competition for oxygen by iron and chlorophenol oxidation......Page 415
24.12 Conclusions......Page 416
References......Page 417
25.1 Introduction......Page 423
25.2 Biological oxidation of iron and sulfur at low temperatures......Page 425
25.3 Biological reduction of sulfate at low temperatures......Page 428
25.4.1 Constructed wetlands......Page 432
25.4.2 In situ remediation......Page 433
25.5.1 Application of Fe2+ oxidation......Page 438
25.5.2 Application of sulfate reduction......Page 439
25.6 Conclusions......Page 443
References......Page 444
Index......Page 449