Microbial Life of the Deep Biosphere (eBook)

Jens Kallmeyer, Dirk Wagner (Herausgeber)

eBook Download: PDF | EPUB

2014 | 1. Auflage
342 Seiten
Walter de Gruyter GmbH & Co.KG (Verlag)
978-3-11-030013-0 (ISBN)

Infos

this book brings together a variety of topics, covering the broad range of issues that are associated with deep biosphere exploration. In order to explain our observations from deep subsurface ecosystems it is necessary to develop interdisciplinary approaches, ranging from microbiology and geochemistry to physics and modeling. This volume will be of high interest to biologists, chemists and earth scientists all working on the deep biosphere.

Jens Kallmeyer, German Research Center for Geosciences; Dirk Wagner, German Research Center for Geosciences;

Inhalt

Preface 5
Contributing authors 15
1 Studies on prokaryotic populations and processes in subseafloor sediments-an update 19
1.1 New sites investigated 19
1.1.1 Southeast Atlantic sector of the Southern Ocean (Leg 177) 19
1.1.2 Woodlark Basin, near Papua New Guinea, Pacific Ocean (Leg 180) 22
1.1.3 Leg 185, Site 1149 in the Izu-Bonin Trench Western Equatorial Pacific 24
1.1.4 Nankai Trough (Leg 190), subduction zone/accretionary prism, Pacific Ocean 25
1.1.5 Eastern Equatorial Pacific and Peru Margin Sites 1225–1231 (Leg 201) 28
1.1.6 Newfoundland Margin (Leg 210) 30
1.1.7 Carbonate mound (IODP Expedition 307) 31
1.2 High-pressure cultivation – DeepIsoBUG, gas hydrate sediments 33
1.3 Subseafloor biosphere simulation experiments 36
1.4 Conclusions 38
2 LifeintheOceanicCrust 47
2.1 Introduction 47
2.2 Sampling tools 48
2.2.1 Tools for accessing the deep basement biosphere 50
2.3 Contamination 54
2.3.1 Contamination induced during drilling 54
2.3.2 Contamination during fluid sampling 56
2.4 Direct evidence for life in the deep ocean crust 56
2.4.1 Textural alterations 57
2.4.2 Geochemical evidence from fluids 58
2.4.3 Geochemical evidence from rocks 59
2.4.4 Genetic surveys 63
2.5 Future directions 69
3 Microbial life in terrestrial hard rock environments 81
3.1 Hard rock aquifers from the perspective of microorganisms 81
3.2 Windows into the terrestrial hard rock biosphere 82
3.2.1 Sampling methods for microbes in hard rock aquifers 82
3.2.2 Yesterday marine – terrestrial today 83
3.2.3 Basalts and ophiolites 84
3.2.4 Granites 86
3.2.5 Hard rocks of varying origin 88
3.3 Energy from where? 89
3.3.1 Deep reduced gases 90
3.4 Activity 91
3.4.1 Stable isotopes 91
3.4.2 Geochemical indicators 92
3.4.3 In vitro activity 92
3.4.4 In situ activity 92
3.4.5 Phages may control activity rates 94
3.5 What’s next in the exploration of microbial life in deep hard rock aquifers? 94
4 Technological state of the art and challenges 101
4.1 Basic concepts and difficulties inherent to the cultivation of subseafloor prokaryotes 101
4.2 Microbial growth monitoring,method detection limits and innovative cultivation methods 109
4.3 Challenges and research needs (instrumental, methodological and logistics needs) 110
5 Detecting slow metabolism in the subseafloor: analysis of single cells using NanoSIMS 119
5.1 Introduction 119
5.2 Overview of ion imaging with a NanoSIMS ion microprobe 120
5.3 Detecting slow metabolism: bulk to single cells 123
5.3.1 Bulk measurement of subseafloor microbial activity using radiotracers 123
5.3.2 Observing radioactive substrate incorporation at the cellular level: microautoradiography 124
5.3.3 Quantitative analysis of stable isotope incorporation using NanoSIMS 125
4 Bridging identification and functional analysis of microbes using elemental labeling 128
5.5 Critical step for successful NanoSIMS analysis: sample preparation 130
5.6 Future directions 132
6 Quantifying microbes in the marine subseafloor: some notes of caution 139
6.1 Introduction 139
6.2 Quantification of specific microbial groups in marine sediments 142
6.3 Assessment of quantitative methods in marine sediments: the Leg 201 Peru Margin example 146
6.4 Global meta-analysis of FISH, CARD-FISH and qPCR quantifications of bacteria and archaea 150
6.5 Future outlook 152
7 Archaea in deep marine subsurface sediments 161
7.1 Introduction 161
7.2 Archaeal Ribosomal RNA phylogeny 161
7.3 Marine subsurface Archaea 162
7.4 Archaeal habitat preferences in the subsurface 167
7.5 Methanogenic and methane-oxidizing archaea 170
7.6 Archaeal abundance and ecosystem significance in the subsurface 172
8 Petroleum: from formation to microbiology 179
8.1 Introduction 179
8.2 Petroleum formation 179
8.2.1 Petroleum system 181
8.3 Petroleum microbiology 184
8.3.1 The sulfate-reducing prokaryotes 186
8.3.2 The methanoarchaea 189
8.3.3 The fermentative prokaryotes 192
8.3.4 Other metabolic lifestyle bacteria 195
8.4 Conclusion 197
9 Fungi in the marine subsurface 205
9.1 Introduction 205
9.2 The concept of marine fungi 205
9.3 Fungi in marine near-surface sediments in the deep sea 207
9.4 Fungi in the deep subsurface 208
9.4.1 Initial whole community and prokaryote-focused studies of the marine subsurface yielding information on eukaryotes 208
9.4.2 Eukaryote-focused studies yielding information on fungi in the deep subsurface 209
9.5 How deep do fungi go in the subsurface? 215
9.6 Summary 215
10 Microbes in geo-engineered systems: geomicrobiological aspects of CCS and Geothermal Energy Generation 221
10.1 Introduction 221
10.1.1 Carbon Capture and Storage (CCS) 222
10.1.2 Geothermal energy and aquifer energy storage 223
10.2 Microbial diversity in geo-engineered reservoirs 224
10.3 Interactions between microbes and geo-engineered systems 226
10.3.1 General considerations 226
10.3.2 Microbial processes in the deep biosphere potentially affected by CCS 227
10.3.3 Examples from a CCS pilot site, CO2 degasing sites and laboratory experiments 229
10.3.4 Impact of microbially-driven processes on CO2 trapping mechanisms 231
10.3.5 Impact of microbially-driven processes on CCS facilities 232
10.3.6 Impact of microbially-driven processes on geothermal energy plants 232
10.4 Methods to analyze the interaction between geo-engineered systems and the deep biosphere 234
10.4.1 Sampling of reservoir fluids and rock cores 234
10.4.2 Methods to analyze microbes in geo-engineered systems 234
11 The subsurface habitability of terrestrial rocky planets: Mars 243
11.1 Introduction 243
11.2 The subsurface of Mars – our current knowledge 244
11.3 Martian subsurface habitability, past and present 251
11.3.1 Vital elements (C, H, N, O, P, S) 251
11.3.2 Other micronutrients and trace elements 252
11.3.3 Liquid water through time 253
11.3.4 Redox couples 256
11.3.5 Radiation 257
11.3.6 Other physical and environmental factors 257
11.3.7 Acidity 258
11.4 Impact craters and deep subsurface habitability 260
11.5 The near-subsurface habitability of present and recent Mars – an empirical example 261
11.6 Uninhabited, but habitable subsurface environments? 263
11.7 Ten testable hypotheses on habitability of the Martian subsurface 265
11.8 Sampling the subsurface of Mars 268
11.9 Conclusion 269
12 Assessing biosphere-geosphere interactions over geologic time scales: insights from Basin Modeling 279
12.1 Introduction 279
12.2 Basin Modeling 280
12.3 Modeling processes at the deep bio-geo interface 282
12.3.1 Feeding the deep biosphere (biogenic gas) 282
12.3.2 Petroleum biodegradation 285
12.4 Modeling processes at the shallow bio-geo interface 292
12.5 Conclusions 293
13 Energetic constraints on life in marine deep sediments 297
13.1 Introduction 297
13.2 Previous work 298
13.3 Study site overview 298
13.3.1 Juan de Fuca (JdF) 299
13.3.2 Peru Margin (PM) 299
13.3.3 South Pacific Gyre (SPG) 300
13.4 Overview of catabolic potential 300
13.5 Comparing deep biospheres 306
13.6 Electron acceptor utilization 308
13.7 Energy demand 310
13.8 Concluding remarks 311
13.9 Computational methods 311
13.9.1 Thermodynamic properties of anhydrous ferrihydrite and pyrolusite 312
14 Experimental assessment of community metabolism in the subsurface 321
14.1 Introduction 321
14.1.1 The energy source 321
14.1.2 The carbon budget 322
14.1.3 Distribution vertical of microbial metabolism the sediment pile 323
14.2 Quantifiable metabolic processes 324
14.2.1 Reaction diffusion modeling and mass balances 325
14.2.2 Measurements of rates of energy metabolism with exotic isotopes 330
14.3 Summary 333
Index 337

Produkt-Details

• Erscheint lt. Verlag: 1.4.2014
• Co-Autor: Karine Alain, Fumio Inagaki, Motoo Ito, Sean Jungbluth, Douglas LaRowe, Mark Lever, Karen G. Lloyd, Yuki Morono, Philippe Oger, Bernard Ollivier, William Orsi, Mashal Alawi, R. John Parkes, Karsten Pedersen, Michael Rappe, Erwan Roussel, Hans Roy, Henrik Sass, Andreas P. Teske, Laurent Toffin, Gordon Webster, Andrew Weightman, Jan Amend, Jennifer Biddle, Jean Borgomano, Charles Cockell, Barry Cragg, Rolando DiPrimio, Virginia Edgcomb
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Naturwissenschaften ► Biologie ► Ökologie / Naturschutz
• Themenwelt: Technik
• ISBN-10: 3-11-030013-3 / 3110300133
• ISBN-13: 978-3-11-030013-0 / 9783110300130