Kallmeyer / Wagner Microbial Life of the Deep Biosphere

1. Auflage 2014
ISBN: 978-3-11-030013-0
Verlag: De Gruyter
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, Band 1, 342 Seiten

Reihe: Life in Extreme Environments

Over the last two decades, exploration of the deep subsurface biosphere has developed into a major research area. New findings constantly challenge our concepts of global biogeochemical cycles and the ultimate limits to life. In order to explain our observations from deep subsurface ecosystems it is necessary to develop truly interdisciplinary approaches, ranging from microbiology and geochemistry to physics and modeling. This book aims to bring together a wide variety of topics, covering the broad range of issues that are associated with deep biosphere exploration. Not only does the book present case studies of selected projects, but also treats questions arising from our current knowledge. Despite nearly two decades of research, there are still many boundaries to exploration caused by technical limitations and one section of the book is devoted to these technical challenges and the latest developments in this field. This volume will be of high interest to biologists, chemists and earth scientists all working on the deep biosphere.

Zielgruppe

Research scientists and graduate students in microbiology, geomircobiology, ecology, environmental sciences

Autoren/Hrsg.

Kallmeyer, Jens

Wagner, Dirk

Weitere Mitwirkende

Alain, Karine

Alawi, Mashal

Amend, Jan

Biddle, Jennifer

Borgomano, Jean

Cockell, Charles

Cragg, Barry

DiPrimio, Rolando

Edgcomb, Virginia

Inagaki, Fumio

Ito, Motoo

Jungbluth, Sean

LaRowe, Douglas

Lever, Mark

Lloyd, Karen G.

Morono, Yuki

Oger, Philippe

Ollivier, Bernard

Orsi, William

Parkes, R. John

Pedersen, Karsten

Rappe, Michael

Roussel, Erwan

Røy, Hans

Sass, Henrik

Teske, Andreas P.

Toffin, Laurent

Webster, Gordon

Weightman, Andrew

Fachgebiete

• Naturwissenschaften Biowissenschaften Biowissenschaften Ökologie
• Naturwissenschaften Biowissenschaften Bakteriologie
• Naturwissenschaften Biowissenschaften Mikrobiologie
• Geowissenschaften Umweltwissenschaften Angewandte Ökologie

Inhaltsverzeichnis

1;Preface;5
2;Contributing authors;15
3;1 Studies on prokaryotic populations and processes in subseafloor sediments-an update;19
3.1;1.1 New sites investigated;19
3.1.1;1.1.1 Southeast Atlantic sector of the Southern Ocean (Leg 177);19
3.1.2;1.1.2 Woodlark Basin, near Papua New Guinea, Pacific Ocean (Leg 180);22
3.1.3;1.1.3 Leg 185, Site 1149 in the Izu-Bonin Trench Western Equatorial Pacific;24
3.1.4;1.1.4 Nankai Trough (Leg 190), subduction zone/accretionary prism, Pacific Ocean;25
3.1.5;1.1.5 Eastern Equatorial Pacific and Peru Margin Sites 1225–1231 (Leg 201);28
3.1.6;1.1.6 Newfoundland Margin (Leg 210);30
3.1.7;1.1.7 Carbonate mound (IODP Expedition 307);31
3.2;1.2 High-pressure cultivation – DeepIsoBUG, gas hydrate sediments;33
3.3;1.3 Subseafloor biosphere simulation experiments;36
3.4;1.4 Conclusions;38
4;2 LifeintheOceanicCrust;47
4.1;2.1 Introduction;47
4.2;2.2 Sampling tools;48
4.2.1;2.2.1 Tools for accessing the deep basement biosphere;50
4.3;2.3 Contamination;54
4.3.1;2.3.1 Contamination induced during drilling;54
4.3.2;2.3.2 Contamination during fluid sampling;56
4.4;2.4 Direct evidence for life in the deep ocean crust;56
4.4.1;2.4.1 Textural alterations;57
4.4.2;2.4.2 Geochemical evidence from fluids;58
4.4.3;2.4.3 Geochemical evidence from rocks;59
4.4.4;2.4.4 Genetic surveys;63
4.5;2.5 Future directions;69
5;3 Microbial life in terrestrial hard rock environments;81
5.1;3.1 Hard rock aquifers from the perspective of microorganisms;81
5.2;3.2 Windows into the terrestrial hard rock biosphere;82
5.2.1;3.2.1 Sampling methods for microbes in hard rock aquifers;82
5.2.2;3.2.2 Yesterday marine – terrestrial today;83
5.2.3;3.2.3 Basalts and ophiolites;84
5.2.4;3.2.4 Granites;86
5.2.5;3.2.5 Hard rocks of varying origin;88
5.3;3.3 Energy from where?;89
5.3.1;3.3.1 Deep reduced gases;90
5.4;3.4 Activity;91
5.4.1;3.4.1 Stable isotopes;91
5.4.2;3.4.2 Geochemical indicators;92
5.4.3;3.4.3 In vitro activity;92
5.4.4;3.4.4 In situ activity;92
5.4.5;3.4.5 Phages may control activity rates;94
5.5;3.5 What’s next in the exploration of microbial life in deep hard rock aquifers?;94
6;4 Technological state of the art and challenges;101
6.1;4.1 Basic concepts and difficulties inherent to the cultivation of subseafloor prokaryotes;101
6.2;4.2 Microbial growth monitoring,method detection limits and innovative cultivation methods;109
6.3;4.3 Challenges and research needs (instrumental, methodological and logistics needs);110
7;5 Detecting slow metabolism in the subseafloor: analysis of single cells using NanoSIMS;119
7.1;5.1 Introduction;119
7.2;5.2 Overview of ion imaging with a NanoSIMS ion microprobe;120
7.3;5.3 Detecting slow metabolism: bulk to single cells;123
7.3.1;5.3.1 Bulk measurement of subseafloor microbial activity using radiotracers;123
7.3.2;5.3.2 Observing radioactive substrate incorporation at the cellular level: microautoradiography;124
7.3.3;5.3.3 Quantitative analysis of stable isotope incorporation using NanoSIMS;125
8;4 Bridging identification and functional analysis of microbes using elemental labeling;128
8.1;5.5 Critical step for successful NanoSIMS analysis: sample preparation;130
8.2;5.6 Future directions;132
9;6 Quantifying microbes in the marine subseafloor: some notes of caution;139
9.1;6.1 Introduction;139
9.2;6.2 Quantification of specific microbial groups in marine sediments;142
9.3;6.3 Assessment of quantitative methods in marine sediments: the Leg 201 Peru Margin example;146
9.4;6.4 Global meta-analysis of FISH, CARD-FISH and qPCR quantifications of bacteria and archaea;150
9.5;6.5 Future outlook;152
10;7 Archaea in deep marine subsurface sediments;161
10.1;7.1 Introduction;161
10.2;7.2 Archaeal Ribosomal RNA phylogeny;161
10.3;7.3 Marine subsurface Archaea;162
10.4;7.4 Archaeal habitat preferences in the subsurface;167
10.5;7.5 Methanogenic and methane-oxidizing archaea;170
10.6;7.6 Archaeal abundance and ecosystem significance in the subsurface;172
11;8 Petroleum: from formation to microbiology;179
11.1;8.1 Introduction;179
11.2;8.2 Petroleum formation;179
11.2.1;8.2.1 Petroleum system;181
11.3;8.3 Petroleum microbiology;184
11.3.1;8.3.1 The sulfate-reducing prokaryotes;186
11.3.2;8.3.2 The methanoarchaea;189
11.3.3;8.3.3 The fermentative prokaryotes;192
11.3.4;8.3.4 Other metabolic lifestyle bacteria;195
11.4;8.4 Conclusion;197
12;9 Fungi in the marine subsurface;205
12.1;9.1 Introduction;205
12.2;9.2 The concept of marine fungi;205
12.3;9.3 Fungi in marine near-surface sediments in the deep sea;207
12.4;9.4 Fungi in the deep subsurface;208
12.4.1;9.4.1 Initial whole community and prokaryote-focused studies of the marine subsurface yielding information on eukaryotes;208
12.4.2;9.4.2 Eukaryote-focused studies yielding information on fungi in the deep subsurface;209
12.5;9.5 How deep do fungi go in the subsurface?;215
12.6;9.6 Summary;215
13;10 Microbes in geo-engineered systems: geomicrobiological aspects of CCS and Geothermal Energy Generation;221
13.1;10.1 Introduction;221
13.1.1;10.1.1 Carbon Capture and Storage (CCS);222
13.1.2;10.1.2 Geothermal energy and aquifer energy storage;223
13.2;10.2 Microbial diversity in geo-engineered reservoirs;224
13.3;10.3 Interactions between microbes and geo-engineered systems;226
13.3.1;10.3.1 General considerations;226
13.3.2;10.3.2 Microbial processes in the deep biosphere potentially affected by CCS;227
13.3.3;10.3.3 Examples from a CCS pilot site, CO2 degasing sites and laboratory experiments;229
13.3.4;10.3.4 Impact of microbially-driven processes on CO2 trapping mechanisms;231
13.3.5;10.3.5 Impact of microbially-driven processes on CCS facilities;232
13.3.6;10.3.6 Impact of microbially-driven processes on geothermal energy plants;232
13.4;10.4 Methods to analyze the interaction between geo-engineered systems and the deep biosphere;234
13.4.1;10.4.1 Sampling of reservoir fluids and rock cores;234
13.4.2;10.4.2 Methods to analyze microbes in geo-engineered systems;234
14;11 The subsurface habitability of terrestrial rocky planets: Mars;243
14.1;11.1 Introduction;243
14.2;11.2 The subsurface of Mars – our current knowledge;244
14.3;11.3 Martian subsurface habitability, past and present;251
14.3.1;11.3.1 Vital elements (C, H, N, O, P, S);251
14.3.2;11.3.2 Other micronutrients and trace elements;252
14.3.3;11.3.3 Liquid water through time;253
14.3.4;11.3.4 Redox couples;256
14.3.5;11.3.5 Radiation;257
14.3.6;11.3.6 Other physical and environmental factors;257
14.3.7;11.3.7 Acidity;258
14.4;11.4 Impact craters and deep subsurface habitability;260
14.5;11.5 The near-subsurface habitability of present and recent Mars – an empirical example;261
14.6;11.6 Uninhabited, but habitable subsurface environments?;263
14.7;11.7 Ten testable hypotheses on habitability of the Martian subsurface;265
14.8;11.8 Sampling the subsurface of Mars;268
14.9;11.9 Conclusion;269
15;12 Assessing biosphere-geosphere interactions over geologic time scales: insights from Basin Modeling;279
15.1;12.1 Introduction;279
15.2;12.2 Basin Modeling;280
15.3;12.3 Modeling processes at the deep bio-geo interface;282
15.3.1;12.3.1 Feeding the deep biosphere (biogenic gas);282
15.3.2;12.3.2 Petroleum biodegradation;285
15.4;12.4 Modeling processes at the shallow bio-geo interface;292
15.5;12.5 Conclusions;293
16;13 Energetic constraints on life in marine deep sediments;297
16.1;13.1 Introduction;297
16.2;13.2 Previous work;298
16.3;13.3 Study site overview;298
16.3.1;13.3.1 Juan de Fuca (JdF);299
16.3.2;13.3.2 Peru Margin (PM);299
16.3.3;13.3.3 South Pacific Gyre (SPG);300
16.4;13.4 Overview of catabolic potential;300
16.5;13.5 Comparing deep biospheres;306
16.6;13.6 Electron acceptor utilization;308
16.7;13.7 Energy demand;310
16.8;13.8 Concluding remarks;311
16.9;13.9 Computational methods;311
16.9.1;13.9.1 Thermodynamic properties of anhydrous ferrihydrite and pyrolusite;312
17;14 Experimental assessment of community metabolism in the subsurface;321
17.1;14.1 Introduction;321
17.1.1;14.1.1 The energy source;321
17.1.2;14.1.2 The carbon budget;322
17.1.3;14.1.3 Distribution vertical of microbial metabolism the sediment pile;323
17.2;14.2 Quantifiable metabolic processes;324
17.2.1;14.2.1 Reaction diffusion modeling and mass balances;325
17.2.2;14.2.2 Measurements of rates of energy metabolism with exotic isotopes;330
17.3;14.3 Summary;333
18;Index;337

Über Autor(innen)

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