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E-raamat: Microbial Life of the Deep Biosphere

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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.
Preface v
Contributing authors xv
1 Studies on prokaryotic populations and processes in subseafloor sediments -- an update
1(28)
R. John Parkes
Henrik Sass
Barry Cragg
Gordon Webster
Erwan Roussel
Andrew Weightman
1.1 New sites investigated
1(14)
1.1.1 Southeast Atlantic sector of the Southern Ocean (Leg 177)
1(3)
1.1.2 Woodlark Basin, near Papua New Guinea, Pacific Ocean (Leg 180)
4(2)
1.1.3 Leg 185, Site 1149 in the Izu-Bonin Trench, Western Equatorial Pacific
6(1)
1.1.4 Nankai Trough (Leg 190), subduction zone/accretionary prism, Pacific Ocean
7(3)
1.1.5 Eastern Equatorial Pacific and Peru Margin Sites 1225--1231 (Leg 201)
10(2)
1.1.6 Newfoundland Margin (Leg 210)
12(1)
1.1.7 Carbonate mound (IODP Expedition 307)
13(2)
1.2 High-pressure cultivation -- DeeplsoBUG, gas hydrate sediments
15(3)
1.3 Subseafloor biosphere simulation experiments
18(2)
1.4 Conclusions
20(9)
2 Life in the Oceanic Crust
29(34)
Jennifer F. Biddle
Sean P. Jungbluth
Mark A. Lever
Michael S. Rappe
2.1 Introduction
29(1)
2.2 Sampling tools
30(6)
2.2.1 Tools for accessing the deep basement biosphere
32(4)
2.3 Contamination
36(2)
2.3.1 Contamination induced during drilling
36(2)
2.3.2 Contamination during fluid sampling
38(1)
2.4 Direct evidence for life in the deep ocean crust
38(13)
2.4.1 Textural alterations
39(1)
2.4.2 Geochemical evidence from fluids
40(1)
2.4.3 Geochemical evidence from rocks
41(4)
2.4.4 Genetic surveys
45(6)
2.5 Future directions
51(12)
3 Microbial life in terrestrial hard rock environments
63(20)
Karsten Pedersen
3.1 Hard rock aquifers from the perspective of microorganisms
63(1)
3.2 Windows into the terrestrial hard rock biosphere
64(7)
3.2.1 Sampling methods for microbes in hard rock aquifers
64(1)
3.2.2 Yesterday marine -- terrestrial today
65(1)
3.2.3 Basalts and ophiolites
66(2)
3.2.4 Granites
68(2)
3.2.5 Hard rocks of varying origin
70(1)
3.3 Energy from where?
71(2)
3.3.1 Deep reduced gases
72(1)
3.4 Activity
73(3)
3.4.1 Stable isotopes
73(1)
3.4.2 Geochemical indicators
74(1)
3.4.3 In vitro activity
74(1)
3.4.4 In situ activity
74(2)
3.4.5 Phages may control activity rates
76(1)
3.5 What's next in the exploration of microbial life in deep hard rock aquifers?
76(7)
4 Technological state of the art and challenges
83(18)
Laurent Toffin
Karine Alain
4.1 Basic concepts and difficulties inherent to the cultivation of subseafloor prokaryotes
83(8)
4.2 Microbial growth monitoring, method detection limits and innovative cultivation methods
91(1)
4.3 Challenges and research needs (instrumental, methodological and logistics needs)
92(9)
5 Detecting slow metabolism in the subseafloor: analysis of single cells using NanoSIMS
101(20)
Yuki Morono
Motoo Ito
Fumio Inagaki
5.1 Introduction
101(1)
5.2 Overview of ion imaging with a NanoSIMS ion microprobe
102(3)
5.3 Detecting slow metabolism: bulk to single cells
105(5)
5.3.1 Bulk measurement of subseafloor microbial activity using radiotracers
105(1)
5.3.2 Observing radioactive substrate incorporation at the cellular level: microautoradiography
106(1)
5.3.3 Quantitative analysis of stable isotope incorporation using NanoSIMS
107(3)
5.4 Bridging identification and functional analysis of microbes using elemental labeling
110(2)
5.5 Critical step for successful NanoSIMS analysis: sample preparation
112(2)
5.6 Future directions
114(7)
6 Quantifying microbes in the marine subseafloor: some notes of caution
121(22)
Karen G. Lloyd
6.1 Introduction
121(3)
6.2 Quantification of specific microbial groups in marine sediments
124(4)
6.3 Assessment of quantitative methods in marine sediments: the Leg 201 Peru Margin example
128(4)
6.4 Global meta-analysis of FISH, CARD-FISH and qPCR quantifications of bacteria and archaea
132(2)
6.5 Future outlook
134(9)
7 Archaea in deep marine subsurface sediments
143(18)
Andreas Teske
7.1 Introduction
143(1)
7.2 Archaeal Ribosomal RNA phylogeny
143(1)
7.3 Marine subsurface Archaea
144(5)
7.4 Archaeal habitat preferences in the subsurface
149(3)
7.5 Methanogenic and methane-oxidizing archaea
152(2)
7.6 Archaeal abundance and ecosystem significance in the subsurface
154(7)
8 Petroleum: from formation to microbiology
161(26)
Bernard Ollivier
Jean Borgomano
Philippe Oger
8.1 Introduction
161(1)
8.2 Petroleum formation
161(5)
8.2.1 Petroleum system
163(3)
8.3 Petroleum microbiology
166(13)
8.3.1 The sulfate-reducing prokaryotes
168(3)
8.3.2 The methanoarchaea
171(3)
8.3.3 The fermentative prokaryotes
174(3)
8.3.4 Other metabolic lifestyle bacteria
177(2)
8.4 Conclusion
179(8)
9 Fungi in the marine subsurface
187(16)
Virginia Edgcomb
William Orsi
Jennifer F. Biddle
9.1 Introduction
187(1)
9.2 The concept of marine fungi
187(2)
9.3 Fungi in marine near-surface sediments in the deep sea
189(1)
9.4 Fungi in the deep subsurface
190(7)
9.4.1 Initial whole community and prokaryote-focused studies of the marine subsurface yielding information on eukaryotes
190(1)
9.4.2 Eukaryote-focused studies yielding information on fungi in the deep subsurface
191(6)
9.5 How deep do fungi go in the subsurface?
197(1)
9.6 Summary
197(6)
10 Microbes in geo-engineered systems: geomicrobiological aspects of CCS and Geothermal Energy Generation
203(22)
Mashal Alawi
10.1 Introduction
203(3)
10.1.1 Carbon Capture and Storage (CCS)
204(1)
10.1.2 Geothermal energy and aquifer energy storage
205(1)
10.2 Microbial diversity in geo-engineered reservoirs
206(2)
10.3 Interactions between microbes and geo-engineered systems
208(8)
10.3.1 General considerations
208(1)
10.3.2 Microbial processes in the deep biosphere potentially affected by CCS
209(2)
10.3.3 Examples from a CCS pilot site, CO2 degasing sites and laboratory experiments
211(2)
10.3.4 Impact of microbially-driven processes on CO2 trapping mechanisms
213(1)
10.3.5 Impact of microbially-driven processes on CCS facilities
214(1)
10.3.6 Impact of microbially-driven processes on geothermal energy plants
214(2)
10.4 Methods to analyze the interaction between geo-engineered systems and the deep biosphere
216(9)
10.4.1 Sampling of reservoir fluids and rock cores
216(1)
10.4.2 Methods to analyze microbes in geo-engineered systems
216(9)
11 The subsurface habitability of terrestrial rocky planets: Mars
225(36)
Charles S. Cockell
11.1 Introduction
225(1)
11.2 The subsurface of Mars -- our current knowledge
226(7)
11.3 Martian subsurface habitability, past and present
233(9)
11.3.1 Vital elements (C, H, N, 0, P, S)
233(1)
11.3.2 Other micronutrients and trace elements
234(1)
11.3.3 Liquid water through time
235(3)
11.3.4 Redox couples
238(1)
11.3.5 Radiation
239(1)
11.3.6 Other physical and environmental factors
239(1)
11.3.7 Acidity
240(2)
11.4 Impact craters and deep subsurface habitability
242(1)
11.5 The near-subsurface habitability of present and recent Mars -- an empirical example
243(2)
11.6 Uninhabited, but habitable subsurface environments?
245(2)
11.7 Ten testable hypotheses on habitability of the Martian subsurface
247(3)
11.8 Sampling the subsurface of Mars
250(1)
11.9 Conclusion
251(10)
12 Assessing biosphere-geosphere interactions over geologic time scales: insights from Basin Modeling
261(18)
Rolando di Primio
12.1 Introduction
261(1)
12.2 Basin Modeling
262(2)
12.3 Modeling processes at the deep bio-geo interface
264(10)
12.3.1 Feeding the deep biosphere (biogenic gas)
264(3)
12.3.2 Petroleum biodegradation
267(7)
12.4 Modeling processes at the shallow bio-geo interface
274(1)
12.5 Conclusions
275(4)
13 Energetic constraints on life in marine deep sediments
279(24)
Doug LaRowe
Jan Amend
13.1 Introduction
279(1)
13.2 Previous work
280(1)
13.3 Study site overview
280(2)
13.3.1 Juan de Fuca (JdF)
281(1)
13.3.2 Peru Margin (PM)
281(1)
13.3.3 South Pacific Gyre (SPG)
282(1)
13.4 Overview of catabolic potential
282(6)
13.5 Comparing deep biospheres
288(2)
13.6 Electron acceptor utilization
290(2)
13.7 Energy demand
292(1)
13.8 Concluding remarks
293(1)
13.9 Computational methods
293(10)
13.9.1 Thermodynamic properties of anhydrous ferrihydrite and pyrolusite
294(9)
14 Experimental assessment of community metabolism in the subsurface
303(16)
Hans Røy
14.1 Introduction
303(3)
14.1.1 The energy source
303(1)
14.1.2 The carbon budget
304(1)
14.1.3 Distribution vertical of microbial metabolism the sediment pile
305(1)
14.2 Quantifiable metabolic processes
306(9)
14.2.1 Reaction diffusion modeling and mass balances
307(5)
14.2.2 Measurements of rates of energy metabolism with exotic isotopes
312(3)
14.3 Summary
315(4)
Index 319
Jens Kallmeyer, German Research Center for Geosciences; Dirk Wagner, German Research Center for Geosciences;
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