Microbial Life of the Deep Biosphere (eBook)

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

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

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Book Review:

Microbial Life of the Deep Biosphere (2014) edited by Jens Kallmeyer and Dirk Wagner, Walter de Gruyer GmbH, Berlin/Boston

Thomas L. Kieft
New Mexico Tech

Subseafloor sediments and crust as well as the groundwater environments beneath the continents comprise something of a last frontier among the Earth's ecosystems in terms of scientific exploration and discovery. Early reports of microbes in deep Earth environments, e.g., John Parkes' meticulous microscopic counts of microbes in subseafloor sediments, were often met with skepticism that these microbes were merely drilling contaminants or dead cells; but now, happily, deep life studies have matured such that the existence of the deep biosphere is widely accepted. The Ocean Drilling Program and its successors, currently the International Ocean Discovery Program (IODP), have devoted considerable resources to biological aspects of subseafloor environs; the International Continental Scientific Drilling Program and various other initiatives, including probes of the deep Earth via mines and underground research labs, have made similar progress in exploring and understanding the highly varied on-shore groundwater environments. Expanded drilling opportunities and biotechnological advances have enabled clear demonstrations that deep microbes are phylogenetically and metabolically diverse and that they're alive and well and actively contribute to biogeochemical cycling. Given the recent progress in deep life studies, the publication of Microbial Life of the Deep Biosphere, edited by Jens Kallmeyer and Dirk Wagner, as the first volume in a series on Life in Extreme Environments, is extremely timely. The book can serve as an introduction to the deep biosphere for neophytes or as an update on the latest findings for those who are already knowledgeable in the field.
The book opens with an update on the past 10 years of IODP seafloor sediment studies by Parkes and colleagues and continues to other subsurface habitats with chapters on basaltic ocean crust by Jennifer Biddle and coauthors and continental hard rock environments by Karsten Pedersen. Parkes' more recent counts continue to show a logarithmic decrease in microbial abundance with depth; he and coauthors also review recent findings of a dominant core group of microbial taxa that are widespread in marine sediments. As a whole, the book focuses more attention on marine than continental systems, but Pedersen's chapter and also later chapters on petroleum reservoirs by Bernard Ollivier and coauthors, on carbon sequestration and geothermal energy development by Masal Alawi, and on Mars (and Earth analogs) by Charles Cockell give a good picture of the geologically and microbiologically varied subterranean habitats. Specialized groups of microbes to which chapters are devoted are the Archaea (Andreas Teske) and fungi, which some still consider to be artifacts or merely buried, dead cells, but Virginia Edgecomb and coauthors present strong arguments for their being indigenous and active, similar to their prokaryotic counterparts. There's growing evidence for the importance of viruses as controllers of prokaryotic biomass and as vectors for gene transfer (touched on briefly by Pedersen), so this reviewer would like to have seen a chapter devoted to them. Technical issues addressed in separate chapters include the challenges of cultivating subsurface microbes, a comparison of methods for quantifying subsurface microbes by Karen Lloyd, and nanoSIMS (secondary ion mass spectrometry) and other approaches for querying the activities of single cells, by Yukio Marono and coauthors. As Morono points out, the potential for combining these methods, e.g., single cell genomics with nanoSIMS is especially exciting. Final chapters are devoted to quantitative, ecosystem-level issues of basin-scale modeling of microbial processes in petroleum hydrocarbon reservoirs (Rolando di Primio), estimating rates of catabolism of various functional groups in the subsurface based on Gibbs free energy calculations (Doug LaRowe and Jan Amend), and quantidying rates of metabolism and carbon turnover in subsurface sediments where the available energy may only barely meet maintenance requirements (Hans Røy).
In summary, Kallmeyer and Wagner recruited active researchers, each with expertise in an important area of subsurface microbiology, to write richly referenced overview chapters. Each details the current state of knowledge and most also identify major gaps in our understanding and directions for future research. Microbial Life of the Deep Biosphere is a fine addition to a university library or the personal library of a geologist, biologist, naturalist, or any combination thereof.