Microbial Life of the Deep Biosphere (Life in Extreme Environments, 1)

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

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.

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, Dirk Wagner (eds.). Includes Bibliographical References And Index.