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

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 1