دانلود کتاب Microbial Life of the Deep Biosphere

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Preface\nContributing authors\n1 Studies on prokaryotic populations and processes in subseafloor sediments-an update\n 1.1 New sites investigated\n 1.1.1 Southeast Atlantic sector of the Southern Ocean (Leg 177)\n 1.1.2 Woodlark Basin, near Papua New Guinea, Pacific Ocean (Leg 180)\n 1.1.3 Leg 185, Site 1149 in the Izu-Bonin Trench Western Equatorial Pacific\n 1.1.4 Nankai Trough (Leg 190), subduction zone/accretionary prism, Pacific Ocean\n 1.1.5 Eastern Equatorial Pacific and Peru Margin Sites 1225–1231 (Leg 201)\n 1.1.6 Newfoundland Margin (Leg 210)\n 1.1.7 Carbonate mound (IODP Expedition 307)\n 1.2 High-pressure cultivation – DeepIsoBUG, gas hydrate sediments\n 1.3 Subseafloor biosphere simulation experiments\n 1.4 Conclusions\n2 LifeintheOceanicCrust\n 2.1 Introduction\n 2.2 Sampling tools\n 2.2.1 Tools for accessing the deep basement biosphere\n 2.3 Contamination\n 2.3.1 Contamination induced during drilling\n 2.3.2 Contamination during fluid sampling\n 2.4 Direct evidence for life in the deep ocean crust\n 2.4.1 Textural alterations\n 2.4.2 Geochemical evidence from fluids\n 2.4.3 Geochemical evidence from rocks\n 2.4.4 Genetic surveys\n 2.5 Future directions\n3 Microbial life in terrestrial hard rock environments\n 3.1 Hard rock aquifers from the perspective of microorganisms\n 3.2 Windows into the terrestrial hard rock biosphere\n 3.2.1 Sampling methods for microbes in hard rock aquifers\n 3.2.2 Yesterday marine – terrestrial today\n 3.2.3 Basalts and ophiolites\n 3.2.4 Granites\n 3.2.5 Hard rocks of varying origin\n 3.3 Energy from where?\n 3.3.1 Deep reduced gases\n 3.4 Activity\n 3.4.1 Stable isotopes\n 3.4.2 Geochemical indicators\n 3.4.3 In vitro activity\n 3.4.4 In situ activity\n 3.4.5 Phages may control activity rates\n 3.5 What’s next in the exploration of microbial life in deep hard rock aquifers?\n4 Technological state of the art and challenges\n 4.1 Basic concepts and difficulties inherent to the cultivation of subseafloor prokaryotes\n 4.2 Microbial growth monitoring,method detection limits and innovative cultivation methods\n 4.3 Challenges and research needs (instrumental, methodological and logistics needs)\n5 Detecting slow metabolism in the subseafloor: analysis of single cells using NanoSIMS\n 5.1 Introduction\n 5.2 Overview of ion imaging with a NanoSIMS ion microprobe\n 5.3 Detecting slow metabolism: bulk to single cells\n 5.3.1 Bulk measurement of subseafloor microbial activity using radiotracers\n 5.3.2 Observing radioactive substrate incorporation at the cellular level: microautoradiography\n 5.3.3 Quantitative analysis of stable isotope incorporation using NanoSIMS\n4 Bridging identification and functional analysis of microbes using elemental labeling\n 5.5 Critical step for successful NanoSIMS analysis: sample preparation\n 5.6 Future directions\n6 Quantifying microbes in the marine subseafloor: some notes of caution\n 6.1 Introduction\n 6.2 Quantification of specific microbial groups in marine sediments\n 6.3 Assessment of quantitative methods in marine sediments: the Leg 201 Peru Margin example\n 6.4 Global meta-analysis of FISH, CARD-FISH and qPCR quantifications of bacteria and archaea\n 6.5 Future outlook\n7 Archaea in deep marine subsurface sediments\n 7.1 Introduction\n 7.2 Archaeal Ribosomal RNA phylogeny\n 7.3 Marine subsurface Archaea\n 7.4 Archaeal habitat preferences in the subsurface\n 7.5 Methanogenic and methane-oxidizing archaea\n 7.6 Archaeal abundance and ecosystem significance in the subsurface\n8 Petroleum: from formation to microbiology\n 8.1 Introduction\n 8.2 Petroleum formation\n 8.2.1 Petroleum system\n 8.3 Petroleum microbiology\n 8.3.1 The sulfate-reducing prokaryotes\n 8.3.2 The methanoarchaea\n 8.3.3 The fermentative prokaryotes\n 8.3.4 Other metabolic lifestyle bacteria\n 8.4 Conclusion\n9 Fungi in the marine subsurface\n 9.1 Introduction\n 9.2 The concept of marine fungi\n 9.3 Fungi in marine near-surface sediments in the deep sea\n 9.4 Fungi in the deep subsurface\n 9.4.1 Initial whole community and prokaryote-focused studies of the marine subsurface yielding information on eukaryotes\n 9.4.2 Eukaryote-focused studies yielding information on fungi in the deep subsurface\n 9.5 How deep do fungi go in the subsurface?\n 9.6 Summary\n10 Microbes in geo-engineered systems: geomicrobiological aspects of CCS and Geothermal Energy Generation\n 10.1 Introduction\n 10.1.1 Carbon Capture and Storage (CCS)\n 10.1.2 Geothermal energy and aquifer energy storage\n 10.2 Microbial diversity in geo-engineered reservoirs\n 10.3 Interactions between microbes and geo-engineered systems\n 10.3.1 General considerations\n 10.3.2 Microbial processes in the deep biosphere potentially affected by CCS\n 10.3.3 Examples from a CCS pilot site, CO2 degasing sites and laboratory experiments\n 10.3.4 Impact of microbially-driven processes on CO2 trapping mechanisms\n 10.3.5 Impact of microbially-driven processes on CCS facilities\n 10.3.6 Impact of microbially-driven processes on geothermal energy plants\n 10.4 Methods to analyze the interaction between geo-engineered systems and the deep biosphere\n 10.4.1 Sampling of reservoir fluids and rock cores\n 10.4.2 Methods to analyze microbes in geo-engineered systems\n11 The subsurface habitability of terrestrial rocky planets: Mars\n 11.1 Introduction\n 11.2 The subsurface of Mars – our current knowledge\n 11.3 Martian subsurface habitability, past and present\n 11.3.1 Vital elements (C, H, N, O, P, S)\n 11.3.2 Other micronutrients and trace elements\n 11.3.3 Liquid water through time\n 11.3.4 Redox couples\n 11.3.5 Radiation\n 11.3.6 Other physical and environmental factors\n 11.3.7 Acidity\n 11.4 Impact craters and deep subsurface habitability\n 11.5 The near-subsurface habitability of present and recent Mars – an empirical example\n 11.6 Uninhabited, but habitable subsurface environments?\n 11.7 Ten testable hypotheses on habitability of the Martian subsurface\n 11.8 Sampling the subsurface of Mars\n 11.9 Conclusion\n12 Assessing biosphere-geosphere interactions over geologic time scales: insights from Basin Modeling\n 12.1 Introduction\n 12.2 Basin Modeling\n 12.3 Modeling processes at the deep bio-geo interface\n 12.3.1 Feeding the deep biosphere (biogenic gas)\n 12.3.2 Petroleum biodegradation\n 12.4 Modeling processes at the shallow bio-geo interface\n 12.5 Conclusions\n13 Energetic constraints on life in marine deep sediments\n 13.1 Introduction\n 13.2 Previous work\n 13.3 Study site overview\n 13.3.1 Juan de Fuca (JdF)\n 13.3.2 Peru Margin (PM)\n 13.3.3 South Pacific Gyre (SPG)\n 13.4 Overview of catabolic potential\n 13.5 Comparing deep biospheres\n 13.6 Electron acceptor utilization\n 13.7 Energy demand\n 13.8 Concluding remarks\n 13.9 Computational methods\n 13.9.1 Thermodynamic properties of anhydrous ferrihydrite and pyrolusite\n14 Experimental assessment of community metabolism in the subsurface\n 14.1 Introduction\n 14.1.1 The energy source\n 14.1.2 The carbon budget\n 14.1.3 Distribution vertical of microbial metabolism the sediment pile\n 14.2 Quantifiable metabolic processes\n 14.2.1 Reaction diffusion modeling and mass balances\n 14.2.2 Measurements of rates of energy metabolism with exotic isotopes\n 14.3 Summary\nIndex