Chapter
1.3 Subseafloor biosphere simulation experiments
2.2.1 Tools for accessing the deep basement biosphere
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
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
3.2.5 Hard rocks of varying origin
3.4.2 Geochemical indicators
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
5.2 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
6 Quantifying microbes in the marine subseafloor: some notes of caution
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
7 Archaea in deep marine subsurface sediments
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
8.3 Petroleum microbiology
8.3.1 The sulfate-reducing prokaryotes
8.3.3 The fermentative prokaryotes
8.3.4 Other metabolic lifestyle bacteria
9 Fungi in the marine subsurface
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?
10 Microbes in geo-engineered systems: geomicrobiological aspects of CCS and Geothermal Energy Generation
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
11.2 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
11.3.6 Other physical and environmental factors
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
12 Assessing biosphere-geosphere interactions over geologic time scales: insights from 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
13 Energetic constraints on life in marine deep sediments
13.3.1 Juan de Fuca (JdF)
13.3.3 South Pacific Gyre (SPG)
13.4 Overview of catabolic potential
13.5 Comparing deep biospheres
13.6 Electron acceptor utilization
13.9 Computational methods
13.9.1 Thermodynamic properties of anhydrous ferrihydrite and pyrolusite
14 Experimental assessment of community metabolism in the subsurface
14.1.3 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
Microbial Life of the Deep Biosphere
( Life in Extreme Environments )
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