Contents. Preface V. Contributing authors-----xiii

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1 Contents Preface V Contributing authors-----xiii Stefan Krause, Helge Niemann, and Tina Treude 1 Methane seeps in a changing climate Introduction What is a cold seep and what drives it? Methane seeps Oil seeps Pockmarks Mud volcanoes Brine seeps Seep chemistry and biology Cold seeps and gas hydrate Gas hydrates, methane bubbles Anaerobic methane oxidation, sulfide oxidation, and large seep fauna Carbonate depositions at cold seeps Effects of climate change on methane seeps and vice versa Methane and past climate Cold seeps and recent global climate change Heat transfer from the atmosphere to marine sediment Gas hydrate destabilization in the near future Areas most affected by gas hydrate destabilization The Arctic Blake Plateau The fate of methane Methane in the sediment Methane in the water column Methane seeps - relevant for climate change? Atmospheric methane concentration overtime Closing remarks

2 Samantha B. Joye and Sara Kleindienst 2 Hydrocarbon seep ecosystems Overview Introduction - discovery of hydrocarbon seeps Geology of hydrocarbon seeps Types and formation mechanism Gas hydrates Authigenic carbonates Biology and biogeochemistry of hydrocarbon seeps Biogeochemistry Biology Microbiology Closing remarks Walter Menapace, Achim Kopf, Matthias Zabel, and Dirk de Beer 3 Mud volcanoes as dynamic sedimentary phenomena that host marine ecosystems Abstract Introduction Types of MV, expelled products, morphologies and dimensions Identification on the seafloor and classification Geological significance MV number estimation and distribution Formation models and long-term evolution Mass transfer and fluid cycling fuel ecosystems Composition and sources of gas, water, mud, and clasts Seafloor and subseafloor ecosystems on MVs MV episodicity MV short term evolution Methane in MVs: the Häkon Mosby case study Conclusion Solveig I. Bühring and Stefan M. Sievert 4 The shallow submarine hot vent system off Milos (Greece) - a natural laboratory for the study of hydrothermal geomicrobiology Abstract Introduction Background Shallow marine systems: overview Milos - an extreme environment as a model system Geophysical and geochemical conditions Seabed features

3 4.4 General aims in hydrothermal geomicrobiology and how they could be addressed by using Milos as a natural laboratory Conclusions and future directions Matthew 0. Schrenk 5 Life in serpentinite hosted alkaline springs Abstract Introduction to serpentinization influenced ecosystems Serpentinization is common Chemical reactions associated with serpentinization Inorganic geochemistry of serpentinites Hydrogeology of serpentinite springs Interfaces associated with serpentinization Mediators of carbon exchange Where do serpentinization processes occur? Submarine systems Continental serpentinite springs Wells in serpentinization influenced aquifers Serpentine cores Serpentine soils Constraints upon the microbial ecology of serpentinite habitats Challenges of hyperalkaliphily Plenty to eat, nothing to breathe Carbon availability Are there endemic species in serpentinite hosted systems? Serpentinomonas, here, there, and everywhere? What about the Clostridiales? Evidence of activity and function Relevance to early Earth, deep biosphere and mineral carbonation Carbon sequestration in serpentinites Summary and future perspectives Mingyang Niu, Qianyong Liang, Dong Feng, and Fengping Wang 6 Ecosystems of cold seeps in the South China Sea Introduction Framework geology Southwest of Taiwan Dongsha area Shenhu area Qiongdongnan Basin Xisha area

4 6.3 Macroecology in cold seeps of the northern South China Sea Microbial community Formosa Ridge Jiulong Reef and Haima Seep Outlook Jian Ding and Yu Zhang 7 Life at the hydrothermal vent field of the Southwest Indian Ridge Overview of the hydrothermal vents Hydrothermal vents on the Southwest Indian Ridge The biologic communities distributed on the SWIR Faunal communities Microbial communities A case study on the microbial communities at the Longqi field Scott D. Wankel, Annie Bourbonnais, and Chawalit Charoenpong 8 Microbial nitrogen cycling processes at submarine hydrothermal vents Introduction Hydrothermal fluid venting and mixing Nitrogen species found in hydrothermal vent fluids Energetic considerations Microbially catalyzed nitrogen cycling processes Stable isotopes as indicators of microbial processes Genetic evidence for nitrogen cycling processes at vents Nitrogen fixation Nitrogen assimilation Denitrification and anammox Dissimilatory nitrate reduction to ammonium (DIMA) Nitrification Concluding remarks and future directions Jeffrey Marlow and Roland Hatzenpichler 9 Assessing metabolic activity at methane seeps: a testing ground for slow growing environmental systems Introduction Observational approaches to quantifying seep hosted activity Modeling rates of activity from geochemical profiles Colonization Rates Catabolism based methods Tracking methane catabolism Tracking sulfur catabolism

5 9.3.3 Tracking catabolism of *nontraditional' electron acceptors Anabolism based methods Cell quantification Stable isotope probing BON CAT Key outstanding issues and challenges Linking the lab with the real world Metabolic activity and tools of the future Preserving microscale spatial arrangements Single-cell growth rate Microcalorimetry Raman spectroscopy Replication rates from metagenomic data Single-cell omics Conclusions Barbara J. MacGregor, Beverly Flood, Jake Bailey, and Matthew Kanke 10 Multiplication is vexation: a genomic perspective on cell division and DNA replication in the large sulfur bacteria Abstract Introduction Overview of sequenced large sulfur bacteria Septation The division and cell wall (dew) gene cluster is fragmented in several of the large sulfur Beggiatoaceae compared to close relatives The available Thiomargarita genomes are missing genes for septum formation What might substitute for ZipA and FtsA as an FtsZ membrane anchor in Thiomargarita septum formation? How might central vacuoles divide? Disruption of some gene clusters seems characteristic of marine LSB DNA replication LSB are lacking some or all of the typical gene features of bacterial replication origins The two complete LSB genomes lack GC skew Parallels to Cyanobacteria Alternatives to DnaA Summary and perspectives

6 Weishu Zhao and Xiao Xiang 11 Life in multiextreme environments: cross-stress response in Thermococcales Abstract Introduction and background Basic characteristics of Thermococcales Physiological traits Genome traits Adaptation related pathways of Thermococcales Energy conversion Amino acid metabolism Compatible solute Composition of membrane lip id Antioxidant pathway Common adaptation strategies for different stresses Common adaptation strategy Summary of adaptation strategy Index