Marine Hydrocarbon Seeps: Microbiology and Biogeochemistry of a Global Marine Habitat (Springer Oceanography)

Foreword
Acknowledgements
Contents
1 Microbial Communities and Metabolisms at Hydrocarbon Seeps
	Abstract
	Life at Hydrocarbon Seeps
	Life Styles at Hydrocarbon Seeps
		Aerobic Methanotrophy
		Anaerobic Methanotrophy Coupled to Sulfate Reduction
		Anaerobic Methanotrophy Coupled to Nitrate, Nitrite, and Metal Oxides
		Aerobic and Anaerobic Oxidation of Non-methane Hydrocarbons
		Thiotrophy
		Heterotrophy
	Microbial Community Assembly and Biogeography
	References
2 Anaerobic Hydrocarbon-Degrading Sulfate-Reducing Bacteria at Marine Gas and Oil Seeps
	Abstract
	Characteristics of Habitats Suitable for Microbial Hydrocarbon Degradation
	In Situ Evidence for Anaerobic Hydrocarbon Degradation by Sulfate-Reducing Bacteria
	Anaerobic Hydrocarbon-Degrading Microorganisms
		Anaerobic Hydrocarbon-Degrading Sulfate-Reducing Bacteria
		Detection and In Situ Quantification of Hydrocarbon-Degrading Sulfate-Reducing Bacteria
			SCA1
			SCA2
			LCA1
			LCA2
			Desulfatiglans anilini and Relatives
			Seep-Endemic Sulfate-Reducing Bacteria
	Pathways for Anaerobic Hydrocarbon Degradation
	Diversity and Distribution of Fumarate-Adding Marker Genes
	Outlook
	References
3 Guaymas Basin, a Hydrothermal Hydrocarbon Seep Ecosystem
	Abstract
	General Characteristics of Guaymas Basin
	Microbial Communities of Guaymas Basin Sediments
		Sulfur-Oxidizing Mat-Forming Bacteria in Guaymas Basin
		Microbial Nitrogen Cycling in Surficial Sediments and Mats of Guaymas Basin
	Microbial Cycling of Methane and Other Hydrocarbons in Guaymas Basin
		Microbial Communities of Guaymas Basin Hydrothermal Mounds, and Chimneys
		Methanogens and Methane Oxidizers in Guaymas Basin
		Alkane-Oxidizing Bacteria and Archaea in Guaymas Basin
		Genomic Surveys of Guaymas Basin Microbial Communities
	Challenging Conditions for Microbial Life in Guaymas Basin Hydrothermal Sediments
	References
4 The Gulf of Mexico: An Introductory Survey of a Seep-Dominated Seafloor Landscape
	Abstract
	Bathymetry and Fluid Geochemistry in the Gulf of Mexico
	Microbial Communities and Their Environmental Constraints in Gulf of Mexico Sediments
	Microbial Communities at Selected Northern Gulf of Mexico Seep Sites
		Alaminos Canyon 601
		Garden Banks 425
		Garden Banks 697
		Green Canyon 246
		Green Canyon 600
		Mississippi Canyon 118
		Mississippi Canyon 252
	References
5 Benthic Deep-Sea Life Associated with Asphaltic Hydrocarbon Emissions in the Southern Gulf of Mexico
	Abstract
	Introduction
	The Hydrocarbon Province in the Southern Gulf of Mexico
		The Chapopote Asphalt Volcano
		Asphalt Geochemistry and Compositional Changes Related to Biodegradation
		Asphalt-Derived Hydrocarbons Induce Increased Microbial Activity
		Microorganisms Associated to Asphalt Volcanism
		Chemosynthetic and Grazing Macrofauna
	Summary and Outlook
	Acknowledgements
	References
6 Archaea in Mediterranean Sea Cold Seep Sediments and Brine Pools
	Abstract
	Introduction
	Geological Structures in Cold Seeps
	Geochemical Conditions in Cold Seeps
	Mud Volcanoes in the Mediterranean Sea
		Microorganisms in the Center of the Amsterdam Mud Volcano
		Microorganisms in the Center of the Napoli Mud Volcano
		Microorganisms in Microbial Mats Associated with the Napoli Mud Volcano
	Microorganisms in Pockmark Sediments of the Nile Deep Sea Fan
	References
7 The Microbial Communities of the East Mediterranean Sea Mud Volcanoes and Pockmarks
	Abstract
	Introduction
	The Eastern Mediterranean Sea Mud Volcanoes and Pockmarks: Sites and Methods Used
		Bacterial Diversity
		Archaeal Diversity
	Future Perspectives
	References
8 Large Sulfur-Oxidizing Bacteria at Gulf of Mexico Hydrocarbon Seeps
	Abstract
	Initial Surveys
		Pigmented and Unpigmented Filamentous Beggiatoaceae
		Unicellular Thiomargarita
		Sessile Filamentous “Candidatus Marithrix”
	New Findings of Beggiatoaceae Types in the Gulf of Mexico
		Discovery of Thioploca-like Organisms
		Macroscopic Aggregates of Curled Filamentous Sulfide Oxidizers
		Enriching Thiomargarita-Like Organisms
	Conclusions
	Acknowledgements
	References
9 Growth Patterns of Giant Deep Sea Beggiatoaceae from a Guaymas Basin Vent Site
	Abstract
	Autotrophic CO2 Fixation in Beggiatoaceae: Gaps in the Evidence
	Experiments with Filamentous Beggiatoaceae from Guaymas Basin, Gulf of California
	Inorganic Carbon Assimilation by Giant Guaymas Beggiatoaceae
	Acknowledgements
	References
10 Uncovering Microbial Hydrocarbon Degradation Processes: The Promise of Stable Isotope Probing
	Abstract
	Introduction
	SIP Methodology
		DNA-SIP
		RNA-SIP
	Coupling DNA-/RNA-SIP with Other Techniques
	Applications to Benthic Systems
		Aerobic SIP
		Anaerobic SIP
	Summary
	References