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This chapter summarizes the physiology of bacterial respiration with an emphasis on topics relevant for understanding processes at a cellular level, as well as for understanding the larger-scale implications of respiration within aquatic ecosystems. The analysis begins with definitions and examples of respiratory systems, and reviews essential aspects of their biochemistry. Modes of respiration and aspects of their dynamics are surveyed next, with a brief consideration of the organisms involved, their distribution, and constraints on their activity.

This chapter discusses the nature of life on ancient Earth before the evolution of oxygen production. It suggests that the Earth enjoyed an active and diverse biosphere well before the evolution of oxygen-producing cyanobacteria. This biosphere was fueled, mainly, by chemical compounds liberated during volcanism, underscoring again the importance of plate tectonics in shaping life on our planet. Geological evidence indicates that many of the processes that we have imagined were part of the early biosphere that was in place 3.5 billion years ago. These processes include methanogenesis, sulfate reduction, and decomposition of dead organic biomass, which was likely aided by a host of different fermenting bacteria. It seems likely, though, that this early biosphere was much less active than what we enjoy at present.

Organisms that live with ice are extremophiles, and are viewed as analogues for potential life on other planets and their moons in our solar system. Extraterrestrial cryospheric environments are found on Mars, Europa (a Jovian moon), and Enceladus and Titan (small and large Saturnian moons, respectively). This chapter describes their potential for supporting both water and life, along with the types of chemical reactions that might be exploited as energy sources, which include methanogenesis on Mars, Enceladus, and Titan; and oxidation of organic matter on Europa. Finally, the weaknesses of using terrestrial environments as analogues for those in the extraterrestrial cryosphere are discussed.

During organic material degradation in oxic environments, electrons from organic material (the electron donor) are transferred to oxygen (the electron acceptor) in the process of aerobic respiration. Other compounds, such as nitrate, iron, sulphate, and carbon dioxide, take the place of oxygen during anaerobic respiration in anoxic environments. The order in which these compounds are used by bacteria and archaea is set by thermodynamics. However, concentrations and chemical state also determine the relative importance of electron acceptors in organic carbon oxidation. Oxygen is most important in the biosphere, while sulphate dominates in marine systems, and carbon dioxide in environments with low sulphate concentrations. Nitrate respiration is important in the nitrogen cycle but not in organic material degradation, because of low nitrate concentrations. Organic material is degraded and oxidized by a complex consortium of organisms – the anaerobic food chain – in which the byproducts from physiological type of organisms becomes the starting material of another. The consortium consists of biopolymer hydrolysis, fermentation, hydrogen gas production, and the reduction of either sulphate or carbon dioxide. The byproduct of sulphate reduction – sulphide and other reduced sulphur compounds – is oxidized back eventually to sulphate by either non-phototrophic, chemolithotrophic organisms or by phototrophic microbes. The byproduct of another main form of anaerobic respiration – carbon dioxide reduction – is methane, which is produced only by specific archaea. Methane is degraded aerobically by bacteria and anaerobically by some archaea, sometimes in a consortium with sulphate-reducing bacteria.

During organic material degradation in oxic environments, electrons from organic material, the electron donor, are transferred to oxygen, the electron acceptor, during aerobic respiration. Other compounds, such as nitrate, iron, sulfate, and carbon dioxide, take the place of oxygen during anaerobic respiration in anoxic environments. The order in which these compounds are used by bacteria and archaea (only a few eukaryotes are capable of anaerobic respiration) is set by thermodynamics. However, concentrations and chemical state also determine the relative importance of electron acceptors in organic carbon oxidation. Oxygen is most important in the biosphere, while sulfate dominates in marine systems, and carbon dioxide in environments with low sulfate concentrations. Nitrate respiration is important in the nitrogen cycle but not in organic material degradation because of low nitrate concentrations. Organic material is degraded and oxidized by a complex consortium of organisms, the anaerobic food chain, in which the by-products from physiological types of organisms becomes the starting material of another. The consortium consists of biopolymer hydrolysis, fermentation, hydrogen gas production, and the reduction of either sulfate or carbon dioxide. The by-product of sulfate reduction, sulfide and other reduced sulfur compounds, is oxidized back eventually to sulfate by either non-phototrophic, chemolithotrophic organisms or by phototrophic microbes. The by-product of another main form of anaerobic respiration, carbon dioxide reduction, is methane, which is produced only by specific archaea. Methane is degraded aerobically by bacteria and anaerobically by some archaea, sometimes in a consortium with sulfate-reducing bacteria. Cultivation-independent approaches focusing on 16S rRNA genes and a methane-related gene (mcrA) have been instrumental in understanding these consortia because the microbes remain uncultivated to date. The chapter ends with some discussion about the few eukaryotes able to reproduce without oxygen. In addition to their ecological roles, anaerobic protists provide clues about the evolution of primitive eukaryotes.

The vast majority of the seafloor is covered not in rocky or biogenic reefs but in unconsolidated sediments and, consequently, the majority of marine biodiversity consists of invertebrates either residing in (infauna) or on (epifauna) sediments (Snelgrove 1999). The biodiversity within these sediments is a result of complex interactions between the underlying environmental conditions (e.g. depth, temperature, organic supply, and granulometry) and the biological interactions operating between organisms (e.g. predation and competition). Not only are sediments important depositories of biodiversity but they are also critical components in many key ecosystem functions. Nowhere is this more apparent than in shallow coastal seas and oceans which, despite covering less than 10% of the earth’s surface, deliver up to 30% of marine production and 90% of marine fisheries (Gattuso et al. 1998). These areas are also the site for 80% of organic matter burial and 90% of sedimentary mineralization and nutrient–sediment biogeochemical processes. They also act as the sink for up to 90% of the suspended load in the world’s rivers and the many associated contaminants this material contains (Gattuso et al. 1998). Human beings depend heavily on the goods and services provided, for free, by the marine realm (Hassan et al. 2005 ) and it is no coincidence that nearly 70% of all humans live within 60 km of the sea or that 75% of all cities with more than 10 million inhabitants are in the coastal zone (Small and Nicholls 2003; McGranahan et al. 2007) Given these facts, it is clear that any broad-scale environmental impact that affects the diversity, structure, and function of sediment ecosystems could have a considerable impact on human health and well-being. It is therefore essential that the impacts of ocean acidification on sediment fauna, and the ecosystem functions they support, are adequately considered. This chapter will first describe the geochemical environment within which sediment organisms live. It will then explore the role that sediment organisms play as ecosystem engineers and how they alter the environment in which they live and the overall biodiversity of sediment communities.