Showing papers by "Bo Thamdrup published in 2005"

The Phosphorus Cycle

Abstract: Publisher Summary The chapter focuses on the biochemical processes by which phosphorus is incorporated into cells and those processes responsible for both phosphorus release and phosphorus sequestration in nature. Phosphorus is a vital functional and structural component of all living organisms. It occurs universally in living cells as phosphate in essential biomolecules such as nucleic acids (DNA and RNA), in energy transfer systems (NAD(P)H and ATP), and in cell membranes (phospholipids). Many of the biochemical processes are microbially mediated, and the chapter highlights the role of microbes in the phosphorus cycle. Microorganisms with active membrane-transport systems regulate the acquisition of phosphate from the environment, such as the Pts phosphate transport system of Escherichia coli. Microbial processes largely control the mobilization and immobilization of phosphorus in aquatic environments. Organic-bound phosphorus is partly assimilated and partly released as dissolved inorganic phosphorus (DIP) by the heterotrophic microbial community during organic matter mineralization. The chapter compares and contrasts phosphorus cycling in a number of representative freshwater and marine systems.

Systematics and Phylogeny

Abstract: Publisher Summary The chapter reviews some key aspects of basic genetics and molecular evolution to appreciate the construction and interpretation of phylogenies based on molecular sequence comparisons. Phylogenies are constructed from genetic elements with the same function (homologous function). Phylogenies are constructed from a range of different DNA, RNA, and protein sequences. By far, the most widely used and comprehensive phylogenies are constructed from the small subunits of the rRNA molecule. Phylogenies constructed from genetic elements are only as inclusive as the distribution of the given genetic element among organisms. The more widely distributed the element, the more inclusive the phylogeny and the less widely distributed, the more specialized the phylogeny. If a phylogeny is constructed, for example, from the nitrogenase enzyme, then the phylogeny will include only those organisms capable of fixing nitrogen. A phylogenetic grouping of prokaryotic organisms became possible after the structure of DNA was discovered and its role in inheritance was made clear. The chapter also discusses the tree of life from small subunit (SSU) rRNAs. Molecular sequences from the SSU rRNAs divide all life into three principal domains: Bacteria , Archaea , and Eukarya .

Effect of Low Sulfate Concentrations on Lactate Oxidation and Isotope Fractionation during Sulfate Reduction by Archaeoglobus fulgidus Strain Z

Abstract: The effect of low substrate concentrations on the metabolic pathway and sulfur isotope fractionation during sulfate reduction was investigated for Archaeoglobus fulgidus strain Z. This archaeon was grown in a chemostat with sulfate concentrations between 0.3 mM and 14 mM at 80°C and with lactate as the limiting substrate. During sulfate reduction, lactate was oxidized to acetate, formate, and CO2. This is the first time that the production of formate has been reported for A. fulgidus. The stoichiometry of the catabolic reaction was strongly dependent on the sulfate concentration. At concentrations of more than 300 μM, 1 mol of sulfate was reduced during the consumption of 1 mol of lactate, whereas only 0.6 mol of sulfate was consumed per mol of lactate oxidized at a sulfate concentration of 300 μM. Furthermore, at low sulfate concentrations acetate was the main carbon product, in contrast to the CO2 produced at high concentrations. We suggest different pathways for lactate oxidation by A. fulgidus at high and low sulfate concentrations. At about 300 μM sulfate both the growth yield and the isotope fractionation were limited by sulfate, whereas the sulfate reduction rate was not limited by sulfate. We suggest that the cell channels more energy for sulfate uptake at sulfate concentrations below 300 to 400 μM than it does at higher concentrations. This could explain the shift in the metabolic pathway and the reduced growth yield and isotope fractionation at low sulfate levels.

34S/32S and 18O/16O Fractionation During Sulfur Disproportionation by Desulfobulbus propionicus

Abstract: In the present study, coupled stable sulfur and oxygen isotope fractionation during elemental sulfur disproportionation according to the overall reaction: 4H2O + 4Sˆ → 3H2S + SO4 2 − + 2H+, was experimentally investigated for the first time using a pure culture of the sulfate reducer Desulfobulbus propionicus at 35ˆC Bacterial disproportionation of elemental sulfur is an important process in the sulfur cycle of natural surface sediments and leads to the simultaneous formation of sulfide and sulfate A dual-isotope approach considering both sulfur and oxygen isotope discrimination has been shown to be most effective in evaluating specific microbial reactions The influence of iron- and manganese bearing-solids (Fe(II)CO3, Fe(III)OOH, Mn(IV)O2) acting in natural sediments as scavengers for hydrogen sulfide, was considered, too Disproportionation of elemental sulfur was observed in the presence of iron solids at a cell-specific sulfur disproportionation rate of about 10− 95± 04 μ mol Sˆ cell− 1 h− 1 No

The Sulfur Cycle

Abstract: Publisher Summary The chapter discusses the biologically mediated sulfur metabolisms, which involve the reduction of sulfur compounds, the oxidative processes, and the disproportionation of sulfur compounds. Sulfur is an essential nutrient element and constitutes around 0.5 to 1.0% of the dry weight of prokaryotic organisms. Sulfur is most abundant in the amino acids cysteine and methionine, the key building blocks of proteins. The chapter focuses on the process of assimilatory sulfate reduction. This process, by contrast to dissimilatory sulfate reduction, is an energy-requiring process. The chapter reviews the ecology and phylogeny of sulfate reducers in nature and looks at the principal factors regulating the process. Dissimilatory sulfate reduction is a widespread anaerobic mineralization process. The phylogenies and ecology of sulfur metabolizing organisms are discussed. The chapter also studies global significance of sulfate reduction in the mineralization organic matter. It outlines some of the main enzymatic steps involved in the phototrophic oxidation of sulfide. The main steps in sulfide oxidation are the oxidation of sulfide to elemental sulfur or sulfite, the oxidation of elemental sulfur to sulfite, and the oxidation of sulfite to sulfate. The chapter discusses various class of organisms involved in sulfur compound disproportionation.

The Silicon Cycle

Abstract: Publisher Summary The chapter outlines some of the basics surrounding the chemistry of dissolved silica and the mineralogy of biological phases formed from silica Silicon is the second most abundant element in the Earth's crust, 27% by weight, exceeded only by oxygen Silica forms the skeleton structures of a variety of aquatic plankton including many diatoms, radiolarians, and silicoflagellates, and the spicules of sponges Therefore, silica is an important nutrient controlling primary production in aquatic systems, and its cycling is controlled by the interplay between biological and physiochemical processes The chapter considers the processes by which silica is formed into biogenic structures and also the processes controlling the dissolution and preservation of biogenic silica in aquatic environments, including the role of microorganisms The chapter presents some case studies of silica cycling in aquatic systems and reviews the evolution of the silica cycle through geologic time

The Iron and Manganese Cycles

Abstract: Publisher Summary The chapter discusses the processes regulating the transformations of iron and manganese in nature and the relationship between the cycling of these and other biologically active elements. Both the oxidation and the reduction of iron and manganese in natural environments is, to a large extent, promoted by microbial catalysis, but abiotic transformations are also important and may compete with the biological processes. In the Earth's crust, iron and manganese are mainly found as minor components of rock-forming silicate minerals such as olivine, pyroxenes, and amphiboles. Iron has a high abundance of 4.3% by mass in the continental crust. At a 50-fold lower crustal abundance than iron, manganese is the second most abundant redox-active metal. There are many similarities between iron and manganese in terms of both geochemistry and microbiology. Microbes play an important role in the oxidation of reduced iron and manganese. Dissimilatory iron- and manganese-reducing microorganisms catalyze the reduction of Fe (III) to Fe (II), and of Mn (III) or Mn (IV) to Mn(II). The chapter discusses the microbial manganese and iron reduction in aquatic environments. Three basic conditions—absence of oxygen and presence of electron donors and oxidized manganese or iron in an appropriate form—are required to fulfill for microbial iron or manganese reduction to thrive in normal aquatic environments of near neutral pH. The chapter discusses the two experimental approaches used to determine rates of microbial Fe reduction in aquatic sediments. The first is a direct quantification of changes in Fe(III) or Fe(II) pools during sediment incubations. The second approach determines rates of dissimilatory iron and manganese reduction by comparing the depth distribution of total carbon oxidation, based on production of dissolved inorganic carbon, to measured rates of sulfate reduction.

The Methane Cycle

Abstract: Publisher Summary The chapter discusses the biogeochemistry and microbial ecology of the methane cycle. It begins by considering some of the dynamics of methane as a greenhouse gas and the role of clathrate hydrates in climate change. The processes of methane formation, paying particular attention to the various microbial pathways involved are explored. The chapter outlines some of the basic features of the biochemistry of methanogenesis. The process begins with the activation of CO2 with a methanofuran and the reduction of the carbon to the level of formyl. The formyl carbon is transferred to methanopterin, where it is reduced first to a methylene carbon and next to methyl carbon. The methyl carbon is transferred to an enzyme containing coenzyme M (CoM), forming CoM-S-CH3. The chapter discusses the pathways of methane oxidation and anaerobic methane oxidation. Methanotrophy refers to the microbial oxidation of methane. The chapter considers aspects of the microbiology, phylogeny, biogeochemistry, and environmental significance of methanotrophic processes. Finally, it describes the isotope fractionations accompanying methane formation and oxidation.

Heterotrophic Carbon Metabolism

Abstract: Publisher Summary The chapter focuses on the heterotrophic processes of carbon mineralization. The relationship between microbial activity and carbon source are considered and the role of microorganisms in the detritus food chain is studied. The chapter outlines the various pathways of both aerobic and anaerobic organic carbon mineralization. When oxygen is present, all catabolic reactions occur by aerobic processes—that is, aerobic respiration. The intracellular mineralization process involves the generation of reduced pyridine nucleotides through the tricarboxylic acid (TCA) cycle with a terminal acetate oxidation to carbon dioxide. Then while transferring the reducing power via the electron transport chain, some of the energy is liberated and conserved in ATP during oxidative phosphorylation. Most aerobic heterotrophs are capable of completely oxidizing particulate polymers to carbon dioxide, water, and inorganic nutrients. In oxygen deficient environments, catabolic reactions are coupled to terminal electron acceptors other than oxygen. Anaerobic decomposition is accomplished by mutualistic consortia of different types of heterotrophic microorganisms. The chapter reemphasizes some of the important fermentation processes involved in anaerobic carbon mineralization. These fermentation reactions are performed by a number of fungi, yeast, and prokaryotes such as clostridia, enterobacteria, lactobacilli, streptococci, and propionibacteria. The chapter also discusses carbon assimilation, degradability and decomposition kinetics, and processes leading to the preservation of organic carbon in sediments.

The Nitrogen Cycle

Abstract: Publisher Summary The chapter focuses on the various microbial pathways that promote the transformation of nitrogen compounds and on environmental factors that regulate the operation and intensity of these pathways. The various microbial nitrogen-transforming processes start with N fixation, followed by microbial ammonification, nitrogen assimilation, nitrification and finally dissimilatory nitrate reduction. The chapter explores how the interplay between microbial processes and the geochemical environment controls the cycling of nitrogen in aquatic environments. Cyanobacteria are responsible for most planktonic nitrogen fixation in open marine and lake waters. Rates of nitrogen fixation are low to moderate in the sediments of most lakes and estuaries, but are high in particularly organic-rich estuarine sediments. The chapter also explores how nitrogen isotopes are fractionated during microbial transformation, however it first considers the aspects of the global nitrogen cycle and the influence of human activities.

Thermodynamics and Microbial Metabolism

Abstract: Publisher Summary The chapter considers basic aspects of chemical thermodynamics as relevant for understanding microbial metabolisms in nature and for defining the chemical environments of the microbial world. The chapter describes enthalpy, entropy, and Gibbs free energy. All thermodynamically favorable chemical reactions proceed, barring kinetic barriers, until the distribution of reacting components in the system reaches equilibrium. The chapter discusses influence of temperature on thermodynamic properties, activity coefficient calculations, gas solubility and Henry's law, oxidation-reduction reactions. Cellular architecture and its relationship to show how organisms gain energy for their growth and metabolism are discussed. The chapter examines how catabolic (also called dissimilatory) processes and light provide the energy for the anabolic (also called assimilatory) synthesis of cellular material. It discusses some of the basic aspects of cellular metabolism and explains how different metabolisms are named. A vast array of different energy-providing metabolisms exist in nature, and a common nomenclature is adopted whereby these metabolisms are named based on their (1) energy source, (2) electron source, and (3) carbon source.

Carbon Fixation and Phototrophy

Abstract: Publisher Summary The chapter focuses on the processes whereby organisms fix CO 2 into organic biomass. This chapter, therefore, explores how energy is gained through both chemotrophic and phototrophic metabolisms and how this energy is used to fix CO 2 . Some attention is also given to the principal known CO 2 fixation pathways. These include the reductive pentose phosphate cycle, which is the predominant pathway of carbon fixation on Earth; used by all oxygenic photosynthetic organisms, including cyanobacteria, land plants, and algae. The reductive citric acid cycle is used in carbon fixation by the anoxygenic photosynthetic green sulfur bacteria. The reductive acetyl-CoA pathway is found among many anaerobic organisms utilizing H 2 as an electron donor. The chapter also speculates the evolutionary history of the CO 2 fixation processes. Aspects of isotope fractionation during CO 2 fixation are explored. The ecology of photosynthetic and chemoautotrophic organisms conducting CO 2 fixation are woven into many of the future discussions of element cycling. The chapter highlights few specific examples of active ecosystems fueled by chemoautotrophic organisms such as hydrothermal vent systems, chemoautotrophic cave ecosystem, and subsurface biosphere.

The Oxygen Cycle

Abstract: Publisher Summary The chapter discusses oxygenic photosynthesis by bacteria, the physiology of oxygen respiration, and the effects of oxygen on other microbial processes. Oxygen gas, O 2 is a prerequisite for life. While oxygen is essential to almost all eukaryotes, this chapter describes a great diversity of metabolic strategies for life without oxygen, and for many organisms, the high oxygen concentrations at the Earth's surface are toxic and may in fact be deadly. Among the prokaryotes, oxygenic photosynthesis is known only from the cyanobacteria. In these organisms, just as in eukaryotic algae and plants, water is oxidized to oxygen by chlorophyll a in the reaction center of photosystem II, and CO 2 is reduced to organic matter by Rubisco in the reductive pentose phosphate cycle. Oxygen respiration is by far the most important oxygen-consuming reaction in living organisms and in the biogeochemical oxygen cycle. In oxygen respiration, the reduction of oxygen to water is the terminal step in a series of coupled oxidation-reduction reactions involving cell membrane-bound redox couples that make up an electron transport chain.

Structure and Growth of Microbial Populations

Abstract: Publisher Summary The chapter documents how prokaryotes play an environmentally significant to dominant role in the cycling of numerous important redox-sensitive elements such as carbon, iron, manganese, oxygen, nitrogen, and sulfur. This chapter explores some of the principles outlining the structure and growth of the populations conducting these transformations. The factors regulating population growth and population size are considered and the chapter explores how populations with overall similar physiology can occupy an enormous range of environmental conditions, including extremes of temperature, salinity, and pH. It also focuses on the factors influencing the ecology of microbial populations although little is known about the details of microbial interactions in nature. The chapter explores how cells communicate with each other and how they cooperate to effectively utilize available resources in some circumstances. The recognition that prokaryotes can display community behavior is an important revelation in microbial ecology. The microbial interactions are numerous, often complex, and highly interesting. The chapter discusses different types of interactions with examples from the microbial world. These are competition, synergism and syntrophy, predation and parasitism, commensalism, amensalism, neutralism, and symbiosis.