1. Biological diversity: a geobiological view




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普通高等教育“十一五”国家级规划教材


Lecture Notes of Geobiology

地球生物学教程

张兴亮 编

高等教育出版社

Higher Education Press

Contents

Preface

1. Biological diversity: A geobiological view

1.1 Introduction

1.2 Classification of living organisms

1.2.1 Three domains of life

1.2.2 Six kingdoms of Life

1.2.3 Life and rocks

1.3 Diversity of biological metabolism

1.3.1 Metabolic classification of organisms

1.3.2 Photosynthesis

1.3.2.1 Oxygenic photosynthesis

1.3.2.2 Anoxygenic photosynthesis

1.3.3 Nitrogen fixation

1.3.4 Chemolithoautotrophic pathways

1.3.4.1 Hydrogen-oxidation: using the chemical energy in H2 to fix carbon

1.3.4.2 Methanogenesis and acetogenesis: CO2 as an electron acceptor

1.3.4.3 Sulfur-Oxidation

1.3.4.4 Fe(II)-Oxidation

1.3.4.5 Manganese-oxidation

1.3.4.6 Ammonium and nitrite-oxidation

1.3.5 Catabolism

1.3.5.1 Glycolysis and fermentation

1.3.5.2 Aerobic respiration

1.3.5.3 Nitrate reduction and denitrification process

1.3.5.4 Reduction of manganese and other inorganic substance

1.3.5.5 Ferric iron reduction

1.3.5.6 Sulfate reduction

1.3.5.7 Methanogenesis

1.3.5.8 Methanotrophs and methylotrophs

1.4 Biologically induced isotopic fractionation

1.4.1 Carbon isotopic fractionation

1.4.2 Sulfur isotopic fractionation

1.5 Life in extreme environments

1.5.1 Classification

1.5.1.1 Acidophiles

1.5.1.2 Alkaliphiles

1.5.1.3 Barophiles

1.5.1.4 Halophiles

1.5.1.5 Psychrophiles

1.5.1.6 Radiodurans

1.5.1.7 Thermophiles

1.5.1.8 Xerophiles

1.5.2 Communities in hydrothermal systems and cold seeps

1.5.2.1 Hydrothermal vents and cold seeps

1.5.2.2 Microorganisms around hydrothermal vents

1.5.2.3 Animals living at thermal vents

2 Fossil and recent biofilms and biomats

2.1 Introduction

2.1.1. Specific features

2.1.1.1 Genetic variations and cell-cell communications

2.1.1.2 EPS

2.1.1.3 Preservation potential

2.1.2 Similarities and differences

2.2 Fossil and recent biofilms

2.2.1 What are biofilms? Where are biofilms found?

2.2.2 Why learn about biofilms?

2.2.3 Types of biofilms

2.2.4 Development of biofilms

2.2.4.1 Surface conditioning

2.2.4.2 Adhesion of ‘pioneer’ bacteria

2.2.4.3 Microcolonies and ‘slime’ formation

2.2.5 Fully functioning biofilm: cooperate, grow and spread

2.2.6 Biofilm architecture

2.2.7 Biochemistry of biofilm bacteria

2.2.8 Factors that affect biofilm attachment and growth

2.2.8.1 Surface

2.2.8.2 Flow velocity

2.2.8.3 Nutrients

2.2.9 Fossilized biofilms

2.2.9.1 Biofilm and soft-tissue preservation

2.2.9.2 Calcified biofilms in carbonate crypts: A case study

2.3 Fossil and recent microbial mats

2.3.1 Structure of microbial mats

2.3.2 Morphology and physical behaviors

2.3.3 Microenvironment within the microbial mats

2.3.3.1 Light microenvironment

2.3.3.2 Chemical gradients

2.3.4 Biogeochemistry of microbial mats

2.3.4.1 Carbon, oxygen, and sulfur budgets

2.3.4.2 Gas production

2.3.5 Recognition in ancient sediments

2.3.6 Geological record of microbial mats and evolution of microbiota

3. Environment as a system and biogeochemical cycles

3.1 Introduction

3.2 Energy flows

3.2.1 Law of thermodynamics

3.2.2 Earth’s energy budget

3.2.3 Human use of energy flows

3.3 The environment as a system: an overview:

3.3.1 A system approach

3.3.2 Three key traits of the environmental system

3.3.2.1 Openness

3.3.2.2 Integration

3.3.2.3 Complexity

3.4 Biogeochemical cycles

3.4.1 Concept

3.4.2 Element abundance

3.4.3 Carbon cycle

3.4.3.1 Carbon reservoirs

3.4.3.2 Withdrawal of carbon

3.4.3.3 Addition of carbon

3.4.3.4 Isotopic distributions

3.4.4 Oxygen cycle

3.4.4.1 Distribution of O2 among earth surface reservoirs

3.4.4.2 O2 production

3.4.4.3 O2 consumption

3.4.4.4 Global oxygen budgets and the global oxygen cycle

3.4.5 Nitrogen cycle

3.4.5.1 Nitrogen fixation

3.4.5.2 Ammonification

3.4.5.3 Nitrification

3.4.5.4 Denitrification

3.4.5.5 Nitrogen reservoirs and their exchanges

3.4.5.6 Remarks on nitrogen cycle

3.4.6 Sulfur cycle

3.4.6.1 Reservoirs and fluxes

3.4.6.2 Hydrogen sulfide and sulfate reduction

3.4.6.3 Sulfide and elemental sulfur oxidation

3.4.6.4 Organic sulfur compounds

3.4.6.5 Isotopic distributions

3.4.7 Phosphorus cycle

3.4.7.1 Reservoirs and flux

3.4.7.2 Phosphorus limitation for primary production

3.4.7.3 Diagenesis and burial of phosphorus in marine sediments

3.4.7.4 Tectonic roles in the global phosphorus cycle

3.4.7.5 Human impact on the global P cycle: Eutrophication

3.4.8 Iron cycle

3.4.8.1 Iron flux

3.4.8.2 Bacterial iron reduction and oxidation

3.4.8.3 Pyrite oxidation

3.4.8.4 Acid mine drainage

3.4.9 Major features of biogeochemical cycles

3.4.9.1 A variety of pathways

3.4.9.2 Variable rates of cycling

3.4.9.2 The effects of human activity

4 Biomineralization and organomineralization

4.1 Introduction

4.2 Biominerals

4.2.1 Concept and unique characters

4.2.2 Major groups of biominerals

4.2.2.1 Carbonate minerals

4.2.2.2 Phosphate minerals

4.2.2.3 Silica minerals

4.2.2.4 Sulfate minerals: gypsum, celestite and barite

4.2.2.5 Sulfide minerals

4.2.2.6 Oxide and hydroxide minerals

4.2.2.7 Organic biominerals

4.3 Basic processes of biomineralization

4.3.1 Biologically induced mineralization (BIM)

4.3.2 Biologically controlled mineralization (BIM)

4.3.2.1 Biologically controlled extracellular mineralization

4.3.2.2 Biologically controlled intercellular mineralization

4.3.2.3 Biologically controlled intracellular mineralization

4.4 Principles of biomineralization

4.4.1 Supersaturated localized zone and fluid influence

4.4.2 Organic-mineral interface in biominerals

4.4.2.1 The organic-mineral interface

4.4.2.2 Prokaryotic biominerals

4.4.2.3 Eukaryotic biominerals

4.4.2.4 Carboxyl group: bonding positive ions

4.5 Origin and evolutionary history of biomineralization

4.5.1 History of major groups of biominerals

4.5.2 Multiple origins of biomineralized skeletons

4.6 Organomineralization

4.6.1 Recognition

4.6.2 Organomineralization of cirratulid annelid Tubes

5 Biogenic sedimentation

5.1 Introduction

5.2 Biogenic sediments

5.2.1 Carbonates

5.2.1.1 Limestones are biological sediments

5.2.1.2 Microbialites

5.2.1.3 Methane-seep carbonates

5.2.1.4 Microbial dolomite model

5.2.2 Siliceous sediments

5.2.2.1 Primary sediments

5.2.2.2 Formation of chert

5.2.3 Phosphorites and phosphatic sediments

5.2.3.1 Phosphorus source

5.2.3.2 Phosphorus uptake

5.2.3.3 Phosphorus concentration

5.2.3.4 Apatite precipitation

5.2.3.5 Microbial structures in phosphatic rocks

5.2.3.6 Grains and groundmasses

5.2.4 Iron sediments (BIFs and pyrites)

5.2.4.1 Sedimentary pyrite

5.2.4.2 Banded iron formations (BIFs)

5.3. Biological diagenesis

5.3.1 Biogeochemical zonation of sediment column

5.3.2 Diagenetic mineralization

5.3.2.1 Diagenetic carbonate minerals

5.3.2.2 Diagenetic phosphate minerals

5.3.2.3 Amorphous silica

5.4 Microbially induced sedimentary structures (MISS)

5.4.1 Classification

5.4.2 Biological processes in MISS formation

5.4.2.1 Microbial leveling

5.4.2.2 Biostabilization

5.4.2.3 Biofilm imprinting

5.4.2.4 Microbial grain separation

5.4.2.5 Baffling, trapping, and binding

6 Bioerosion, biological weathering, biocorrosion, and soil formation

6.1 Introduction

6.2 Bioerosion

6.2.1 Macroborers.

6.2.1.1 Macroboring groups

6.2.1.2 Insight into boring sponges

6.2.1.3 Insight into boring bivalves

6.2.2 External grazers and scrapers (raspers)

6.2.2.1 External grazers

6.2.2.2 External scrapers

6.2.3 Microborers

6.2.3.1 Microbial endolithic groups

6.2.3.2 Geological importance and records of microborings

6.3 Microbial corrosion

6.3.1 Mechanisms of microbial corrosion

6.3.2 Microbial contributors to corrosion

6.4 Biological weathering

6.4.1 Biological mechanisms that influence and increase rates of rock weathering

6.4.1.1 Plant roots

6.4.1.2 Animals

6.4.1.3 Microbial communities

6.4.2 Silicate weathering

6.4.2.1 Feldspar

6.4.2.2 Silica

6.4.2.3 Olivine, pyroxene, amphibole and biotite

6.4.2.4 Basalts

6.4.3 Carbonate weathering

6.4.4 Insight in to biological weathering: lichens’ weathering

6.4.4.1 Physical processes

6.4.4.2 Biochemical processes

6.4.4.3 A zone model

6.5 Biological contributions to the soil formation

6.5.1 The soil profile

6.5.2 Soil development and humus

7. Synergic evolution of geosphere and biosphere

7.1 Introduction

7.2 Earth’s earliest records and surface environment

7.2.1 Hadean

7.2.1.1 Oldest zircons and implications

7.2.1.2 Four billion years old Acasta Gneiss, Canada

7.2.1.3 Surface environment

7.2.2 Archean (~4.0 Ga-2.5 Ga)

7.2.2.1 Eoarchean (~4.0-3.6 Ga) Isua-Akilia green stone belt, SW Greenland

7.2.2.2 Paleoarchean (3.6-3.2 Ga) records

7.2.2.3 Mesoarchean (3.2-2.8 Ga) records

7.2.2.4 Neoarchean (2.8-2.5 Ga) records

7.2.2.5 Surface environment of earliest Archean

7.3. Evolution of atmosphere

7.3.1 The primitive atmosphere: prebiotic

7.3.2 The atmosphere at the time of the origin of life

7.3.3 Long-term climate evolution: The faint young Sun problem and concentration of greenhouse gases

7.3.3.1 The faint young Sun problem

7.3.3.2 Precambrian atmosphere CO2 change

7.3.3.3 Methane-rich Precambrian atmosphere

7.3.3.4 Phanerozoic CO2 concentrations

7.3.4 The rise of atmospheric O2

7.3.4.1 Net accumulation of O2 in atmosphere

7.3.4.2 Constraints on Precambrian atmospheric O2 levels

7.3.4.3 Evidence for the Paleoproterozoic rise of atmospheric O2

7.3.4.4 Neoproterozoic second rise of atmospheric O2

7.3.4.5 Phanerozoic variations of atmospheric O2

7.4. Evolution of ocean

7.4.1 Origin of the oceans

7.4.2 Cooling of ocean temperature: evidence from δ18O of cherts

7.4.3 Salinity history

7.4.3.1 Total salinity

7.4.3.2 Secular variations of Ca2+, Mg2+ and SO42- concentrations

7.4.3.3. Trace metals Fe and Mo

7.4.4 Oxygenation

7.5. Evolution of biosphere

7.5.1 The origin of life

7.5.1.1 Evidence for life beginning 4.0 billion years ago

7.5.1.2 The organic soup model

7.5.1.3 The hydrothermal model

7.5.1.4 Mineral templates

7.5.2 The framework of life history

7.5.2.1 Prokaryotes dominated evolutionary history from 3.5 to 2.0 billion years ago

7.5.2.2 Eukaryotic life began by 2.1 billion years ago

7.5.2.3 Multicellular eukaryotes evolved by 1.2 billion years ago

7.5.2.4 Animal diversity exploded during the Early Cambrian

7.5.2.5 Phanerozoic events

7.5.3 Evolution of metabolism

7.6. Schematic evolution of Earth and life, a summary


Preface

Geobiology is an exciting and rapidly developing research discipline that opens new perspective in understanding Earth as a system. This relatively new interdiscipline, which is more of a research agenda than a formal discipline, focuses on the processes of and evolution of the coupled Earth-life system through time, especially attacking problems which are inextricable for a single discipline like geology and biology, alone. At its heart, geobiological research merges disciplines in the earth and biological sciences including, but not restricted to, microbiology, microbial ecology, plant physiology, molecular biology, paleontology, early evolutionary ecology, geology, mineralogy, sedimentology, geochemistry, oceanography, and astrobiology. Therefore, geobiological research can be viewed as a synergism between Earth science and life science, which explores the interface between the geosphere (Earth’s surface environment) and the biosphere. Seemingly, it is a simple blending of numerous disciplines. Owing to providing us a more holistic way of thinking, this blending is expected to be particularly powerful for our understanding the present and past interactions between life and inanimate matter, and promises to reveal the co-evolution of geosphere and biosphere. Besides, such studies hold enormous practical potential as well.

Students might have some knowledge of ecology (including paleoecology), also a study of organisms in relation to the environment in which they live. However, ecology is in a much narrower sense. Ecologists, those who study ecology, are always aiming to understand how an organism fits into its environment. They may be interested in asking questions like: Why does this organism live or grow here and not there? How does the organism obtain its food? Is a particular nutrient limiting its growth or number? Does it reproduce in this site and if so how? Is it absent from parts of the site due to some factors? How and when do the young disperse? What cause the death of the organisms? It may be effortless for a student to cite numerous possible questions. Obviously, most of these questions are about the study of environments from the point of view of various organisms. Geobiology is in a much broader sense, dealing with interactions of life with the earth’s surface environment, present and past, which works in two directions: life has had an enormous impact on the chemical and physical evolution of this planet, and in turn, evolutionary changes in the Earth’s surface environment have left their imprint on the ecosystem. Theoretically and methodologically, it seems that there is nothing new in Geobiology, an artificial mixture of diverse sub-disciplines selected from the earth and life sciences. There is neither a unified theory nor a specific method for Geobiology. However, it is of great importance that this cross-discipline provides us a holistic view thinking the Earth as a system, in which life and inanimate world are intimately interacted in present and past.

Over the past two decades or more geobiological research has truly exploded. Many research centers have been established and enormous advances have been published in scientific journals of geology and biology, and many special volumes as well. Meanwhile, professional journals have been launched by leading publishers, e.g., Geobiology by the Blackwell Science and Virtual Journal of Geobiology by Elsevier. An Encyclopedia of Geobiology is now under compiling by the Springer. However, this field of research has remained relatively neglected in China, and it would behove students majoring in geology to devote more attention to this discipline. Currently, most geobiological research achievements are published in English, while relevant Chinese literatures are quite rare. Under this circumstance, the Department of Geology, Northwest University launched a bilingual teaching and learning course of Geobiology at the beginning of this century. It is designed as a half-semester introductory course for students requiring knowledge of geobiology as a trigger for further interests in this field.

This research subject, however, is far from maturity. Comprehensive books e.g. Introduction to Geomicrobiology (by K. Konhauser, 2007), are rare and a formal textbook is presently not available worldwide. Lecture Notes of Geobiology has been written as a text for senior students of geology major in the Department of Geology, Northwest University. Research topics of geobiology are all-inclusive. Studies of astrobiology (investigating exterrestrial life), environmental microbiology, biogeomorphology, global changes, etc., are all considered by some authors as sub-branches of geobiology. Lecture Notes of Geobiology regards geobiology as a subdiscipline of geology, covering the following topics.

  • Current classification of organisms, geological importance of metabolic diversity, biologically induced isotopic fractionation and extremophiles (life in extreme environments).

  • Fossil and recent biofilms and biomats—development, characteristics, distribution, geological record, and taphonomic roles.

  • Environment (geosphere and biosphere) as a system, energy flow and biogeochemical cycles of elements that are of geobiological importance.

  • Biogenic minerals and, processes, principles and evolution of biomineralization, and concept of organomineralization.

  • Biogenic sedimentation—major types of biogenic sediments, biological diagenesis, and microbially induced sedimentary structures (MISS).

  • Biological deconstruction of rocks and minerals—bioerosion, microbial weathering, and soil formation.

  • Co-evolution between life and Earth’s surface environment—geological record of early Earth, formation of oxygenic atmosphere, evolution of ocean chemistry, and how the biosphere evolved during the Precambrian.

Lecture Notes of Geobiology is a contribution to the bilingual teaching and learning course at the Department of Geology, Northwest University. Its sources are mostly from English publications. Audiences are seniors who have good knowledge of geology, and their English are good as well. The majority of them passed CET-6 (College English Test, Band 6). Therefore, Lecture Notes of Geobiology was prepared in English, well suitable for a bilingual teaching and learning course. Frankly speaking, this contribution is far from a complete introduction to Geobiology, nothing but a patchwork of lecture notes. The major feature of the lecture notes focuses on the geological consequences of biological activity. The aim of this course is to stir up students’ attention to many growing fields of Geobiology, to foster students a holistic view on the evolution of Earth, as well as to train their capabilities of learning and communicating professional knowledge through English.

The preparation of the lecture notes was greatly encouraged by several deans of the Department of Geology, NWU. Financial supports from Higher Education Press, Natural Science Foundation of China, and Northwest University, are acknowledged. Special thanks go to Liu Wei for preparing numerous figures in this book, and Dai Tao for linguistic assistance.


Xingliang Zhang

Northwest University, Xian

1. Biological diversity: A geobiological view

1.1 Introduction

Life! It's everywhere on Earth; you can find living organisms from the poles to the equator, from the bottom of the sea to several kilometers in the air, from freezing waters to dry valleys to undersea thermal vents to groundwater thousands of meters below the Earth's surface. Over the last 3.5 billion years or so, living organisms on the Earth have diversified and adapted to almost every environment imaginable. The diversity of life is truly amazing, but all living organisms do share certain similarities. All living organisms can replicate, and the replicator molecule is DNA. As well, all living organisms contain some means of converting the information stored in DNA into products used to build cellular machinery from fats, proteins, and carbohydrates.

Virtually every month, new discoveries are made about surprising occurrences and modes of microbial life on Earth, ranging from proteorhodopsin-based phototrophy in the open ocean to methanogenesis driven by geochemical reactions in Earth's interior. Niches once considered to be uninhabitable (such as those with pH of 0 in extremely rich metal solutions) have been found to harbor thriving microbial communities; compounds once thought to be refractory (such as kerogen, or long-chain alkanes under anaerobic conditions) are now known to serve as microbial growth substrates; organisms previously believed to be unculturable (such as anaerobic benzene oxidizers or soil bacteria that produce medically relevant natural products) have been brought into culture and/or their genetic content has been expressed in recombinant strains; and enigmatic geochemical transformations (such as the anaerobic oxidation of methane or ammonium) are now attributed to the activity of consortia of bacteria and archaea. The importance and extent of microbial diversity have captured the attention of Earth scientists, and now the geoscience community is helping to define and explore interesting biogeochemical problems.

Up until now, we have been familiar with microorganisms that can be said to have a “conventional” metabolism. These are organisms that use organic compounds as energy sources, primarily via aerobic (respiratory) metabolism. To replenish insufficient knowledge of geological students, this chapter will discuss current classification and metabolic diversity of living organisms, as well as life in extreme environments, which are crucial for students understanding geobiological processes

1.2 Classification of living organisms

1.2.1 Three domains of life

Until comparatively recently, living organisms were divided into two kingdoms: animal and vegetable, or the Animalia and the Plantae. In the later half of 20th century, evidence began to accumulate that these were insufficient to express the diversity of life, and various schemes were proposed with three, four, or more kingdoms. The scheme in widest current use divides all living organisms into five kingdoms: Monera (bacteria), Protista, Fungi, Plantae, and Animalia. This coexisted with a scheme dividing life into two main divisions: the Prokaryota (bacteria, etc.) and the Eukaryota (animals, plants, fungi, and protists).

However, with the advent of molecular taxonomy (sequence comparison of genes coding for 16S ribosomal RNA), our view of life on Earth changed radically. What were once called "prokaryotes" are far more diverse than anyone had suspected. The Prokaryotae is now divided into two domains, the Bacteria and the Archaea, as different from each other as either is from the Eukaryota, or eukaryotes. No one of these groups is ancestral to the others, and each shares certain features with the others as well as having unique characteristics of its own (Table 1.1). Within the last two decades, a great deal of additional work has been done to resolve relationships within the Eukaryota. It now appears that most of the biological diversity of eukaryotes lies among the protists, and many scientists feel it is just as inappropriate to lump all protists into a single kingdom as it was to group all prokaryotes. Although many revised systems have been proposed, no single one of them has yet gained a wide acceptance. A fourth group of biological entities, the viruses, are not organisms in the same sense that eukaryotes, archaeans, and bacteria are. It is true that viruses are of considerable biological importance, but they are less important in geobiological context, and therefore, not discussed in this book.

1.2.2 Six kingdoms of Life

Before 1970, taxonomists classified all forms of life into two kingdoms: Animalia and Plantae. Bacteria, fungi, and photosynthetic protists were considered plants, and the protozoa were classified as animals. In 1969, Robort H. Whittaker proposed a five-kingdom classification scheme that is widely used today, and which we follow in this text.

Whittaker identified two kingdoms of primarily unicellular microorganisms based on whether they showed prokaryotic or eukaryotic cellular organization. The kingdom Monera consists of generally single prokaryotic cells, whereas the kingdom Protista consists of generally single eukaryotic cells. All of the organisms in the remaining three kingdoms (Plantae, Fungi and Animalia) are eukaryotic, and most of them are multicellular. They may be classified further on the basis of their way of acquiring nutrients. Members of the kingdom Plantae photosynthesize, and members of the kingdom Fungi secrete enzymes outside their bodies and then absorb the externally digested nutrients. In contrast, members of the kingdom Animalia ingest their food and then digest it, either within an internal cavity or within individual cells.

Recently, a sixth kingdom has been proposed. Many microbiologists argue that the cell structure of the Archaea is so different from that of prokaryotic and eukaryotic cells that they should occupy their own kingdom. Following the fashion, this text adopts the updated six-kingdom classification system (Fig. 1.1).

1.2.3 Life and rocks

The interactions between life and minerals are many, including both energy-yielding and energy-consuming processes. With regard to the evolution of metabolism, life can be divided by consideration of “use” of the mineral by the organism. On the one hand, the prokaryotes have developed a wide array of abilities to utilize geochemical compounds either as energy sources (electron donors) or oxidants (electron acceptors) for respiration, many of which are mineral-forming and/or geochemically important elements. As we like to say, they “eat and breathe” anything, including the rocks. On the other hand, the eukaryotes do not indulge in the redox metabolism of minerals; their interactions involve structure or behavior—synthesizing minerals and “rocks” for structures involved primarily with predation or the escape from it (bones, teeth, shells, frustules, etc.). In general, these cases do not involve a change of redox state, but do require the input of energy for the synthesis (Nealson and Rye, 2005).

1.3 Diversity of biological metabolism

Organisms, especially microbes, show an impressive metabolic diversity in the ways in which they obtain the energy needed for growth. The process involves two basic kinds of transformations, building up or biosynthetic processes mostly via Calvin Cycle (the biochemical route of CO2 fixation in many autotrophic organisms), called anabolism, and breaking down or degradative processes, called catabolism. In the process of anabolism, microbial cells use energy to convert nutrients and simple compounds into more complex structural and functional macromolecules, which include the formation of protein from amino acids, nucleic acids from nucleotides, polysaccharides from simple sugars, and lipids from glycerol and fatty acids. The opposing process, catabolism, oxidizes organic or inorganic compounds, accompanied by the release of chemical energy and excretion of waste products into the environment. Some of the energy is captured and utilized by organisms for movements, transport of nutrients, and anabolic reactions, while the remaining energy is lost to the environment in the form of heat.

1.3.1 Metabolic classification of organisms

The living world can be divided into two metabolic groups: prokaryotes possess rather remarkable metabolic plasticity, and eukaryotes are much more monolithic in their approach to metabolism (i.e. metabolizing only a few different carbon compounds for energy, and respiring only oxygen). For the most part, this division also holds with regard to mineral metabolism, separating the prokaryotes, which harvest energy from minerals (and inadvertently dissolve or precipitate them) from the eukaryotes, which invest energy in biomineral synthesis (Nealson and Rye, 2005).

On the basis of energy usage, we can divide metabolic life into three groups. Many microorganisms resemble animals and humans, using organic chemicals as energy sources. We call these organisms chemoorganotrophs (heterotrophs). An interesting collection of microorganisms, exclusively prokaryotic (bacteria and archaea), use inorganic compounds as energy sources. These organisms are called chemolithotrophs. Another major class of living organisms, called phototrophs, use light as an energy source, which include green plants and also many microorganisms, both prokaryotic and eukaryotic. We will see that there are two distinct types of photosynthesis, that typified by green plants but also found in both eukaryotic and certain prokaryotic microorganisms, and that found exclusively in special groups of bacteria, the purple and green bacteria.

Life can also be categorized according to the carbon sources utilized. Organisms that use inorganic chemicals or light as energy sources are frequently able to grow in the complete absence of organic materials, using carbon dioxide as their sole source of carbon. Autotrophs (meaning literally, “self-feeding”) are able to obtain all the carbon they need from inorganic sources (CO2 or bicarbonate). Note that autotrophy does not refer to the energy source used but to the carbon source. Autotrophs are of great importance in the functioning of the biosphere because they are able to bring about the synthesis of organic matter from inorganic (nonliving) sources; this process is called primary production. Chemolithoautotrophs (in general, are chemolithotrophs) are organisms that obtain energy by degrading reduced inorganic compounds and use CO2 as a carbon source. Photoautotrophs use light as the energy source and CO2 as the major carbon source. Heterotrophs utilize energetically rich organic carbon as their carbon sources, breaking down and resynthesizing polymers. Chemoheterotrophs are organisms that use chemicals as a source of energy and organic compounds as carbon sources. Chemoorganoheterotrophs (in general, are chemoorganotrophs) obtain both energy and carbon from organic compounds. Photoheterotrophs use light as the energy source and organic compounds as the carbon source.

In addition to alternate styles of energy metabolism, we also discuss in this chapter a number of specialized aspects of catabolism. As for respiratory metabolism, when O2 is used as an electron acceptor (a substance that accepts electrons during an oxidation-reduction reaction), the process is called aerobic respiration. There are also a number of other electron acceptors that can participate in the electron transport process in particular groups of microorganisms. The process in which an electron acceptor other than molecular oxygen is used is called anaerobic respiration and will be one of the significant features of metabolic diversity considered here.

Finally, although the major thrust of this chapter is carbon metabolism, our discussion would not be complete without a consideration of one of the important metabolic reactions of microorganisms that involves nitrogen. This is the utilization of N2 as a source of nitrogen for biosynthesis, a process called nitrogen fixation. This important process that is unique to prokaryotes contributes to the recycling of nitrogen into living matter and is important not only agriculturally but also in the total function of the biosphere.

1.3.2 Photosynthesis

Photosynthesis is utilization of solar energy by plants, algae and certain bacteria for the synthesis of organic molecules. Photosynthetic organisms have large molecules chlorophyll (that makes plants look green) in higher plants, algae and cyanobacteria, or bacteriochlorophyll in green and purple bacteria. Both are able to capture light energy from the sun and use it to make ATP (adenosine triphosphate) and NADPH (abbreviations for the oxidized/reduced forms of nicotinamide adenine dinucleotide, a diffusible electron carrier). Photosynthesis can be considered in terms of two separate sets of reactions, the light reactions, in which light energy is converted to chemical energy, and the dark reactions, in which this chemical energy is used for CO2 fixation. The photosynthesis also spins off the energetic molecule, NADPH, which is used by green plants to convert nitrate into the more useable ammonia (in assimilative nitrate reduction). Photosynthesis contributes to big changes in the global environment, mainly as a producer of oxygen gas. Virtually all of the oxygen gas in our atmosphere came from photosynthesis. Photosynthesis also has played a minor role as a remover of carbon dioxide gas from the atmosphere (calcium carbonate precipitation greatly overshadows it). Photosynthesis occurs in two main ways: anoxygenic and oxygenic photosynthesis (see Table 1.2 for comparison).
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