Microbial Ecology E-Book

Larry L. Barton

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 702

Veröffentlichungsjahr: 2011

Beschreibung

This book covers the ecological activities of microbes in the biosphere with an emphasis on microbial interactions within their environments and communities

In thirteen concise and timely chapters, Microbial Ecology presents a broad overview of this rapidly growing field, explaining the basic principles in an easy-to-follow manner. Using an integrative approach, it comprehensively covers traditional issues in ecology as well as cutting-edge content at the intersection of ecology, microbiology, environmental science and engineering, and molecular biology.

Examining the microbial characteristics that enable microbes to grow in different environments, the book provides insights into relevant methodologies for characterization of microorganisms in the environment. The authors draw upon their extensive experience in teaching microbiology to address the latest hot-button topics in the field, such as:

• Ecology of microorganisms in natural and engineered environments
• Advances in molecular-based understanding of microbial phylogeny and interactions
• Microbially driven biogeochemical processes and interactions among microbial populations and communities
• Microbial activities in extreme or unusual environments
• Ecological studies pertaining to animal, plant, and insect microbiology
• Microbial processes and interactions associated with environmental pollution

Designed for use in teaching, Microbial Ecology offers numerous special features to aid both students and instructors, including:

• Information boxes that highlight key microbial ecology issues
• "Microbial Spotlights" that focus on how prominent microbial ecologists became interested in microbial ecology
• Examples that illustrate the role of bacterial interaction with humans
• Exercises to promote critical thinking
• Selected reading lists
• Chapter summaries and review questions for class discussion

Various microbial interactions and community structures are presented through examples and illustrations. Also included are mini case studies that address activities of microorganisms in specific environments, as well as a glossary and key words. All these features make this an ideal textbook for graduate or upper-level undergraduate students in biology, microbiology, ecology, or environmental science. It also serves as a highly useful reference for scientists and environmental professionals.

Leseprobe

Table of Contents

Title Page

Copyright

Dedication Page

Preface

Glossary

Chapter 1: Microbial Ecology: Beginnings and the Road Forward

1.1 Central Themes

1.2 Introduction

1.3 Timeline

1.4 Microfossils

1.5 Early Life

1.6 Characteristics of Microbial Life

1.7 Classification and Taxonomy: The Species Concept

1.8 The Three Domains: Tree of Life

1.9 Relationship of Microbial Ecology to General Ecology

1.10 Changing Face of Microbial Ecology

1.11 Summary

1.12 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 2: Diversity of Microorganisms

2.1 Central Themes

2.2 The Ubiquity of Microorganisms

2.3 The Amazing Diversity of Morphologies

2.4 Diversity of Bacterial Groups

2.5 Discovery of Archaea as a Separate Domain

2.6 Archaeal Diversity

2.7 Archaea–Bacteria Differences

2.8 Eukarya: A Changing Picture of Phylogenetic Diversity

2.9 Protist Diversity

2.10 Fungal Diversity

2.11 Algal Diversity

2.12 Viral Diversity

2.13 Summary

2.14 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 3: Complexity and Simplicity of Cell Systems

3.1 Central Themes

3.2 Introduction

3.3 Cell Parameters

3.4 Cell Movement and Chemotaxis

3.5 Structures of Sporulation

3.6 Nutrient Reserves and Storage Materials

3.7 Cell–Cell Associations

3.8 Cell Physiology and Metabolism

3.9 Energetics and Environment

3.10 Bioelectrochemical Activities

3.11 Summary

3.12 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 4: The Microbial Habitat: An Ecological Perspective

4.1 Central Themes

4.2 Habitats: An Overview

4.3 Aquatic Habitats

4.4 Soil Habitats

4.5 Rock and Subsurface Habitats

4.6 Atmospheric Habitats

4.7 Population Ecology Across Habitats

4.8 Summary

4.9 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 5: The How of Microbial Ecology Studies

5.1 Central Themes

5.2 Introduction

5.3 Sampling and Sample Storage

5.4 Microscopy

5.5 Cultivation of Microorganisms

5.6 Molecular Phylogenetics

5.7 Culturing Versus Molecular Techniques: Comparisons from Soil Studies

5.8 Community Fingerprinting Methods

5.9 Metagenomics: A New Tool for Answering Community Ecology Questions

5.10 Environmental Proteomics

5.11 Stable-Isotope Studies

5.12 Summary

5.13 Delving Deeper: Critical Thinking Questions

Bibliographic Sources

Chapter 6: Microbe–Microbe Interactions

6.1 Central Themes

6.2 Introduction

6.3 Classification of Microbial Interactions

6.4 Symbiotic Associations

6.5 Fungus–Bacterium Symbiosis

6.6 Prokaryote–Prokaryote Interactions

6.7 Establishing a Symbiosis: the Nostoc–Geosiphon Association

6.8 Sexual Interactions

6.9 Summary

6.10 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 7: Interactions Between Microorganismsand Plants

7.1 Central Themes

7.2 Introduction

7.3 Symbiotic Associations with Cyanobacteria

7.4 Interactions in the Rhizosphere

7.5 Mycorrhizae

7.6 Nitrogen-Fixing Bacteria and Higher Plants

7.7 Bacteria Supporting Plant Growth

7.8 Leaf Surfaces and Microorganisms

7.9 Detrimental Activities of Microorganisms on Plants

7.10 Fungi Promoting Increased heat Tolerance in Plants

7.11 Biocontrol of Pests and Pathogens

7.12 Summary

7.13 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 8: Interactions Between Microorganismsand Animals

8.1 Central Themes

8.2 Introduction

8.3 Primary and Secondary Symbionts

8.4 Microbe–Animal Interactions: Parasitism

8.5 Microbe–Animal Interactions: Mutualism

8.6 Lessons from the Deep: Evolutionary and Ecosystem Insights from Deep-Sea Vents Symbioses

8.7 Microbial–Vertebrate Interactions

8.8 Grazing and Predation by Animals

8.9 Summary

8.10 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 9: Living Together: Microbial Communities

9.1 Central Themes

9.2 Introduction

9.3 Metagenomics: A New Tool for Answering Community Ecology Questions

9.4 Biomats and Biofilms

9.5 Formation of Organized Communities: Quorum Sensing

9.6 Colonization and Recolonization by Microorganisms

9.7 Dispersal, Succession, and Stability

9.8 Species Diversity

9.9 Food Webs

9.10 Primary Production and Energy Flow

9.11 Microbial Community Examples

9.12 Summary

9.13 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 10: Microbial Processes Contributing to Biogeochemical Cycles

10.1 Central Themes

10.2 Introduction

10.3 Energy Flow

10.4 Oxygen and Carbon Cycling

10.5 Nitrogen Cycling

10.6 Sulfur Cycling

10.7 Phosphorus Cycling

10.8 Iron Cycling

10.9 Cycling of Manganese and Selenium

10.10 Cycling of Hydrogen

10.11 Transformation of Mercury

10.12 Closed Systems

10.13 Summary

10.14 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 11: Microbes at Work in Nature: Biomineralization and Microbial Weathering

11.1 Central Themes

11.2 Introduction

11.3 Cell Characteristics and Metal Binding

11.4 Energy Flow: Shuffling Electrons; Redox Reactions

11.5 Dissolution Versus Precipitation

11.6 Formation of Ores and Minerals

11.7 Microbial Participation in Silicification

11.8 Biomineralization of Ferromanganese Deposits

11.9 Microbial Carbonate Microbialites

11.10 Stromatolites

11.11 Summary

11.12 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 12: Decomposition of Natural Compounds

12.1 Central Themes

12.2 Introduction

12.3 Decomposition of Wood

12.4 Digestion of Plant Cell Wall Structures

12.5 Starch Hydrolysis

12.6 Inulin Hydrolysis

12.7 Decomposition of Diverse Biopolymers Including Animal Fibrous Proteins

12.8 Ecology of Fermented Foods

12.9 Ecology of Bioenergy Production

12.10 Waste Treatment Systems

12.11 Composting of Plant Organic Matter

12.12 Impact of Microbial Degradation on Humans

12.13 Summary

12.14 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Chapter 13: Microbes at Work: Bioremediation

13.1 Central Themes

13.2 Introduction

13.3 Bioremediation as a Technology

13.4 Genetic Engineering

13.5 Design and Implementation of Bioremediation

13.6 Bioremediation of Organic Compounds

13.7 Degradation of Hydrocarbons

13.8 Degradation of Xenobiotics

13.9 Bioremediation with Inorganic Pollutants

13.10 Summary

13.11 Delving Deeper: Critical Thinking Questions

Bibliographic Material

Index

Copyright © 2011 by Wiley-Blackwell. All rights reserved.

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Published simultaneously in Canada.

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Library of Congress Cataloging-in-Publication Data:

Barton, Larry, 1940-

Microbial ecology / Larry L. Barton and Diana E. Northup.

p. cm.

Includes index.

ISBN 978-0-470-04817-7 (hardback)

1. Microbial ecology. I. Northrup, Diana E. II. Title.

QR100.B37 2011.

579'.17–dc22

2010043470

Dedicated to

Sandra, Kenneth,

and the many students who

inspired us to write this book

Preface

This book was written with the objective of including it as a central part of a higher-education program that offers a semester course in microbial ecology. This book is appropriate for upper-level undergraduate or graduate students pursuing majors in biology, microbiology, ecology, or environmental science. In our presentation, we have assumed that students have backgrounds in chemistry, biology, and microbiology. Our approach is to present basic principles, provide an insight into relevant methodologies, and discuss interactions that are characteristic of microorganisms. We have used an integrative approach to relate new topics that are addressed in the book to the broader scientific field. As an outgrowth of our teaching numerous courses of microbiology, we understand the importance of providing specifics for different topics and, therefore, have included many examples associated with microbial ecology. We broadly cover the environments where microorganisms are found and include community activities in processes that are important in commercial and environmental events. Since this book is designed for use in teaching, each chapter contains a summary, bibliographic sources for additional reading, and review questions appropriate for class discussion. Numerous bibliographic references are cited throughout the text to provide access to additional information on topics covered. It is our hope that this book will stimulate the study of microbial ecology and development of new approaches to evaluate microbes in a natural setting.

We provide an overview of the field of microbial ecology, and while we focus on bacteria, we include numerous examples of other microorganisms. Chapter 1 provides a perspective on historical developments and more recent activities of microbial ecology. The diversity of the organisms in the “tree of life” and the distinctions between Archaea and Bacteria are covered in Chapter 2. To assist in the understanding of cellular processes for specific environments, Chapter 3 covers the structural, physiological, and metabolic characteristics of microorganisms. The ubiquity of microorganisms in various habitats and techniques for studying them are the topics of Chapters 4 and 5, respectively. Microbe–microbe interactions, including dominance in a population, are discussed in Chapter 6. Plant–microbial interactions are relatively unique, and features of these activities are discussed in Chapter 7. To illustrate the many different interactions between microorganisms and animals, we have provided information on several of these in Chapter 8. Community structure, colonization activities, and species diversity are covered in Chapter 9. Microorganisms are important in several of the major nutrient cycles, and in Chapter 10 we cover the influence of microorganisms on biogeochemical cycles. Since microorganisms may have considerable impact on the environment, we have designated Chapter 11 as a summary of the activities of biomineralization and microbial weathering. The beneficial activities of natural polymer decomposition and use of microbes in bioenergy production are discussed in Chapter 12. The final chapter, Chapter 13, discusses the participation of microorganisms in various types of bioremediation and processes to achieve microbial detoxification of the environment.

We appreciate the support of our colleagues and friends who have contributed to this book. Most of the photographs and other images used in this text are original and were provided by many scientists working in microbial ecology. We also acknowledge these scientists for providing highlights of their microbial ecology activities, biographic and these sketches are presented in the chapters as microbial “spotlight” events. Selection of individuals for spotlights was based on our desire to cover a diversity of areas of microbial ecology, and we wish that we had more space to include additional spotlights. We gratefully acknowledge these contributors as follows:

Photographs provided by

Esther Angert

Sue Barns

Sandra Barton

Dennis Bazylinski

Rebecca Bixby

Cliff Dahm

Airidas Dapkevicius

Armand Dichosa

Martin Dworkin

Jane Gillespie

Girhsorn

Dale Griffin

G. Hirson

Kenneth Ingham

Gordon Johnson

Brian Jones

Peter Jones

Leslie Melim

Yauoi Nishiyama

T.C. Onstott

Robin Renaut

Adam W. Rollins

Janet Shagam

Holly Simon

David Scott Simonton

Jessica Snider

Michael Spilde

Helga Stan-Lotter

Ward's Natural Science

John Waterbury

Microbial spotlights provided by

Dominique Expert

Gill Geesey

Dale Griffin

Jared Leadbetter

Lynn Margulis

David Mills

Michael O'Connell

T.C. Onstott

Norman Pace

Anna-Louise Reysenbach

Mitch Sogin

Joseph Sufleta

Brad Tebo

Lily Young

We are most appreciative of the assistance, patience, and professional contributions of Karen Chambers and the editorial staff at John Wiley.

Larry L. Barton

Diana E. Northup

Glossary

actinomycete A group of chemoorganotrophic soil bacteria that may grow as filaments and display branching.

adhesins Microbial surface antigens, often in the form of filamentous pili or proteins, that bind one cell to another.

air stripping The injection of air into soil with the purpose of carrying volatile materials into the atmosphere.

alkane Referring to saturated hydrocarbons with carbon atoms in a chain without double bonds.

alkene Referring to unsaturated hydrocarbons with carbon atoms in a chain containing double bonds between the carbon atoms.

allelopathy Inhibition of growth of one species by another species by production of secondary metabolites known as allelochemicals. Commonly allelopathy is associated with plants but in a broad sense may be associated with microorganisms and coral.

amensalism The state of one microorganism having a negative effect on another microorganism.

anaerobic microorganisms Bacteria, archaea, or yeast growing in the absence of oxygen.

anammox reaction A bacterial reaction involving the anaerobic oxidation of ammonium with reduction of nitrite to produce N2.

anoxygenic Referring to activity that contributes to the anaerobic environment.

antagonism The state of one organism inhibiting the growth of another organism.

anthropogenic Referring to chemicals that result from human influence in contrast to chemicals resulting from natural processes.

Arthropoda Animals with exoskeletons, segmented bodies, and jointed appendages. They include Acari, arachnids that include mites and ticks; Annelida, segmented worms such as earthworms (Enchytraeida), and Nematoda, unsegmented worms (also termed roundworms).

assimilation The incorporation of compounds into cellular materials.

augmentation With respect to bioremediation, the addition of desired bacteria to a bioreactor or to a contaminated site.

azo dyes Brightly colored dyes used in the textile industry that contain the azo (–N—N–) group.

bacteriome A specialized organelle in insects that hosts bacterial endosymbionts.

bacteriophages Viruses that attack bacteria.

benthic Referring to habitats at the bottom of aquatic environments.

biodiesel An extract of algal cells containing oils; suitable for use in engines.

biofarming The addition of contaminated soil to agricultural soil with the purpose of soil microorganisms mineralizing the organic contaminant.

biofilm Film containing microbial cells of diverse genera that are localized on a surface by extracellular matrix material.

biofuel A biological product (ethanol, methane, H2, etc.) that can be used as an engines fuel.

biogeochemical cycle The path that a nutrient or element takes as it moves through the biosphere, hydrosphere, lithosphere, and atmosphere.

biogeography The spatial distribution of organisms and the processes that bring about this distribution.

biolomics The study of all biological systems and biochemical components of a cellular system.

biomineralization The process by which microorganisms form mineral phases.

biomining The use of microorganisms to aid in the extraction and recovery of metals from ores.

bioremediation The application of microorganisms (or biological material) to detoxify organic substances or inorganic compounds.

biosignatures Characteristic morphologies or attributes, such as biominerals, found in rocks; reveal the presence of microorganisms in the past.

biosorption Metablism-independent binding of metal ions or radionuclide species to cellular components.

biosphere An entity that includes all ecosystems of Earth.

cellulose A biopolymer that consists of several dozen chains of microfibrils where each chain of glucose is held by β-1,4-glucosidic bonds.

cellulosome The structure containing enzymes for cellulose digestion; may occur on the surface of some bacterial cells.

chemoautotrophy The process in which carbon dioxide is used as the source of carbon.

chemolithotrophs Microorganisms that couple electron flow to oxidation or reduction of inorganic materials.

chemolithotrophy The process in which inorganic compounds are oxidized to generate energy for organisms.

chemoorganotrophs Organisms that utilize organic compounds as their energy sources.

chert Microcrystalline quartz that may contain microfossils.

codon Three bases in RNA that code for a specific amino acid in the synthesis or proteins.

coenocytic Referring to multinucleated cells resulting from incomplete crosswalls as is the case with some fungi.

colonization resistance The ability of the host's gut to prevent colonization by nonnative microorganisms, due at least in part to the native microbiota's actions.

commensalism Situation in which one partner benefits, while the other neither benefits nor is harmed; in mutualism both partners benefit; and in parasitism one partner is harmed while the other benefits.

community An association of species that interact and live within a physical environment.

community ecology The study of interactions among species that live together in a defined physical area and the biogeography, abundance, and distribution of the coexisting populations.

competition Activity involving two or more microorganisms seeking the same niche or nutrients.

compost A process using aerobic microbial decomposition of plant material for the production of a soil conditioner.

conjugation The genetic exchange resulting from cell–cell contact; occurs in both prokaryotic and eukaryotic microorganisms.

coprophilic Referring to organisms that have a preference for growing on fecal material.

creosote A distillation of coal tar that contains polyaromatic hydrocarbons; has been used to preserve wood in poles and railroad ties.

cryptomonad A flagellated cell with a chloroplast that may be considered as a member of either algae or protozoa.

cyanobionts Intracellular or extracellular associations of cyanobacteria with diatoms.

cyst A resting cell produced by a few bacterial or protest species; this structure is less resistant than a bacterial endospore.

dehydrogenase An enzyme that oxidizes molecules by transferring electrons to an electron carrier of NAD or cytochromes.

denitrification The conversion of nitrate to atmospheric nitrogen.

desert varnish The darkened surface on rocks in desert environments, also called rock varnish.

dinitrogen Atmospheric nitrogen, N2.

dissimilation Activity leading to the conversion of an electron acceptor to a metabolic end product; not associated with incorporation of chemicals into cell biomass.

dissimilatory reduction In microbiology, the transfer of a large number of electrons to an electron acceptor with the consequence of producing a high quantity of product from respiration.

dissimilatory sulfate reduction The use of sulfate as the final electron acceptor by chemolithotrophic organisms with the production of H2S.

disturbance An event that causes the death, displacement, or harm of or to individuals within a given population, community, or ecosystem; leads to opportunities for new individuals to replace them.

DMRB Dissimilatory metal-reducing bacteria, in which electrons from an organic are passed to an oxidized metal ion.

ecotype A group of individuals (population or subspecies) that have adapted to a particular ecological niche in which they live, becoming genetically similar.

endolithic Referring to microorganisms that live within rock in the pore spaces.

endospore The most resistant biological structure; is produced by specific bacteria.

epilimnion The surface layer of lakes, which is warmer, less dense, and sunlit.

epiphyte A microorganism growing on the surface, usually leaves, of a plant.

Eukarya One of the three phylogenomic domains of the tree of life; contains all of the eukaryotes.

eukaryote A cell or organism that has a true nuclear nucleus and internal membranes and is a member of Eukarya.

eutrophic habitats Habitats that are nutrient-rich, potentially leading to eutrophication in which oxygen levels become very low and algal blooms occur.

extracellular polymeric matrix (EPM) Polysaccharide material surrounding bacterial cells along with other polymeric material.

extremophiles Organisms that live in and have adapted to extreme conditions of pH, temperature, or salinity.

fermentation An anaerobic metabolic process of bacteria and yeast resulting in the production of desired end products including ethanol and lactic acid.

ferritin A protein consisting of 24 subunits; used to store iron in the cytoplasm of animals and a few bacteria.

filament A cluster of cells arranged in a linear form.

food chain A representation of the flow of energy within a food web, from one level to the next, showing the sequence of what is eaten by what.

food web A system representing feeding relationships within a community and linkages among food chains.

fruiting body An asexual reproductive structure produced by soil fungi and a few bacteria.

genetic engineering Activity involving the transfer of desired genes into a microorganism for the purpose of exploiting the activity of the gene product.

genomics Study of the gene content of an organism.

genotype The gene content of an organism.

glutathione A peptide consisting of three amino acids (glycine, cysteine, and glutamate); functions to protect cells against various toxicities.

Gram-negative/Gram-positive bacteria Bacteria distinguished under a microscope by differential staining procedures. Generally Gram-negative bacteria have a more diverse metabolism and grow faster than do Gram-positive bacteria.

guild A group of species that share a common ecological niche.

haustaria Specialized branches extending from a parasitic fungal cell that may be extended into a host cell.

hemicellulose The material extracted from the cell walls of plants consisting of xylose–glucose polymers or glucose–arabinose–xylose polymers.

herbicide Chemical agents that are used to kill plants.

heterocyst A specialized cell that occurs in some filamentous cyanobacteria, providing oxygen-free environments in which nitrogen fixation can take place.

heterotrophs (Or chemoorganotrophs) organisms that use organic compounds as energy sources and to obtain carbon for cellular processes.

hopanoids Heterocyclic lipids found in the membranes of bacteria. The chemical structure is similar to that of sterols such as cholesterol.

horizontal gene transfer The movement of genes between different organisms rather than by vertical transmission during cell division.

horizontal transmission A process in which endosymbionts are transferred from one individual of the host species to another or even to other species.

hydrogel A substance in which the biofilm polymer is hydrated with water, forming a viscous jelly-like matrix.

hydrogenase An enzyme that cleaves molecular hydrogen to two protons and two electrons.

hydrogenosomes Organisms found in some anaerobic microbial eukaryotes; ferment pyruvate, yielding carbon dioxide, hydrogen, and acetate. Like mitochondria, hydrogenosomes generate energy in the form of ATP.

hydrolytic reaction An enzymatic process in which water is added across a covalent bond to produce monomeric units from a dimer or polymer.

hyperthermophiles Organisms that live above 80°C.

hyphae The thread-like web of fungal cells making up the mycelium (singular hypha).

hypolimnion The bottom layer of lakes, which is colder, more dense, and darker than the epilimnion.

indigenous bacteria Bacteria normally present in the environment.

kerogen A mixture of complex organic compounds of high molecular weight that are found in sedimentary rocks.

lateral gene transfer A term often applied to horizontal gene transfer.

lignin An amorphous polymer present in woody tissue that functions to secure the cellulose fibrils together.

lyase A class of enzyme that releases a small molecule from a large compound.

magnetosomes Magnetic structures found in cells of specific bacterial species.

magnetotaxis The ability of magnetotactic bacteria to align themselves and swim along magnetic field lines.

manganese nodules Rock-like deposits of manganese and other metals found on the sea floor.

melanin An organic molecule with a complex structure that is responsible for brown to black pigmentation.

metabiomics The study of small molecules and intermediate compounds produced from metabolism.

metagenomics The culture-independent whole-genome analysis of all members of a community of microorganisms to determine the composition and functions of the microorganisms.

metallomics The study of metal ions and their activities in a biological system.

metallothionein A cytoplasmic protein containing numerous cysteine residues that bind toxic metal ions; found in eukaryotic cells and a few cyanobacteria.

metaproteomics The analysis of all proteins present in a specific environment.

methane hydrate Also known as methane clathrate; ice-containing methane in a water crystal.

methanobacteria Bacteria that grow by obtaining energy from the oxidation of methane.

methanotroph A microorganism that grows with methane as the electron donor.

methylobacteria Bacteria that grow with methanol as the electron donor.

micrite Very fine-grained (1–5-μm) calcite crystals.

microbialites Microbially produced organosedimentary benthic deposits.

microbially influenced corrosion (MIC) Also termed biocorrosion; the process by which microorganisms deteriorate metal.

microbiomics The study of all microorganisms and their interactions in an environment.

microfossils Fossils that contain cyanobacteria or other microorganisms.

microorganisms Prokaryotic, eukaryotic, and other organisms that are microscopic in nature.

mitosomes Double-membrane sacs that contain clustered mitochondria-like proteins.

mold A general name for filamentous fungi.

MTBE Methyl-(tert)-tertiary butyl ether; a gasoline additive that increases the oxygen content of the fuel.

mutualism The state where both partners benefit from a relationship.

mycelium The entire mass resulting from aggregation of fungal hyphae.

mycobiont The fungal partner in a symbiotic relationship (e.g., fungi in lichen).

nanobacteria Organisms of a specific species that have a normal growing size of 0.2–0.4 μm.

neutralism The state of two microorganisms growing in close proximity to each other without any effect (positive or negative) on the other.

nitrification The production of nitrate from nitrite or other reduced nitrogen compounds.

nitrogen fixation Also called diazotrophy; the process of reducing atmospheric nitrogen to ammonia, carried out by various bacteria and archaea in order to supply nitrogen for building proteins and nucleic acids.

nitrogenase The enzyme that converts atmospheric nitrogen to ammonia.

nucleoid The nuclear material in a prokaryotic organism.

oligotrophic Referring to habitats that are nutrient-poor and hence exhibit low productivity; a term often applied to low levels of organic carbon.

oxygenase An enzyme that incorporates molecular oxygen directly into a substrate.

oxygenic Referring to activity resulting in the generation of molecular oxygen.

parasitism The state of one organism benefiting at the expense of another organism.

pectin A mixture of branched heterogenous polysaccharides containing galacturonic acid with the polysaccharide held in the cell wall by Ca2+.

pelagic Term referring to habitats above the bottom of aquatic environments.

pesticide A chemical effective in killing unwanted agents in the environment.

phenotype The characteristics of an organism that are readily observed.

pheromones Low-molecular-weight compounds secreted by cells that are important for mating.

phosphonate A compound with phosphorus covalently linked to a carbon atom.

photobiont The photosynthetic partner in a symbiotic relationship.

photosynthesis A process in which solar energy is used to reduce carbon dioxide to carbohydrates.

phototrophy The type of metabolism in which energy from light is converted to chemical energy.

phycobilin Light-capturing molecules in red algae and cyanobacteria that transmit light energy to chlorophylls.

phylogenetics The study of relationships among organisms based on evolutionary differences and similarities.

phytic acid Common name for inositol hexaphosphate, a major storage phosphorus compound in plants.

phytochelator A cytoplasmic protein found in plant cells that contains several cysteine residues and binds toxic metal ions.

phytoplanktonMarine phytoplankton include the microscopic algae and diatoms that float in the ocean and are responsible for the bulk of marine photosynthesis.

picoplankton Very small organisms (<2 μm) that float free in the water column.

pili Linear structures of protein that extend from the surface of Gram-negative bacteria.

planktonic organisms Organisms that are not attached to surfaces.

plasmid DNA found in the cytoplasm of bacterial cells that provides the cell with special benefits.

polyaromatic hydrocarbon A water-insoluble molecule consisting of several ring structures.

POP Persistent organic pollutant.

predation The preying of one microorganism on another microorganism.

prokaryote A microorganism that does not have a true nucleus but in which DNA is distributed in the cell cytoplasm.

proteomics Study of the protein content of an organism.

Redfield ratio Our oceans show a ratio of 16–1 of nitrogen to phosphorus, which corresponds to the average ratio seen in marine phytoplankton; this is called the Redfield ratio.

resilience The ability of an ecosystem to return to its former state following a disturbance (derived from the Latin resilire, to rebound).

rhizosphere The area of soil surrounding plant roots.

ribozyme An RNA molecule with enzymatic activity.

selenomethionine An amino acid that has a selenium element substituting for sulfur in methionine.

sensory systems Systems consisting of a cascade of proteins that enable cells to respond to physical or chemical stimuli.

siderophores Small organic compounds produced by bacteria or fungi; these compounds facilitate cellular uptake of Fe3+.

silicalemma The membrane of the silica deposition vesicle in diatoms.

sludge Solid material containing a high concentration of microorganisms, inorganic precipitates, and undigested organic solids.

sorption A term used to includes adsorption and absorption; a process where a chemical moves from a soluble phase to an insoluble phase.

species A genus subdivision consisting of closely related organisms.

stability The ability of a community to return to its prior species composition, diversity, and abundance and to retain its genetic traits following a disturbance.

stromatolite The layered limestone structure developed in shallow water that results from inorganic precipitation. Some stromatolites contain fossilized microbes.

succession The replacement of one community by another over time.

sulfureta The zones in an aquatic environment where sulfur bacteria grow in association with sulfate-reducing bacteria (singular sulfuretum.

symbiogenesis A phenomenon that occurs when new physiological processes, tissues, or organs evolve as a result of a symbiotic relationship.

symbiosis A long-term association between organisms of different species; derived from the terms biosis (living) and sym (with).

syntrophism The relationship where the metabolism of one microorganism enables a second microorganism to grow.

thallus The structure or body of lichen, large fungus, or algae.

thrombolites Microbialites with macroscopically clotted mineral fabrics.

transcriptomics The study evaluating the presence of specific mRNA produced by an organism.

trichome A linear array of cells that function as a single unit.

UMB Ultramicroscopic bacteria; cells of reduced size that are produced as a result of starvation.

vegetative cells Actively metabolizing and dividing cells.

vertical transmission A process in which endosymbionts are transferred from the mother to the egg or embryo.

xenobiotic A chemical produced in the laboratory and not produced by any living system.

Chapter 1

Microbial Ecology: Beginnings and the Road Forward

1.1 Central Themes

Interdisciplinary studies addressing the origin and evolution of life stimulate many ongoing conversations and research activities.Prokaryote classification is based on biochemical and physiological activities as well as structures including cell morphology. Classification within Bacteria and Archaea domains is complicated because the definition for a prokaryotic species is currently under review.Our knowledge of the microbial diversity of Earth is growing exponentially with the discovery and implementation of molecular phylogeny to study environmental microbiology.Configuration of the “tree of life” has changed since the 1990s with the use of molecular and genomic techniques to evaluate microbial relationships.Microbial ecology as a discipline will benefit substantially from the development of a theoretical basis that draws on principles identified in general ecology.

1.2 Introduction

The study of microbial ecology encompasses topics ranging from individual cells to complex systems and includes many different microbial types. Not only is there a visual difference in examining pure cultures and unique microbial environments (see Figure 1.1), but also there is a difference in study approach in each of these images. Microbial ecology has benefited from studies by scientists from many different scientific fields addressing environments throughout the globe. At this time there is considerable interest in understanding microbial community structure in the environment. To achieve this understanding, it is necessary to identify microbes present; this can be accomplished by using molecular methods even though the microbes have not been cultivated in the laboratory. Enzymatic activities of microorganisms and microbial adaptations to the environment are contributing to our knowledge of the physiological ecology of microorganisms.

Figure 1.1 Understanding our environment through the study of cells and systems: (A) Fischerella sp; (B) electron micrographs of the triangular archaea, Haloarcula japonica TR-1 (provided by Yayoi Nishiyama); (C) Mammoth Hot Springs in Yellowstone National Park. (Photos A and B courtesy of Sue Barns). See insert for color representation

Persistent questions about microorganisms in the environment include:

Which microbes are present?What is the role of each species?What interactions occur in the microbial environment?How do microbes change the environment?

While this book provides some answers to these questions, each discovery brings with it more questions. The objective of this book is to emphasize the basics of microbial ecology and to explain how microorganisms interact in and with the environment.

1.2.1 Roots of Microbial Ecology

For centuries and long before bacteria were known, people from different regions around the world used selective procedures to influence the production of desired foods. Starter cultures were passed throughout a community to make fermented milk, and common procedures were used for fermentation of fruit juices. Pickling procedures involving normal fermentations were customary for food preservation. In various regions of the world, increased production of rice resulted from specific practices that we now understand select for the growth of nitrogen-fixing cyanobacteria. Some consider that microbiology started with the reports by Anton van Leeukenhoek (1632–1723) in 1675 with the description of “very little animacules” that have the shape of bacteria, yeast, and protozoa. The environments that van Leeuwenhoek examined included saliva, dental plaque, and contaminated water. Gradually, information on microorganisms appeared as scientists in various countries explored the environment through direct observations or experimentation (Brock 1961; Lechecalier and Solotorovsky 1965). Early discoveries relevant to microbial ecology are listed in Table 1.1 (Schlegel and Köhler 1999). The contributions of scientists to disprove the “doctrine of spontaneous generation” had a great impact on microbiology, and especially important was the presentation by Louis Pasteur (1822–1895) in 1864 at the Sorbonne in Paris. In addition to studying the role of microorganisms in diseases and their impact on our lives, Pasteur emphasized the importance of microorganisms in fermentation. Many consider that the founders of microbial ecology were Sergei Winogradsky (1845–1916) and Martinus Beijerinck (1851–1931), who were the first to demonstrate the role of bacteria in nutrient cycles and to formulate principles of microbial interactions in soil. Beijerinck worked at the Delft Polytechnic School in The Netherlands, where he developed the enrichment culture technique to isolate several bacterial cultures, including those now known as Azotobacter, Rhizobium, Desulfovibrio, and Lactobacillus. Also, Beijerinck's early studies contributed to the demonstration of the tobacco mosaic virus and provided insight into the principles of virology. Winogradsky was a Russian soil microbiologist who developed the concept of chemolithotrophy while working with nitrifying bacteria. In addition to demonstrating that bacteria could grow autotrophically with CO2 as the carbon source, Winogradsky established the concept of nitrogen fixation resulting from his experimentation with Clostridium pasteuranium. With an increased interest in microbiology, it became apparent that there was a highly dynamic interaction among microorganisms and also between microorganisms with their environment. Today the study of microbial ecology includes many different fields, and these are addressed in subsequent chapters of this book.

Table 1.1 Pioneers in the Field of Microbial Ecology

YearIndividualContribution1683Antonie van LeeuwenhoekPublished drawings of bacteria showing rods, cocci, and spirals1786Otto Friedrich MüllerReported the characteristics of 379 different species in his publication Animalcules of Infusions, Rivers and the Sea1823Bartholomeo BizioDescribed the “blood” drops in “bleeding” bread used in communion rites as attributed to Serratia marcescens1837FriedrichTraugott Küzing, Charles Cagniard-Latour, and Theodor SchwannIndependently published papers stating that microorganisms were responsible for ethanol production1838Christian Gottfried EhrenbergDescribed Gallionella ferruginea as responsible for ocher1843Friedrich Traugott KützingDescribed Leptothrix ochracea, a filamentous iron-oxidizing bacterium1852Maximilian PertyDescribed several species of Chromatium including C. vinosum1866Ernst HaeckelProposed the term ecology1877Theophile Schoesing and Achille MuntzDemonstrated that microorganisms were responsible for nitrification (NO3− → NH3)1878Anton de BerryProposed concepts of mutalistic and antagonistic symbiosis1885A. B. FrankDescribed the fungus–root symbiosis known as mycorrhiza1886H. Hellriegel and H.WilfarthDemonstrated that root nodules on legumes supplied nitrogen to plants1889Matrinus W. BeijerinckDeveloped enrichment technique that produced pure cultures of many bacteria in nitrogen–sulfur cycle1889Sergus N. WinogradskyEstablished concept of chemolithotrophy and autotrophic growth of bacteria1904L. HiltnerStudied the biology of the root zone and proposed the term rhizosphere1909Sigurd Orla-JensenPresented a natural system for arrangement of bacteria with lithoautotrophs as the most primitive bacteria

1.2.2 Current Perspectives

The study of microbial ecology includes the influence of environment on microbial growth and development. Not only do physical and chemical changes in the environment select for microorganisms, but biological adaptation enables bacteria and archaea to optimize the use of nutrients available to support growth. The prokaryotic cell was the perfect system for early life forms because it had the facility for rapid genetic evolution. As we now understand, horizontal gene transfer (Section 4.7.2) between prokaryotes serves as the mechanism for cellular evolution of early life forms to produce progeny with diverse genotypes and phenotypes. While fossils provide evidence of plant and animal evolution, fossils can also provide evidence of early animal forms that have become extinct. It is an irony in biology that the same prokaryotic organisms that evolved to produce eukaryotic organisms also participated in the decomposition of dinosaurs and other prehistoric forms. The prokaryotic form of life not only persists today but thrives and continues to evolve. It has been estimated that there are more living microbial cells in the top one inch of soil than the number of eukaryotic organisms living above ground. William Whitman and colleagues have estimated that there are 5 × 1030 (five million trillion trillion) prokaryotes on Earth, and these cells make up over half of the living protoplasm on Earth (Whitman et al. 1998). The number of bacteria growing in the human body exceeds the number of human cells by a factor of 10 (Curtin 2009). While it is impossible to assess the role of each of these prokaryotic cells, collectively groups of prokaryotic cells can have considerable impact on eukaryotic life. Analysis of the human microbiome reveals that although the microbial flora of the skin is similar, each human has a bacterial biome that is unique for that individual (Curtin 2009). Not only are microorganisms important in cycling of nutrients but they have an important role in community structure and interactions with other life forms. It would be impossible to envision life on Earth without microorganisms. Before addressing important divisions in microbial ecology, it is useful to reflect on the development of microbes on Earth.

1.3 Timeline

Formation of Earth occurred about 4.5 billion years ago, and this was followed by development of Earth's crust and oceans. Volcanic and hydrothermal activities of Earth released various gases into the atmosphere. In addition to water vapor, dinitrogen (N2), carbon dioxide (CO2), methane (CH4), and ammonia (NH3) were the major atmospheric gases, while hydrogen (H2), carbon monoxide (CO), and hydrogen cyanide (HCN) were present at trace levels. Chemical developments of prebiotic Earth relevant to the evolution of life have been critically reviewed by Williams and Fraústo da Silva (2006). The anaerobic environment on Earth provided the reducing power for the formation of the first organic compounds.

Early life forms were anaerobes that included thermophilic H2-utilizing chemolithotrophs, methanogens, and various microbes displaying dissimilatory mineral reduction. Hyperthermophilic prokaryotes are proposed to have been one of the earliest life forms, and Karl Stetter has collected over 1500 strains of these organisms from hot terrestrial and submarine environments (Stetter 2006). There is considerable abundance of these microorganisms in the environment, with 107 cells of Thermoproteus found in a gram of boiling muds near active volcanoes, 108 cells of Methanopyrus found in a gram of hot vent chimney rock, and 107 cells of Archaeoglobus and Pyrococcus found per milliliter (mL) of deep subterranean fluids under the North Sea (Stetter 2006). While the hyperthermophiles characteristically grow at 80–113°C with a range of pH 0–9.0, one archaeal species, Pyrolobus fumarii, withstands one hour in an autoclave that has a temperature of 121°C. Currently, about 90 species of microorganisms are hyperthermophiles, and some of these species are listed in Table 1.2. Most hyperthermophiles are chemolithotrophic organisms using molecular hydrogen (H2) as the electron source for energy-yielding reactions. While many of the hyperthermophilic archaea use S0 as the electron acceptor, some hyperthermophiles can couple growth to the use of Fe3+,  SO42−,  NO3−,  CO2, or O2 as electron acceptors. Molecular oxygen (O2) is a suitable electron acceptor for a few hyperthermophilic archaea, and in these cases only under microaerophilic conditions. Hyperthermophilic bacteria usually require organic material to support their anaerobic or aerobic growth. Many of the anaerobes have active systems using H2 as the electron donor.

Table 1.2 Examples of Hyperthermophilic Prokaryotes

Genera of ArchaeaGenera of BacteriaAcidianusArchaeoglobusAquifexFerroglobusDesulfurobacteriumIgniococcusThermocrinisMetallosphaeraThermotogaMethanopyrusThermovibrioMethanothermusNanoarchaeumPyrococcusPyrodictiumPyrolobusSulfolobusThermococcusThermofilumThermoproteus

The biological production of methane is considered to be an ancient process and would have been attributed to prokaryotes catalyzing the following reaction:

When organic compounds such as acetate accumulated in the environment, methanogens could have produced methane from methanol, formate, or acetate. Only members of the Archaea domain are capable of methane production.

Chemoautotrophic microbes could have evolved to grow on the energy from oxidation of molecular hydrogen and reduction of carbon dioxide according to the following reaction:

In addition to the production of H2 from geologic formations, ultraviolet radiation could have released H2 according to the following reaction:

Another source of H2 would be the radiolysis of water attributed to alpha radiation (Landström et al. 1983). With the accumulation of diverse organic compounds in the environment, heterotrophic prokaryotes metabolizing organic carbon materials would have appeared sometime after the chemoautotrophs were established.

As presented in Figure 1.2, anaerobic photodriven energy activities may have been present ∼3 billion years ago, using light to activate bacteriorhodopsin-like proteins to pump ions across cell membranes. The bacteriorhodopsin type of photodriven energetics would have been followed by chlorophyll-containing anoxygenic bacterial photosynthesis involving purple and green photosynthetic bacteria where H2S was the electron source. While microbial evolution was initially in the marine environment, microorganisms may have migrated to dry land about 2.75 billion years ago (Rasmussen et al. 2009). Cyanobacteria with oxygenic photosynthesis produced the aerobic atmosphere, and this has been called the “great oxidation event.” Since O2 was produced from water by the photocatalytic process, the rate of O2 released was not limited by availability of water.

Figure 1.2 Early development of life.

Once molecular oxygen was released into the atmosphere, it reacted with reduced iron and sulfur compounds (i.e., FeS and FeS2) to produce oxidized inorganic compounds by both microbial and abiotic processes. Gradually the O2 level in Earth's atmosphere increased and by ∼1.78–1.68 billion years ago oxygen respiration could have been used to support the growth of the first single-cell eukaryotes (Rasmussen et al. 2008). Another important development of an aerobic atmosphere was the generation of ozone (O3) from O2 due to a reaction with ultraviolet light. Ozone absorbs ultraviolet light and forms a protective layer in the atmosphere to shield Earth from destructive activity of ultraviolet radiation (Madigan et al. 2009). Prior to the development of an ozone layer, microorganisms would have been growing only in subsurface areas or in environments shielded by rocks.

1.4 Microfossils

Fossils are important for understanding the evolution of plants and animals; however, there are few fossils available for microorganisms. Dating of dinosaur presence can be derived from bone fragments or footprints left in mud (Figure 1.3). As depicted in Figure 1.4, footprints can provide considerable information about the presence of life; however, the early history of microorganisms is relatively sparse. Electron microscopy of aggregates found in the Archean Apex chert of Western Australia revealed cell-like structures characteristic of cyanobacterial trichomes, and these were reported to be 3.5 billion years old (Schopf 1993). However, the inability to demonstrate appropriate biomarkers in the microfossils has generated concern about the dating of these images (Rasmussen et al. 2008). Fossilized stromatolites (see Section 11.9 for additional information) consisting of mats of cyanobacteria and other microorganisms were reported to be present in rocks from the Warrawoona Group in Western Australia. Images of bacteria are suggested in scanning electron micrographs of rocks that are 3.4 billion years old from the Barberton Greenstone Belt, South Africa. From carbonaceous chert in the Ural Mountains there are structures resembling the bacterium Gleodiniopsis, and this has been dated to be 1.5 billion years old. Microfossils of the cyanobacterium Palaeolyngbya are 950 million years old and were found in the Khabarousk region in Siberia.

Figure 1.3 Dinodaur footprints present on surface stone in Texas (A) and Arizona (B). [Photograph (A) by Diana Northup, (B) by Larry Barton]. See insert for color representation.

Figure 1.4 Examples of organisms present in a specific environment: footprints of several animals and shell records; exhibit at the educational center in Albuquerque museum (photograph by Larry Barton). See insert for color representation.

Konhauser (2007) has critiqued the use of Archean microfossils in dating primitive aerobic phototrophs. Some scientists maintain that the mere presence of kerogen in microfossils is not sufficient to indicate biogenic origin. Biomarkers useful in suggesting the presence of prokaryotes would be the lipid soluble hopanes and steranes that would be derivatives of hopanoids and sterols, respectively. Degradation products of these compounds are useful in assessing the biogenic character of microfossils because hopanoids are lipids characteristically found in the plasma membrane of prokaryotes and sterols are typically found in the membranes of eukaryotic cells. An additional significance in finding derivatives of sterols in microfossils is that molecular O2 is required for one of the final enzyme steps in the biosynthesis of sterols. Of course, definitive proof of life in the microfossils would be the detection of DNA or decomposition products of DNA.

1.5 Early Life

The origin of life on Earth is a topic that has attracted the attention of many scientists and has resulted in publication of numerous fascinating opinions. In a more recent review, Koch and Silver (2005) discuss the stages required in development of chemical processes into a biological unit. The transition from an abiotic environment to a world with microorganisms is summarized in Figure 1.5. Using cellular evolution as a perspective, early development of the evolutionary tree of life could be divided into various phases (Koch and Silver 2005): (1) the pre-Darwinian phase, which represents Earth's environment prior to the formation of a cell; (2) the proto-Darwinian phase, during which the first cell was formed; and (3) the Darwinian phase, which involved selective pressures on cell development that favored diverse forms of prokaryotes and eukaryotes.

Figure 1.5 Evolutionary development of early life [modified from Koch and Silver (2005)].

1.5.1 The Precellular World

The precellular phase would involve astrophysical and geochemical activities at a time before the presence of biological cells. The activities involved in formation of small organic molecules (e.g., sugars, amino acids, lipids, porphyrins, nucleotides, heterocyclic bases) may have been unrelated. There are several different opinions concerning the energy sources and sites or regions where synthesis of organic molecules may have occurred. Wächtershäuser (1990) proposed that the organic macromolecules were produced on clay-like surfaces, while Koch (1985) and Deamer (1997) supported the idea that vesicles enclosed with membrane-like structures were involved in the formation of organic molecules. Some have supported the idea that life arose from a “primordial soup” in a lake on the surface of Earth, while others consider that life arose from a subsurface spring. All of these theories provide for an interesting interplay of geochemical processes that may have culminated in biological activity.

1.5.2 The First Cell

Prior to the first living cell, various organic compounds presumably accumulated in the environment. Koch and Silver (2005) propose that prebiotic compounds could have included nucleic acid inside a vesicle and that the vesicle had a mechanism for generating an ionic charge across the membrane barrier. It was not necessary for this first cell-like unit to have enzymes for metabolism, nor was there a requirement for ATP, ribosomes, proteins, or DNA. The presence of a self-replicating single-stranded RNA with autocatalytic activity, also known as ribozyme, could provide a basis for development of molecular biology in this evolutionary process. The membrane provided a lipid closure for the vesicle, and in terms of structure and composition the early membrane may have been different from current unit membranes.

Energy is paramount for development of life and could have resulted from the following reaction:

The oxidation of inorganic compounds (see Section 11.3 for additional information), such as given in the reaction above, could have provided the potential for various reactions, including the generation of an ionic gradient across the membrane. This vesicular structure would not yet be a cell but could evolve into a cell after acquiring DNA, proteins for metabolism, ribosomes, ATP, and related components. The presence of RNA in the first membrane vesicle would have been useful because even a small RNA molecule is highly charged and could nonspecifically bind protein and small organic molecules found in the environment. DNA replaced RNA as the molecule carrying genetic information and was more stable than RNA. Undoubtedly, the time required for development of the first self- replicating unit (cell) was considerable, but once this process was achieved, cellular evolution proceeded at an accelerated rate. The extent of evolution by eukaryotes is apparent when reviewing the diversity of eukaryotic life forms, but it should be recalled that eukaryotes have been on Earth for only one-third as long as prokaryotes.

1.5.3 Development of Cellular Biology

With the presence of DNA and other protein-synthesizing materials inside the membrane vesicle, the cell had the capability for heredity with new phenotypes expressed. Evolution leading to different lifestyles and life forms could follow selection based on the hypothesis of Alfred Wallace and Charles Darwin. The bacterial and archaeal species surviving and reproducing in an environment were the ones capable of dealing with that environment. The evolutionary process was not continuous, but changes in genetic information would have been displayed by periodic environmental changes providing the selective pressure that led to new cell types. Genetic variation in these asexual microorganisms would be attributed to mutations and horizontal (lateral) gene transfer (Section 4.7.2). There is no record suggesting the events responsible for the universal ancestor to produce two lineages of prokaryotes (i.e., Bacteria and Archaea). Many of the biomolecules and biochemical processes found in Bacteria and Archaea are similar, but numerous details in accomplishing certain activities distinguish organisms of these two domains. Since prokaryotes were the only living organisms on Earth for over 2 billion years, it is rather remarkable that only two prokaryotic cell types were produced.

One theory for the formation of a eukaryotic cell is the establishment of a nucleus prior to the development of mitochondria and chloroplasts by endosymbiosis (see Section 8.2 for additional information). The genome fusion hypothesis has been developed to explain the formation of the eukaryotic nucleus where the eukaryotic genome arose from a combination of archaeal and bacterial genes. An examination of energy production and chemistry of lipids in the cell membrane reveals that eukaryotic cells are more similar to Bacteria than to Archaea. However, when examining transcription and translation processes, eukaryotes have characteristics of the Archaea. As the genome of the ancestral eukaryote increased in size, chromosomes were developed to enhance organization of DNA, and it has been proposed that the nuclear membrane arose spontaneously to segregate DNA from the cytoplasm. More recently it has been discovered that one bacterial species has a “primitive” nuclear membrane (see Section 3.8.3), and the function of this internal membrane is unresolved.

The endosymbiotic hypothesis (see Section 8.2) addresses the origin of chloroplasts and mitochondria where both of these organelles developed from bacteria. Lynn Margulis (see “Microbial spotlight” in Chapter 8) suggests that the formation of the eukaryotic cell is a product of several sequential endosymbiotic steps. Spirochete bacteria were an early surface symbiont with an anaerobic organism resulting in motility of the eukaryotic cell. Endosymbiotic activity contributed to the development of mitochondria and chloroplasts. The endosymbyote provided the host with a capability useful to the host cell, while the endosymbiont benefited from nutrients and a safe environment provided by the host. Some have proposed that the primitive eukaryotic cell receiving the endosymbiont was derived from the archaeal cell line. Genes for the synthesis of bacterial-like membranes may have been transferred to the host archaeal cell and may have promoted the early development of cytoplasmic membranes. The genome of Rickettsia prowazekii, a member of the Alphaproteobacteria, is remarkably similar to the mitochondrial genome, and additional inspection is required to determine whether it was the source of the mitochondria or if both the mitochondria and rickettsia evolved from a common ancestor. Most likely chloroplasts developed in the cell line producing higher plants. Chloroplasts in green algae and higher plants could have evolved from Prochloron, a cyanobacterium, because it is the only aerobic photosynthetic cell that has both chlorophyll a and b.

An alternate idea pertaining to development of organelles in eukaryotes is the hydrogen hypothesis. The endosymbiont in this situation is proposed to be an anaerobic member of the Alphaproteobacteria that releases CO2 and H2 as end products. This endosymbiont is proposed to evolve along two distinct lines to produce a hydrogenosome for anaerobic metabolism and a mitochondrion for aerobic respiration. The hydrogenosome (Figure 1.6) would obtain ATP from pyruvate metabolism with the release of CO2 and H2. From genome analysis, it appears that there is considerable similarity between the genomes of hydrogenosomes and mitochondria.

Figure 1.6 Hydrogenosome in the eukaryotic cell.

1.5.4 Evolution of Metabolic Pathways

The origin and evolution of metabolic pathways were important for molecular evolution and are attracting considerable attention (Canfield et al. 2006; Falkowski et al. 2008; Fani and Fondi 2009; Fondi et al. 2009). Many consider that ancestral cells, in comparison to current prokaryotic cells, had relatively few genes, no gene regulation, and no mobile genetic elements. While early cells may have had only a few hundred genes, the expansion of the genome to several thousand genes per cell could be explained by the “patchwork” hypothesis (Jensen 1976; Ycas 1974), in which genes encoding for enzymes of low specificity were duplicated, and through selective pressures evolved into genes encoding for enzymes of considerable specificity. In terms of gene duplication there could be duplication of the entire gene, a part of a gene, or several genes from the same or different metabolic pathway. Gradually the primordial cells expanded their metabolic capabilities and established regulatory mechanisms. Cells with efficient metabolic pathways were selected through pressures of population growth. Genetic exchange between cells involving horizontal gene transfer and fusion of protoplasmic prokaryotic cells would have been important in early evolutionary processes. Initially it may have been more important for transfer of operational genes than for transfer of genes involved in information processing (transcription, translation, etc.). Abiotic geochemical cycles were replaced (or supplemented) by biotic processes, resulting in interconnection of biogeochemical cycles.

1.6 Characteristics of Microbial Life

The characteristics of life that have become associated with microorganisms are similar to those of higher plants and animals. A distinguishing feature is that for microorganisms a cell constitutes the individual while with higher forms of life the individual is multicellular and even contains numerous tissues. The biochemical and physiological processes seen in microorganisms are compared in Table 1.3. Introductory courses in biology include a listing of the characteristics defining life, and it is important to reflect on these characteristics of life since they also pertain to prokaryotes. The following discussion addresses how bacteria and archaea conform to the requirements of a defined structure, metabolism, growth, reproduction, and response to stimulus.

Table 1.3 Selected Phenotypic Characteristics of Bacteria, Archaea, and Eukarya

1.6.1 Structure and Evolution of Cell Shape

Cells of microorganisms have a precise organization and their structure is continuous with their progeny. While crystals of minerals show organization due to alignment of inorganic atoms, differences in crystal organization occur as seen in the differences in the structure of snowflakes. Structural organization in microbial cells reflects the molecular alignment in membranes, ribosomes, protein cell walls, DNA, and other macromolecules. The molecular architecture in the cell walls of microorganisms is reproduced in the progeny of each species. An example of this structural organization is seen in the mosaic arrangement seen on the surface of bacteria and archaea that have been designated as the S layer. Glycoproteins form a lattice with the precision of crystalline minerals, and models of the lattice are shown in Figure 1.7.

Figure 1.7 S layer of microorganisms as examined with freeze-etched preparations or atomic force microscopy displays a surface composed of proteins in four different lattice formations: (A) oblique lattice; (B) square lattice; (C) hexagonal–triangular lattice; (D) hexagonal rosette lattice [modifed from Sleytr et al. (1996)].

Another example of an important structure in prokaryotes is the plasma membrane or cell membrane, which functions as a barrier to segregate molecules essential for cellular growth from the extracellular environment. The chemical structure of the plasma membrane includes lipids that form a hydrophobic barrier and proteins that contribute to solute transport, metabolic processes, and communication between the cytoplasm and the environment. Lipids found in prokaryotes consist of phospholipids and fatty acids or fatty acyl groups attached to the glycerol backbone. Although there is a molecular distinction in the lipids found in archaeal and bacterial cells, lipophilic affinity of these molecules functions to stabilize the plasma membrane (Madigan et al. 2009). Phosphate moieties and other charged groups on the surface of the membranes are important for carrying the charge on the membrane. Integrity of the membrane structure is required for cell viability, and disruption of this organization results in cell death.

The cell wall is an important structure for bacterial and archaeal cells in that it prevents osmotic disruption of the cell and contributes to cell shape. For bacteria, rigidity of the cell wall is attributed to a macromolecule called peptidoglycan that consists of a sugar polymer with a covalent crossbridge to peptides. Even after disruption of the bacterial cell, the structure of the peptidoglycan is evident (see Figure 1.8). N-Acetylglucosamine and N-acetylmuramic acid make up the dimer that contributes to the linear strength of the peptidoglycan molecule. As discussed in general texts (Madigan et al. 2009), the crossbridge peptide in the peptidoglycan contains alternating d and l forms of amino acids. Considerable similarity of cell wall composition is found in all of the various types of bacteria; the quantity of peptidoglycan surrounding Gram-positive bacteria is greater than that found with Gram-negative cells. While the cell wall in archaea does not contain peptidoglycan, the covalent bonds attributed to polymers of l forms of amino acids and sugars provide for structural stability of the archaeal cell.

Figure 1.8 Remnants of the peptidoglycan structure of Bacillus stearothermophilus after distrution of bacterial cell by high-pressure treatment (electron micrograph provided by Sandra Barton).

Specific proteins account for cell division and cellular form for prokaryotic cells. For cell division, there are a series of proteins located on the inner side of the cell membrane, and prior to binary fission many of these proteins polymerize to form the FtsZ ring located at the midpoint of the cell. The FtsZ ring recruits other proteins for the division process and is present in both archaea and bacteria. To underscore the evolutionary relationship between prokaryotes and eukaryotes, FtsZ-like proteins are also found in chloroplasts, mitochondria, and cell division proteins in eukaryotes. Additional proteins on the inner side of the cell membrane in bacteria and archaea are the MreB proteins (Figure 1.9). The MreB proteins influence the localized synthesis of the cell wall and account for the rod-shaped cell form. Bacteria without the genes for the production of MreB proteins are of the coccus form. Scientists speculate that the ancestral cell was spherical and the rod form appeared with the development of the specific gene for MreB synthesis. Some bacteria have a curved rod shape also known as a vibrio form. In one vibrio-shaped bacterium, Caulobacter crescentus (Section 3.6), the cell shape is attributed to crescentin in addition to MreB. The crescentin proteins accumulate on the concave face of the vibrio cell and contribute to the curvature of the cell. Since proteins similar to crescentin have been found in another vibrio, Helicobacter, some have suggested that unique proteins are needed to produce a curved bacterial cell.

Figure 1.9 Localization of FtsZ and MreB proteins in a bacterial cell.

1.6.2 Metabolism and Use of Energy

Microbial cells use chemical energy from organic compounds, minerals, and light-driven reactions. While solar energy is restricted to microorganisms at Earth's surface, the use of reduced organic compounds or inorganic materials provides energy for metabolic reactions in anaerobic and aerobic environments. A hallmark characteristic of living systems is the flow of electrons from electron donors to electron acceptors, and this characteristic is observed in both aerobic and anaerobic cultures (see discussion on energetics in Chapter 3). The generation of ATP and establishment of a charge on the cell membrane are coupled to this electron flow. As indicated in the model in Figure 1.10, energy from cell metabolism is also used for motility and nutrient transport. As with other life forms, metabolism in microorganisms is the summation of incremental changes. Additionally, there is a similarity in all forms of life in that electron transfer is mediated by cytochromes, quinones, and proteins with iron–sulfur centers; however, considerable variability of these electron carriers distinguishes prokaryotes from mitochondria-containing life forms. In terms of transmembrane movement, nutrient transport is driven by chemiosmotic or ion gradients in all living cells with prokaryotes commonly relying on H+- or Na+-driven transporters.

Figure 1.10 Energy flow in microorganisms.

1.6.3 Growth, Reproduction, and Development