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Processes in Microbial Ecology - Expanded Table of Contents

PME2012-FinalFrontcover.jpgby David L. Kirchman

Oxford University Press

First Edition, March 2012

Order it from: OUP USA, OUP UK, or Amazon

368 pages; 200 illustrations; 9.7 x 7.4


Table of Contents: Expanded


Chapter 1 Introduction

What is a Microbe?
Why Study Microbial Ecology?

Microbes cause diseases of macroscopic organisms, including humans
Much of our food depends on microbes.
Microbes degrade or detoxify pollutants.
Microbes can be useful model systems for exploring general principles in ecology and evolution.
Some microbes are examples of early life on earth and perhaps of life on other planets.
Microbes mediate many biogeochemical processes that affect global climate.
Microbes are everywhere, doing nearly everything.

How do we Study Microbes in Nature?
The Three Kingdoms of Life: Bacteria, Archaea, and Eucarya
Functional Groups of Microbes

Autotroph versus heterotroph
Phototroph versus chemotroph

Sources of Background Information

Chapter 2 - Elements, Biochemicals, and Structures of Microbes

Elemental Composition of Microbes
Elemental Ratios in Biogeochemical Studies
C:N and C:P Ratios for Various Microbes
Biochemical Composition of Bacteria
Biochemical Composition of Eukaryotic Microbes
Explaining Elemental Ratios
Architecture of a Microbial Cell

Membranes of microbes and active transport
Cell walls in prokaryotes and eukaryotes

Components of Microbial Cells as Biomarkers
Contribution of Microbes to Detrital Organic Material

Aquatic microbes and DOM
Soil organic material and microbes

Extracellular Structures

Extracellular polymers of microbes
Flagella, cilia, fimbriae and pili

Chapter 3 - Physical-Chemical Environment of Microbes

The effect of temperature on reaction rates
Salt and Osmotic Balance
Oxygen and Redox Potential
The Consequences of Being Small
Microbial Life In Natural Aquatic Habitats
Motility and taxis
Submicron- and micron-scale patchiness in aqueous environments
Microbial Life in Soils

Water content of soils
Interactions between temperature and water content in soils

The Biofilm Environment

Chapter 4 - Microbial Primary Production and Phototrophy

Basics of Primary Production and Photosynthesis

Light and algal pigments
Transport of inorganic carbon
The carbon dioxide-fixing enzyme

Primary Production, Gross Production and Net Production
Primary Production by Terrestrial Higher Plants and Aquatic Microbes
The Spring Bloom and Controls of Phytoplankton Growth
Major Groups of Bloom-Forming Phytoplankton

Coccolithophorids and the biological pump
Phaeocystis and dimethylsulfide
Diazotrophic filamentous cyanobacteria

After the Bloom: Picoplankton and Nanoplankton
Competition for limiting nutrients
Primary Production by Coccoid Cyanobacteria
Photoheterotrophy in the Oceans

Uptake of DOM by algae
Aerobic anoxygenic phototrophic bacteria
Rhodopsin in photoheterotrophic bacteria
Ecological and biogeochemical impacts of photoheterotrophy

Chapter 5 - Degradation of Organic Material

Mineralization of Organic Material in Various Ecosystems
Who Does Most of the Respiration on the Planet?

Slow and fast carbon cycling pathways

Chemical Characterization of Detrital Organic Material

Dissolved organic material

Detrital Food Webs
DOM and the Microbial Loop
Hydrolysis of High Molecular Weight Organic Compounds

Lignin degradation

Uptake of Low Molecular Weight Organic Compounds: Turnover versus Reservoir Size
Chemical Composition and Organic Material Degradation
Release of Inorganic Nutrients and its Control
Photo-Oxidation of Organic Material
Refractory Organic Matter

Chapter 6 - Microbial Growth, Biomass Production and Controls

Are Bacteria Alive or Dead?

Activity state of bacteria in soils and sediments
Activity state of soil fungi

Microbial Growth and Biomass Production

Growth of pure cultures in the lab: batch cultures
Growth of pure cultures in the lab: continuous cultures

Measuring Growth and Biomass Production in Nature
Bacterial Biomass Production In Aquatic Environments
Bacterial growth rates in aquatic environments
Growth Rates of Bacteria and Fungi in Soils
What Sets Biomass Production and Growth by Microbes in Nature?

Temperature effects on growth and carbon cycling
Temperature effects on fungi versus bacteria in soils
Limitation by organic carbon
Limitation by inorganic nutrients
Co-limitation and interactions between controlling factors

Competition and Chemical Communication Between Organisms

Chapter 7 - Predation and Protists
Bacterivory and Herbivory in Aquatic Habitats
Grazers of Bacteria and Fungi in Soils and Sediments
Grazing Mechanism for Protists
Factors Affecting Grazing

Prey number and predator-prey cycles
Size relationships of predator and prey
Chemical recognition and composition

Defenses Against Grazing
Effect of Grazing on Prey Growth
Grazing by Ciliates and Dinoflagellates

Ciliates as herbivores in aquatic ecosystems
Ciliates in soils and sediments
Heterotrophic dinoflagellates

Fluxes from Microbial Food Webs to Higher Trophic Levels
Mixotrophic Protists and Endosymbiosis
Phagotrophy, endosymbiosis and algal evolution

Chapter 8 - Ecology of Viruses

What Are Viruses?
Viral Replication
Temperate Viruses in Nature
Contact Between Host and Virus at the Molecular Scale
The Number of Viruses in Natural Environments

Counting viruses by the plaque assay
Counting viruses by microscopy
Variation in viral abundance in nature

Mortality of Bacteria Due to Viruses

Percentage of infected cells
The viral reduction method

Contribution of Viruses Versus Grazers to Bacterial Mortality
Viral Production and Turnover
Viral Decay and Loss
Viruses of Phytoplankton
Viruses are not Grazers

Viral shunt and DOM production
Population dynamics of a virus and its host

Genetic Exchange Mediated by Viruses

Chapter 9 - Community Structure of Microbes in Natural Environments

Taxonomy and Phylogeny via Genes
Introduction to 16S rRNA-based methods
The Species Problem
Diversity of Bacterial Communities
The Paradox of the Plankton
Differences Between Cultivated and Uncultivated Microbes
Types of Bacteria in Soils, Freshwaters and the Oceans
Archaea in Non-Extreme Environments
Everything, Everywhere?
What Controls Diversity Levels and Bacterial Community Structure?

Temperature, salinity, and pH
Moisture and soil microbial communities
Organic material and primary production
Predation and viral lysis

Problems with 16S rRNA as a Taxonomic and Phylogenetic Tool
Community Structure of Protists and Other Eukaryotic Microbes
Types of protists and other eukaryotic microbes in nature
Relevance of Community Structure to Understanding Processes

Chapter 10 - Genomes and Metagenomes of Microbes and Viruses

What are Genomics and Environmental Genomics?
Turning Genomic Sequences into Genomic Information
Lessons from Cultivated Microbes

Similar rRNA genes, dissimilar genomes
Genome size
Organization of eukaryotic versus prokaryotic genomes
Growth rates and genomics
Chromosomes, plasmids and replicons
Lateral gene transfer

Genomes from Uncultivated Microbes: Metagenomics

Metagenomic approaches
The proteorhodopsin story and others

Metagenomics of a Simple Community in Acid Mine Drainage
Useful Compounds from Metagenomics and Activity Screening
Metatranscriptomics and Metaproteomics
Proteomics and metaproteomics
Metagenomics of Viruses
RNA viruses

Chapter 11 - Introduction to Anaerobic Processes

Introduction to Anaerobic Respiration
The Order of Electron Acceptors
Oxidation of Organic Carbon by Various Electron Acceptors

Limited by concentrations and supply
Effect of chemical form

The Anaerobic Food Chain

Interspecies hydrogen transfer and syntrophy

Sulfate Reduction
Electron donors for sulfate reduction
Sulfur Oxidation and the Rest of the Sulfur Cycle
Non-phototrophic sulfur oxidation
Sulfide Oxidation by Anoxygenic Photosynthesis
The Carbon Source for Sulfur Oxidizers
Methane and Methanogenesis

Aerobic methane degradation
Anaerobic methane oxidation

Anaerobic Eukaryotes

Chapter 12 - The Nitrogen Cycle

Nitrogen Fixation

Nitrogenase, the nitrogen-fixing enzyme
Solving the oxygen problem
N2 fixation in nature
Limitation of N2 fixation

Ammonium Assimilation, Regeneration, and Fluxes

Ammonium release in anoxic systems
Ammonium uptake versus regeneration, immobilization versus mobilization

Ammonia Oxidation, Nitrate Production and Nitrification

Aerobic ammonia oxidation by bacteria
Archaeal ammonia oxidation
Controls of aerobic ammonia oxidation

Nitrite Oxidation and the Second Step In Nitrification
Anaerobic Ammonia Oxidation
Dissimilatory Nitrate Reduction and Denitrification
Ammonium versus N2 as final products of dissimilatory nitrate reduction
Denitrification Versus Anaerobic Ammonium Oxidation
Sources and Sinks of Nitrous Oxide
Balancing N Loss and N2 Fixation

Chapter 13 - Introduction to Geomicrobiology

Cell Surface Charge, Metal Sorption, and Microbial Attachment

Metal sorption
Iron uptake mediated by siderophores and other metal ligands

Attachment of Microbes to Surfaces
Biomineralization by Microbes

Carbonate minerals
Phosphorus minerals
Iron mineral formation by non-enzymatic processes
Magnetite and magnetotactic bacteria

Manganese and Iron-Oxidizing Bacteria

Iron oxidation
Manganese-oxidizing bacteria

Weathering and Mineral Dissolution by Microbes

Dissolution by acid and base production
Dissolution by low and high molecular weight chelators

Geomicrobiology of Fossil Fuels

Chapter 14 - Symbiosis and Microbes

Microbial Residents of Vertebrates
Microbial Symbioses with Insects

Microbial symbionts in termites
Aphids-Buchnera symbiosis
Symbiotic relationship between ants and fungi

Symbiotic Microbes in Marine Invertebrates

Endosymbionts in Riftia and other sulfide-oxidizing symbionts
Bioluminescent symbionts in the oceans

Microbe-Plant Symbioses

Diazotrophic bacteria and plant symbioses
Fungi-plant symbioses

Concluding Remarks


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