Microbial Ecology of the Oceans, 2nd Edition

by Editor: David L. Kirchman (Graduate College of Marine Studies, Univ. of Delaware, Lewes, Delaware); Ralph Mitchell (Harvard Univ., Cambridge, Massachusetts)

• ISBN13: 9780470438626
• ISBN10: 0470438622
• Format: eBook
• Copyright: 2010-06-01
• Publisher: Wiley-Liss

Summary

"I would strongly recommend it for library purchase and the reading list of advanced students in this field." -Microbiology Today, May 2009Nearly a decade since its landmark publication, this book has been thoroughly revised in this valuable new editionLike the successful first edition, Microbial Ecology of the Oceans, Second Edition is unique and fills a void in the rapidly growing fields of marine microbiology, microbial ecology, and microbial oceanography. Here, a carefully selected team of international experts explores issues of enduring importance to microbial ecologists, including: Genomes and metagenomes of marine microbes Microbial evolution, as revealed by molecular techniques Microbes in carbon budgets and cycles Viruses and grazers of bacteria Microbes and N cycle reactions in sediments The role of microbes in food web dynamics Biogeochemical cycles in the oceanIn addition to drawing on the long history of microbiology, the contributors also include discussions of the latest advances in biological and chemical oceanography to examine the role of microbes and viruses in the oceans.Richly illustrated with black-and-white photographs and drawings, and complemented with a comprehensive list of additional reading for each chapter, this important new edition provides readers with current information in the fields of marine microbiology and microbial ecology. It is designed for students and researchers in biological and chemical oceanography, geochemistry, marine chemistry, freshwater ecology, and general microbiology. It is also appropriate for professionals and advanced students in related fields.

Table of Contents

Preface

ContributorS

Introduction and Overview

Eukaryotic Phytoplankton and Cyanobacteria

Photoheterotrophic Bacteria

Dissolved Organic Material

Heterotrophic Bacteria

Marine Archaea

Heterotrophic Protists

Nanoflagellates (2-20 µm)

Microzooplanktonic Protists (20-200 µm)

Dinoflagellates

Marine Fungi

Marine Viruses

N2 Fixers

Nitrifiers and Other Chemolithotrophs

Denitrifiers

Understanding Roles of Microbes In Marine Pelagic Food Webs: A Brief History

Pre-1950s: The Early Years

1950-1974

1970s-1980s

Improvement in Methods

Bacterial Abundance

Bacterial Activity

Marine Heterotrophic Protists

The "Microbial Loop"

1990-Present: The Molecular Revolution

Bacterial and Archaeal Community Structure and Its Patterns

Major Groups of Prokaryotes in Seawater

"Classically" Culturable Bacteria

The Roseobacter Clade of Marine Alphaproteobacteri a

Gammaproteobacteria

Bacteroidetes

Cyanobacteria

"Sea Water" Culturable Bacteria

SAR11 Cluster

Not-Yet-Cultured Bacteria

Marine Gammaproteobacterial Clusters

Actinobacteria

SAR116 Cluster

SAR202

Marine Group A

Marine Group B

Betaproteobacteria

Marine Archaea

Bacterioplankton Diversity

Species Concept

Microdiversity

Components of Diversity: Richness and Evenness

Community Structure: Description and Factors

Bottom-Up Control

Sideways Control

Top-Down Control

"Kill the Winner" Hypothesis

Temporal Variation (Days to Seasonal)

Short-Term Variation

Seasonal Variation

Spatial Variation

Microscale Patterns

Global Distribution

Latitudinal Gradient and Degree of Endemism

Patchiness and Large Eddies

Genomics and Metagenomics of Marine Prokaryotes

The Basics of Prokaryotic Genomics

Genome Sequence and Assembly

Finding Genes

Finding Operons

Functional Annotation

Tame or Wild? Pure-Culture Genomics Versus Metagenomics

Genomics in Marine Microbial Ecology

The Ecology of Genome Composition

Reverse Biogeochemistry: Discovery of New Ecological Processes

Environmental Reductionism: New Details About Recognized Processes

Comparative Genomics and Metagenomics

Future Directions

Photoheterotrophic Marine Prokaryotes

Facultative Photoheterotrophy by Unicellular Cyanobacteria

Cyanobacteria as Facultative Heterotrophs

Uptake of Urea and DMSP

Uptake of Nucleosides and Amino Acids

Field Studies Using Light and Dark Incubations

Implications of Facultative Photoheterotrophy by Cyanobacteria

Marine AAnP Bacteria: Habitats and Diversity

Rediscovery of the Marine AAnP Bacteria

Diversity of AAnP Bacteria

Physiology of AAnP Bacteria

AAnP Bacterial Abundance and Ecological Significance

Proteorhodopsin-Containing Prokaryotes

Proteorhodopsin Genotypes and Taxonomic Distributions

Proteorhodopsin Spectral Tuning

Proteorhodopsin-Containing Prokaryotes: Abundance and Activity

Proteorhodopsin-Containing Prokaryotes: Ecological Significance

Ecology and Diversity of Picoeukaryotes

Functional Roles, Classification, and Biological Traits

Photoautotrophs

Heterotrophs and Alternative Lifestyles

Environmental Diversity and Molecular Phylogenetics

Diversity of Uncultured Populations

Methodological Issues for envPCR Studies

Distribution, Abundance, and Activities

Methods for Quantifying Mixed Assemblages

Distribution, Abundance, and Activity of Mixed Picophytoplankton Assemblages

Quantifying Specific Picoeukaryote Populations

Methodological Challenges to Quantifying Specific Populations and Resolving Dynamics

Mortality, Contributions to Microbial Food Webs, and Microbial Interactions

Genomic Approaches to Picoeukaryote Ecology

Integration of Picoeukaryotes to the Microbial Food Web: Research Directions

Organic Matter-Bacteria Interactions in Seawater

Organic Matter Inventory and Fluxes

DOM-Bacteria Interactions

Labile Low-Molecular Weight (LMW) DOM

Extracellular Hydrolytic Enzymes

Polymeric DOM-Protein as a Model

Refractory DOM

POM-Bacteria Interactions

POM Continuum

POM Fluxes

POM-Mineral Interactions

Bacterial Community Structure and Utilization of Organic Matter

Future Challenges

Physiological Structure and Single-Cell Activity in Marine Bacterioplankton

Distribution of Physiological States in Bacterioplankton Assemblages

The Concept of "Physiological Structure" of Bacterioplankton Assemblages

Starvation, Dormancy, and Viability in Marine Bacterioplankton

Describing the Physiological Structure of Bacterioplankton

Single-Cell Properties and Methodological Approaches

Operational Categories of Single-Cell Activity

Regulation of Physiological Structure of Marine Bacterioplankton

Factors Influencing Physiological State of Bacterial Cells in Marine Ecosystems

Factors Influencing Loss and Persistence of Physiological Fractions

Distribution of Single-Cell Characteristics in Marine Bacterioplankton Assemblages

Distribution of Single-Cell Activity and Physiological States in Marine Bacterioplankton

Simultaneous Determination of Several Aspects of Single-Cell Activity and Physiology

Patterns in Distribution of Single-Cell Activity and Physiology Along Marine Gradients

Distribution of Activity and Growth Among Bacterial Size Classes

Distribution of Activity Across and Within Major Phylogenetic Groups

Dynamics of Single-Cell Activity and Physiological States

Ecological Implications of Patterns in Bacterioplankton Single-Cell Activity

Community Versus Individual Cell Growth and Metabolic Rates

Linking the Distribution of Single-Cell Parameters and the Bulk Assemblage Response

Ecological Role of Different Physiological Fractions

Heterotrophic Bacterial Respiration

Measurement of Bacterial Respiration and Production

Routine Measurement Techniques for Bacterial Respiration and Their Limitations

Routine Measurement Techniques for Bacterial Production and Their Limitations

Magnitude and Variability of Bacterial Respiration

Temporal Variability

Spatial Variability

Relationship Between Bacterial Respiration and Environmental and Ecological Factors

Bacterial Respiration as a Proportion of Community Respiration

Predicting Bacterial Respiration

Comparison Between Measurements and Predictions of Bacterial Respiration

Magnitude of Bacterial Respiration in Relation to Primary Production

Bacterial Respiration in a Changing Environment

Resource Control of Bacterial Dynamics in The Sea

Growth in the Sea

Growth and Nutrient Uptake Kinetics

Approaches to Understanding Resource Control of Growth

Comparative Approaches

Experimental Approaches for Defining Limitation of Bacterial Growth

Limitation by Dissolved Organic Matter

Bacterial Growth on Bulk DOM Pools

Limitation by Specific DOM Compounds

Limitation by Inorganic Nutrients

Nitrogen

Phosphorus

Trace Nutrients

Temperature-DOM Interactions

Light

Resource Control of Specific Bacterial Populations in the Sea

Protistan Grazing on Marine Bacterioplankton

New Insights into Phylogenetic Organization

Functional Size Classes of Protists

Natural Assemblages of Marine Heterotrophic Nanoflagellates

Functional Ecology of Bacterivorous Flagellates

Living in a Dilute Environment

Using Culture Experiments to Infer the Ecological Role of HNF

Impact of Protistan Bacterivory on Marine Bacterioplankton

Search for the Perfect Method to Quantify Protistan Bacterivory

Rates of Protistan Bacterivory in the Sea

Balance of Bacterial Production and Protistan Grazing

Bottom-Up Versus Top-Down Control of Bacteria and Bacterivorous Protists

Ecological Functions of Bacterial Grazers

Grazing as a Shaping Force of Bacterial Assemblages

Bacterial Cell Size Determines Vulnerability Towards Grazers

Other Antipredator Traits of Prokaryotes

Grazing-Mediated Changes in Bacterial Community Composition

Molecular Tools for Protistan Ecology

Culturing Bias and Molecular Approaches

Global Distribution and Diversity of Marine Protists

Linking Diversity and Function for Uncultured Heterotrophic Flagellates

Marine Viruses: Community Dynamics, Diversity and Impact on Microbial Processes

Viruses and the Marine Microbial Food Web

Direct Counts and Viral Numbers

Viral Production and Decay Rates

Viral Decay and Rates of Production in Pelagic Systems

Measurements of Viral Production in Marine Sediments

General Rates of Viral Production

Role of Viruses in Biogeochemical Cycling

Impact of Viruses on Bacterial Diversity and Community Dynamics

Marine Viral Diversity

Methods for Examining Marine Viral Diversity

Culture-Based Studies of Viral Diversity

The Need for Culture-Independent Methods

Culture-Independent Studies of Viral Diversity Using Transmission Electron Microscopy

Whole-Genome Profiling of Viral Communities Based on Genome Size

Studies of Viral Diversity Using Signature Genes

Metagenomic Studies of Viral Diversity

A Vision for the Future

Molecular Ecological Aspects of Nitrogen Fixation in The Marine Environment

Chemistry, Biochemistry, and Genetics of N2 Fixation

Genetics and Enzymology

Evolution of N2 Fixation

Phylogeny of Nitrogenase

Genomics of N2 Fixation

Diversity of N2-Fixing Microorganisms

Regulation in Diazotrophs

Methods for Assessing Diazotroph Diversity, Gene Expression, and N2 Fixation Activity

Ecophysiological Aspects of N2 Fixation

Ecology of Diazotrophs in the Open Ocean

Estuarine and Coastal Waters

Benthic Habitats, Including Microbial Mats and Reefs

Deep Water and Hydrothermal Vents

Nitrogen Cycling in Sediments

Inputs

Transformations

Microbes and Microbial Processes

Processes Involving Mn and Fe

Nitrogen Budgets

Benthic Budgets

Oceanic Budgets

Summary

References

Index

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