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Introduction

Introduction

Microbial Ecology: Beginnings and the Road Forward

DNA Reassociation Yields Broad‐Scale Information on Metagenome Complexity and Microbial Diversity

Viral Metagenomics

Methods in Viral Metagenomics

Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes

Metagenomic Contrasts of Viruses in Soil and Aquatic Environments

Diversity of Microorganisms

Use of the rRNA Operon and Genomic Repetitive Sequences for the Identification of Bacteria

Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites

Use of Different PCR Primer‐Based Strategies for Characterization of Natural Microbial Communities

Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co‐Evolution

Horizontal Gene Transfer and Recombination Shape Mesorhizobial Populations in the Gene Center of the Host Plants <fi>Astragalus Luteolus</fi> and <fi>Astragalus Ernestii</fi> in Sichuan, China

Amplified rDNA Restriction Analysis (ARDRA) for Identification and Phylogenetic Placement of 16S‐rDNA Clones

Complexity and Simplicity of Cell Systems

Next‐Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology

Clustering‐Based Peak Alignment Algorithm for Objective and Quantitative Analysis of DNA Fingerprinting Data

Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High‐Throughput Sequencing Approach

Population Genomics Informs Our Understanding of the Bacterial Species Concept

Soil‐Based Metagenomics

The Microbial Pangenome: Implications for Vaccine Development

Metagenomic Insights into Bacterial Species

Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil

Reports of Ad Hoc Committees for the Reevaluation of the Species Definition in Bacteriology

The Microbial Habitat: An Ecological Perspective

Metagenomic Approaches for the Identification of Microbial Species

Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications

Microbial Ecology in the Age of Metagenomics

Application of PCR‐DGGE and MetagenomeWalking to Retrieve Full‐Length Functional Genes from Soil

The Enduring Legacy of Small Subunit rRNA in Microbiology

Actinobacterial Diversity Associated with Antarctic Dry Valley Mineral Soils

Pitfalls of PCR‐Based rRNA Gene Sequence Analysis: An Update on Some Parameters

The how of Microbial Ecology Studies

Empirical Testing of 16S PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy not Suggested by <fi>In Silico</fi> Analysis

Targeting Major Soil‐Borne Bacterial Lineages Using Large‐Insert Metagenomic Approaches

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

The Impact of Next‐Generation Sequencing Technologies on Metagenomics

Accuracy and Quality of Massively Parallel DNA Pyrosequencing

Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters

Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes

Microbe–Microbe Interactions

A Comparison of Random Sequence Reads Versus 16S rDNA Sequences for Estimating the Biodiversity of a Metagenomic Sample

The Antibiotic Resistome: Origins, Diversity, and Future Prospects

Metagenomic Libraries for Functional Screening

Functional Intestinal Metagenomics

GC Fractionation Allows Comparative Total Microbial Community Analysis, Enhances Diversity Assessment, and Facilitates Detection of Minority Populations of Bacteria

Interactions Between Microorganisms and Plants

Assessment and Improvement of Methods for Microbial DNA Preparation from Fecal Samples

Enriching Plant Microbiota for a Metagenomic Library Construction

The Role of Dysbiosis in Inflammatory Bowel Diseases

Towards Automated Phylogenomic Inference

Culture‐Independent Analysis of the Human Gut Microbiota and their Activities

Integron First Gene Cassettes: A Target to Find Adaptive Genes in Metagenomes

INTERACTIONS BETWEEN MICROORGANISMS AND ANIMALS

Complete Genome of an Uncultured Endosymbiont Coupling Nitrogen Fixation to Cellulolysis within Protist Cells in Termite Gut

High‐Resolution Metagenomics: Assessing Specific Functional Types in Complex Microbial Communities

Cloning and Identification of Genes Encoding Acidic Cellulases from the Metagenomes of Buffalo Rumen

Gene‐Targeted Metagenomics (GT Metagenomics) to Explore the Extensive Diversity of Genes of Interest in Microbial Communities

Living Together: Microbial Communities

Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere”

Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease Restriction and Marker Insertion

ArrayOme‐ and tRNAcc‐Facilitated Mobilome Discovery: Comparative Genomics Approaches for Identifying Rich Veins of Bacterial Novel DNA Sequences

Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia

Microbes at Work: Bioremediation

Sequence‐Based Characterization of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST)

Adaptation to Nutrient Availability in Marine Microorganisms by Gene Gain and Loss

Microbial Processes Contributing to Biogeochemical Cycles

The Metagenomics of Plant Pathogen‐Suppressive Soils

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

Metagenomic Approach Studying the Taxonomic and Functional Diversity of the Bacterial Community in a Lacustrine Ecosystem

Soil Metagenomic Exploration of the Rare Biosphere

Metagenomics of the Marine Subsurface: The First Glimpse from the Peru Margin, ODP Site 1229

Microbes at Work in Nature: Biomineralization and Microbial Weathering

The BIOSPAS Consortium: Soil Biology and Agricultural Production

A Targeted Metagenomic Approach to Determine the “Population Genome” of Marine <fi>Synechococcus</fi>

The Human Microbiome Project

Diversity and Role of Bacterial Integron/Gene Cassette Metagenome in Extreme Marine Environments

The Ribosomal Database Project: Sequences and Software for High‐Throughput rRNA Analysis

The <fi>Olavius algarvensis</fi> Metagenome Revisited: Lessons Learned from the Analysis of the Low‐Diversity Microbial Consortium of a Gutless Marine Worm

The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes

Decomposition of Natural Compounds

The EBI Metagenomics Archive, Integration and Analysis Resource

Microbiome Diversity in Human Saliva

Approaches to Understanding Population Level Functional Diversity in a Microbial Community

Comparative Metagenome Analysis Using MEGAN

Phylogenetic Binning of Metagenome Sequence Samples

A Functional Metagenomic Approach for Discovering Nickel Resistance Genes from the Rhizosphere of an Acid Mine Drainage Environment

Gene Prediction in Metagenomic Fragments with Orphelia: A Large‐Scale Machine Learning Approach

The Microbiome of Leaf‐Cutter Ant Fungus Gardens

Binning Metagenomic Sequences Using Seeded GSOM

Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly

Diversity of Archaea in Terrestrial Hot Springs and Role in Ammonia Oxidation

Ribosomal RNA Identification in Metagenomic and Metatranscriptomic Datasets

SILVA: Comprehensive Databases for Quality Checked and Aligned Ribosomal RNA Sequence Data Compatible with ARB

Colonization of Nascent, Deep‐Sea Hydrothermal Vents by a Novel Archaeal and Nanoarchaeal Assemblage

Index

ARB: A Software Environment for Sequence Data

Analysis of the Metagenome from a Biogas‐Producing Microbial Community by Means of Bioinformatics Methods

The Phyloware Project: A Software Framework for Phylogenomic Virtue