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The first comprehensive synthesis of genomic techniques in earth sciencesThe past 15 years have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into biology. Although this technological revolution has been driven by the biomedical sciences, it also offers extraordinary opportunities in the earth and environmental sciences. In particular, the application of "omics" methods (genomics, transcriptomics, proteomics) directly to environmental samples offers exciting new vistas of complex microbial communities and their roles in environmental and geochemical processes. This unique book fills the gap where there exists a lack of resources and infrastructure to educate and train geoscientists about the opportunities, approaches, and analytical methods available in the application of omic technologies to problems in the geosciences.Genomic Approaches in Earth and Environmental Sciences begins by covering the role of microorganisms in earth and environmental processes. It then goes on to discuss how omics approaches provide new windows into geobiological processes. It delves into the DNA sequencing revolution and the impact that genomics has made on the geosciences. The book then discusses the methods used in the field, beginning with an overview of current technologies. After that it offers in-depth coverage of single cell genomics, metagenomics, metatranscriptomics, metaproteomics, and functional approaches, before finishing up with an outlook on the future of the field.* The very first synthesis of an important new family of techniques* Shows strengths and limitations (both practical and theoretical) of the techniques* Deals with both theoretical and laboratory basics* Shows use of techniques in a variety of applications, including various aspects of environmental science, geobiology, and evolutionGenomic Approaches in Earth and Environmental Sciences is a welcome addition to the library of all earth and environmental scientists and students working within a wide range of subdisciplines.

Genomic Approaches in Earth and Environmental Sciences

Preface ixAcknowledgments xAbbreviations xi1 Introduction 11.1 Exploring the Microbial World 11.2 The DNA Sequencing Revolution: Historical Perspectives 4References 72 The Architecture of Microbial Genomes 11Introduction 112.1 Genome Size, Organization, and Replication 112.2 Nucleotide Composition 142.3 Ecological and Evolutionary Aspects of Microbial Genomes 162.3.1 The Role of Viruses in Promoting Genomic Diversity 182.4 Genomic Diversity in Microbial Communities 192.5 Does Genomic Diversity Matter? 21References 213 Application of Omics Approaches to Earth and Environmental Sciences: Opportunities and Challenges 27Introduction 273.1 New Perspectives on Microbial Biogeochemistry 273.1.1 Redefining the Carbon and Nitrogen Cycles 273.1.2 Omics as Sensitive and Efficient Tracers of Biogeochemical Processes 293.1.3 Omics Data is Valuable for Biogeochemical Models 293.1.4 Understanding Biotic Responses and Feedbacks to Global Change 293.2 A Genomic Record of Biological and Geochemical Evolution 303.3 Challenges and Limitations of Omics Approaches 323.4 Omics as a Complement to Other Approaches 33References 344 Overview of Approaches: From Whole-Community Shotgun Sequencing to Single-Cell Genomics 41Introduction 414.1 Choosing the Right Approach 414.1.1 Whole-Community Approaches 414.1.2 Targeted Approaches: Physical, Microbiological,and Isotopic Enrichment 434.1.3 Single-Cell Genomics 444.2 Experimental Design and Sampling Considerations 454.2.1 Replication 454.2.2 Estimating Sequencing Effort: How Much Sequencing Do I Need to Do? 464.2.3 From Sample to Data: Biases Due to Preservation,Storage, Extraction, and Sequencing 474.2.4 Estimating Absolute Abundance with Internal Standards 494.3 Overview of Current DNA Sequencing Technologies 494.4 Quality Control and Sequence Processing 514.4.1 Dereplication 514.4.2 Trimming 52References 535 Genomics of Single Species and Single Cells 59Introduction 595.1 Algorithms for Genome Assembly 605.2 Challenges of Genome Assembly 615.3 Scaffolding 635.4 Programs and Pipelines for Genome Assembly 635.5 Evaluation of Genome Assemblies 665.6 Single-Cell Genomics 67References 696 Metagenomics: Assembly and Database-Dependent Approaches 73Introduction 736.1 To Assemble or Not To Assemble? 736.2 Database-Dependent Approaches 756.3 Database-Independent Approaches: De Novo Assembly 786.4 Evaluation of Metagenomic Assemblies 826.5 A Philosophy of Metagenome Assemblies 82References 837 Metagenomic Binning 89Introduction 897.1 Genomic Signatures of Nucleotide Composition 907.2 Binning Programs 917.3 Additional Signal and Steps for Binning: Coverage,Taxonomic Data, and Mini?]Assemblies 937.4 Identifying, Evaluating, and Assessing the Completeness of Genomic Bins 95References 978 Annotation: Gene Calling, Taxonomy, and Function 101Introduction 1018.1 Gene Calling 1028.2 Determining Taxonomic Composition 1038.3 Functional Annotation 1068.3.1 Overall Approach to Functional Annotation 1068.3.2 Predicting Metabolic Pathways 1078.3.3 The Importance of Experimental Annotation 108References 1099 Metatranscriptomics 113Introduction 1139.1 Sample Collection 1149.2 RNA Extraction and Preparation of cDNA Libraries 1159.2.1 Should rRNAs Be Removed Prior to Library Preparation and Sequencing? 1159.3 Assigning Transcripts to Genes or Other Features 1159.4 De Novo Assembly 1169.5 Absolute Versus Relative Abundance and Normalization 1189.6 Detecting Differential Expression 122References 12310 Metaproteomics 127Introduction 12710.1 Methodologies for Basic Proteomics 12810.2 The Importance of Genomic Databases for Interpreting Proteomics Data 13010.3 Quantitative Proteomics 13110.4 Combining Stable Isotope Probing with Proteomics to Track Microbial Metabolism 133References 13311 Lipidomics and Metabolomics 137Introduction 13711.1 Lipidomics 13711.2 Metabolomics 139References 14012 Downstream and Integrative Approaches and Future Outlook 145Introduction 14512.1 Comparative Omics 14512.2 Statistical Approaches 14612.3 Visualization 14712.4 Cyberinfrastructure for Environmental Omics 14812.4.1 Software Platforms for Integrated Analyses and Data Storage 14912.5 Data and Sample Archival 15112.6 Modeling 15112.7 Emerging Trends and Future Outlook 153References 155Index 161