{"product_id":"genomic-approaches-in-earth-and-environmental-sciences-isbn-9781118708248","title":"Genomic Approaches in Earth and Environmental Sciences","description":"\u003cp\u003e\u003cb\u003eThe first comprehensive synthesis of genomic techniques in earth sciences\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eThe 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. \u003c\/p\u003e \u003cp\u003e\u003ci\u003eGenomic Approaches in Earth and Environmental Sciences \u003c\/i\u003ebegins 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. \u003c\/p\u003e \u003cul\u003e \u003cli\u003eThe very first synthesis of an important new family of techniques\u003c\/li\u003e \u003cli\u003eShows strengths and limitations (both practical and theoretical) of the techniques\u003c\/li\u003e \u003cli\u003eDeals with both theoretical and laboratory basics\u003c\/li\u003e \u003cli\u003eShows use of techniques in a variety of applications, including various aspects of environmental science, geobiology, and evolution\u003c\/li\u003e \u003c\/ul\u003e \u003cp\u003e\u003ci\u003eGenomic Approaches in Earth and Environmental Sciences\u003c\/i\u003e is a welcome addition to the library of all earth and environmental scientists and students working within a wide range of subdisciplines.\u003c\/p\u003e \u003cp\u003ePreface ix \u003c\/p\u003e \u003cp\u003eAcknowledgments x \u003c\/p\u003e \u003cp\u003eAbbreviations xi \u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 Introduction 1\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003e1.1 Exploring the Microbial World 1 \u003c\/p\u003e \u003cp\u003e1.2 The DNA Sequencing Revolution: Historical Perspectives 4 \u003c\/p\u003e \u003cp\u003eReferences 7 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 The Architecture of Microbial Genomes 11\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 11 \u003c\/p\u003e \u003cp\u003e2.1 Genome Size, Organization, and Replication 11 \u003c\/p\u003e \u003cp\u003e2.2 Nucleotide Composition 14 \u003c\/p\u003e \u003cp\u003e2.3 Ecological and Evolutionary Aspects of Microbial Genomes 16 \u003c\/p\u003e \u003cp\u003e2.3.1 The Role of Viruses in Promoting Genomic Diversity 18 \u003c\/p\u003e \u003cp\u003e2.4 Genomic Diversity in Microbial Communities 19 \u003c\/p\u003e \u003cp\u003e2.5 Does Genomic Diversity Matter? 21 \u003c\/p\u003e \u003cp\u003eReferences 21 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Application of Omics Approaches to Earth and Environmental Sciences: Opportunities and Challenges 27\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 27 \u003c\/p\u003e \u003cp\u003e3.1 New Perspectives on Microbial Biogeochemistry 27 \u003c\/p\u003e \u003cp\u003e3.1.1 Redefining the Carbon and Nitrogen Cycles 27 \u003c\/p\u003e \u003cp\u003e3.1.2 Omics as Sensitive and Efficient Tracers of Biogeochemical Processes 29 \u003c\/p\u003e \u003cp\u003e3.1.3 Omics Data is Valuable for Biogeochemical Models 29 \u003c\/p\u003e \u003cp\u003e3.1.4 Understanding Biotic Responses and Feedbacks to Global Change 29 \u003c\/p\u003e \u003cp\u003e3.2 A Genomic Record of Biological and Geochemical Evolution 30 \u003c\/p\u003e \u003cp\u003e3.3 Challenges and Limitations of Omics Approaches 32 \u003c\/p\u003e \u003cp\u003e3.4 Omics as a Complement to Other Approaches 33 \u003c\/p\u003e \u003cp\u003eReferences 34 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 Overview of Approaches: From Whole-Community Shotgun Sequencing to Single-Cell Genomics 41\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 41 \u003c\/p\u003e \u003cp\u003e4.1 Choosing the Right Approach 41 \u003c\/p\u003e \u003cp\u003e4.1.1 Whole-Community Approaches 41 \u003c\/p\u003e \u003cp\u003e4.1.2 Targeted Approaches: Physical, Microbiological, and Isotopic Enrichment 43 \u003c\/p\u003e \u003cp\u003e4.1.3 Single-Cell Genomics 44 \u003c\/p\u003e \u003cp\u003e4.2 Experimental Design and Sampling Considerations 45 \u003c\/p\u003e \u003cp\u003e4.2.1 Replication 45 \u003c\/p\u003e \u003cp\u003e4.2.2 Estimating Sequencing Effort: How Much Sequencing Do I Need to Do? 46 \u003c\/p\u003e \u003cp\u003e4.2.3 From Sample to Data: Biases Due to Preservation, Storage, Extraction, and Sequencing 47 \u003c\/p\u003e \u003cp\u003e4.2.4 Estimating Absolute Abundance with Internal Standards 49 \u003c\/p\u003e \u003cp\u003e4.3 Overview of Current DNA Sequencing Technologies 49 \u003c\/p\u003e \u003cp\u003e4.4 Quality Control and Sequence Processing 51 \u003c\/p\u003e \u003cp\u003e4.4.1 Dereplication 51 \u003c\/p\u003e \u003cp\u003e4.4.2 Trimming 52 \u003c\/p\u003e \u003cp\u003eReferences 53 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Genomics of Single Species and Single Cells 59\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 59 \u003c\/p\u003e \u003cp\u003e5.1 Algorithms for Genome Assembly 60 \u003c\/p\u003e \u003cp\u003e5.2 Challenges of Genome Assembly 61 \u003c\/p\u003e \u003cp\u003e5.3 Scaffolding 63 \u003c\/p\u003e \u003cp\u003e5.4 Programs and Pipelines for Genome Assembly 63 \u003c\/p\u003e \u003cp\u003e5.5 Evaluation of Genome Assemblies 66 \u003c\/p\u003e \u003cp\u003e5.6 Single-Cell Genomics 67 \u003c\/p\u003e \u003cp\u003eReferences 69 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Metagenomics: Assembly and Database-Dependent Approaches 73\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 73 \u003c\/p\u003e \u003cp\u003e6.1 To Assemble or Not To Assemble? 73 \u003c\/p\u003e \u003cp\u003e6.2 Database-Dependent Approaches 75 \u003c\/p\u003e \u003cp\u003e6.3 Database-Independent Approaches: De Novo Assembly 78 \u003c\/p\u003e \u003cp\u003e6.4 Evaluation of Metagenomic Assemblies 82 \u003c\/p\u003e \u003cp\u003e6.5 A Philosophy of Metagenome Assemblies 82 \u003c\/p\u003e \u003cp\u003eReferences 83 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Metagenomic Binning 89\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 89 \u003c\/p\u003e \u003cp\u003e7.1 Genomic Signatures of Nucleotide Composition 90 \u003c\/p\u003e \u003cp\u003e7.2 Binning Programs 91 \u003c\/p\u003e \u003cp\u003e7.3 Additional Signal and Steps for Binning: Coverage, Taxonomic Data, and Mini‐Assemblies 93 \u003c\/p\u003e \u003cp\u003e7.4 Identifying, Evaluating, and Assessing the Completeness of Genomic Bins 95 \u003c\/p\u003e \u003cp\u003eReferences 97 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Annotation: Gene Calling, Taxonomy, and Function 101\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 101 \u003c\/p\u003e \u003cp\u003e8.1 Gene Calling 102 \u003c\/p\u003e \u003cp\u003e8.2 Determining Taxonomic Composition 103 \u003c\/p\u003e \u003cp\u003e8.3 Functional Annotation 106 \u003c\/p\u003e \u003cp\u003e8.3.1 Overall Approach to Functional Annotation 106 \u003c\/p\u003e \u003cp\u003e8.3.2 Predicting Metabolic Pathways 107 \u003c\/p\u003e \u003cp\u003e8.3.3 The Importance of Experimental Annotation 108 \u003c\/p\u003e \u003cp\u003eReferences 109 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Metatranscriptomics 113\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 113 \u003c\/p\u003e \u003cp\u003e9.1 Sample Collection 114 \u003c\/p\u003e \u003cp\u003e9.2 RNA Extraction and Preparation of cDNA Libraries 115 \u003c\/p\u003e \u003cp\u003e9.2.1 Should rRNAs Be Removed Prior to Library Preparation and Sequencing? 115 \u003c\/p\u003e \u003cp\u003e9.3 Assigning Transcripts to Genes or Other Features 115 \u003c\/p\u003e \u003cp\u003e9.4 De Novo Assembly 116 \u003c\/p\u003e \u003cp\u003e9.5 Absolute Versus Relative Abundance and Normalization 118 \u003c\/p\u003e \u003cp\u003e9.6 Detecting Differential Expression 122 \u003c\/p\u003e \u003cp\u003eReferences 123 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Metaproteomics 127\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 127 \u003c\/p\u003e \u003cp\u003e10.1 Methodologies for Basic Proteomics 128 \u003c\/p\u003e \u003cp\u003e10.2 The Importance of Genomic Databases for Interpreting Proteomics Data 130 \u003c\/p\u003e \u003cp\u003e10.3 Quantitative Proteomics 131 \u003c\/p\u003e \u003cp\u003e10.4 Combining Stable Isotope Probing with Proteomics to Track Microbial Metabolism 133 \u003c\/p\u003e \u003cp\u003eReferences 133 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Lipidomics and Metabolomics 137\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 137 \u003c\/p\u003e \u003cp\u003e11.1 Lipidomics 137 \u003c\/p\u003e \u003cp\u003e11.2 Metabolomics 139 \u003c\/p\u003e \u003cp\u003eReferences 140 \u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Downstream and Integrative Approaches and Future Outlook 145\u003c\/b\u003e \u003c\/p\u003e \u003cp\u003eIntroduction 145 \u003c\/p\u003e \u003cp\u003e12.1 Comparative Omics 145 \u003c\/p\u003e \u003cp\u003e12.2 Statistical Approaches 146 \u003c\/p\u003e \u003cp\u003e12.3 Visualization 147 \u003c\/p\u003e \u003cp\u003e12.4 Cyberinfrastructure for Environmental Omics 148 \u003c\/p\u003e \u003cp\u003e12.4.1 Software Platforms for Integrated Analyses and Data Storage 149 \u003c\/p\u003e \u003cp\u003e12.5 Data and Sample Archival 151 \u003c\/p\u003e \u003cp\u003e12.6 Modeling 151 \u003c\/p\u003e \u003cp\u003e12.7 Emerging Trends and Future Outlook 153 \u003c\/p\u003e \u003cp\u003eReferences 155 \u003c\/p\u003e \u003cp\u003eIndex 161\u003c\/p\u003e \u003cp\u003e\u003cb\u003eGregory J. Dick,\u003c\/b\u003e is Associate Professor of Earth and Environmental Sciences at the University of Michigan.\u003c\/p\u003e \u003cp\u003e\u003cb\u003eThe first comprehensive synthesis of genomic techniques in earth sciences\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eThe 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.\u003c\/p\u003e \u003cp\u003e\u003ci\u003eGenomic Approaches in Earth and Environmental Sciences \u003c\/i\u003ebegins 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.\u003c\/p\u003e \u003cul\u003e \u003cli\u003eThe very first synthesis of an important new family of techniques\u003c\/li\u003e \u003cli\u003eShows strengths and limitations (both practical and theoretical) of the techniques\u003c\/li\u003e \u003cli\u003eDeals with both theoretical and laboratory basics\u003c\/li\u003e \u003cli\u003eShows use of techniques in a variety of applications, including various aspects of environmental science, geobiology, and evolution\u003c\/li\u003e \u003c\/ul\u003e \u003cp\u003e\u003ci\u003eGenomic Approaches in Earth and Environmental Sciences\u003c\/i\u003e is a welcome addition to the library of all earth and environmental scientists and students working within a wide range of subdisciplines.\u003c\/p\u003e","brand":"Wiley-Blackwell","offers":[{"title":"Default Title","offer_id":47989279588581,"sku":"NP9781118708248","price":114.0,"currency_code":"USD","in_stock":false}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/1842\/7735\/files\/9781118708248.jpg?v=1761783496","url":"https:\/\/k12savings.com\/products\/genomic-approaches-in-earth-and-environmental-sciences-isbn-9781118708248","provider":"K12savings","version":"1.0","type":"link"}