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Genomic Approaches in Earth and Environmental Sciences [Hardback]

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Genomic Approaches in Earth and Environmental SciencesPalielināt
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Permanent link: https://www.kriso.lv/db/9781118708248.html
The 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 evolution

Genomic Approaches In Earth And Environmental Sciences

The first comprehensive synthesis of genomic techniques in earth sciences

The 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 otters 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. I he book then discusses the methods used in the held, beginning with an overview of current technologies. After that it offers in depth coverage of single cell genomics, metagenonics, metatranscriptomics, metaproteomics, and functional approaches, before finishing up with an outlook on the future of the field.

Genomic 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

The first comprehensive synthesis of genomic techniques in earth sciences The past 15 years have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into biology.

The first comprehensive synthesis of genomic techniques in earth sciences

The 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 evolution

Genomic 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.

Preface ix
Acknowledgments x
Abbreviations xi
1 Introduction 1(10)
1.1 Exploring the Microbial World
1(3)
1.2 The DNA Sequencing Revolution: Historical Perspectives
4(3)
References
7(4)
2 The Architecture of Microbial Genomes 11(16)
Introduction
11(1)
2.1 Genome Size, Organization, and Replication
11(3)
2.2 Nucleotide Composition
14(2)
2.3 Ecological and Evolutionary Aspects of Microbial Genomes
16(3)
2.3.1 The Role of Viruses in Promoting Genomic Diversity
18(1)
2.4 Genomic Diversity in Microbial Communities
19(2)
2.5 Does Genomic Diversity Matter?
21(1)
References
21(6)
3 Application of Omics Approaches to Earth and Environmental Sciences: Opportunities and Challenges 27(14)
Introduction
27(1)
3.1 New Perspectives on Microbial Biogeochemistry
27(3)
3.1.1 Redefining the Carbon and Nitrogen Cycles
27(2)
3.1.2 Omics as Sensitive and Efficient Tracers of Biogeochemical Processes
29(1)
3.1.3 Omics Data is Valuable for Biogeochemical Models
29(1)
3.1.4 Understanding Biotic Responses and Feedbacks to Global Change
29(1)
3.2 A Genomic Record of Biological and Geochemical Evolution
30(2)
3.3 Challenges and Limitations of Omics Approaches
32(1)
3.4 Omics as a Complement to Other Approaches
33(1)
References
34(7)
1 Overview of Approaches: From Whole-Community Shotgun Sequencing to Single-Cell Genomics 41(18)
Introduction
41(1)
4.1 Choosing the Right Approach
41(4)
1.1.1 Whole-Community Approaches
41(2)
4.1.2 Targeted Approaches: Physical, Microbiological, and Isotopic Enrichment
43(1)
4.1.3 Single-Cell Genomics
44(1)
4.2 Experimental Design and Sampling Considerations
45(4)
4.2.1 Replication
45(1)
4.2.2 Estimating Sequencing Effort: How Much Sequencing Do I Need to Do?
46(1)
4.2.3 From Sample to Data: Biases Due to Preservation, Storage, Extraction, and Sequencing
47(2)
4.2.4 Estimating Absolute Abundance with Internal Standards
49(1)
4.3 Overview of Current DNA Sequencing Technologies
49(2)
4.4 Quality Control and Sequence Processing
51(2)
4.1.1 Dereplication
51(1)
4.1.2 Trimming
52(1)
References
53(6)
5 Genomics of Single Species and Single Cells 59(14)
Introduction
59(1)
5.1 Algorithms for Genome Assembly
60(1)
5.2 Challenges of Genome Assembly
61(2)
5.3 Scaffolding
63(1)
5.4 Programs and Pipelines for Genome Assembly
63(3)
5.5 Evaluation of Genome Assemblies
66(1)
5.6 Single-Cell Genomics
67(2)
References
69(4)
6 Metagenomics: Assembly and Database-Dependent Approaches 73(16)
Introduction
73(1)
6.1 To Assemble or Not To Assemble?
73(2)
6.2 Database-Dependent Approaches
75(3)
6.3 Database-Independent Approaches: De Novo Assembly
78(4)
6.4 Evaluation of Metagenomic Assemblies
82(1)
6.5 A Philosophy of Metagenome Assemblies
82(1)
References
83(6)
7 Metagenomic Binning 89(12)
Introduction
89(1)
7.1 Genomic Signatures of Nucleotide Composition
90(1)
7.2 Binning Programs
91(2)
7.3 Additional Signal and Steps for Binning: Coverage, Taxonomic Data, and Mini-Assemblies
93(2)
7.4 Identifying, Evaluating, and Assessing the Completeness of Genomic Bins
95(2)
References
97(4)
8 Annotation: Gene Calling, Taxonomy, and Function 101(12)
Introduction
101(1)
8.1 Gene Calling
102(1)
8.2 Determining Taxonomic Composition
103(3)
8.3 Functional Annotation
106(3)
8.3.1 Overall Approach to Functional Annotation
106(1)
8.3.2 Predicting Metabolic Pathways
107(1)
8.3.3 The Importance of Experimental Annotation
108(1)
References
109(4)
9 Metatranscriptomics 113(14)
Introduction
113(1)
9.1 Sample Collection
114(1)
9.2 RNA Extraction and Preparation of cDNA Libraries
115(1)
9.2.1 Should rRNAs Be Removed Prior to Library Preparation and Sequencing?
115(1)
9.3 Assigning Transcripts to Genes or Other Features
115(1)
9.4 De Novo Assembly
116(2)
9.5 Absolute Versus Relative Abundance and Normalization
118(4)
9.6 Detecting Differential Expression
122(1)
References
123(4)
10 Metaproteomics 127(10)
Introduction
127(1)
10.1 Methodologies for Basic Proteomics
128(2)
10.2 The Importance of Genomic Databases for Interpreting Proteomics Data
130(1)
10.3 Quantitative Proteomics
131(2)
10.4 Combining Stable Isotope Probing with Proteomics to Track Microbial Metabolism
133(1)
References
133(4)
11 Lipidomics and Metabolomics 137(8)
Introduction
137(1)
11.1 Lipidomics
137(2)
11.2 Metabolomics
139(1)
References
140(5)
12 Downstream and Integrative Approaches and Future Outlook 145(16)
Introduction
145(1)
12.1 Comparative Omics
145(1)
12.2 Statistical Approaches
146(1)
12.3 Visualization
147(1)
12.4 Cyberinfrastructure for Environmental Omics
148(3)
12.4.1 Software Platforms for Integrated Analyses and Data Storage
149(2)
12.5 Data and Sample Archival
151(1)
12.6 Modeling
151(2)
12.7 Emerging Trends and Future Outlook
153(2)
References
155(6)
Index 161
Gregory J. Dick, is Associate Professor of Earth and Environmental Sciences at the University of Michigan.