Cover Page

Genomic Approaches in Earth and Environmental Sciences

 

Gregory Dick

University of Michigan
Michigan, USA

 

 

 

 

 

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New Analytical Methods in Earth and Environmental Science Series

 

Introducing New Analytical Methods in Earth and Environmental Science, a new series providing accessible introductions to important new techniques, lab and field protocols, suggestions for data handling and in-terpretation, and useful case studies.

New Analytical Methods in Earth and Environmental Science represents an invaluable and trusted source of information for researchers, advanced students, and applied earth scientists wishing to familiarize themselves with emerging techniques in their field.

All titles in this series are available in a variety of full-color, searchable e-book formats.

See below for the full list of books from the series.

 

Digital Terrain Modelling

John P. Wilson

 

Structure from Motion in the Geosciences

Jonathan L. Carrivick, Mark W. Smith, Duncan J. Quincey

 

Ground-penetrating Radar for Geoarchaeology

Lawrence B. Conyers

 

Rock Magnetic Cyclostratigraphy

Kenneth P. Kodama, Linda A. Hinnov

 

Techniques for Virtual Palaeontology

Mark Sutton, Imran Rahman, Russell Garwood

Preface

In recent years we 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. However, there is currently 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. This book aims to begin to fill this gap. Due to the rapidly advancing nature of DNA sequencing technologies, this book will almost certainly be well out of date by the time of publication. Nevertheless, my hope is that the accompanying e‐book format will allow relatively frequent updates and will serve as a foundation and a gateway for students and other scientists to access this exciting field. I apologize in advance to the many researchers whose excellent work was inevitably not cited, due to either my own ignorance or constraints on space. I welcome suggestions for citations, additions, and corrections that can be incorporated into future editions.

Gregory Dick
Ann Arbor, Michigan, USA
August, 2017

Acknowledgments

This book is the product of many interactions with numerous people over several years. It was developed from lecture notes for a graduate class that I teach at the University of Michigan, Earth 523, and thus benefited from numerous questions, comments, and input from students during class over the years. Several students, including Shilva Shrestha and Matthew Hoostal, provided direct detailed comments and edits for which I am most grateful. Sunit Jain was a bioinformatician in my lab who assisted with and substantially contributed to Earth 523, thus he indirectly contributed to the content of this book as well, particularly Chapter 4. Other current and former lab members including Brett Baker, Karthik Anantharaman, and Sharon Grim also provided valuable material and feedback. Vincent Denef provided insightful feedback and edits to Chapter 2, especially the section on the ecological and evolutionary aspects of microbial genomes. Mike Wilkins, Mary Ann Moran, Frank Stewart, Mak Saito, Jake Waldbauer, Ann Pearson, Murat Eren, and Titus Brown also provided thoughtful comments and suggested edits on individual chapters. Illustrations were drafted by Stephanie O'Neil, an undergraduate student at the time. Chapters 1 and 3 drew on early material from drafts of an article now published in Elements magazine (Dick and Lam 2015, Elements 11: 403–408) with permission from the Mineralogical Society of America. I am grateful for permission to reuse this material as well as figures from other papers as described herein.

I owe several people thanks for their patience. First, the publisher, Wiley, including Ian Francis, Delia Sandford, Ramya Raghaven, and Sonali Melwani, for their assistance and for tolerating the tardiness of this book. Finally, thanks to my wife, Jenna, and kids, Adeline and Ben, for their support and patience.

Abbreviations

BAC
bacterial artificial chromosome
DNA
deoxyribonucleic acid
dnGASP
de novo genome assembly project
GAGE
genome assembly gold standard evaluations
GMG
geomicrobiology and microbial geochemistry
IGV
Integrative Genomics Viewer
mRNA
messenger RNA
OLC
overlap‐layout‐consensus
ORF
open reading frames
OTU
operational taxonomic unit
PCR
polymerase chain reaction
RAM
random access memory
RNA
ribonucleic acid
rrn
ribosomal RNA