Defrosting Ancient Microbes-Emerging Genomes in a Warmer World

255 Pages·2019·6.307 MB·\255

by  Scott Rogers (Author), John D. Castello (Author)

Defrosting Ancient
Microbes

Defrosting Ancient
Microbes
Emerging Genomes in a Warmer World
Scott O. Rogers
Professor of Molecular Biology and Evolution
Bowling Green State University
John D. Castello
Professor Emeritus of Microbiology and Forest Pathology
SUNY College of Environmental Science and Forestry
CRC Press
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Contents
Preface..................................................................................................................xi
Acknowledgments ...............................................................................................xv
Authors ..............................................................................................................xvii
List of Figures ....................................................................................................xix
List of Tables ......................................................................................................xxi
Abbreviations ...................................................................................................xxiii
Chapter 1 Reaching Backwards .......................................................................1
Reviving the “Dead” ........................................................................1
How Ice Affects Life .......................................................................4
Chapter 2 Questions and Answers ...................................................................9
Enigmas ...........................................................................................9
Frozen Knowledge ..........................................................................9
Evolutionary Implications .............................................................11
Applications ..................................................................................12
Extraterrestrial Life .......................................................................12
Moving Forward ............................................................................13
Chapter 3 The Importance of Water and Ice .................................................15
Liquid and Solid Water ..................................................................15
What Is in That Water? ..................................................................17
Why Are Water and Ice So Important for Life? ............................17
Ice as a Microbial Archive .............................................................20
Preservation of Microbes in Glaciers ............................................21
Microbes and Aliens ......................................................................23
Chapter 4 The Diversity of Ice .......................................................................25
Snow and Ice Diversity ..................................................................25
Glaciers ..........................................................................................27
Ice Fields and Domes ....................................................................32
Lake and Sea Ice ............................................................................32
Surface and Subglacial Lake Ice ...................................................33
v
vi Contents
Chapter 5 Permafrost .....................................................................................37
Frozen Soils ...................................................................................37
Life in Permafrost ..........................................................................37
Release of Greenhouse Gases and Other Chemicals .....................41
Chapter 6 What Is Life? .................................................................................43
What Is Causing the Disease? .......................................................43
Microbes in Ice ..............................................................................44
Classification of Life .....................................................................46
Chapter 7 Fossils: Marking Time ..................................................................53
Reading Fossils ..............................................................................53
Fossils in Ice ..................................................................................54
Living Fossils ................................................................................55
How Old? ......................................................................................56
Ancient Biomolecules ...................................................................59
Problems with Degradation ...........................................................60
Real or Imagined? .........................................................................61
Chapter 8 Walking into the Past ....................................................................63
Obtaining the Core Sections ..........................................................63
Storage ...........................................................................................64
What to Look For ..........................................................................66
Decontamination ...........................................................................70
Most Effective Methods ................................................................74
Chapter 9 Isolating and Characterizing Microbes from Ice ..........................79
How to Study Life .........................................................................79
Culture Methods ............................................................................79
Nucleic Acid Methods ...................................................................80
Metagenomics, Metatranscriptomics, and Genomics....................83
Other Methods ...............................................................................86
Chapter 10 A Brief History of Research on Life in Ice ...................................89
Longevity .......................................................................................89
A Brief History ..............................................................................92
International Geophysical Year and Beyond .................................98
Serendipity Strikes ......................................................................101
Contents vii
Chapter 11 Ice Core Discoveries....................................................................107
All Ice Is Not the Same ...............................................................107
IGY ..............................................................................................107
1950’s and 1960’s ........................................................................108
1970’s ..........................................................................................110
1980’s ..........................................................................................111
1990’s ..........................................................................................112
2000’s ..........................................................................................116
2010’s ..........................................................................................118
Future ..........................................................................................120
Chapter 12 Subglacial Lake Vostok ...............................................................123
Walking on Thick Ice ..................................................................123
Initial Characterization of the Vostok Ice Core ...........................125
Bacteria in the Lake .....................................................................128
Metagenomics and Metatranscriptomics .....................................130
Metabolic Processes ....................................................................131
Eukaryotes in Lake Vostok ..........................................................132
Lake Water Sampling ..................................................................133
Chapter 13 Discoveries from Other Ice-Covered Lakes ................................135
Subglacial Environments .............................................................135
Surface Lake Ice ..........................................................................139
Chapter 14 Life Is Everywhere .......................................................................143
Hard Times ..................................................................................143
Adaptable Species in Ice .............................................................144
Sensitivity to Freezing, Thawing, and Temperature ....................146
Pressure Tests ..............................................................................147
Other Adaptations ........................................................................147
Anabiosis and Spores ..................................................................148
Yeasts and Filamentous Fungi .....................................................149
Bacteria in Permafrost .................................................................151
Viruses .........................................................................................152
Chapter 15 Pathogens in the Environment: Viruses ......................................157
Exposure to Pathogens ................................................................157
Influenza A ..................................................................................158
Other Viruses ...............................................................................160
viii Contents
Ice as a Virus Reservoir ...............................................................161
Ice Cubes to Glaciers ...................................................................163
Don’t Eat That Ice .......................................................................163
Detecting Viruses Emerging from Ice .........................................164
Chapter 16 Pathogens, Hazards, and Dangers ...............................................167
Pathogens .....................................................................................167
Bacteria ........................................................................................168
Archaea ........................................................................................170
Eukarya ........................................................................................171
Hazards and Dangers ...................................................................174
Chapter 17 Everything Old Is New Again, the Ultimate in
Recycling .....................................................................................179
An Unfortunate Accident.............................................................179
Stops and Starts of Life ...............................................................180
Glacial Cycles..............................................................................181
The 1918 Influenza A Pandemic .................................................183
Pathogen Cycling ........................................................................183
Mutation Rates, Gene Flow, and Populations .............................184
Implications .................................................................................187
Chapter 18 Astrobiology—Out of This World ..............................................189
Probing the Solar System ............................................................189
Seeking Signs of Life ..................................................................190
Where in the Solar System to Look? ...........................................192
Inner Planets ................................................................................192
The Moon ....................................................................................193
Mars .............................................................................................193
Ceres ............................................................................................194
Jupiter and Its Moons ..................................................................195
Saturn and Its Moons ...................................................................196
Uranus and Its Moons..................................................................197
Neptune and Its Moons................................................................198
Pluto and Its Moons .....................................................................198
A Question of Life .......................................................................198
Chapter 19 Disappearing Ice—Global Climate Change ...............................201
Pollution and Melting ..................................................................201
Receding Glaciers and Ice Shelves .............................................203
Greenhouse Effect .......................................................................206
Misconceptions ............................................................................207
Contents ix
Global Climate and Hominins .....................................................209
Other Planets and the Future of Earth .........................................211
Plusses and Minuses ....................................................................213
Chapter 20 Epilogue........................................................................................217
Ignoring the Dangers ...................................................................217
Pathogens, Epidemics, and Pandemics ........................................218
Microbial Survival .......................................................................220
Preservation of Species, and Extinctions ....................................220
Subglacial Environments .............................................................221
A Look into the Future ................................................................222
Index .................................................................................................................225