Astrobiology Camp�Extremophiles and the Span of the Terrestrial Biotic Environments

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Extremophiles and the Span of Terrestrial Biotic Environments

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(1)Extremophiles

(2)Extreme Environments

Temperature, Salinity, Acidity, Radiation, etc.

3) Implications of Extremophiles for Life Elsewhere

in the Solar System

4) Significance of Extremophiles in the Earliest History

of Life on Earth

What are the Characteristics of Life?

In biology, a lifeform has traditionally been considered to be a member of a population whose members can exhibit all the following phenomena at least once during their existence:

• Growth
• Metabolism, consuming, transforming and storing energy/mass; growing by absorbing and reorganizing mass; excreting waste
• Motion, either moving itself, or having internal motion
• Reproduction, the ability to create entities that are similar to, yet separate from, itself
• Response to stimuli - the ability to measure properties of its surrounding environment, and act upon certain conditions.
• Exceptions: mules, fire, stars, crystals, computer programs, viruses

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What are the Properties of Life?

• Hierarchical organization and emergent properties
• Regulatory capacity leading to homeostasis
• Medium for life: water (H₂O) as a solvent
• Information processing
• Undergo Darwinian evolution

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What are the necessities for life?

• Life on Earth thrives in a wide range of environments, and in general seems to require three things:
• a source of raw materials
• a source of energy
• and liquid water

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The Early Earth was �an Extreme Environment

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Before oceans,

Before oxygen,

Before photosynthesis,

There was chemosynthesis…..

Methanogenesis:

CO₂ + 4 H₂ → CH₄ + 2 H₂O

http://www.agen.ufl.edu/~chyn/age4660/lect/lect_08x/lect_08.htm

Sulfur Reducing Bacteria:

S + H₂ → H₂S

What are Extremophiles?

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• Extremophiles are organisms that live in extreme environments.

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• Early in Earth history all life was extremophilic.

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• The study of extremophiles provide insight into the early evolution of life.

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• Extremophiles illustrate the adapatability of terrestrial-type life.

Grant Prismatic Spring - Yellowstone

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http://upload.wikimedia.org/wikipedia/en/3/3f/Grand_Prismatic_Spring_and_Midway_Geyser_Basin_from_above.jpg

Characteristics of Cells

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What are Extremophiles?

• Extremophiles are microorganisms
• viruses, prokaryotes, or eukaryotes
• Extremophiles live under unusual environmental conditions
• atypical temperature, pH, salinity, pressure, nutrient, oxic, water, and radiation levels

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

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Types of Extremophiles

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

More Types of Extremophiles

• Barophiles -survive under high pressure levels, especially in deep sea vents
• Osmophiles –survive in high sugar environments
• Xerophiles -survive in hot deserts where water is scarce
• Anaerobes -survive in habitats lacking oxygen
• Microaerophiles -thrive under low-oxygen conditions
• Endoliths –dwell in rocks and caves
• Toxitolerants -organisms able to withstand high levels of damaging agents. For example, living in water saturated with benzene, or in the water-core of a nuclear reactor

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Kinds of Extremophiles

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Environmental Parameter Example of

Parameter Type of Behavior Definition Organism

Hyperthermophile Growth > 80^oC Pryolobus fumarii (113^oC)

Temperature Thermophile Growth 60-80^oC Synechoccus lividis

Psychrophile < 15^oC Psychrobacteria, some insects

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Radiation Atomophile Up to 6000 rad/hr Deinococcus radiodurans

15 Mrad total

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Pressure Pizeophiles Up to Gigapascals Sh. Oneidensis, E. coli

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Desiccation Xerophile Anhydrobiotic Artemia salina, fungi, etc

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Salinity Halophile High Salt Halobacteriaceae, D. salina

(2-5 Molar NaCl)

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pH Alkaliphile pH > 9 Natronobacterium, B. firmus

(acidity/alkalinity) Acidophile pH < 0 Cyanadium caldarim (pH 0)

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Oxygen pressure Anaerobe O₂ intolerant Methanococcus jannaschii

Microaerophile Tolerates low O₂ Clostridium

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Chemical extremes Gases Pure CO₂ gas Cyanidium caldarium

Metals High metal concs Ferroplasmic acidarmanus

Environmental Requirements

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

EXTREME PROKARYOTES Hyperthermophiles

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• Members of domains Bacteria and Archaea
• Possibly the earliest organisms
• Early earth was excessively hot, so these organisms would have been able to survive

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Hyperthermophiles: How do they survive?

• Heat stable proteins that have more hydrophobic interiors prevents unfolding or denaturation at higher temperatures

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• Chaperonin proteins maintain folding

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• Monolayer membranes of dibiphytanyl tetraethers saturated fatty acids which confer rigidity, prevent degradation in high temperatures

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• A variety of DNA-preserving substances that reduce mutations and damage to nucleic acids e.g., reverse DNA gyrase and Sac7d

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• Can live without sunlight or organic carbon as food survive on sulfur, hydrogen, and other materials that other organisms cannot metabolize

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The red on these rocks is produced by Sulfolobus solfataricus, near Naples, Italy

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Hyperthermophiles

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Thermus aquaticus 1μm

Pyrococcus abyssi 1μm

Frequent habitats include volcanic vents and hot springs.

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Deep Sea Extremophiles

• Deep-sea floor and hydrothermal vents involve the following conditions:
• low temperatures (2-3º C) – where only psychrophiles are present
• low nutrient levels – where only oligotrophs present
• high pressures – which increase at the rate of 1 atm for every 10 meters in depth (as we have learned, increased pressure leads to decreased enzyme-substrate binding)
• barotolerant microorganisms live at 1000-4000 meters
• barophilic microorganisms live at depths greater than 4000 meters

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A black smoker, i.e. a submarine hot spring, which can reach 518- 716°F (270-380°C)

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Extremophiles of Hydrothermal Vents

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A cross-section of a bacterium isolated from a vent. Often such bacteria are filled with viral particles which are abundant in hydrothermal vents

A bacterial community from a deep-sea hydrothermal vent near the Azores

Natural springs vent warm or hot water on the sea floor near mid-ocean ridges

Associated with the spreading of the Earth’s crust. High temperatures and pressures

0.2μm

1μm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Psychrophiles

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Some microorganisms thrive in temperatures below the freezing point of water

(this location in Antarctica)

Some people believe that psychrophiles live in conditions mirroring those found on Mars – but is this true?

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

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• Proteins rich in α-helices and polar groups
• allow for greater flexibility
• “Antifreeze proteins”
• maintain liquid intracellular conditions by lowering freezing points of other biomolecules
• Membranes that are more fluid
• contain unsaturated cis-fatty acids which help to prevent freezing
• active transport at lower temperatures

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Characteristics of Psychrophiles

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Halophiles

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• Divided into classes
• mild (1-6%NaCl)
• moderate (6-15%NaCl)
• extreme (15-30%NaCl)

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• Mostly obligate aerobic archaea

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• Survive high salt concentrations by
• interacting more strongly with water such as using more negatively charged amino acids in key structures
• making many small proteins inside the cell, and these then compete for the water
• accumulating high levels of salt in the cell in order to outweigh the salt outside

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Barophiles

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• Survive under levels of pressure that are lethal to most organisms
• Found deep in the Earth, in deep sea hydrothermal vents, etc.

A sample of barophilic bacteria from the earth’s interior

1μm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Xerophiles

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• Extremophiles which live in water-scarce habitats, such as deserts
• Produce desert varnish as seen in the image to the left, which is a thin coating of Mn, Fe, and clay on the surface of desert rocks, formed by colonies of bacteria living on the rock surface for thousands of years

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Desert “Varnish”

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http://www.livingwilderness.com/southwest/petroglyphs.jpg

SAMPLE PROKARYOTE EXTREMOPHILES

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Thermotoga

Aquifex

Halobacterium

Methanosarcina

Thermoplasma

Thermococcus

Thermoproteus

Pyrodictium

Ignicoccus

2um

1.8um

1um

0.6um

0.9um

0.9um

1.3um

0.6um

0.7um

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Deinococcus Radiodurans

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Possess extreme resistance to up to 4 million rad of radiation, genotoxic chemicals (those that harm DNA), oxidative damage from peroxides/superoxides, high levels of ionizing and ultraviolet radiation, and dehydration

It has from four to ten DNA molecules compared to only one for most other bacteria

DR contain many DNA repair enzymes, such as RecA, which matches the shattered pieces of DNA and splices them back together. During these repairs, cell-building activities are shut off and the broken DNA pieces are kept in place.

0.8μm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Cyanobacteria

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Cyanobacteria, also known as blue-green algae, blue-green bacteria or Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria.

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They are a significant component of the marine nitrogen cycle and an important primar producer in many areas of the ocean, but are also found on land.

Chroococcidiopsis

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• A cyanobacteria which can survive in a variety of harsh environments
• hot springs, hypersaline habitats, hot, arid deserts, and Antarctica 
• Possesses a variety of enzymes which assist in such adaptation

1.5μm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Other Prokaryotic Extremophiles

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Gallionella ferrugineaand (iron bacteria), from a cave

Anaerobic bacteria

1μm

1μm

Current efforts in microbial taxonomy are isolating more and more previously undiscovered extremophile species, in places where life was least expected.

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

EXTREME EUKARYOTES�THERMOPHILES/ACIDOPHILES

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2μm

EXTREME EUKARYOTES�PSYCHROPHILES

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Snow Algae

(Chlamydomonas nivalis)

A bloom of Chloromonas rubroleosa in Antarctica

These algae have successfully adapted to their harsh environment through the development of a number of adaptive features which include pigments to protect against high light, polyols (sugar alcohols, e.g. glycerine), sugars and lipids (oils), mucilage sheaths, motile stages and spore formation

2μm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

EXTREME EUKARYOTES�ENDOLITHS

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Quartzite (Johnson Canyon, California) with green bands of endolithic algae.

The sample is 9.5 cm wide.

Endoliths (also called hypoliths) are usually algae, but can also be prokaryotic cyanobacteria, that exist within rocks and caves.

Often are exposed to anoxic (no oxygen) and anhydric (no water) environments.

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

EXTREME EUKARYOTES�Parasites as extremophiles

-Members of the Phylum Protozoa, which are regarded as the earliest eukaryotes to evolve, are mostly parasites

-Parasitism is often a stressful relationship on both host and parasite, so they are considered extremophiles

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Trypanosoma gambiense, causes African sleeping sickness

Balantidium coli, causes dysentery-like symptoms

15μm

20μm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

What are Viruses?

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Viruses consist of genetic materials

(DNA or RNA) surrounded by a

protective coat of proteins. They

are capable of latching onto cells

and penetrating them. ��They can't multiply on their own, so they must invade a 'host' cell and take over its machinery in order to be able to reproduce. �

The cells of the mucous membranes, such as those lining the respiratory passages that we breathe through, are particularly open to virus attacks because they are not covered by protective skin.

http://static.howstuffworks.com/gif/light-virus-1.jpg

Major Types of Viruses

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http://www.daviddarling.info/images/virus_types.gif

Further Types of Viruses

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http://blogs.ipswitch.com/archives/viruses%202.jpg

HIV Retrovirus

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http://www.sciam.com/media/inline/F1C30FB9-F95F-8B4E-9FAF03A0503D1ABA_1.jpg

Viruses – continued�Bacteriophage

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http://www.cosmosmagazine.com/files/imagecache/feature/files/20070207_virus.jpg

Virus Replication

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EXTREME VIRUSES

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Virus-like particles isolated from Yellowstone National Park hot springs

Viruses are currently being isolated from habitats where temperatures exceed 200°F

Instead of the usual icosahedral or rod-shaped capsids that known viruses possess, researchers have found viruses with novel propeller-like structures

These extreme viruses often live in hyperthermophile prokaryotes such as Sulfolobus

40nm

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Phylogenetic Relationships

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Extremophiles are present among Bacteria; form the majority of Archaea; and, also a few among the Eukarya

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

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• Members of Domain Bacteria (such as Aquifex and Thermotoga) that are closer to the root of the “tree of life” tend to be hyperthermophilic extremophiles
• The Domain Archaea contain a multitude of extremophilic species:
• Phylum Euryarchaeota-consists of methanogens and extreme halophiles
• Phylum Crenarchaeota-consists of thermoacidophiles, which are extremophiles that live in hot, sulfur-rich, and acidic solfatara springs
• Phylum Korarchaeota-new phylum of yet uncultured archaea near the root of the Archaea branch, all are hyperthermophiles
• Most extremophilic members of the Domain Eukarya are red and green algae

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PHYLOGENETIC RELATIONSHIPS

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Extremophiles and the Chronology of Life

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• The early Earth was largely inhospitable.
• high CO₂/H₂S/H₂ etc, low oxygen, and high temperatures
• Lifeforms that could evolve in such an environment needed to adapt to these extreme conditions.
• H₂ was present in high abundance in the early atmosphere.
• Many hyperthermophiles and archaea are H₂ oxidizers

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

What were the first organisms?

• Extremophiles may represent the earliest forms of life with non-extreme forms evolving after cyanobacteria had accumulated enough O₂ in the atmosphere.
• Results of rRNA and other molecular techniques have placed hyperthermophilic bacteria and archaea at the roots of the phylogenetic tree of life.

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

What is Evolution?

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Biological evolution in its simplest sense, evolution is descent with change.

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This definition encompasses small-scale evolution (changes in gene frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations).

http://evolution.berkeley.edu/evosite/evo101/IIntro.shtml

What is Evolution?

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Biological evolution is not simply a matter of change over time.

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Lots of things change over time: trees lose their leaves, mountain ranges rise and erode, but they aren't examples of biological evolution because they don't involve descent through genetic inheritance.

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The central idea of biological evolution is that all life on Earth shares a common ancestor.

http://evolution.berkeley.edu/evosite/evo101/IIntro.shtml

Evolutionary Theories Must be Consistent With:

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

What Causes (Drives) Evolution?

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• Adaptation (becoming better fit to the environment)
• Genetic drift (random events change the gene pool)
• Gene flow (section of gene transfer)
• Mutation (change in nucleotide sequence)
• Natural selection (favorable traits become more common)
• Speciation (formation of new species)

Mechanisms of Evolution

• Consortia/Symbiosis - symbiotic relationships between microorganisms, allows more than one species to exist in extreme habitats because one species provides nutrients to the others and vice versa.

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Consortia

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Symbiosis and Mitrochondria

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http://thebrain.mcgill.ca/flash/a/a_05/a_05_cl/a_05_cl_her/a_05_cl_her_1b.jpg

Mechanisms of Evolution

• Genetic drift appears to have played a major role in how extremophiles evolved, with allele frequencies randomly changing in a microbial population.
• So alleles that conferred adaptation to harsh habitats increased in the population, giving rise to extremophile populations.

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

An allele is one member of a pair or series of different forms of a gene. Usually alleles are coding sequences, but sometimes the term is used to refer to a non-coding sequence.

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An individual's genotype for that gene is the set of alleles it happens to possess.

Mechanisms of Evolution

• Geographic isolation may also be a significant factor in extremophile evolution.
• Microorganisms that became isolated in more extreme areas may have evolved biochemical and morphological characteristics which enhanced survival as opposed to their relatives in more temperate areas.
• This involves genetic drift as well.

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

The Pace of Evolution

Extremophiles, especially hyperthermophiles, possess slow “evolutionary clocks”

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• They have not evolved much from their ancestors as compared to other organisms
• Hyperthermophiles today are similar to hyperthermophiles of over 3 billion years ago

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

The Pace of Evolution

• Slower evolution may be the direct result of living in extreme habitats and little competition
• Other extremophiles, such as extreme halophiles and psychrophiles, appear to have undergone faster modes of evolution since they live in more specialized habitats that are not representative of early earth conditions.

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Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Mat Consortia (Microbial Mats)

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A mat consortia in Yellowstone National Park

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Microbial mats consist of an upper layer of photosynthetic bacteria, with a lower layer of nonphotosynthetic bacteria.

Mat Consortia

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These consortia may explain some of the evolution that has taken place: extremophiles may have relied on other extremophiles and non-extremophiles for nutrients and shelter

Hence, evolution could have been cooperative

Adapted from H. A. Zorkot, R. Williams and A. Ahmad, University of Michigan-Dearborn

Stromatolites

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http://cas.bellarmine.edu/tietjen/images/microfossils.htm

Cyanobacteria and Oxygen

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Stromatolites of fossilized oxygen-producing cyanobacteria have been found from 2.8 billion years ago.

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The ability of cyanobacteria to perform oxygenic photosynthesis is thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the life forms on Earth and provoked an explosion of biodiversity.

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Chloroplasts in plants and eukaryotic algae have evolved from cyanobacteria via endosymbiosis.

Earth’s Earliest History

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Evidences for Life in Early Earth History

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http://www.exobio.cnrs.fr/IMG/jpg/Image1-14.jpg

Evolution of Oxygen

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http://www.prism.gatech.edu/~gh19/b1510/f202a.jpg

Cyanobacteria and Oxygen

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Cyanobacteria and BiFs

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http://hsc.csu.edu.au/earth_environmental/core/time/9_3_1/Image2.gif

Extremophiles and Life on other planets?

• Major requirements for life:
• water
• energy
• carbon
• Requirements for extremophiles are found on Mars, Jupiter’s moon Europa, and Saturn’s moons Titan and Mimas.
• Such life, if like terrestrial life, would have to consist of extremophiles that can withstand the cold and pressure differences of these worlds.

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Where to Look for Extremophiles?

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Mars: most like Earth

Europa: largest liquid water

Ocean in the solar system

Titan: Hydrocarbon seas

Life on other planets?

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Europa maybe has an ice crust above a 30-mile deep ocean.

• Reddish cracks (left) are visible in the ice – what are they?

Titan is enveloped with hazy nitrogen (left)

• Contains organic molecules
• May provide sustenance for life?
• Information from Huygens

Images courtesy of Current Science & Technology Center

Conclusions

How are extremophiles important to astrobiology?

• reveal much about the earth’s history and origins of life
• possess amazing capabilities to survive in extreme environments
• are beneficial to both humans and the environment.
• Are good candidates for life elsewhere in the solar system, such as Mars, Europa, Mimas, etc.

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