Microbial Evolution Lecture 2

Lecture 2: Microbial Evolution

• Environmental Microbiology (BI 304)
• Instructor: Dr. Nalina Nadarajah
• Email: [email protected]

Today's Agenda

• Earth's history and evolution
• Plausible stages in the development of early life
• Panspermia Theory (life reaching Earth from space)
• Early biosynthesis (iron/sulfur world)
• Encapsulation – key to cellular life
• "Last universal common ancestor"
• The rise of oxygen
• Eukaryotic evolution

What Do We Know

• Earth
  • First Earth-size planet orbiting a star discovered by NASA (2013) in the "habitable zone".
  • NASA's Kepler Mission discovered a larger, older cousin to Earth (2015).
• Solar System
  • Astronomers have found over 3200 stars with orbiting planets.
  • Milky Way Galaxy contains 125 billion galaxies (3,000 visible).
• Universe
  • Expansion of space (redshift).

The Big Bang Theory

• The universe began from a point-source of infinite mass.
• 13.7 billion years ago.
• Exploded, spewing intense radiation and energy.
• 380,000 years: Protons and neutrons merged to form helium nuclei.
• Gravity caused hydrogen and helium to coalesce, forming larger clumps and eventually galaxies.
• Stars formed, died, and released heavy elements into space.

Physical Evolution of Earth

• Big Bang led to our solar system & early Earth.
• All matter concentrated as one immense point-source.
• Exploded and spewed intense energy and radiation.
• 380,000 years later, protons and neutrons formed.
• Formed hydrogen and helium nuclei.
• Density of hydrogen clumped together to form larger objects (stars/galaxies).
• Some stars disintegrated, creating interstellar matter.

Patchy Condensation Formed Solar System – 4.6 bya

• Most matter clumped together near the center of the condensed objects.
• This formed the Sun.
• Remaining matter formed orbiting planetismals, planetoids, planets.
• Planet Earth Formed 4.54 billion years ago.
• Not too close or far from Sun – crucial for liquid water.
• About 60 million years later, Earth's moon was formed.

How to Calculate the Age of Earth & Biota

• Radioactive decay in rocks: Zircon contains trace amounts of uranium-238 and decays into lead-206. The half-life of Uranium-238 (4.5 x 10⁹ years) is used to determine rock ages. By measuring the ratio of lead-206 to uranium-238, scientists can estimate how old the rock is.

• Carbon dating of life: Carbon-14 (14C) is radioactive, with a half-life of 5760 years. 14CO₂ is incorporated into living organisms and the ratio of radioactive carbon to non-radioactive carbon is used to estimate age. 1g of carbon will decay down to 0.5g after 5760 years

What info can we get from Zircon?

• Origin of rocks (Greenland)
• Zircon's hardness (resistant to melting)
• Analysis location (Swedish museum of natural history)
• Age estimation based on Pb/U ratio
• Tree age (oldest inside)
• Synthetic Zircon Analysis (Rensselaer Polytechnic Institute, New York) Ti proportional to temperature

Early Earth (Hadean Period): 3.8-4.6 billion years ago

• Extremely hot Earth with abundant volcanism, lightning, and high UV radiation.
• Oceans were hot.
• Atmosphere was reducing (lacking oxygen). Gases like N₂, H₂, NH₃, CH₄, and HCN were present.
• Ocean chemistry included H₂S, Fe²⁺, and heavy metals.
• Oldest meteorites and lunar rocks are 4.5 billion years old.
• Oldest known Earth rocks are from the Hadean period (3.8bya).
• Cooled from liquid magma to a solid crust over 700 million years.

Archean Eon: 3.8-2.5 billion years ago

• Lasted 1.3 billion years.
• Origin of life.
• Formation of continents.

Conditions for Early Life to Originate

• Elements (Carbon, Oxygen, Hydrogen, Nitrogen) combined to form organic molecules.
• Early atmosphere provided raw material for life-essential molecules.
• Sun’s energy (heat, UV, lightning) was essential for chemical reactions to create organic molecules such as nucleotides and amino acids.

The Oparin-Haldane Hypothesis

• (1920s) Suggested early Earth's reducing atmosphere provided the necessary building blocks.
• UV light converted these atmospheric chemicals to organic molecules (sugars & amino acids).
• Primitive oceans functioned as a "primordial soup" facilitating complex organic molecules.
• Life may have originated through a series of stages, including metabolism and replication through the fusion of self-replicating droplets.

Prebiotic Soup Theory

• Early Earth’s atmosphere was chemically reducing.
• Energy produced simple organic molecules (monomers).
• Monomers accumulated in concentrated soups (e.g., shorelines, oceanic vents).
• Further transformations created complex organic polymers and ultimately life.
• 1951 Harold Urey speculated that early Earth's atmosphere contained NH₃, CH₄, & H₂
• 1953 Miller-Urey experiment successfully created amino acids from simple inorganic molecules.

Miller-Urey Experiment

• Simulated early Earth conditions in a closed system.
• Water vapor, gases (CH₄, NH₃, H₂), and energy (electric discharge) were used.
• Identified 5 amino acids (aspartic acid, glycine, a-amino-butyric acid & 2 versions of alanine).

Other Discoveries

• 1980s Leslie Orgel (Salk Institute) produced DNA-like molecules.
• Nobel Prize Winners (1989) Thomas Cech & Sidney Altman demonstrated that RNA can act as an enzyme (ribozyme).
• Manfred Eigen (Gottingen Institute) created short RNA molecules that self-replicated.

Did Life Reach Earth from Space?

• Panspermia Theory: Life arrives from space, possibly on meteorites.
• Supported by the survival of bacterial spores in outer space.

Evidence of Panspermia

• Bacteria can survive harsh space environments (UV radiation, cold temperatures).
• Prebiotic chemicals are found in interstellar matter (clouds, comets and meteorites).
• Organic molecules such as amino acids (left-handed), liquid water, hydrocarbons and organic matter have been identified on the surface of meteorites.
• Protected within the rocks of meteorites, bacterial spores can survive long periods.

Biomolecules from Meteorite

• Murchison meteorite (Australia 1969): contained many amino acids (predominantly left-handed).
• Studied the composition of the meteorite to determine the biomolecules found within the material.

Possibility of Life in Other Planets

• Research on prebiotic synthesis and the possibility of life on places like Europa, one of Jupiter's moons.

What Was the First Biomolecule? (DNA/Protein?)

• DNA replication requires proteins.
• DNA is a blueprint for protein construction.
• RNA potentially was the first biomolecule capable of both information storage and enzymatic function.

May Be it Was RNA

• RNA is composed of nucleotides.
• RNA plays multiple roles, both as an information carrier and as an enzyme (ribozyme).
• RNA can form a double helix or be folded into a single strand similar to a protein.

General Model of Biochemical Evolution

• Chemical synthesis (organic molecules)
• Surface-catalyzed reactions
• RNA world
• Last Universal Common Ancestor and community
• Compartmentalization to form free-living. cells

Where in Early Earth Did Life Form?

• Two main theories:
  • Hydrothermal vents at the bottom of the ocean
  • Volcanic pools on the surface of the earth
• These locations provided necessary building blocks and the right environment - high temperatures, catalytic surfaces, and other environmental factors for primitive life.

Encapsulation - Formation of Cells

• Proto-life (organic catalysis and replication) existed in RNA world.
• Self-assembled membranes into membrane-like vesicles.
• Lab studies suggest that simple polymers of RNA and other biomolecules encased themselves within vesicles.
• This helped protect the molecules, allowing the evolution of more advanced biological components – the formation of free-living cells.

Last Universal Common Ancestor (LUCA)

• All living organisms on Earth share a single common ancestor.
• This ancestor, likely a community of pre-cellular entities.
• Estimated to have lived 3.5 to 3.8 billion years ago
• Represents the end point of prebiotic evolution, and the beginning of life as we now know it.

Evidence of LUCA

• Genetic code (based on DNA) expressed via RNA intermediates, translated into proteins.
• Many properties of living organisms are due to protein functions.
• Cells functioned using ATP energy intermediates.

Last Common Ancestor (LCA) of All Life

• Phylogenetic trees show evolutionary relationships among different groups of organisms.
• Shared characteristics suggest common ancestry
• Branches based on genetic relationships.
• Demonstrates all life forms evolved from shared ancestral lineages.

Difference in Membrane Composition

• Archaea membranes use isoprenoid chains, branching side-chains, L-glycerol, and ether linkages.
• Bacteria and Eukaryotes use ester-linked fatty acids and D-glycerol-based phospholipids.

The Rise of Oxygen

• Early Earth had a highly reducing atmosphere – lacked oxygen (0% O₂).
• Pyrite (FeS₂) is unstable in the presence of oxygen.
• Oxygen levels slowly increased over many millions of years, due to oxygenic photosynthesis by organisms.
• Red beds (iron oxide minerals) showed evidence of increasing oxygen.

Stromatolites

• Layered accretionary structures formed in shallow water by sedimentation.
• These structures can form both abiotically and biogenically, from the trapping and binding of sedimentary grains.
• Stromatolites from 3.5 to 3.8 billion years ago (Western Australia, Eastern Andies).

Evidence of Oldest Life

• Zircon crystals (4.4 billion years old)
• Stromatolites (3.5 billion years old)
• Microfossils (3.8 billion years old).

Earth’s Biological Clock

• Photosynthetic bacteria appeared well before 2.8 billion years ago

Endosymbiotic Theory for the Origin of Eukaryotic Cells

• An endosymbiont is an organism that lives inside another one.
• The theory proposes that mitochondria and chloroplasts, which are membrane-bound organelles, evolved from prokaryotic endosymbionts.
• Lynn Margulis proposed the theory in 1967, stating that endosymbiotic relationships resulted in the evolution of eukaryotic cells.

Evolution since LUCA

• Mitochondria and chloroplasts evolved from free-living prokaryotic cells, becoming organelles within eukaryotic cells.

Our Microbial Ancestors

• Many current microbes descended from 3 billion year old microbes.
• These organisms formed symbiotic relationships and became permanent parts of the larger biological systems (human bodies) and ecosystems.

Summary - Timescale

• Big Bang (13.7 billion years ago)
• Earth formation (4.54 billion years ago)
• Life origin (3.8 billion years ago)
• Bacteria's emergence (3.45 billion years ago)
• Oxygen-producing organisms (2.7-2.9 billion years ago)
• Dinosaurs appeared (230 million years ago), disappeared (66 million years ago)
• Early Humans (2.3 million years ago)
• Homo sapiens (200,000 years ago)

References

• Various academic papers, university courses, and other publications are cited. Information on the sources are not provided within the notes.