Lecture 03 (2 09-2021) early earth
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The lecture on microbiology of early earth covers the formation of the planet, the origins of life theories, and key evolutionary events. It discusses the early earth environment, including the big bang, accretion, and the significance of RNA and protocells in life's development. Evidence for early life is presented through isotopic records, microfossils, and molecular fossils, illustrating the scientific foundations of these topics.
Lecture 03 (2 09-2021) early earth
- 1. MICROBIOLOGY OF EARLY EARTH Lecture 3, 2.09.2021 Reading for today: Brown Ch. 24 & 7 Reading for next class: Brown Ch. 12, White Ch. 21 Dr. Kristen DeAngelis by appointment deangelis@microbio.umass.edu
- 2. Unit 3: Microbiology of Early Earth LECTURE LEARNING GOALS • Describe the early Earth environment, and prevailing theories for the origins of life. • Describe the major events in the evolution of cellular life, and when they happened. • Explain the lines of evidence that lead us to know when early life arose, and the scientific basis behind each line. 4
- 3. Unit 3: Microbiology of Early Earth LECTURE LEARNING GOALS • Describe the early Earth environment, and prevailing theories for the origins of life. • Describe the major events in the evolution of cellular life, and when they happened. • Explain the lines of evidence that lead us to know when early life arose, and the scientific basis behind each line. 5
- 4. Early Earth: the first few million years…
- 5. History of Earth • The Big Bang Theory is the prevailing cosmological model that describes the formation of the Universe. – This occurred approximately 13.8 billion years ago, which is thus considered the age of the universe. – The Earth is estimated 4.54 billion years old (4.54 × 10^9 years ± 1%) • The first few million years 1. Radioactivity – Short-lived radiogenic isotopes are released and absorbed 2. Accretion – Impacting bodies, including moon formation 3. Differentiation – Formation of the Earth’s heavy metal core and light element crust 4. Self-compression – Extra gravity produces heat 7
- 6. 8 You are made of stars http://science.nasa.gov/science-news/science-at-nasa/2015/01may_halleyids/
- 7. “You are made of stars” • Two prevailing theories on the origins of life on earth: (1) Could the process of accretion, or impacting bodies, “seeded” our planet with life? • In 1986, Europe's Giotto spacecraft encountered and photographed the nucleus of Halley's Comet it approached the sun. • http://science.nasa.gov/science-news/science-at- nasa/2015/01may_halleyids/ (2) the alternative hypothesis is abiogenesis… 9
- 8. The Miller-Urey experiments demonstrated abiogenesis – life from organic matter 10
- 9. Miller-Urey experiments • simulated the early earth ocean-atmosphere interface and produced amino acids • It has been known for over 100 years that mixtures of many types of sugar molecules can be obtained by warming an alkaline solution of formaldehyde (CH2O), which also would have been available on the young planet. • Under the right conditions some building blocks of proteins, the amino acids, form easily from simpler chemicals, as Stanley L. Miller and Harold C. Urey of the University of Chicago discovered in pioneering experiments in the 1950s 11
- 10. RNA the first biological molecule 12
- 11. RNA the first biological molecule • Exposure to ultraviolet light destroys the “incorrect” nucleotides and leaves behind the “correct” ones • These are the same solar UV rays that hit shallow waters on the early earth • This provides a clean route to the C and U nucleotides • Ribosomes are “fossil” evidence of a primordial RNA world • Some roles of modern RNA: Translation, DNA replication, Splicing, Protein translocation, RNA interference 13
- 12. RNA is an autocatalytic network 14
- 13. Clay layers catalyze RNA polymerization • Soils are made of minerals (including clay), organic matter, water and microbes • Clay minerals enhance polymerization, producing chains of up to 50 nucleotides 15
- 14. The primordial sandwich hypothesis • Surfaces can concentrate organics by adsorption • Polymerization is favored on surfaces • Surface chemistry is stereospecific • Activated precursors are not required 16
- 15. Activity for Review of Unit 03.1 Place the following events in the history of Earth in order: ____ Radioactivity and self-compression of the early earth ____ The Big Bang ____ RNA World ____ First land plants 17
- 16. Unit 3: Microbiology of Early Earth LECTURE LEARNING GOALS • Describe the early Earth environment, and prevailing theories for the origins of life. • Describe the major events in the evolution of cellular life, and when they happened. 18
- 17. History of Life on Earth 19
- 18. History of Earth • Hadean Eon – 4.5 Ga – age of earth (Accretion & Moon; Self compression; Differentiation; radiogenic isotopes for the first few million years) • Archaean Eon – 3.5 Ga – First prokaryotes, including LUCA? (based on fossil evidence) • Proterozoic Eon – 2.5 Ga – First eukaryotes (cells with nuclei) – 2.45-0.85 Ga – The Great Oxygenation Event (in stages) – 1.5 Ga – First eukaryotes containing endosymbiotic Rickettsiales (Sar11 clade) bacteria, now mitochondria – 1.0 Ga – First plants, containing endosymbiotic cyanobacteria, now chloroplasts • Phanerozoic Eon – 600 Ma – First animals – 475 Ma – First land plants – 60 Ma – First primates – 0.2 Ma – First genus Homo (humans and predecessors) *Ga = Billion years ago, Ma = Million years ago 20
- 20. Assisted reproduction of protocells 22
- 21. Assisted reproduction of protocells • Amphipathic lipids (one end hydrophilic, another hydrophobic) can spontaneously form bilayers. Lipid bilayer spheres are known as liposomes. • Liposomes could have been early ‘cell compartments’. • Assisted reproduction could have occurred in waters circulating between cold and warm sides of ponds, for example. 23
- 22. From protocells to cells… 24
- 23. From protocells to cells… 25
- 24. From protocells to cells 1. Evolution starts with a liposome with RNA trapped inside. 2. RNA catalysis begins as ribozymes strengthen the membrane and speed up reproduction. 3. Metabolism begins as ribozymes incorporate nutrients from the environment into their reproduction and the protocell membrane. 4. Proteins appear and take over some ribozyme functions. 5. Proteins replace most ribozyme functions, because they are more efficient and more stable. 6. Other enzymes make DNA, and it takes over in encoding proteins, with RNA acting as the intermediate. 26
- 25. Pre-cellular Earth was an RNA world • RNA can fold and have catalytic capabilities • Proteins are more efficient enzymes • DNA is a more stable information- coding molecule 27
- 26. The Great Oxygenation Event 28 aka the Oxygen Catastrophe ~2.3 Ga, one of the great extinction events Red and green lines represent the range of the estimates while time is measured in billions of years ago (Ga).
- 27. The Great Oxygenation Event 29 Red and green lines represent the range of the estimates while time is measured in billions of years ago (Ga).
- 28. Great Oxygenation Event • Stage 1 (3.85–2.45 Ga) – Practically no O2 in the atmosphere. – In the pre-3.0 Ga biosphere photosynthetic bacteria almost certainly used photosystem-I (PS-I) and used H2, H2S and/or Fe2+ to reduce CO2 to organic matter • Stage 2 (2.45–1.85 Ga) – O2 produced, but absorbed in oceans & seabed rock. – The Oxygen Catastrophe (~2 Ga), when atmospheric oxygen jumps to ~0.01 atm (~5% of today’s levels) – Reactive Oxygen Species (ROS) can be formed by UV light or heat, and damage cell structures – Antioxidant enzymes like catalase and superoxide dismutase are present in all living cells, to combat oxygen stress 30
- 29. Great Oxygenation Event • Stage 3 (1.85–0.85 Ga) – O2 build-up in the Earth's atmosphere begins about 2.3 Ga. – O2 starts to gas out of the oceans, but is absorbed by land surfaces. • Stages 4 & 5 (0.85–present) – O2 sinks filled and the gas accumulates. • Oxygen build-up ENDS the Archaean Eon – 3.5 Ga – First prokaryotes, or the LUCA – 2.3 Ga– The Great Oxygenation Event begins • … and begins the Proterozoic Eon – 2.5 Ga – First eukaryotes (cells with nucleus) – 1.5 Ga – First eukaryotes with endosymbiotic Rickettsiales (Sar11 clade) bacteria, now mitochondria: symbiogenesis – 1.5-1 Ga – First plants with endosymbiotic cyanobacteria, now chloroplasts 31
- 30. 1.5 Ga - Mitochondria Class Alphaproteobacteria • Order Rickettsiales • Has DNA, performs respiration, has an electron transport system that occurs across membranes, and produces ATP • endosymbiotic theory – thought to have once been a bacterial cell that colonized a eukaryotic cell – Mitochondria originated as a symbiosis between separate single-celled organisms
- 31. 1.0 Ga – Chloroplasts Phylum Cyanobacteria • Found only in plant cells to provide energy from light • Derived from endosymbiosis of a cyanobacteria of the Prochlorales • Primary chloroplasts have 2 membranes • Secondary chloroplasts have 3 or 4 membranes
- 32. Activity for Review of Unit 03.2 • What were some characteristics of protocells? In answering, describe if it had: – DNA – RNA – Lipids – Membranes – Proteins – Replication • Was LUCA a protocell? Why or why not? 34
- 33. Unit 3: Microbiology of Early Earth LECTURE LEARNING GOALS • Describe the early Earth environment, and prevailing theories for the origins of life. • Describe the major events in the evolution of cellular life, and when they happened. • Explain the lines of evidence that lead us to know when early life arose, and the scientific basis behind each line. 35
- 34. THE EVIDENCE for Early Life 1. Isotopic record 2. Microfossils 3. Molecular fossils 4. Molecular evolution 36
- 35. Isotopic fractionation • Bonds involving “light” isotopes break more readily than those involving “heavy” isotopes. 37
- 36. Isotopic fractionation • Bonds involving “light” isotopes break more readily than those involving “heavy” isotopes. • Rate determining step which includes breaking of bond dictates isotopic fractionation of entire process • Typical of processes which are unidirectional and irreversible Example: Breathing - we use 16O preferentially for respiration, so 17O and 18O become progressively more abundant in lung air and exhaled air) Example: Preferential incorporation of 12C in CO2 fixing plants -passed on to herbivores and up the food chain Example: Methane has a very light δ13C signature, and differs whether it is biogenic methane of −60‰ or thermogenic methane −40‰. 38
- 37. Isotopic records of microfossils Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life J. William Schopf Science, New Series, Vol. 260, No. 5108. (Apr. 30, 1993), pp. 640-646 39
- 38. Isotopic records of microfossils • The sole source of direct, fossil evidence is from rocks deposited during the Archaean Eon of Earth history (>2.5 Ga). • “In order to establish the authenticity of Archean micro- fossils, five principal criteria must be satisfied. The putative microfossils must – (I) occur in rocks of known provenance and – (ii) established Archean age; – (iii) be demonstrably indigenous to and – (iv) syngeneic with the primary deposition of the enclosing rock; and – (v) be of assured biological origin.” Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life J. William Schopf Science, New Series, Vol. 260, No. 5108. (Apr. 30, 1993), pp. 640-646 40
- 39. Stromatolites 41 A P Nutman et al. Nature 1–4 (2016) doi:10.1038/nature19355
- 40. Stromatolites • Stromatolites are fossils that form through the activity of microbial communities including cyanobacteria and algae – These grow through sediment and sand, binding the sedimentary particles together, resulting in successive layers. – Over a long period of time, these layers harden to form rock. • Rapid emergence of life shown by discovery of 3,700- million-year-old microbial structures – newly exposed outcrop of 3,700-Myr-old metacarbonate rocks contain 1-4 cm-high stromatolites – Rare earth elements suggest that they formed in a shallow marine environment – Isotopic analysis demonstrates biotic CO2 fixation • https://www.nature.com/articles/nature19355 42
- 41. “Molecular fossils” organic geochemical markers • Organic biomarkers from 2.7 billion year old shales A. Steranes (cholestane) = eukaryotes B. 2-methyl hopanes = cyanobacteria • Lots of care has to be taken to ensure organics are derived from the rock was buried – and not contaminating material. • Hard stuff to do !!! – See also Archaean Molecular Fossils and the Early Rise of Eukaryotes Jochen J. Brocks, Graham A. Logan, Roger Buick, Roger E. Summons – Science, Vol 285, Issue 5430, 1033-1036 , 13 August 1999 43
- 42. Molecular evolution: Reconstructing past events 44 David & Alm, Nature 2011
- 43. Molecular evolution: Reconstructing past events • evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. – Molecular clock of genes associated with living in early Earth – Colors indicate abundance normalized to present-day values. Values in parentheses give the overall number of gene families in each group. • gradual increase in the fraction of enzymes that bind molecular oxygen predicted to be present over Earth history • Rapid evolutionary innovation during an Archaean genetic expansion. – coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. – A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways 45
- 44. THE EVIDENCE for Early Life 1. Isotopic record – Isotopic fractionation of C in old rock 2. Microfossils – Microbially-shaped fossils (small or large) in old rock with organic isotopic signature 3. Molecular fossils – Organic geochemical markers 4. Molecular Evolution – Use the molecular clock to time the evolution of oxygen usage 46
- 45. Activity for Review of Unit 03.3 47 Place the following events in the history of Earth in order: ____ First eukaryotes with endosymbiotic Rickettsiales (first mitochondria) ____ First plants with endosymbiotic cyanobacteria (first chloroplasts) ____ First eukaryotes ____ First land plants
- 46. Unit 3: Microbiology of Early Earth LECTURE LEARNING GOALS • Describe the early Earth environment, and prevailing theories for the origins of life. • Describe the major events in the evolution of cellular life, and when they happened. • Explain the lines of evidence that lead us to know when early life arose, and the scientific basis behind each line. 48 Next Class: Biofilms and motility Reading for next class: Brown Ch. 12, White Ch. 21