Earth System Science PDF

Earth System Science Dr. Jerome Harlay [email protected] Readings: Geosystems: An Introduction to Physical Geography, 8th Edition- Robert W. Christopherson, American River College - ©2012 Pearson An Introduction to Physical Geography and...

Earth System Science Dr. Jerome Harlay [email protected] Readings: Geosystems: An Introduction to Physical Geography, 8th Edition- Robert W. Christopherson, American River College - ©2012 Pearson An Introduction to Physical Geography and the Environment – 3rd Edition – J. Holden - ©2012 Pearson   Origin of the atmosphere Summary 1. Formation of the Earth by Accretion (4.5 Ga) This event lasted 50-100 million years 2. Differentiation The elements are sorted by their density and this period corresponds to the formation of the layers:  Crust  Mantle  Core  Atmosphere 3. Degassing of the mantle (changes in redox status) Release of CO2 and H2O (T0 ± 70 Million years).  Origin of the atmosphere Summary 4. The Primitive atmosphere is composed of H2O, CO2, CH4, N2 and O2. 5. Evolution of the atmosphere… What caused the Early Life to kick off ? Establishing conditions for life After the Intense Bombardment episode (at 4.4 Ga, early Hadean), a cooling of the Earth’s surface coincided with the condensation of water vapor and produced the first Ocean. The hydrogen isotope features of our contemporary ocean water suggest the source of water on Earth is icy asteroids*, not the condensation of water vapor during the cooling. The Cool Early Earth covers a range from about 4.4 Ga to 4.0 Ga. *Referred to as Carbonaceous Chondrites (rocky meteorites with less than 35% metal)  Evolution of the atmosphere  The second atmosphere is compatible with the conditions that supported life on Earth:  Second atmosphere (CO2, CH4, H2O, O2 and N2) – Warm climate (4.5 – 3.5 Ga)  Weathering of rocks Although no O2 had been produced by photosynthetic organisms, the atom of O was present as a radical, formed by UV radiation effects on water vapor and carbon dioxide.  Weathering of Rocks and the Long-term C Cycle Le long-term C-cycle Early oceans and atmosphere were in equilibrium in concentration with atmospheric CO2 levels. But what caused the atmospheric and oceanic CO2 to decrease? Weathering involves the chemical reactions between compounds in the atmosphere and compounds on the planet's surface. As a consequence, large-scale weathering is a process that takes place on a timescale of millions of years, over which it constitutes a critically important carbon sink for the atmosphere (T0 ± 200 Million years).  Weathering of Rocks and the Long-term C Cycle Why a carbon-sink for the atmosphere? Because, via the weathering of rocks and the re-precipitation of weathering products as carbonate sediments (e.g. limestones), huge quantities of atmospheric CO2 end up locked away from the atmosphere for a very, very long time. The process begins when CO2 dissolves in droplets of water, up there in the clouds. The resulting solution, which reaches the surface as rainwater, is weakly acidic: CO2 + H2O = H2CO3 (carbonic acid) Carbonic acid is able to react with most minerals at varying rates according to their chemical stability.  Weathering of Rocks and the Long-term C Cycle Chemical stability of minerals There exists a whole spectrum of mineral stabilities, but an important point is that most of the mineral species that make up rocks tend to the stable end of that spectrum: whilst they do react with carbonic acid, they do so at a very slow rate.  Most stable minerals Gold and quartz (silicon dioxide) are accumulating in river beds and are very difficult to erode.  Less stable minerals On the other side of the solubility spectrum are sulphides and sulfur compounds with various metals. Sulphides readily weather in the surface or near-surface environment, leaving their accompanying metal salt behind.  Equations of weathering Major reactions  H2CO3 ⇌ HCO3− + H+ [Acid rains] Carbonic acid dissociates into bicarbonate and protons (acid rains)  H2CO3 + CaCO3 = Ca(HCO3)2 [Weathering of carbonate rocks] carbonic acid + calcium carbonate = calcium bicarbonate (in solution)  2CO2 + 3H2O + CaSiO3 = Ca2++ 2HCO3– + H4SiO4 [Weathering of silicate rocks] carbon dioxide + water + calcium silicate = calcium ions + bicarbonate ions + silicic acid (in solution)  Ca2++2HCO3- = CaCO3 + CO2 + H2O [re-precipitation in the Ocean] Precipitation of calcium carbonate in seawater releases carbon dioxide  First organic molecules The first organic molecules appeared in the earliest times of Earth’s formation. Some authors believe that life was prevented to develop because of the Intense Bombardment episode when the first organic molecules were formed. What mechanisms lead to the synthesis or organic molecules? A demonstration of the feasibility of organic molecule synthesis is provided by the Miller-Urey experiment (1953) and the following experiments that were conducted in this vein. The swan-neck experiment (Pasteur, 1850)  Coacervates (Bungenberg de Jong, 1932) The term “Coacervate” is sometimes used to refer to spherical aggregates of colloidal droplets held together by hydrophobic forces. The process of coacervation was proposed by Alexandr Oparin and John Haldane as crucial in the early theory of abiogenesis (origin of life). This theory proposes that metabolism predated information replication, although the discussion as to whether metabolism or molecules capable of template replication came first in the origins of life remains open. And for decades the theory of Oparin and Haldane was the leading approach to the origin of life question.  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The Miller–Urey Experiment Electrodes discharge Water vapor sparks Reducing atmosphere (lightning mixture (H2O, N2, NH3, simulation) CO2, CO, CH4, H2) Many cycles Condenser Samples tested during one for analysis week Cool water Boiler Condensed liquid with complex molecules Heated water (“ocean”) Small organic molecules Heat source including amino acids  The Miller-Urey experiment They found that within a week:  15% of the carbon originally present as methane gas (CH4) had converted into other simple carbon compounds.  Among these compounds were formaldehyde (CH2O) and hydrogen cyanide (HCN).  These compounds then combined to form simple molecules, such as formic acid (HCOOH) and urea (NH2CONH2), and more complex molecules containing carbon–carbon bonds, including the amino acids glycine and alanine.  The Miller-Urey experiment Similar experiments followed  Tested different gas mixtures: Hydrogen cyanide contributed to the production of a complex ring-shaped molecule called adenine — one of the bases found in DNA and RNA.  Tested different sources of energy like lightning, UV, radiations…  The Miller-Urey experiment The table below summarized the different sources of energy tested so far. One of the major constraints is to deliver enough energy without raising the temperature to a level where the organic material is degraded. Ebisuzaki, T., & Maruyama, S. (2017). Nuclear geyser model of the origin of life: Driving force to promote the synthesis of building blocks of life. Geoscience Frontiers, 8(2), 275-298.  The Miller-Urey experiment The Miller-Urey experiment tended to demonstrated that the synthesis of simple organic molecules was possible in the primitive atmosphere of the Hadean Earth. However, some detractors pretended that their initial mixture did not reflect that of the Hadean. Further experiments showed that even thought the composition differs, the synthesis or organic products is still effective. But producing organic molecules is not yet the same as producing life. The most accepted definition for life is three-fold: 1. metabolism, 2. membrane, and 3. self-replication  The origin of life Before the Biogenesis theory was commonly accepted, other theories flourished: 1. Panspermia: hypothesis proposing that microscopic life forms that can  survive the effects of space, such as extremophiles,  become trapped in debris ejected into space after collisions between planets and small Solar System bodies that harbor life. 2. Spontaneous Generation: Believed that life came out of decaying and rotting matter such as straw and mud e.g. Virchow’s experiment with broth in an open jar  The origin of life 3. Biogenesis: hypothesis that opposed to spontaneous generation, supported by Francesco Redi (1668) and Louis Pasteur (1850) e.g. rotten meat experiment (1668) and the swan-neck experiment (1850) 4. Chemical evolution: hypothesis developed in the 1920s by the Russian Alexandr Ivanovich Oparin. He suggested that different types of coacervates could have formed in the Earth's primordial ocean and been subject to a selection process that led, eventually, to life. This does not contradict Biogenesis. The latter hypothesis has gained credit among scientists over the last few years  Natural synthesis versus extraterrestrial origin However the “Nuclear geyser model of the origin of life” that suggest a terrestrial origin of the first organic molecules is opposed to other models in which the same molecules could be of extraterrestrial origin. Ebisuzaki, T., & Maruyama, S. (2017). Nuclear geyser model of the origin of life: Driving force to promote the synthesis of building blocks of life. Geoscience Frontiers, 8(2), 275-298.  Natural synthesis versus extraterrestrial origin Another theory born in the 1990s evokes an extra- terrestrial origin for organic molecules – Abiogenesis - Christopher Chyba and Carl Sagan, suggested a new source of organic material – the continuous ‘drizzle’ of very small dust particles that reach Earth from space. Very small particles, according to their publication in Nature (1992), less than 1 micrometer, do not burn up when crossing the atmosphere, but gently fall to the ground. Chyba, C., & Sagan, C. (1992). Endogenous production, exogenous Many of these particles come from comets and are delivery and impact-shock synthesis of organic molecules: an inventory rich in organic compounds. for the origins of life. Nature, 355(6356), 125. Natural synthesis versus extraterrestrial origin Chyba, C., & Sagan, C. (1992). Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an inventory for the origins of life. Nature, 355(6356), 125.  Natural synthesis versus extraterrestrial origin The Murchison meteorite (1969) The meteorite was rich in organic compounds similar to that generated during the Miller-Urey experiment. A more recent analysis (2010) of the meteorite confirmed the presence of 14,000 molecular compounds including 70 amino acids. The study also showed the presence of di-amino acids that are considered as good candidates for the first genetic material on Earth. Di-amino acids are used for the synthesis of specific peptide nucleic acids, capable of forming duplex structures with individual DNA- and RNA-strands Schmitt-Kopplin, P., Gabelica, Z., Gougeon, R. D., Fekete, A., Kanawati, B., Harir, M.,... & Hertkorn, N. (2010). High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall. Proceedings of the National Academy of Sciences, 107(7), 2763-2768.  Natural synthesis versus extraterrestrial origin Although the meteorite contained a racemic mixture (of left- handed and right-handed amino acids), most amino acids used by living organisms are left-handed in chirality, and most sugars right-handed. A team of chemists in Sweden demonstrated in 2005 that this homochirality could have been triggered or catalyzed, by the action of a left-handed amino acid such as Glycine. Córdova, A., Engqvist, M., Ibrahem, I., Casas, J., & Sundén, H. (2005). Plausible origins of homochirality in the amino acid catalyzed neogenesis of carbohydrates. Chemical Communications, (15), 2047-2049.  Natural synthesis versus extraterrestrial origin Chirality is a geometric property of some molecules and ions to be non-superposable on its mirror image. The presence of a tetravalent C at the center is often a condition for chirality. The two molecules are called enantiomers or optical isomers. Many biologically active molecules are chiral, including the naturally occurring amino acids (the building blocks of proteins) and sugars. In biological systems, most of these compounds are of the same chirality: most amino acids are levorotatory (l) and sugars are dextrorotatory (d).  Natural synthesis versus extraterrestrial origin In the most recent developments of this theory (2015), scientists found an explanation for the chirality of molecules and especially the reason why they are generally levorotatory in the living.  Natural synthesis versus extraterrestrial origin Abstract: We report experimental evidence that chiral glycine (NH2CHDCOOH) is formed by the surface reaction of normal glycine (NH2CH2COOH) solid with deuterium (D) atom at 12 K under the simulative conditions of interstellar molecular clouds. Chiral glycine formation is most likely initiated by the tunneling abstraction reaction of H atom by D atom followed by the addition of D atom to the glycine radical (NH2CHCOOH). Given that chiral glycine can form in such a primordial low-temperature environment, it might source molecular chirality as molecular clouds evolve into planetary systems.  Natural synthesis versus extraterrestrial origin Purine and pyrimidine compounds were found in the Murchison meteorite. Carbon isotope ratios for uracil and xanthine at δ13C +44.5‰ and +37.7‰, respectively, indicate a non-terrestrial origin for these compounds. This specimen demonstrates that many organic compounds were delivered by early Solar System bodies and may have played a key role in life's origin. Martins, Z., Botta, O., Fogel, M. L., Sephton, M. A., Glavin, D. P., Watson, J. S.,... & Ehrenfreund, P. (2008). Extraterrestrial nucleobases in the Murchison meteorite. Earth and planetary science Letters, 270(1), 130-136.  Origin of life The most accepted definition for life is three-fold: 1. metabolism, 2. membrane, 3. self-replication The current theory accepts that coacervation may explain the appearance of membranes but how to account for self-replication and for metabolism? Origin of life Coacervation = process of encapsulating hydrophilic compounds in a lipidic membrane  Origin of life In all organisms alive today, the hard work is done by proteins. Proteins can twist and fold into a wild diversity of shapes, so they can do just about anything, including acting as enzymes, substances that catalyze a huge range of chemical reactions. However, the information needed to make proteins is stored in DNA molecules: You can’t make new proteins without DNA, and you can’t make new DNA without proteins. So which came first, proteins or DNA?  Origin of life In the 1960s scientists found that RNA could fold like a protein, albeit not into such complex structures. Many questions flourished: Can RNA catalyze reactions? Can RNA store and transmit information? Some RNA molecules might well be capable of making more RNA molecules. … and if that was the case? RNA replicators would have had no need for proteins: they could do everything themselves.  Origin of life Nucleic acids & DNA-RNA Adenine was one of the products of the Miller-Urey experiment, it is also a common base in DNA and RNAs. The genetic pairing code is also common for DNA and RNA: A/U-T and G-C Could have RNA been the first genetic material? Origin of life  Origin of life The first RNA enzyme or ribozyme was finally discovered in 1982 in a primitive aquatic creature (Zaug & Cech, 1986). RNA might not be as good for storing information as DNA (less stable, nor as versatile as proteins) but it was turning out to be a molecular jack-of-all-trades. This was a huge boost to the idea that the first life consisted of RNA molecules that catalyzed the production of more RNA molecules – “the RNA world” (Gilbert, 1986) Zaug, A., & Cech, T. (1986). The intervening sequence RNA of Gilbert, W. (1986). Origin of life: The RNA Tetrahymena is an enzyme. Science, 231(4737), 470-475. world. nature, 319(6055).  Origin of life The “RNA world” hypothesis The “RNA world” preceded today’s “DNA world”. RNA may have been the first genetic material but not all the reactions leading to self-replication have been checked in vitro. The first genes could have been abiotically produced RNA, whose base sequences served as templates for both alignment of amino acids in polypeptide synthesis and self-replication of an RNA-chain (alignment of complementary nucleotide bases). For more information refer to discussion in Orgel (2004). Orgel Leslie E. (2004) Prebiotic Chemistry and the Origin of the RNA World, Critical Reviews in Biochemistry and Molecular Biology, 39:2, 99-123  Origin of life Putting the nucleotides together is the hardest part of the “RNA Theory”; There does not seem to be any way to join the components without the help of specialized enzymes. Because of the shapes of the molecules, it is almost impossible for the sugar to join to a base, and even when it does happen, the combined molecule quickly breaks apart. Many began exploring the possibility that the “RNA world” was preceded by a “TNA world”, or a “PNA world”, or perhaps an “ANA world”… all molecules similar to RNA but whose basic units are thought to have been much more likely to form spontaneously. POSITIVE SELECTION of RNA against others  Origin of life Prof. John Sutherland said: “In each nucleotide, you see a sugar, a base and a phosphate group, so you assume you need to make those building blocks first and then stick them together… and it doesn’t work.” In 2009, he proved it was possible that simpler molecules might assemble into a nucleotide without ever becoming sugars or bases (Powner et al., 2009). Powner, M. W., Gerland, B., & Sutherland, J. D. (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459(7244), 239-242.  Origin of life Although Sutherland has achieved the de novo synthesis 2 of the 4 nucleotides present in nature, the issue of an RNA replicator is not totally solved! No fossilized vestiges remain of the first replicators as far as we know. But scientists try recreating the RNA world to demonstrate how it might have arisen. New insights may come from the chemistry of HCN (hydrogen cyanide) as the C1 block of life… see review in Sutherland, 2016. Sutherland, J. D. (2016). The origin of life—out of the blue. Angewandte Chemie International Edition, 55(1), 104-121. The Chemistry of Life First organic particles  The First Cells Microfossils of cells are fossilized forms of microscopic life  Oldest are 3.5 billion years old  Seem to resemble present-day prokaryotes 100 μm  The Prokaryotes: Bacteria and Archaea Diagram shows some of the ways organisms have been classified into kingdoms over the years. The six-kingdom system includes the following kingdoms: Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Animalia. Changing Number of Kingdoms Introduced Names of Kingdoms 1700’s Plantae Animalia Late 1800’s Protista Plantae Animalia 1950’s Monera Protista Fungi Plantae Animalia Archae- Animalia 1990’s Eubacteria Protista Fungi Plantae bacteria The Prokaryotes: Bacteria and Archaea  The Archaean Eon 3.8 Ga – 2.5 Ga Archean Eon is one of the four principal eons of Earth history. Some scientists argue that, because the Earth was much hotter, tectonic activity was more vigorous than it is today, resulting in a much faster rate of recycling of crustal material. Water bodies on dry land, the atmosphere, beaches, sea ice, the sea surface micro-layer, marine sediments, oceanic crusts and hydrothermal systems all contributing to the Hadean micro-environment, would have a drastic impact on the origin of life in the Archaean.  The Archean Eon 3.8 Ga – 2.5 Ga The surface of the Earth is now solid but the temperature is still hot due to core heat, volcanism and radioactive decay. Water is condensed in the liquid form. The first Prokaryotes appeared between the Hadean and the Archaean Eons:  Oxygen producing bacteria  Cyanobacteria The continents have not formed yet but will form during this Eon, although not in the form we know now. Atmosphere has low levels of free oxygen.  The Development of an Oxidizing Atmosphere Today it is clear that the oxygen in our atmosphere is the result of the process of photosynthesis. Cyanobacteria are the simplest organisms that are able to photosynthesize at that time, followed by green algae. One of the ‘waste’ products of the process of photosynthesis is molecular oxygen (O2), a toxic product for most of the life forms living at that time.  The Development of an Oxidizing Atmosphere Pre-biotic conditions established about 4 Ga and lasted approximately 1.5 billion years. The oldest known fossils of living cells are thought to have formed 3.5 Ba. They consist in fossilized, photosynthetic bacteria that have been found in geological formations called stromatolites on the coasts of South Africa and Western Australia.  The Development of an Oxidizing Atmosphere In an oxidizing atmosphere, it was no longer possible for organic molecules to accumulate over millions of years to be later incorporated into living material. It allowed for the evolution of aerobic respiration. Because the first heterotrophs were anaerobic organisms by necessity, they did not derive large amounts of energy from the organic materials available as food. Aerobic organisms have a significant advantage over anaerobic organisms: They use the newly generated oxygen as a final hydrogen acceptor and, therefore, generate many more ATPs (adenosine triphosphates) from the food molecules they consumed.  The Development of an Oxidizing Atmosphere With the first evidence of life at 3.5 Ga and the development of an oxidizing atmosphere around 2.5 Ga, why is there a 1 billion year delay in the Oxygen build up? 40 oxygen level (%) Atmospheric 30 20 10 Time delay 1 billion y 3.5 3.0 2.0 1.0 0 Time (BYA)  The Development of an Oxidizing Atmosphere Banded Iron Formations - BIFs In the early atmosphere, O2 produced by the obligate anaerobic forms of life reacted with abundant reduced iron III (Fe3+), forming solid minerals (e.g. iron oxides)⟶ strong O2 sink. The structures consist of repeated thin layers of iron oxides, either magnetite or hematite, alternating with bands of silicate-rich rocks. BIFs are a distinctive type of rock often found in primordial sedimentary rocks. The seasonality of the accumulation is suggestive of a feedback oscillation pattern. Movie Movie The Snowball Earth hypothesis An alternative explanation of these deposits has undergone much discussion as part of the Snowball Earth hypothesis during which state the earth's continents, and possibly seas at low latitudes, were subject to an Ice Age: 1. During a Snowball Earth episode sea ice formed over most of the ocean's surface. 2. Mixing of oxygen with underlying water was made difficult by the ice sheet. 3. Over millions of years iron built up in seawater. 4. When the ice started to melt, atmospheric oxygen could mix with the ocean again 5. All the iron was deposited in these unusual iron formations. The Snowball Earth Hypothesis The initiation of a snowball Earth event 1. Involves some initial cooling mechanisms, 2. Which would result in an increase in Earth's coverage of snow and ice. 3. The increase in Earth's coverage of snow and ice would in turn increase Earth's albedo, which would result in positive feedback for cooling. 4. This positive feedback is facilitated by an equatorial continental distribution, which would allow ice to accumulate in the regions closer to the equator, where solar radiation is most direct. The Snowball Earth Hypothesis The presence of ice deposits within the tropics suggests global ice cover The Snowball Earth Hypothesis What processes created that cooling? The residence time of CH4 in the contemporary atmosphere is about 12 years because most of the CH4 is oxidized into CO2 by atmospheric O2. CH4 is also 30 time more potent greenhouse gas than CO2 in an atmospheric lifecycle analysis. This means that if all the CH4 contained in the atmosphere was converted into CO2 during the transition between a reducing to an oxidizing atmosphere, the overall greenhouse effect would decrease. Other initiating effects could have been the triggering of phytoplanktonic activity due:  To lower UV effect  To the burst of nutrients’ after deglaciation  To the niche made available for aerobic organisms after the extinction of obligate anaerobic organisms (raise of O2)  The Snowball Earth Hypothesis What processes resumed normal activity?  Volcanic activity:  Released CO2 to the atmosphere, and in absence of photosynthesis, its accumulation contributed to re-establish a greenhouse warming  Releases of volcanic dust reduced the albedo of the ice cover and dampened the positive feedback loop effect.  Release of methane contained in:  The equatorial permafrost,  Clathrates (methane hydrates)  Weathering of nutrients out of lands during the first deglaciation stages:  Triggered phytoplanktonic activity and the Ocean Biological pump (uptake of atmospheric CO2 and export to the Deep Ocean)  The pressure the ice cover (several km thick) exerts on the crust influences plate tectonics and the position of continents.  The Snowball Earth Hypothesis Neoproterozoic distribution of lands in agreement with the Hyde et al.’s model. Hyde, W. T., Crowley, T. J., Baum, S. K., & Peltier, W. R. (2000). Neoproterozoic'snowball Earth'simulations with a coupled climate/ice-sheet model. Nature, 405(6785), 425.  The Snowball Earth Hypothesis Side effects of O2 production  Allows Ozone formation: protects organisms from the negative effect of solar radiation (especially UV),  O2 inhibits methanogens’ activity but does not “kill” cyanobacteria  O2 is toxic for the first obligate anaerobic organisms,  Oxidize CH4 to CO2, a less potent greenhouse gas,  More CO2 and less UV may lead to excessive photosynthesis and eventually to the development of Snowball Earth.  v CH4 to CO2 + H2O; methane a more efficient greenhouse gas than CO2!  The alternative Slushball Earth Hypothesis An alternative theory has developed that goes by the name “slushball” in which the Earth becomes largely covered with ice, but open water remains near the equator. This hypothesis does not exclude that at least one episode has resulted in a snowball state but the Cryogenian glaciations may have rather been of Image credit: NASA-GISS/Columbia-CCSR slushball type.  Deep freeze and complex life The most complex life forms on Earth at the time of the Neoproterozoic glaciations were primitive algae and protozoa and most of them were undoubtedly wiped out by glacial episodes. However, the intense selective pressures of snowball glaciations may have fostered life forms that were highly adaptable Recent findings have shown that some microscopic organisms can flourish in extremely challenging conditions:  Within the channels inside floating sea ice  Around vents on the ocean floor where superheated water fountains up from Earth's mantle.  In small holes in the ice created by the geothermal heat. They would have been wonderful refuges where life could persist. The last reservoirs of life during Snowball Earth phases?  Ice Ages and Glaciations Global Ice Ages occurred at least four times in the Proterozoic era: 1. 2.4-2.1 Ga: Huronian glaciation (covers the Siderian and the Rhyacian, at the beginning of the Proterozoic eon) 2. 0,85-0.75 Ga: Kaigas glaciation Cryogenian glaciations 3. 0.78-0.67 Ga: Sturtian glaciation 4. 0.65-0.63 Ga: Marinoan glaciation (ended after the release of CH4 out of the equatorial permafrost) The beginning of the Huronian glaciation coincided with the Oxygen Catastrophe that caused a massive extinction of the first obligate anaerobic forms of life. As a result, the entire Earth was covered with ice. The Marinoan glaciation caused the last mass extinction, possibly killing off most Edicarian* life forms (*635-542 mya) and leading to the Cambrian explosion of new life forms (=new evol. Niches). Dickinsonia (560-550 mya): fossil of the Ediacaran biota. It (roughly) resembles a bilaterally symmetrical ribbed oval. Its mode of has been subject to scientific debate, though some have suggested that it belongs to the fungi, or even an "extinct kingdom". Finally, a new study provides strong proof the creature was an indeed an animal1. 1Hoekzema, R. S., Brasier, M. D., Dunn, F. S., & Liu, A. G. (2017, September). Quantitative study of developmental biology confirms Dickinsonia as a metazoan. In Proc. R. Soc. B (Vol. 284, No. 1862, p. 20171348). The Royal Society.  The Great Oxygenation Event What caused the Oxygen burst between 850 My and 540 My? 40 oxygen level (%) Atmospheric 30 20 10 3.0 2.0 1.0 0 Time (BYA)  The Great Oxygenation Event Phase Period (Ga) Characteristics 1 3.85–2.45 No O2 production O2 of biological origin dissolves in the Ocean 2 2.45–1.85 and is scavenged in BIFs O2 is produced by the Oceans, some is 3 1.85–0.85 converted to ozone and the rest is absorbed by lands 0.85–0.54 O2 sinks are saturated and O2 accumulates in 4 and 5 0.54–present the atmosphere The accumulation of O2 into the atmosphere has created an ecologic crisis because of its toxicity The Proterozoic Eon 2.5 Ga – 0.54 Ga The Proterozoic Eon ends 540 million years ago. During the Proterozoic, the Earth cooled down and re-heated several times, offering Life many opportunities to re-create new forms and new processes to cope with free O2. In the late Proterozoic (most recent), the dominant supercontinent was Rodinia (~1000– 750 Ma) that gave birth to Pangea (Pan= complete, gea=Mother Earth (Gaia)) then to Gondwana (~500 Ma). It saw the development of multicellular organisms.  The Textbook Paradigm Biology books tell us that there are two different types of cells:  Prokaryotes, those without nuclei (specifically, without nuclear membranes),  Eukaryotes, those with a classical membrane-bounded nucleus. But the classification was based on the visual aspect of organisms (with E. Haeckel who termed “monera” the group that will become the “Prokaryotes”). Further studies of their genetic sequence (ribosomal RNA – work by Carl R. Woese1) and further biochemical developments contributed to change the view of how things work. 1Woese, C. R., & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), 5088-5090.  The Textbook Paradigm Ribosomal RNA has been useful to reconstruct the earliest evolutionary events because rRNA:  Are ubiquitous  Have a slow rate of evolution This established a 3-Domains model to organize living things:  Eubacteria,  Archaea, and  Eukarya or Eukaryota.  The Textbook Paradigm The kingdom-level classification of life Source Wikipedia Ruggiero, M. A., Gordon, D. P., Orrell, T. M., Bailly, N., Bourgoin, T., Brusca, R. C.,... & Kirk, P. M. (2015). A higher level classification of all living organisms. PloS one, 10(4), e0119248.  The Textbook Paradigm Contemporary understanding of the Tree of Life: Besides rRNA sequencing, other phylogenetic results and biochemical correlates show that the genetic lines of Eukarya and Archaea have a common ancestral branch that is independent of that giving rise to the bacteria. The oldest organisms may have been some bacteria that were able to live in hot situations and that gave rise to the Archaea. The major eukaryotic organelles, mitochondria and chloroplasts, are definitely bacterial in origin, but the nucleus is not. The nucleus appeared later in evolution and is not derived from either Archaea or Bacteria. This makes the 1Pace,N. R. (2006). Time for a change. Nature, Prokaryote/Eukaryote model invalid1. 441(7091), 289-289.  The Textbook Paradigm Archaea and Eukarya share many characteristics suggesting that they are “more closely related to one another than either is to Bacteria”.  The Tree of life Bacteria and Archaea share similar structures:  Plasmid (circular DNA) pili  Flagellum plasma membrane flagellum  Pilli DNA  Cell wall cell wall  Plasma membrane plasmid  Capsule This diagram shows the typical structure of a prokaryote. Archaea and bacteria look very similar, although they have important molecular differences.  The Tree of Life The main differences between Bacteria and Archaea are: Bacteria  Rod-shaped (bacilli)  Spiral (spirilla, spirochete)  Spherical (cocci) Archaea  Have many shapes  The Tree of Life In Archaea and Bacteria, cell wall and cell membrane do not have the same composition: Archaea membrane lipids contain branched long-chain hydrocarbons connected to glycerol by ether linkages.  The Tree of Life Domain Bacteria – Kingdom Eubacteria (“eu” = “true”)  Developed many different metabolic abilities.  Many are able to use organic molecules as a source of energy,  Some are able to carry on photosynthesis,  Others are able to get energy from inorganic chemical reactions similar to Archaea. The Tree of Life The bacterial cell wall is made of Peptidoglycans that are polymers of sugars and amino acids that form a mesh-like layer outside the plasma membrane: The Tree of Life  The Tree of Life Aerobic C fixation – The Calvin cycle The most common pathway for carbon fixation is the Calvin cycle. This is the pathway used by cyanobacteria, algae, and modern land plants that perform oxygenic photosynthesis. The Calvin cycle is also active in green and purple sulfur bacteria that perform anoxygenic photosynthesis. This anoxygenic form of photosynthesis could account for an ancient carbon fixation pathway without the production of O2. 1,3-Bisphospho- glycerate Glyceraldehyde-3- phosphate  The Tree of Life Aerobic pathways and the Cyanobacteria Cyanobacteria, commonly called blue-green algae, is a phylum of bacteria that obtain their energy through photosynthesis. Some structures formed by mats of bacteria are found today and also fossilized from 2 billion years ago (stromatolites). They were initially called Myxophyceae with regard to their diazotrophic ability to fix atmospheric di-nitrogen N2. The Tree of Life Domain Archaea – Kingdom Archaebacteria  Organisms that use inorganic chemical reactions to generate the energy they need to make organic matter.  These reactions result in the production of CH4, the organisms are known as methanogens.  Others use sulfur and produce hydrogen sulfide (H2S)  Most of these organisms are found in extreme environments such as hot springs or in extremely salty or acid environments. The Tree of Life Archaea were originally viewed as the extremophile branch of bacteria with various habitats like:  Deep-sea vents,  Volcano lakes,  Salt lakes,  Hot springs. They are often mutualists or commensals, no clear examples of parasites are known. They may have been playing a major role in early Earth's life and may still play roles in both the Carbon and Nitrogen cycles. Most of them are found in the Ocean where they are associated to phytoplankton blooms.  The Tree of Life 1. Halophiles are referred to as haloarchaea and require high salt concentration to grow. They can develop aerobically or anaerobically and contain a pigment, rhodopsin, which they use to transform light energy into chemical energy. Their high densities in the water often lead to pink or red colorations of the water. 2. Thermophiles can live at very high temperature and are equipped with enzymes that do not degrade with heat. They use the sulfur instead of oxygen as an electron acceptor during cellular respiration.  Obligate thermophiles (also called extreme thermophiles) require such high temperatures for growth,  Facultative thermophiles (also called moderate thermophiles) can thrive at high temperatures, but also at lower temperatures (below 50 °C).  Hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80 °C.  The Tree of Life 3. Methanogens are Archaea that produce CH4 as a metabolic byproduct in anoxic conditions, methanogenesis is a form of anaerobic respiration where the terminal electron acceptor is not oxygen but carbon:  𝐶𝐻3𝐶𝑂𝑂𝐻 → 𝐶𝑂2 + 𝐶𝐻4 (Acetic acid)  𝐶𝑂2 + 4𝐻2 → 2𝐻2𝑂 + 𝐶𝐻4 (𝐶𝑎𝑟𝑏𝑜𝑛 𝑑𝑖𝑜𝑥𝑖𝑑𝑒)  The Tree of Life Depending on pH and temperature, methanogenesis has been shown to use carbon from other small organic compounds, such as formic acid, methanol, methylamines, tetramethylammonium, dimethyl sulfide, and methanethiol. Methanogenesis is the final step in the decay of organic matter. During the decay process, electron acceptors (such as oxygen, ferric iron, sulfate, and nitrate) become depleted, while hydrogen (H2) and carbon dioxide accumulate with light organic molecules due to fermentation. Without methanogenesis, a great part of carbon would accumulate in anaerobic environments, especially fermentation products.  The Tree of Life Halorubrum lacusprofundi Researchers, including Carl Woese, sequenced the complete genome of an extreme Halophile within the Archaeal phylum living in Deep Lake in Antarctica1 under temperatures as low as -40˚C and at salinities ranging between 10 and 25 PSU. Members of the genus Halorubrum have been found not only in Antarctica, but also in Africa, Asia, and North America, where they are usually found in saline lakes. Most members of the genus are neutrophiles, but some are haloalkaliphiles. 1Anderson,I. J., DasSarma, P., Lucas, S., Copeland, A., Lapidus, A., Del Rio, T. G.,... & Pitluck, S. (2016). Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Standards in genomic sciences, 11(1), 70.  The Tree of Life Domain Eukarya  Are the most familiar,  Appear to have exploited the metabolic abilities of other organisms by incorporating them into their own structure:  Chloroplasts Bacteria-like structures found inside eukaryotic cells  Mitochondria  Contains five kingdoms (Ruggiero et al., 2015): 1. Protozoa 2. Chromista 3. Plantae 4. Fungi Ruggiero, M. A., Gordon, D. P., Orrell, T. M., Bailly, N., Bourgoin, 5. Animalia T., Brusca, R. C.,... & Kirk, P. M. (2015). A higher level classification of all living organisms. PloS one, 10(4), e0119248.  The Tree of Life Eukaryotic cells have started to exist more than 0.6 billion years ago. Their evolution is viewed by many as one of the most unusual events in biological history because over the same period of time a lot characteristics have been developed, evolved, and changed. To explain such bizarre event, scientist Lynn Margulis proposed the so-called “Endosymbiotic Theory”.  The Endosymbiotic Theory This theory states that the mitochondria (powerhouse of the cell), and the chloroplasts (structure for photosynthesis) were once single-celled organisms that have been engulfed by “proto-eukaryotic” cells. Interestingly, the eukaryotic mitochondria and chloroplasts have a different set of genetic material as compared to the cell itself, hence a compelling evidence that they were once bacterial cells. Their continuous and maintained symbiosis required both cells to reproduce at the same rate and not to digest each other. The resulting cells are equipped to produce their own energy, and fix carbon through the use of light. The Endosymbiotic Theory The Endosymbiotic Theory The Tree of Life The Kingdom Fungi consists of heterotrophic organisms. Instead, they simply acquire all the important nutrients by absorption:  The cell wall of the members of the kingdom is made of chitin, a type of carbohydrate, whereas their carbohydrates (energy) is stored in the form of glycogen.  The Kingdom fungi consists of organisms such as yeast, mushroom, and mold.  Fungi break down the organic materials of dead organisms and as a result, they help continue nutrient cycling in ecosystems. The Tree of Life Coming from the Latin “animalis” (“have breath”) the Kingdom Animalia is comprised of heterotrophic organisms.  A distinguishing characteristic of this kingdom include multi-cellularity and the lack of cell walls.  Most members of this kingdom are capable of movement (locomotion) and reproduction.  Members of this kingdom consist of almost all animals known (e.g. fishes, amphibians, reptiles, birds, mammals, insects, etc). The Tree of Life The Kingdom Plantae consists all multicellular, eukaryotic, and photosynthetic organisms in the planet.  Being photosynthetic, these organisms are autotrophs and are able to make their own food using the energy from the sun.  However, some members are able to be both producer and consumers as they are able to synthesize food and metabolize it from other sources.  Members of this kingdom have made possible the perpetuation of a large number of organisms. Basically, without them, heterotrophic organisms would have never survived.  The Tree of Life The kingdom Chromista, is one of the “newly-considered” kingdoms in the biological world (as proposed by Thomas Cavalier-Smith in 1981, refined in 2017).  This kingdom includes ciliates, dinoflagellates and all chromophyte algae plus some endoparasites and pseudofungi.  It is believed that the members of this kingdom originated from a bikont (a cell with two flagella) and a red alga that became the ancestor of all organisms with plastids having chlorophyll c.  However at present, it is still being debated as some evidences show that this kingdom is not monophyletic (coming from a common ancestor) as it was originally observed. Cavalier-Smith, T. (2017). Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. Protoplasma, 1-61. The Tree of Life The kingdom Protozoa is defined as single-celled animals or organisms with animal-like behaviors, such as motility and predation.  It contains ciliates, amoebae and flagellates.  Some protozoa are sessile, and do not move at all, others are vagile (free-dwelling).  They can feed by osmotrophy or by phagocytosis, either by engulfing particles of food with pseudopodia (e.g. amoebae). Some are taking in food through a mouth-like aperture called a cytostome. They possess vacuoles where digestion occurs.  They possess a pellicle, a thin layer supporting the cell membrane.  Tree of Life Some Protozoa are human pathogens at the origin of severe diseases:  Malaria (Plasmodium),  Amoebiasis (dysentery),  Toxoplasmosis,  African trypanosomiasis, also known as sleeping sickness (Trypanosoma brucei),  Leishmaniasis,…