Biodiversity l2 PDF

TANG Lectures Instructor: Dr. Jessica Tang email: [email protected] Topic 9 Sep (Mon) The History and Origins of Life on Earth 13 Sep (Fri) Introduction to Microorganisms 16 Sep (Mon) Diversity of...

TANG Lectures Instructor: Dr. Jessica Tang email: [email protected] Topic 9 Sep (Mon) The History and Origins of Life on Earth 13 Sep (Fri) Introduction to Microorganisms 16 Sep (Mon) Diversity of Microbial Life: Archaea and Bacteria 20 Sep (Fri) Diversity of Microbial Life: Viruses 23 Sep (Mon) Diversity and Ecological Importance of Fungi 27 Sep (Fri) Microbiomes: Microbial Systems on and around Us 14 Oct (Mon) Mid-term Exam Ko & Tang (coverage from 6th Sep– 7th Oct)  Ilya Bobrovskiy, Australian National University Origins of Life LIFS 2060 Biodiversity Half-Billion-Year-old underwater blob from the White Sea area of Russia. The earliest animal to be discovered!  Lecture Content Geological Time Line of Earth How did Earth begin? Evolution of Life on Earth Mass Extinction Events  How was the Earth formed? The Earth started as swirling gas and dust in the center of the disks space became sun, the other Around 4.6 billion years ago (bya), these rings turned into particles were attracted by gravity forming planets the Earth The hot gas and molten-liquid outside of the sun cooled and condensed to become solid planets, including Earth. Crust Modern Earth The thin crust The atmosphere is now mostly made of supports all life Core Mantle nitrogen and oxygen Including soil The Earth is special as water covers 70% of and water the Earth’s surface Can there be life without water? Can there be life without oxygen?  Beginning of Life The first Era-Hadean Eon (4.6-4 Bya) From Greek “Hades” Greek god of the underworld “hell” During the Hadean Eon, the solar system was still forming. Early Earth Atmosphere Produced by gasses of volcanoes-H2O vapor), CH4 (methane), NH3 (ammonia) No free oxygen (not found in volcanic gases) Lightening, heat and UV radiation (no ozone O3) No liquid water  Beginning of Life 3.9-3.5 Bya Forming of Oceans The Earth was cool enough for liquid water to form How Did Oceans Form? Water vapor from volcanoes condensed to form rain Ice from comets-comets made from ice and rock-collide with Earth, which melted the ice Could organic compounds be generated under conditions similar to those of Early Earth? Primordial Soup Model- It is hypothesized that the oceans, provide all the organic molecules required for life. Primordial-existing since the beginning of time Miller and Urey (1950s) designed an experiment that demonstrated the possibility that building blocks required for life could be formed from gases in early Earth’s atmosphere The Urey-Miller experiment produced all 20 amino acids, which are the building blocks for proteins The primordial soup consisting primarily of an oxygen-free gaseous mixture of containing chiefly water, hydrogen, methane and ammonia.  Life originated in hydrothermal vents? Deep-Sea Hydrothermal Vent Hypothesis Researchers (2013), proposed that life began in deep sea hydrothermal vents oceanexplorer.noaa.gov What Are Hydrothermal Vents? opening in sea floor which heated mineral- rich water flows A deep-sea hydrothermal vent The battery effect Acidic early oceans +alkaline fluids from vent create an electrochemical gradient-> forming organic molecules inc. amino acids and sugars Proto-cells: these organic molecules may have combined to form proto-cells (plasma membrane + RNA)  Unique Life at Antarctic Deep-Sea Vents (Image credit: NERC ChEsSo Consortium) (Image credit: NERC ChEsSo Consortium) (Image credit: (c) Alex Rogers) Hydrothermal vents contain Anemones and barnacles thriving Remotely operated vehicle (ROV) compounds that make the ultra- in warm vent waters. in an Antarctica heated water they spew out smoke-colored. Giant Tubeworms: Life at Hydrothermal Vents Body Structure: No mouth, gut, or anus Feeding: Absorb toxic hydrogen sulfide and oxygen Symbiosis: Host chemosynthetic bacteria in their trophosome Function of Bacteria: Convert hydrogen sulfide (toxic) into sulfur, releasing energy for the tubeworm Growth Rate: Can reach 3 feet in 1.5 years! Can grow over 6 feet long! Timeline of life  Geological Time Scale (GTS) To describe the geology and history of life on Earth, scientists use the geological time scale. Rock layers and fossils were used to develop the time scale. Eons-The largest period of geological time Epoch-The smallest unit on the timescale, encompasses a period of millions of years Ga-giga annum=billion Ma-mega annum=million Ka-kilo annum=thousand  Video-A brief History of Geologic Time https://www.youtube.com/watch?v=rWp5ZpJAIAE Time Eons Era Events Fill in the blanks PRECAMBRIAN 4.6-4 BYA Hadean 4- 2.5 BYA Archean 1. Mammals diversify, humans 2. Earth forms, no life 2.5 BYA Proterozoic 3. Cambrian explosion: first fish, plant diversity, reptiles diversify 541 MYA-present 4. multicellular forms, O2, eukaryotes 541-252 MYA Paleozoic 5. Dinosaurs, first primates, PHANEROZOIC flowering plants 6. First life, mostly CO2, 252-66 MYA Mesozoic cyanobacteria 66 MYA- present Cenozoic https://www.youtube.com/watch?v=rWp5ZpJAIAE  Life, Molecules and the Geological Record First organisms on Earth were prokaryotes (Bacteria and Archaea) What kind of conditions did they live in during Early Earth? (Oxygen, temperature, water, radiation?) Problem one Prokaryotes are very small, so how could you see the fossils? Problem two How can you distinguish between fossil archeans from fossil bacteria? Archaea do not have distinct morphologies, so fossil shapes cannot be used to identify them. Lipid biomarkers used in fossils (chemical fossils) to identify archaea as archaea or bacteria as they have Archaea have unique isoprenoid (carbon side chains) chains and not prone to different lipid composition of their cell membranes decomposition at high temps.  Earth’s Atmosphere and the First Cells/Organisms Rise of early organisms (3.5 Bya)- methanogens (methane producing archaea) Evidence-Fossils (methane in rocks) Addition of methane (CH4) to the atmosphere by methanogens Methane is a greenhouse gas.  Archean Eon (4 to 2.5 Bya) Stromatolite fossils as old as 3.5 Bya found in W. Australia (in 2016) Photosynthetic cyanobacteria (blue green algae) that produce sticky compounds that cement sand and sediment. How do cyanobacteria increase the Earth’s oxygen? Stromatolites oxygenating Earth’s oceans and atmosphere Photo: UNSW Sydney/Brendan Burns Fossilized stromatolite found in W. Australia Modern stromatolites in shallow waters at Shark Bay, Western Australia. Where would you expect to find fresh cyanobacteria on the Cyanobacteria stromatolite?  Stromatolites https://www.youtube.com/watch?v=N-G7IJCkyvg  Oxygen and Cyanobacteria Cyanobacteria (blue green algae) are bacteria Increase in O2 that use photosynthesis producing O2. Oxygen is needed to make ozone, O3- blocks UV from the sun. o Without the ozone layer, life on early Earth was almost impossible. WHY? Due to increased O2, new life forms developed O2 was toxic to anerobic organisms, many died out.  Oxygen Boom! Before O2 in the atmosphere O2 from cyanobacteria reacted with iron in sea water to form iron oxide causing banded iron formations O2 went into the atmosphere when there was no more iron in sea water Image credit: Alex Glass Great Oxygenation Event- Cyanobacteria increased levels of O2 in atmosphere, displacing methane leading to free oxygen in the Earth’s atmosphere. Early Earth’s climate was constantly changing Earth’s temperature over time fluctuated from 2000 °C to -50 °C “Snowball Earth” -extreme drops in temperature Equator at -20 °C Leading to massive extinctions During Snowball Earth, ice covered the entire planet, from the poles to the equator  How do we know when life began? Fossils Extrapolation from molecular clocks Fossils form when: Organism is buried in sediment Calcium in bone or other hard tissue mineralizes Surrounding sediment hardens to form rock Radioactive carbon dating can be used to determine the age of the fossils Plants take in some C-14 by photosynthesis. Animals eat the plants. Amount of C-14 in a dead organism decreases exponentially with time as it decays into nitrogen with a half-life of about 5700 years. By comparing how much C-14 there is in the dead organism with the amount in a living one, the age of the dead organism can be estimated.  Molecular clocks use mutations to estimate evolutionary time Mutations are changes in the genetic material. Different molecules have varying rates of mutation e.g. mitochondrial DNA (fast mutation rate) or ribosomal RNA (low mutation rate) Mutations occur at a constant rate (ticking of the molecular clock) in related species. As time increases, more mutations will accumulate. The number of mutations can indicate how long ago two species shared a common ancestor. Example A length of DNA found in two species differs by 4 bases, it is known that this entire length of DNA changes at a rate of approx. one base per 25 million years How many years do the two DNA versions differ by?  Endosymbiotic theory How did eukaryotic cells evolve? Endosymbiotic theory-explains the evolution of the eukaryotic cell by American biologist, Lynn Margulis in 1970 Endo=inside Endocytosis=eating inside the cell Symbiosis=living together Endosymbiosis=living together inside the cell but not being eaten Her research paper was rejected by 15 journals, but she did not give up!! Symbiosis symbiosis means a close relationship between different species that live together.  Endosymbiotic theory Margulis hypothesized mitochondria are the result of endocytosis of aerobic bacteria chloroplasts are the result of endocytosis of photosynthetic bacteria Mutually beneficial Aerobic bacteria (pre-mitochondria) would have handled the toxic oxygen. Anaerobic ancestor would ingest food and protect the aerobic bacteria Some eukaryotes then acquire photosynthetic bacteria (cyanobacteria) for nutrients. Many lines of evidence to support endosymbiosis theory Both organelles are bounded by a double membrane. The inner membrane probably evolved from the plasma membrane of the engulfed bacterium, the outer membrane is probably derived from the plasma membrane or ER of the host cell. This figure shows how a double membrane may have been created during symbiotic origin of mitochondria or chloroplasts  Many lines of evidence to support endosymbiosis theory Mitochondria and chloroplasts are similar to bacteria in size and in structure. The cristae (inner membrane folds) formed inside of mitochondria resemble the folded membranes in various bacteria. For example, mitochondria resemble purple aerobic bacteria and both use oxygen in the production of ATP  Origin of modern eukaryotes (chloroplast reproduction) Binary fission-they replicate their DNA independently of the cell’s DNA by splitting  Origin of modern eukaryotes Other evidence: The timeline of Earth Anaerobic bacteria-around 3.8 billion years ago-fossils have been found of bacteria. All bacteria would have been anaerobic because there was no oxygen in the environment. Photosynthetic bacteria-around 3.2 billion years ago from fossil evidence of cyanobacteria Eukaryotes appeared shortly after that, around 2.5 billion years ago. Now, the Earth contained oxygen and these cells could use “toxic oxygen” and convert it to ATP and water.  What do we have in common with sponges? Photograph by Reinhard Dirscherl/ullstein bild via Getty  The first multicellular animals? Sponges are thought to be the earliest animal ancestors during the Cambrian period. We all evolved from sponges! Since they are soft-bodied, very rarely preserved as fossils Chemical fossils- Identified by detecting a particular steroid is produced by sponges but not in simpler organisms Water out Sponges are mostly marine, filter feeders that pump water through their matrix to filter food matter They do not have muscles, nerves or internal organs Choanocytes (collar cells) trap nutrients Amoebocytes transport digested food from food vacuoles to other cells Video: Evidence to show that humans evolved from sponges https://www.youtube.com/watch?v=XT8-1fcOc7Y&t=148s  The Cambrian Explosion “Cambrian Explosion” refers to the sudden appearance to the major groups of complex animals that are alive today in the fossil record over 30 million years Cambrian radiation was confined to the ocean The first Cambrian fossils were the trilobites in the early oceans-types of Cambrian fossil finds in Qingjiang in Hubei Province (2019) arthropods Trilobite fossils (University of Oxford, Natural History Museum) Chengjiang biota Cambrian fossils https://www.youtube.com/watch?v=S4DPtf9dwuc  Colonization of Land Fungi Around 360 mya, there were no trees and the only animals were invertebrates Land fungi are thought to have colonized land about 1,300 mya and played a crucial role in shaping the landscape Mega fungi (protoaxites) towered the landscape Fungi decomposed organic matter & minerals to soil Rendition of protoaxites based on fossils, Soil is required for plants towered the land up to 8m in height From algae (water) to land plants. How? A recent study (eLife, 2019) suggests that algae piggybacked on fungi to land, over 500 mya Du et al. studied a strain of marine algae and fungus from ancient lineages Found that the algal cells attached and broke the fungal (eLife, Du et al.) cell walls and enter the fungi-mutually benefit by each the algae (Nannochloropsis oceanica) attaches other’s nutrients itself to the fungus (Mortierella elongate)  Colonization of Land DNA evidence suggests that land plants evolved from a single species of green alga (a type of protist) (lives in water) around 470 mya It took only 75 million years for animals to follow plants out of water Closest living relatives of land plants are the charophytes (green algae) How did plants adapt to life on land?? Need to prevent desiccation, requires structural support Male gametes must meet female gametes (swimming no longer possible) Develop structures to anchor to substrates Charophytes-freshwater green algae  Colonization of Land The green algae split into two major clades Chlorophytes – Never made it to land. Charophytes – Sister to all land plants. Charophytes  How plants crawled out of the sea Genes have been found in algae from water (ancient lineages) allow them to have symbiosis with fungi https://www.youtube.com/watch?v=OyCyIOEyL20&t=85s  What were the first animals to colonize land? Arthropods : Greek: arthro- “joint”, pod- “foot” (invertebrates with jointed legs) including insects were the first animals to colonize land ~ 420 mya Tetrapods : Greek: tetra “ four”, pod- “foot” (vertebrates with 4 limbs) last to colonize land (probably evolved from fish) ~365 mya Includes amphibians, reptiles & mammals Photo: Andrew Wendruff This ancient scorpion is thought to have lived 437mya and may be the first land dwelling animal.  Mentimeter question Please put in the correct order  Major extinction events Lasted millions of years “Age of Fish” The “Great dying” Killed most of ocean and land life What caused the Great Dying? https://www.youtube.com/watch?v=z2sN8O5E_mQ  Recap Earth formed around 4.6 billion years ago from gas and dust, with mostly nitrogen and oxygen atmosphere and 70% water coverage on modern Earth Life originated during Hadean Eon, and first organisms thought to be prokaryotes Early organisms included methanogens and photosynthetic cyanobacteria that produced oxygen, needed to make ozone and protect life Geological time scale used to describe Earth's history, and climate has constantly changed with extreme temperature drops leading to mass extinctions during "Snowball Earth" period. Fossils and molecular clocks used to estimate the timing of evolutionary events and age of species. Endosymbiotic theory provides explanation for origin of eukaryotic cells. Cambrian explosion-represents first appearance of many major animal groups that still exist today. Fungi came before plants “The Great Dying”-most severe mass extinction event in Earth’s history  Video-A brief History of Geologic Time https://www.youtube.com/watch?v=rWp5ZpJAIAE Time Super Eons Era Events eon 4.6-4 BYA Hadean Earth forms, no life PRECAMBRIAN 4- 2.5 BYA Archean First life, mostly CO2, cyanobacteria 2.5 BYA Proterozoic multicellular forms, O2, eukaryotes 541 MYA-present 541-252 MYA Paleozoic Cambrian explosion: first fish, plant diversity, reptiles PHANEROZOIC diversify 252-66 MYA Mesozoic Dinosaurs, first primates, flowering plants 66 MYA- present Cenozoic Mammals diversify, humans