BY451 Introduction to Microorganisms and Plants 2024 SC PDF

BY451 Introduction to Microorganisms and Plants Teaching team Dr Ian Cooper (Module lecturer) Dr Maureen Berg Today’s Learning objectives Know the fundamental properties of life Understand the processes involved for life to evolve on Earth Understand SET Know the differences between Proka...

BY451 Introduction to Microorganisms and Plants Teaching team Dr Ian Cooper (Module lecturer) Dr Maureen Berg Today’s Learning objectives Know the fundamental properties of life Understand the processes involved for life to evolve on Earth Understand SET Know the differences between Prokaryote & Eukaryote Understand the timeframe involved for life to diversify on Earth Understand taxonomic hierarchy Understand binomial nomenclature Use dichotomous keys All living organisms have: 1. Cellular Organization 2. Metabolism 3. Homeostasis 4. Growth & Development 5. Reproduction (Heredity) 6. Responsiveness /Interactions 7. Evolution  All organisms are made of one or more cells; There is a hierarchy of cell organisation Order Fundamental Properties of Life Organic composition Metabolism ➔ obtaining & use of energy anabolic = build catabolic = break down Fundamental Properties of Life Growth & reproduction Ability to respond Ability to evolve and adapt ➔ All organisms respond to their environment Fundamental Properties of Life.. Homeostasis → maintaining stable internal conditions (temperature & fluid balance) within certain pre-set limits Fundamental Properties of Life …. Reproduction / Hereditary Reproduction to continue species existence Heredity = traits passed on from parents to offspring through genes (DNA …mutations….) Evolution → populations of organism change over time leading to great diversity in life Variation in DNA Traits are passed on Overproduction Changing survival pressures 1. Cellular Organization All living things are made of one or more cells. 2. Metabolism Living things break things down then build things back up. 3. Homeostasis Maintaining stable internal conditions when things outside change. 4. Growth & Development Summary Living things grow in size or number in cells and have a Fundamental life cycle, they live and then eventually die. Properties of Life 5. Reproduction/Heredity. 6. Responsiveness/Interaction Living things respond to outside influences. 7. Evolution As generations increase, random mutation and genetic combinations contribute to variability. View of Most Scientists Universe began with the Big Bang Earth is 4.55 billion years old Life arose on earth spontaneously Earliest life were bacteria (3.5 billion years ago) Genetic drift and natural selection pressures caused changes in genetics of populations Millions of species arose on earth over billions of years All life is cellular Life: Geological Time Scale Lots of fossil evidence for presence of life ….…but how did life actually evolve? Current assumption: if life formed spontaneously… Primitive Earth’s chemicals had to combine to form organic molecules Organic molecules had to combine to form primitive cells (proto-cells) Primitive cells had to evolve into a true cells Illustration of the Miller Urey 1953 experiment Evidence that organic molecules could form spontaneously Chemical evolution led to the formation of protocells Miller &Urey created organic compounds Based on: Mader, S., Inquiry Into Life, McGraw-Hill (e.g. amino acids) using gasses and electricity (1953)  Process from inorganic compounds to building blocks for life to polymers Stage 1: the origins of organic molecules ➔ lots of experimental evidence Stage 2: organic monomers becoming ordered into biologically active polymers → the discovery of alkaline vents and the similarity with the "proton pump“. The origin of replication. → work with RNA world Stage 3: how were biological reactions incorporated behind cell walls? → modern work on the self organising capacities (by which cell membranes self-assemble); work on micropores in various substrates. Ongoing research to understand how independent free-living cells developed.  Chemical Evolution Ongoing debate concerning actual path “which came first?” RNA World - Molecules could not have consistently formed without a mechanism of heredity. Scientists have created synthetic nucleic acids able to replicate And make mistakes (mutation) Protein World - Replication would be impossible without enzymes – metabolism first Peptide-Nucleic Acid World - RNA is too unstable, thus a precursor must have existed. Protein – nucleic acid was the basis of life Organic molecules from space – evidence of meteorites containing organic molecules (e.g. carbon with multiple ring structures) or nitrogenous bases (like those found in DNA/RNA) and amino acids) Current Suggestion of the time line  Comparison of two possible views for the path leading from a ‘primordial soup’ to a rudimentary protocellular structure (bottom). A) The ‘biopolymer first’ scenario, according to which the emergence of self‐replicating informational strings such as RNA and proteins are assumed to have had an independent origin from that of lipid encapsulation. B) The ‘Lipid World’ scenario, which maintains that the roots of life could have been aggregates of spontaneously assembling lipid‐like molecules endowed with capabilities for dynamic self‐organization and compositional inheritance. Adapted from Segre & Lancet 2000 – EMBO reports 1(3) Example of how life could have evolved in alkaline hydrothermal vents (Soja et al. (2016) The origin of life in alkaline hydrothermal vents. Astrobiology 16, 181-197) Early cellular life then evolved into more complex life forms Archaea Defined as extreme-condition prokaryotes lack peptidoglycan in cell walls Great variety in metabolism & source of energy: Methanogens – methane producing Anaerobic methane oxidizers Nitrifiers - ammonia & nitrite oxidizing extreme halophiles –salt lovers extreme thermophiles – high temp lovers thought to have split from Bacteria 2 bya – several metabolic pathways more closely related to eukaryotes. Bacteria second major group of prokaryotes strong cell walls simpler gene structure contains most modern prokaryotes includes photosynthetic bacteria cyanobacteria Prokaryotes vs. Eukaryotes Prokaryote Eukaryote Achaea & Bacteria – single celled Cell with nucleus containing organisms without membrane multiple chromosomes; nuclear bound organelles or nucleus envelop and membrane-bound internal cell bodies Sexual reproduction → allows genetic recombination Single celled or multicellular Evolutionary theory states these arose through the endosymbiosis (archaean & eubacterium) Eukaryotes probably arose about 1.5 bya  Energy-producing bacteria were engulfed by larger archaea bacteria → beneficial symbiotic relationship What is the Endosymbiont Theory? first postulated by Lynn Margulis in the 1967 Internal membrane-bound structures such as mitochondria and chloroplasts are thought to have evolved via endosymbiosis Evidence Organelles have their own DNA, and divide independently of the cell they live in; New mitochondria and plastids are formed only through binary fission; They are composed of a peptidoglycan cell wall characteristic of a bacterial cell; These organelles' ribosomes are like those found in bacteria (70S). Mitochondrial DNA (mtDNA) has a unique pattern of inheritance - maternally Great Oxidation Event  Earth is very old, providing plenty of time for evolution to have occurred Radioactive dating shows the earth is 4.6 billion years old Because of continental drift, there has been a long time for different organisms to evolve on different continents ➔ Promotion of biodiversity – lots of species! Varek 2016: Predicted biodiversity for all areas (solid line), areas greater than 250 000 km2 (dotted line) and areas greater than 500 000 km2 (dashed line). Palaeogeographic maps shown for select time periods. Pg, Palaeogene. The Diversity of Life  Finding Order in Diversity Natural Selection and all the other process have led to a staggering diversity of organisms → Biologists have identified and named about 1.7 million species so far → But they estimate that still 2-100 million additional species have yet to be discovered →One needs to organize and group these according to biological significance →WHY????? Improved communication in science One unique name for each organisms Helps organize information about organisms, the relationships between them, adaptation to ecological niches etc….  Approaches to classifying organisms Linnaeus Haeckel Chatton Copeland Whittaker Woese et al. Woese et al. 1735 1866 1937 1956 1969 1977 1990 2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 6 kingdoms 3 domains Eubacteria Bacteria Prokaryota Monera Monera (not treated) Protista Archaebacteria Archaea Protista Protista Protista Fungi Fungi Vegetabilia Plantae Plantae Eukarya Plantae Plantae Plantae Animalia Animalia Animalia Animalia Animalia Tree of Life – based on rRNA sequencing (Domain System) Hierarchical classification “Did King Philip Come Over For Gumbo Sunday?” Taxon (taxa) = the named taxonomic unit(s) at any level in this taxonomic hierarchy Panthera = genus pardus = specific epithet that refers to one species in the genus Panthera Linnaeus’s System of Classification Species - most specific group. Can reproduce among themselves and produce fertile offspring Genus - group of closely related species. Share many characteristics Family - group of related genus Order - broad taxonomic group composed of similar families Class - Composed of similar orders Phylum - made up of several different classes that share important characteristics  Linnaeus convinced us Darwin provided us with the to use a hierarchical mechanism by which evolution classification system results in descent with modification Taxonomy – naming & classifying organisms Systematics – naming & classifying organisms according to their evolutionary relationships Systematic Phylogenetics – reconstructing the Phylogenetics evolutionary relationships among organisms  BINOMIAL Nomenclature Standard name is binomial - developed by Carolus Linneaus Each species is given a two – part scientific name Ursus arctos genus species ‘Binomial’ = two parts = 2 names species – all in lower case Fucus vesiculosus Genus – has a capital letter Italics (or underlined) → Highlights these in any text – easy to recognise binomial nomenclature — Genus species Usually descriptive in Latin (or Latinized) or Greek Improved communication in science as it prevents confusion — e.g. English and American robins Erithacus rubecula Turdus migratorius Dichotomous keys Key used to identify an organism in which each stage present descriptions of two distinguishing characters, with a direction to another stage in the key, until the species is identified Couplets consists of two differentiating choices Choices of YES or NO Choice determines the next step Note: Notice there is always one less step or set of statements than there are items to identify. Examples: Flow chart dichotomous key Bracketed dichotomous key  Examples Multi access keys used if information for a given step in a single access key is not available → allows for free choice of identification steps – typically interactive / computerised keys. Make a dichotomous key Steps – first work out what is in common with all and what not and how they could be linked  compiling a dichotomous key 1 a. With a hole Go to Question 2 b. Without a hole Go to Question 3  Dichotomous key solution 1 a. With a hole Go to Question 2 b. Without a hole Go to Question 3 2 a. Six sided Species #1 b. Four sided Species #6 3 a. With threading Go to Question 4 b. Without threading Species #8 4 a. Pointy tip Go to Question 5 b. No pointy tip Go to Question 6 5 a. Rounded head Species #4 b. Not rounded head Species #7 6 a. Flat head Go to Question 7 b. Not flat head Species #2 7 a. Body length twice the width of head Species #5 b. Body length not twice the width of head Species #3  Now it is your turn – make a dichotomous key for these 6 leaves Genus A: Cydonia B: Quercus C: Ilex D: Fraxinus E: Aesculus F: Magnolia Use leaf shape, number of leaf parts and size (width & length) as characteristics Leaf dichotomous key – set it up as a table Steps (Go To instructions Characteristics or Species identification) 1a 1b Use leaf shape, no of leaf parts and size (width & length) as characteristics Leaf dichotomous key – possible solution Characteristics Steps (Go To instructions or Species identification) 1a Leaf with smooth outline go to 2 1b Leaf with jagged outline go to 3 2a 2b 3a 3b 4a 4n 5a 5b Leaf dichotomous key – potential solution Characteristics Steps (Go To instructions or Species identification) 1a Leaf with smooth outline go to 2 1b Leaf with jagged outline go to 3 2a Leaf about same length as width Cydonia 2b Leaf about twice as long as it is wide Magnolia 3a Leaf divided into more than two distinct parts go to 4 3b Leaf not divided into more than two distinct parts go to 5 4a Leaf divided into 5 parts Aesculus 4n Leaf divided into ten or more parts Fraxinus 5a Leaf pointed spines along its edge Ilex 5b Leaf with rounded lobes along its edge Quercus How well have you understood the concepts of dichotomous key and the binomial nomenclature? Quiz Quiz 1: Identify the following birds using the classification keys shown…. Bird 1: ruby-throated hummingbird Bird 2: red-tailed hawk Bird 3: Kildeer (plover) Quiz 2: An illustration of two fish is provided. Which paired statement could be used to know the difference between fish using a dichotomous key? A. Eyes on side of head. Eyes on top of head B. One set of dorsal fins. Two sets of dorsal fins C. Mouth at front of head. Mouth on underside of head D. Rounded caudal fin. Forked caudal fin Quiz 2: An illustration of two fish is provided. Which paired statement could be used to know the difference between fish using a dichotomous key? A. Eyes on side of head. Eyes on top of head B. One set of dorsal fins. Two sets of dorsal fins C. Mouth at front of head. Mouth on underside of head D. Rounded caudal fin. Forked caudal fin Quiz 3: An illustration of three beetles is given. A student examines three different species of beetles that are related. What structure is identical in all three beetle species? A. Antenna length B. Placement of eyes C. Marking on abdomen D. Width of thorax Quiz 3: An illustration of three beetles is given. A student examines three different species of beetles that are related. What structure is identical in all three beetle species? A. Antenna length B. Placement of eyes C. Marking on abdomen D. Width of thorax Quiz 4 answer these questions A. Give three purposes of dichotomous keys? B. The two word naming system that includes Genus and species is called what? C. What step do we always start when using dichotomous keys? Quiz 4 answers.... A. Give three purposes of dichotomous keys? Organize information, identification of unknown organisms, basis for taxonomy which is defined as a system used to classify organisms. B. The two word naming system that includes Genus and species is called what? C. What step do we always start when using dichotomous keys? Quiz 4 answers..... A. Give three purposes of dichotomous keys? Organize information, identification of unknown organisms, basis for taxonomy which is defined as a system used to classify organisms. B. The two word naming system that includes Genus and species is called what? Binomial nomenclature C. What step do we always start when using dichotomous keys? Quiz 4 answers….... A. Give three purposes of dichotomous keys? Organize information, identification of unknown organisms, basis for taxonomy which is defined as a system used to classify organisms. B. The two word naming system that includes Genus and species is called what? Binomial nomenclature C. What step do we always start when using dichotomous keys? Step 1 – this cannot be skipped Dichotomous Keys How to use them Using a dichotomous key – identify these LIVING CAMINALCULES Adapted from Sokal R.R. (1983a & b) Use this dichotomous key…. Identification Solution B C F D A E H G Adapted from Sokal R.R. (1983a & b) References & Additional reading: Barnes, R.S.K. (ed.) 1998 The Diversity of Living Organisms Blackwell, Oxford Purves W.K., Orians G.H., Heller H.C. and Sadava D., 2008 Life: the Science of Biology, 8th ed., Freeman. Journal articles for the Caminalcules: Sokal R.R. (1983a) A phylogenetic analysis of the Caminalcules. I. The data base. Systematic Zoology 32:159-184. Sokal R.R. (1983b) A phylogenetic analysis of the Caminalcules. II. Estimating the true cladogram. Systematic Zoology 32:185-201. Want more practice – try this interactive plant identification: https://fergusonfoundation.org/resources/game-plant-identification/ Thank you Additional Information Geological Timeframes The primarily defined divisions of time are eons, the Hadean, the Archean, the Proterozoic and the Phanerozoic. The first three of these can be referred to collectively as the Precambrian supereon. Each eon is subsequently divided into eras, which in turn are divided into periods, which are further divided into epochs Life: Geological Time  Hadean Eon: 4.5 – 3.9 bya Earth mainly molten rock; ancient atmosphere did not contain oxygen; 4.567 bya – origin of the solar system 4.55 bya- Earth forms 4.46 bya – origin of moon 3.9 bya - intense bombardment melt parts of the Earth’s crust  Archean Eon: 4 – 2.5 bya Earth crusts had cooled enough to allow the formation of continents; water vapour condenses and first ocean’s form 3.8 bya - oldest known possible markers of life (carbon isotope ratio) 3.7 bya – possible markers of photosynthetic microbes 3.5 bya – possible biomarkers of methane-producing archaea 3.4 bya – fossils of microbial mats in Australia & SA – stromatolites – resulting in rock-like build-up of Stromatolites – microbial mats “colonies” of cyanobacteria Proterozoic Eon: “beginning of life” 2.5 bya – 542 mya Stable continent formation; first abundant fossils of living organisms; evidence of oxygen build-up resulting in explosion of eukaryotic forms; first animals 2.5 bya – earliest known fossils of bacteria on land 2.4 bya – previously oxygen-free atmosphere acquires 1% of today's oxygen level 2.1 bya – possible fossils of multicellular organisms 1.8 bya – oldest know fossils of single-celled eukaryotes (protozoans) 1.6 bya – oldest known fossils of multicellular eukaryotes (alga) 1.2 bya – multicellular fossils of red algae Proterozoic Eon: “beginning of life” 2.5 bya – 542 mya Stable continent formation; first abundant fossils of living organisms; evidence of oxygen build-up resulting in explosion of eukaryotic forms; first animals Snowball Earth Hypothesis – 800-600mya the earth may have been completely frozen over 850 mya - Oxygen levels begin to rise towards modern levels 750 mya – earliest green algae fossils 650 mya – possible fossils of animals (sponges) 635 mya – earliest biomarkers of animals 570 mya – earliest definitive fossils of animals Phanerozoic Eon: ”visible life” 542 mya - present