Diversity of Life Lecture Notes
Diversity of Life Lecture Notes ECOL 182R
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This 10 page Class Notes was uploaded by Camille Hizon on Thursday January 14, 2016. The Class Notes belongs to ECOL 182R at University of Arizona taught by Bonine, Hunter, Martinez in Spring 2016. Since its upload, it has received 112 views. For similar materials see Introductory Biology II in Science at University of Arizona.
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Date Created: 01/14/16
Diversity of Life 1: Prokaryotes and Protists I. Prokaryotes have been alone for most of the history of life on earth. A. How many years? 1. about 2.4 billion years (alone on Earth for) B. Photosynthesis and the arrival of an oxygen atmosphere. 1. The first photosynthetic organisms, first abundant organisms were cyanobacteria. 2. With photosynthesis, arrival of oxygen a) What were the two major consequences of an oxygen atmosphere? (1) Aerobic (effective metabolism) (2) accumulation of ozone (O3) protected life from UV radiation, allowed life on land 3. Prokaryotes and protists a) Prokaryotes Bacteria and Archaea II. Phylogeny A. The three domains: Bacteria, Archaea, and Eukarya B. The Archaea and Bacteria are both rokaryoti but differ more from each other than does the Archaea from the Eukarya. 1. Archaea are thesister group to the Eukarya. C. Kingdoms 1. What are the kingdom(s) in the Bacteria? a) Bacteria 2. What are the kingdom(s) in the Archaea? a) Archaea 3. What are the kingdom(s) in Eukarya? 4. Old idea Protists, Plants, Fungi Animwe will use this classification system, even though outdated. 5. New idea a classification based on current understanding of evolutionary relationships: Excavata, Discicristata, Alveolata, Stramenopila, Rhizaria, Plantae, Opisthokonta, Amoebozoa (in the textbook, don’t need to know these names) D. How and when did we learn of the existence of Archaea? 1. Bacteria and Archaea are superficially similar. But they are morphologically differetacteria have peptidoglycain their cell walls (polysaccharides cross linked with peptides). 2. Archaea have other polysaccharides or glycoproteins in their cell walls. 3. Differences in rRNA sequences, membrane structure, and other differences led to “3 domain concept” in 1996. 4. Many are extremophiles Sulfolobus Archaea that thrives at very high temperatures and acidic environments III. Prokaryotes Bacteria and Archaea A. The prokaryotes are the most numerous (numbers of individuals) and diverse organisms on earth. 1. Diversity in numbers of species, metabolism and ecology 2. Before molecular techniques, only prokaryotes that could be cultured were studied and identified. 3. What percent of prokaryotes do you think can be cultured this way? a) 1% B. New methods involve culturefree, DNA sequencing of complex mixtures many new groups of prokaryotes being discovered. C. Prokaryotes and protists 1. Where are there prokaryotes in the environments? a) Prokaryotes in the gut (1) How many species? (a) 1000 species inside; 1000 species on skin (2) How many prokaryotic cells relative to human cells? (a) 10x (3) How much of our weight is bacteria? (a) 2.5 lb. or 1kg (4) New research: important in normal gut development; calibrate immune system. Different communities: more or less efficient at extracting calories from food. b) Skin prokaryotes (1) Prevent pathogens from invading (2) Stimulate skin immunity; rotect against skin disease (3) Different parts of skin (habitats) have different bacteria. (a) Ex: Forearm bacteria, different from underarm bacteria and forehead bacteria. (b) Fun fact: Highest diversity between people in area between fingers! 2. Morphology of prokaryotes a) What have they got that’s different from (most) protists and animals? (1) Cell Wall b) Cell walls provide structural support, protection, can prevent water loss or rupture of cell from turgor pressure. c) Prokaryotic cells are usually much smaller than eukaryotic cells. Closer to the size of aitochondrion or chloroplast. d) Prokaryotes everything in one compartment, including DNA D. Eukaryotes 1. Nuclear envelope often no cell wall; instead a flexible cell membrane (what does this allow)? 2. Sophisticated cytoskeleton (cell skeleton) 3. Vesicles for digestion 4. Organelles a) organelle a structure enclosed within its own membrane inside a cell b) Ex: nucleus, mitochondrion, the chloroplast, the Golgi apparatus, the lysosome, and the endoplasmic reticulum E. Review of Endosymbiosis 1. The organelles with their own DNA (mitochondria, chloroplasts) have symbiotic origins 2. Where would you look for evidence for endosymbiosis? a) DNA sequences 3. Organelles share features with prokaryotes: a) Have their own DNA, RNA b) Genes most closely related to existing bacteria likely shared ancestors (1) Chloroplasts cyanobacteria (2) Mitochondria proteobacteria F. Physiology/Metabolism of prokaryotes 1. How do prokaryotes reproduce? a) Asexually by fission 2. How do they exchange genetic info? a) Conjugation transfer of DNA via a cytoplasmic bridge. Can also take up extracellular DNA spontaneously. And DNA can be transferred by a bacterial virusbacteriophage. 3. Prokaryotes fairly narrow range of shapes and sizes, and not very exciting movement 4. What have prokaryotes been doing for 4 billion years? a) Learning chemical tricks 5. All ancestral prokaryotes were anaerobic and some still are a) Anaerobic: metabolism in the absence of oxygen b) Aerobic: metabolism involving oxygen 6. Some can shift back and forth. 7. One of the most fundamental things about lill living organisms need a source of carbon in order to survive and grow. 8. What is the source of our energy and carbon? a) Food We eat both; energy from carbon compounds, carbon from carbon compounds b) That makes us heterotrophs 9. Most bacteria and archaea are the same 10. What do plants do for energy and carbon? a) Light for energy and CO2 for carbon 11. Some prokaryotes do as well e.g. Cyanobacteria. These are autotrophs (= photoautotrophs) 12. Others have completely unique solutions not found in eukaryotes 13. Some use simple nitrogen or sulfur compounds for energy, but CO2 for carbon (needing neither light nor organic compounds for foalled chemolithotrophs 14. Have enabled life in extremely inhospitable places. G. Chemolithotrophs (mostly Archaea) 1. Some live near deep sea hydrothermal vents at up to 2500 m deep where there is NO light. 2. Use hydrogen sulfide from deep sea volcanic vents for energy. Form base of food pyramid for an entire bizarre community. H. Photoheterotrophs 1. Lastly,some use light for energ but need to ingest organic compounds for carbon. 2. Many other chemical “tricks” that eukaryotes can’t generally do... a) Digest cellulose (in plant walls) b) Produce amazing toxins like polyketides (many antibiotics, e.g. tetracycline, antitumor drugs) I. Ecology of the prokaryotes chemical tricks used often in symbiosis with other organisms. 1. Ex: Paederus beetles cause rashes. Produce pederin, a polyketide. Pederin has antitumor activit. 2. Some anaerobic Archaea produce methane from CO2 as a key part of their energy metabolisArchaea produce 8090% of methane in atmosphere 3. Methane, a greenhouse gas, important contributor to global warming. 4. About 30% of global methane comes from methane producers in guts of grazing herbivores. 5. If we could get rid of those pesky Archaea would we reduce global warming? a) No; this is a bad idea because Archaea produce methane, but also consume it. 6. Some archaea are heatloving and acidloving and saltloving. 7. Some live in hot sulfur springs and die of “cold”. 131℉ 8. Prokaryotes play key roles in global nutrient cycles, e.g. the nitrogen cycle. a) Nitrogen fixation extract N2 out of the air b) Nitrificatio from one solid form to another better for plants. c) Denitrification back to the air J. Protists: How are they defined? 1. Protists are defined by what they’re not: a) Eukaryotes, butnot animals, plants, or fungi b) Most are unicellular, bome algae are multicellular c) Many independently evolved lineages. Some closely related to animals, some to plants and fungi. 2. Eight major lineages of Eukaryotes a current hypothesis a) The majority of eukaryotic lineages are protists. (1) Why are protists not a monophyletic group? (a) Has descendants that aren’t protists (2) Paraphyletichas common ancestor but not all are descendants (3) We share a lineagepisthokonta, with fungi! 3. Protists Startling diversity of form and lifestyle, and insights into the early experiments in eukaryotes. 4. Like prokaryotes, many protists are involvsymbiotic relationships a) Mutualism cellulose digesting protists in termites b) Parasitism 5. Are all protists singlecelled creatures? a) No; Ex: kelp 6. Kelp a protist giantulticellularrown alga 7. Spectacular singlecelled beauty tiatoms. Diversity of Life 2: Fungi I. Introduction A. What unites all fungi? 1. Absorptive nutrition they absorb stuff! a) Lots of fungi araprobes =decomposers) : absorb nutrients from dead organic matter b) Parasites absorb nutrients from living hosts. c) Mutualists: gain and receive nutrients from their partners. 2. Chitinin their cell walls. a) Chitin nitrogen containing polysaccharide tough and flexible. 3. Fungi are clustered with animals and choanoflagellates, all heterotrophs II. Morphology A. Single celled form: yeasts 1. There are unicellular members of several different groups. B. Multicellular fungi: 1. composed of tubular filaments. Single filament a hypha (plural hyphae) 2. Network of hyphae a ycelium a big absorptive net. 3. Hyphae can grow up to 1 km a day. 4. A fungal mycelium has a large surface areatovolume ratio. a) Fruiting body also composed of hyphae. What we see of fungi is often just the fruiting body (e.g. a mushroom) 5. Would dividing the cube into 27 smaller cubes increase the surface area of the organism? a) No, but end to end would increase 6. What might be a limitation with this large SA: V ratio? a) cells are stretched end to end b) large surface area is good for absorption of nutrients c) would be weaker d) would dry out 7. Where are fungi found? a) Most environments C. Highlights of fungal reproduction 1. Fruiting body produces (haploidpores 2. Asexual reproduction: spores can give rise to haploid hyphae that give rise to more spores. 3. Sexual reproduction: in many fungal groups, fusion hyphae of different mating types. a) “Mating types are not sexes because morphologically identical, and often more than two” b) In many fungal groups, fusion of two haploid hyphae (of different mating types) producesdikaryotic hyphae c) Dikaryon a cell with two genetically different haploid nuclei (one from each parent hypha) d) How is this cell type (a dikaryon) different from a diploid cell? (1) 2 haploid nuclei (2) diploid is chromosomes e) Eventually the nuclei fuse to make a diploid ‘zygote’ and then meiosis occurs to make more (haploid) spores. 4. A generalized Fungal life cycle a) the same sequence of events is common to most fungal life cycles. b) Which type of cell division leads to spores in asexual cycle? (1) Mitosis c) Which type of cell division leads to spores in sexual cycle? (1) Meiosis III. Ecology: Dispersal A. Where are the spores? 1. In grilled mushrooms, spores produced on grill surface 2. Mushrooms are a result of asexual life cycle. B. How are spores dispersed? 1. wind 2. rain a) Ex: Bird’s nest fungus rain splashes ‘eggs’ full of spores and spores themselves out of ‘nest’ 3. animals a) Ex: flies respond to smell of ‘stinkhorns’, mammals can smell underground truffles b) Ballistic dispersal of spores in Pilobolus a fungus that lives in cattle digestive track. c) Fruits on cow manure; needs to get spores to grass that will be eaten by a cow. IV. Ecological Roles: Recyclers, Pathogens, Parasites, and Mutualists A. Roles of Fungi saprobes 1. Fungi and bacteria are the major decomposers on earth 2. Important in soil formation 3. Recycling nutrients 4. We can classify species interactions by who benefits, who loses Type of interaction Commensalism Mutualism Parasitism, predation Species 1 positive positive positive Species 2 no effect positive negative 5. How would we classify saprobes? 6. How would we classify those beneficial bacteria in human guts? B. Roles of Fungi: Mutualists 1. Lichens fungus and photosynthetic organism. a) Are these really species? b) Described by fungal partner 2. Photosynthetic partner yanobacterium or alga, or both. 3. Fungus provides protection, attachmenacquisition of water, mineral. 4. Alga provides carbon compounds, e.g. sugars, amino acids 5. Lichens can surviveharsh environments. a) But sensitive to toxic compounds good indicators of air pollution. b) Remember lichens on trees in England that died as a result of the coalburning factories? 6. Mycorrhizae association between plant roots and fungal hyphae 7. A mycorrhizae plant mutualism was present in some of the earliest land plants helped plants to colonize land. a) Web of fungal mycorrhizae hyphae penetrates soil around roots (1) increase surface area for water and mineral and nutrient absorption b) From plant, receive carbohydrates, amino acids (products of photosynthesis) c) Why do you think this association might have been necessary for plants to colonize land? (1) Initially rocky land, little soil d) What caused the buildup of soil? (1) Fungi degrading rock, bacteria degrading rock 8. Ectomycorrhizae fungus that wraps around the plant roots 9. More common: Arbuscular mycorrhizae hyphae enter root and penetrate cell walls, but not plasma membrane. 10. Almost all vascular plants have mycorrhizae. 11. Complex fungal interactions mycorrhizae on pinon pine. a) Tom Whitham and colleagues studied the pinon community in N. Arizona. Found some trees that areresistant to the most important herbivore, a moth, and these trees also have the most mycorrhizae b) What is causing what? Is the moth depressing mycorrhizae, or are mycorrhizae depressing populations of the moth? c) How would you test this? (1) Manipulate the moth d) Experiment some susceptible trees treated with insecticide for 4 years. e) Hypothesis: herbivory depressesolonization of mycorrhizae. If this is true, trees treated with insecticide will get more colonization of mycorrhizae. (1) What does the study show? (2) Why would herbivory aboveground influence fungal growth below ground? 12. Another mutualism: fungus andeaf cutter ants a) Worker ants harvest huge amounts of leaves and other plant material for their fungus gardens. b) In tropical America, they are the single most important herbivore. c) Can be a major pest as they harvest the plants we nurture in our ‘gardens’ or field crops. d) Their nests can become huge. e) Workers cut leaf circles and carry them back to the nest. f) Assembly line (1) leaves are cut into smaller and smaller pieces by increasingly smaller ants (2) eventually fed to fungnd the ants eat the fungus (3) Why don’t they eat the leaves? (a) indigestible g) New queens take fungus with them, mate, and start a new colony with fungus h) Ants and antfungus coevolving i) Coevolution reciprocal evolution of interacting species j) Each ant species has its own species of fungus, and when ants speciate, so does fungus. k) But… (1) a type of parasitic fungus was discovered in leaf cutter ant nests that can quickly kill the mutualist fungus (2) detectable in most gardens l) So now we have a) a fungus that is a mutualist to the ants and b) a fungus that is a parasite of the first fungus. m) Some researchers noticed white stuff on some ant workers in the fungus gardens. Turned out white stuff is bacteriu (1) Bacteria foundainly on garden tending ants. Produces antibiotic that controls parasitic fungus n) What is the bacterium relative to the ants? o) So leaf cutter ants are dependent on fungus (for fond a bacterium (to control fungus parasitic on food source) C. Fungi are also often parasites of other fungi, of plants, and of animals 1. Generally, hyphae invade plant or animal tissue with enzymes or pressure. Grow inside, absorbing nutrients and then often fruit outside. Example: Cordyceps, a fungal parasite of insects. 2. Microsporidia a singlecelled fungal parasite of insects, fish, crustaceans, with a clever infection strategy a) Spores get consumed by animal b) Microsporidia spores ‘germinate’ in gut a coil of filament comes out forcibly like a harpoon c) The harpoon penetrates gut wall and ‘plants’ the microsporidian nucleus in host cell d) There are even predatory fungi! e) Set up traps for nematodes (round worms) nematodes grow into rings, can’t move, get absorbed.
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