Biology 1015 General Biology Lab Taxonomy Handout Section 1: Introduction Taxonomy is the branch of science concerned with classification of organisms. This involves defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Something that you will learn quickly is there is a lot of uncertainty and debate when it comes to taxonomy. It is important to remember that the system of classification is binomial. This means that the species name is made up of two names: one is the genus name and the other the specific epithet. These names are preferably italicized, or underlined. The scientific name for the human species is Homo sapiens. Homo is the genus name and sapiens is the trivial name meaning wise. For green beans or pinto beans, the scientific name is Phaseolus vulgaris where Phaseolus is the genus for beans and vulgaris means common. Sugar maple is Acer saccharum (saccharum means sugar or sweet), and bread or brewer's yeast is Saccharomyces cerevisiae (the fungus myces that uses sugar saccharum for making beer cerevisio). In taxonomy, we frequently use dichotomous keys. A dichotomous key is a tool for identifying organisms based on a series of choices between alternative characters. Taxonomy has been called "the world's oldest profession", and has likely been taking place as long as mankind has been able to communicate (Adam and Eve?). Over the years, taxonomy has changed. For example, Carl Linnaeus the most renowned taxonomist ever, established three kingdoms, namely Regnum Animale, Regnum Vegetabile and Regnum Lapideum (the Animal, Vegetable and Mineral Kingdoms, respectively). Notice that his system does not include bacteria or other microscopic organisms as microscopes have not yet been invented. Since this time several different classification systems have developed, each with different proposal on the number of kingdoms. For lab we will use a 7-kingdom system with two empires (superkingdoms). The superkingdom Prokaryota will have two kingdoms: Eubacteria and Archaebacteria. The superkingdom Eukaryota with have five kingdoms: Protozoa, Plantae, Chromista, Fungi and Animalia. Prokaryota: DNA is dissolved in cytoplasm to form a nucleoid with no endomembrane system, no cytoskeleton and no mitosis. Eubacteria: Unicellular, peptidoglycan cell wall and ester linkages in their membrane phospholipids. Archaebacteria: Unicellular, adapted to harsh environments, ether linkages in membrane phospholipids, central dogma similar to eukaryotes (i.e. introns). Eukaryota: Linear DNA chromosomes contained in the nuclear envelope, cytoskeleton, ancestrally cilia or flagella, will be able to carry out mitosis, descended from sexual ancestors. Protozoa: Largely unicellular, colonial, filamentous or pseudo-parenchymatous. Plantae: Multicellular, photosynthetic, mostly terrestrial, chloroplast envelope contains two membranes Chromista: Multicellular, photosynthetic, mostly aquatic, chloroplast envelope contains four membranes Fungi: Multicellular, heterotrophic (do not photosynthesize), chitin cell walls, made up of filaments called hyphae, non-motile, absorb food through extracellular enzymes Animalia: Muliticellular, heterotrophic (do not photosynthesize), no cell wall, made up of tissues, motile at least part of their life cycle, ingest food Section 2: Prokaryotoa Overview Prokaryota will have the two kingdoms: Eubacteria and Archaebacteria. Prokaryotes have DNA that is dissolved in the cytoplasm to form a nucleoid with no endomembrane system, no cytoskeleton and no mitosis will be found in either. Eubacteria: These organisms are commonly called bacteria. Eubacteria have ester linkages in their membrane phospholipids, muramic acid and D-amino acids in the peptidoglycan cell wall, One of the most important ways of classifying the eubacteria is based on a staining procedure called the Gram stain. Gram-positive bacteria have a thick out peptidoglycan cell wall that retains crystal violet when stained, whereas the Gram-negative bacteria have a thing peptidoglycan cells wall between and inner and outer membrane and does not hold the satin. Another main characteristic to identify bacteria is the shape. Baccilii (rod) and cooci (sphere) are the most common. Archaebacteria: Archaebacteria live in harsh environments, have ether linkages their membrane phospholipids, and DNA transcription, mRNA translation (protein synthesis) and tDNA introns that resemble eukaryote systems. Section 3: Eubacteria Key Eubacteria Kingdom -- ester linkages in phospholipid bilayer; muramic acid in peptidoglycan cell walls, no protein-spliced tRNA introns; may inhabit a wide range of environments utilizing a vast array of metabolic strategies Negibacteria subkingdom -- (mostly stain Gram-negative) double cell envelope, outer membrane lipid bilayer with porins and separated from cytoplasmic or plasma membrane by cell wall of peptidoglycan Eobacteria infrakingdom --(eos is Greek for dawn) primitive traits Eobacteria division or phylum Class Chlorobacteria -- (khloros is Greek for yellow-green) filamentous green bacteria with bacteriochlorophyll a and usually chlorosomes Example: Chloroflexus - carbon is fixed in photoheterotrophic by unique hydroxypropionate pathway. Class Hadobacteria (hades is Greek for hell) -- heterotrophic thermophiles such Example: Thermus aquaticus from which Taq polymerase is extracted for PCR Example: Deinococcus highly radiation resistant with a thick peptidoglycan cell wall (despite being Gram -) Glycobacteria (glukus is Greek for sweet) infrakingdom Cyanobacteria division or phylum -- (kuanos is Greek for blue-green) oxygenic photosynthesis Gloeobacteria subphylum -- no thylakoids Example: Gloeobacter Phycobacteria subphylum -- thylakoids present; Examples: Fix nitrogen in heterocysts. sometimes in symbiosis with ferns or cycads or fungi; Anabaena, Nostoc and Rivularia, Examples: Major contributors to freshwater food chains. Oscillatoria, Lyngbya, Tolypothrix, Scytonema, Hapalosiphon, Gloeocapsa, Merismopedia, and Stigonema. Example: A protein-rich food source for birds, humans in Lake Chad, Mexico City, spirillum Spirulina Example: Adapted to hot springs; Spirulina, Arthrospira, Oscillatoria, Lyngbya and Synechococcus. Example: Prochlorophyte; sea squirt or ascidian symbiont producing oxygen for the animal Prochloron Example: Free-living pico-phytoplankton (about 100,000 per liter of tropical sea water) Prochlorothrix Spirochaetae division or phylum -- spiral or helical cells with periplasmic flagella; flexible outer membrane; Class Spirochaetes -- aerobic to facultatively anaerobic or obligately anaerobic; motile; many pathogens – Example: Borrelia burgdorferi is tick-borne cause of Lyme disease, Example: Treponema pallidum is cause of the venereal (sexually transmitted) disease syphilis and the tropical skin disease yaws Sphingobacteria division or phylum -- cytoplasmic membrane with sphingolipids; outer membrane with lipopolysaccharide; secondary loss of exoflagella Class Flavobacteria -- aerobic heterotrophs Example: Flavobacterium Class Chlorobea -- anaerobic phototrophs; anoxygenic photosynthesis, green bacteriochlorophyll and yellow to orange carotenoid pigments, diverse environments, some in hot springs Example: Green Sulfur bacteria that lack rubisco and use the reverse or Krebs cycle to fix carbon dioxide into organic molecules; Chlorobium, Pelodictyon Planctobacteria division or phylum -- some lack peptidoglycan; flagella with flagellin protein Class Planctomycea -- protein walls but no peptidoglycan; free-living (saprobes); often (exo)flagellate, aquatic heterotrophs with budding division Examples: Pirellula and Planctomyces have holdfasts and form rosettes, Gemmata Class Verrucomicrobiae -- prosthecate, free-living bacteria with peptidoglycan, or intracellular parasites lacking Example: Verrucomicrobium Class Chlamydiae -- peptidoglycan in cell walls replaced by protein; obligate intracellular parasites of eukaryotes; secondary loss of flagella. Example: Chlamydia is cause of psittacosis in birds and sometimes humans. It is also responsible for a difficult to detect sexually transmitted disease (NGU) Class Spirochaetes -- aerobic to facultatively anaerobic or obligately anaerobic; motile; many pathogens Example: Borrelia burgdorferi is tick-borne cause of Lyme disease, Example: Treponema pallidum is cause of the venereal (sexually transmitted) disease syphilis and the tropical skin disease yaws. Sphingobacteria division or phylum -- cytoplasmic membrane with sphingolipids; outer membrane with lipopolysaccharide; secondary loss of exoflagella Class Flavobacteria -- aerobic heterotrophs Example: Flavobacterium Class Chlorobea -- anaerobic phototrophs (either auto or hetero) Example: Chlorobium, Pelodictyon Planctobacteria division or phylum -- some lack peptidoglycan; flagella with flagellin protein in flagellar shaft present, or secondarily absent Class Planctomycea -- protein walls but no peptidoglycan; free-living (saprobes); often (exo)flagellate, aquatic heterotrophs with budding division Example: Pirellula, Planctomyces, Gemmata Class Verrucomicrobiae -- prosthecate, free-living bacteria Example: Verrucomicrobium with peptidoglycan Class Chlamydiae -- peptidoglycan in cell walls replaced by protein; obligate intracellular parasites of eukaryotes Example: Chlamydia is cause of psittacosis in birds and sometimes humans. It is also responsible for a difficult to detect sexually transmitted disease Proteobacteria division or phylum -- peptidoglycan and lipopolysaccharide