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1015 General Biology Lab Handout

Section 1: Introduction Taxonomy is the branch of science concerned with classification of . 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 name is made up of two names: one is the 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 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 , taxonomy has changed. For example, Carl Linnaeus the most renowned taxonomist ever, established three kingdoms, namely Regnum Animale, Regnum Vegetabile and Regnum Lapideum (the , Vegetable and Mineral Kingdoms, respectively). Notice that his system does not include 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- system with two empires (superkingdoms). The superkingdom Prokaryota will have two kingdoms: Eubacteria and Archaebacteria. The superkingdom Eukaryota with have five kingdoms: , Plantae, , Fungi and Animalia. Prokaryota: DNA is dissolved in cytoplasm to form a nucleoid with no endomembrane system, no cytoskeleton and no mitosis. Eubacteria: Unicellular, wall and ester linkages in their membrane phospholipids. Archaebacteria: Unicellular, adapted to harsh environments, ether linkages in membrane phospholipids, central dogma similar to (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 Animalia: Muliticellular, heterotrophic (do not photosynthesize), no , made up of tissues, motile at least part of their cycle, ingest food

Section 2: Prokaryotoa Overview Prokaryota will have the two kingdoms: Eubacteria and Archaebacteria. 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 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 infrakingdom --(eos is Greek for dawn) primitive traits Eobacteria or Chlorobacteria -- (khloros is Greek for yellow-green) filamentous green bacteria with 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: highly radiation resistant with a thick peptidoglycan cell wall (despite being Gram -) Glycobacteria (glukus is Greek for sweet) infrakingdom 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 with or 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- (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 -- aerobic to facultatively anaerobic or obligately anaerobic; motile; many pathogens – Example: Borrelia burgdorferi is tick-borne cause of Lyme disease, Example: pallidum is cause of the venereal (sexually transmitted) disease syphilis and the tropical skin disease yaws division or phylum -- cytoplasmic membrane with sphingolipids; outer membrane with lipopolysaccharide; secondary loss of exoflagella Class Flavobacteria -- aerobic heterotrophs Example: Class Chlorobea -- anaerobic phototrophs; anoxygenic photosynthesis, green bacteriochlorophyll and yellow to orange carotenoid pigments, diverse environments, some in hot springs Example: that lack rubisco and use the reverse or Krebs cycle to fix carbon dioxide into organic molecules; Chlorobium, Pelodictyon division or phylum -- some lack peptidoglycan; flagella with flagellin protein Class Planctomycea -- protein walls but no peptidoglycan; free-living (saprobes); often (exo), 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 -- 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 division or phylum -- peptidoglycan and lipopolysaccharide always present; many different shapes, divers respiratory pathways Rhodobacteria subdivision or subphylum -- (rhodon is Greek for rose) purple photosynthetic bacteria Class Chromatibacteria -- named for the , diverse environments, some in hot springs and mud pots Example: Chromatium, Thiospirillum, Thiocapsa Class or b-proteobacteria-- aerobic to micro-aerophilic; motile Examples: spirillum (Spirillum volutans – chemoorganoheterotroph); cocci (Neisseria gonorrhoeae STD); (Thiobacillus ferrooxidans oxidizes iron under acidic conditions and Nitrosomonas spp oxidize ammonia to nitrite) Class or g-proteobacteria – Example: ; Example: Pseudomonas species include many pathogens and some beneficials that degrade pesticides in soils, and opportunists in human infections Example: cholerae prefers alkaline waters and causes cholera, both vectored by polluted water or food Example: Agrobacterium tumefaciens is a plant pathogen causing crown gall that is used in genetically engineering . Example: The are Gram negative rods and include the facultative anaerobic coliform Escherichia coli or E. coli, cholerae, Yersinia pestis cause of bubonic plague or Black Death and is vectored from rat fleas to other rodents and to humans Example: Erwinia amylovora causes fire blight in apple and pear . Example: The Methylococcaceae: Bordetella pertussis causes whooping cough. Example: Legionella pneumophilia causes Legionnaires disease The causative agent of Q fever Coxiella burnetii causative agent of Q fever. Example: Haemophilus influenzae the major cause of meningitis in children. Class Alphabacteria (a-proteobacteria) -- purple non-sulfur bacteria also have anoxygenic photosynthesis with other compounds than sulfur ones or water donating electrons Examples: Rhodospirillum, Rhodomicrobium, Rhodocyclus, Rhodobacter Example: Azotobacter fixes nitrogen, Azospirillum symbioses in grasses such as corn fix nitrogen like, rod-shaped species in symbiosis with legume plants. Example: Caulobacter, Rickettsiales (typhus) Example: Rochalimaea quintana trench fever in World War I Example: Rochalimaea prowazekii shares some genetic homology with the genome. Perhaps, the symbiogenetic ancestor of the mitochondrion came from this group. Thiobacteria subdivision or subphylum -- non-photosynthetic relatives Class Deltabacteria (d-proteobacteria) -- anaerobic sulfate reducers Example: Desulfobacterium, Bdellovibrio, Example: (Myxococcus, Stigmatella, Chondromyces) aerobes with gliding motility that flow over the substrate [warm, somewhat dry with neutral soils and normal salt levels and usually found on herbivorous animal dung (cow manure), rotting wood, bark of trees and in fresh water] secreting enzymes to lyse bacteria, , fungi, etc absorbing nutrients Class Epsilobacteria (e-proteobacteria) -- organotrophs, often parasitic Example: Helicobacter pylori spirillum, causes most ulcers Example: inhabits intestinal tracts Example: is hyperthermophile (85 to 95oC) Example: Non-motile Geobacteria subdivision or subphylum -- non-photosynthetic anaerobes and their fermenting descendants; often reduce or oxidize iron, rarely reduce sulfate Class Ferrobacteria – Example: Leptospirillum, Thermodesulfovibrio Example: Magnetospirillum magnetotacticum has particles of (Fe3O4) that allow the bacterium to align parallel to the North-South dipole moment of a magnetic field Class -- (Acidobacterium) Posibacteria (mostly stain Gram-positive) subkingdom -- the outer membrane is missing and the ancestral cell wall of peptidoglycan is usually thick Endobacteria division or phylum -- (develop endospores) low G + C content; ancestrally with endospores; lacking proteasomes (large complexes of proteases that break down proteins). Examples: , , Togobacteria. Class Togobacteria -- (toga is Latin for loose outer garment) Example: Selenomonas, Carboxydobrachium, Heliobacteriales; . Class Teichobacteria -- (teichos is Greek for wall) thick, rigid cell walls of peptidoglycan, stain Gram positive Example: : cocci, aerobic to facultatively anaerobic or strictly anaerobic, usually not motile, free-living saprobic, symbiotic or pathogenic --- in human intestines. Example: is found in dairy and plant products, and is used in dairy food fermentations. Example: Ruminococcus species are found in the rumen and large intestines of mammals. Example: pyogenes is the cause of strep throat, rheumatic fever, pneumonia, and septicemias. Example: Staphylococcus aureus on the harshly dry and acidic surface of the human skin and may cause boils and food poisoning. Example: species are facultatively anaerobic, found in animal, dairy and vegetable food products like pickled fish, yogurt (Lactobacillus delbrueckii) and acidophilus milk (L. acidophilus), sauer kraut and kimchi, and in the gastrointestinal tracts of birds and mammals and in the mammalian vagina. Example: Listeria monocytogenes is motile, facultatively anaerobic coccobacillus found in human gut, soil, water and plant vegetation that is serious cause of food poisoning in commercially prepared cheeses and meats. Example: Carnobacterium and Renibacterium species are pathogenic on Salmonid fish. Example: Bacillus: Rod-shaped aerobic to facultatively anaerobic; B. anthracis cause of anthrax in cattle and humans and B. subtilis and B. cereus causes of food poisoning Example: rod-shaped obligately anaerobic species such as C. botulinum cause of botulism food poisoning (exotoxin used in Botox treatments) and C. tetani cause of tetanus from infected puncture wounds. Class Mollicutes -- are obligate intracellular parasites; no cell walls (lack peptidoglycan and teichoic acids); require cholesterol and fatty acids; no endospores. Example: species are pleomorphic with no cytochromes or quinones. They are pathogenic in mammals and birds, causes atypical pneumonia in humans, pneumonia in mammals. Example: is helical with limited fatty acid synthesis and pathogenic in and vascular plants. S. citri causes citrus stubborn disease. division or phylum -- (actino is Greek for ray) high G + C content; proteasomes present; if spores present, then usually exospores; stain Gram positive; Class Arthrobacteria -- cell walls varied Example: Arthrobacter reproduce as rods-cocci-rods. Some are motile. Detoxify pesticides and other soil pollutants. Example: give off a fishy smell to freshly turned soil as when searching for earthworms to go fishing. Example: Propionibacterium is a facultative anaerobe forming chains or clumps of pleomorphic rods commonly found on human skin where one species is responsible for acne. Another species is used in making Swiss cheese imparting a distinctive flavor to the cheese because of its propionic acid . Example: is used as a probiotic in including humans. Example: Clavibacter species are aerobic pathogens on flowering plants. Class Arabobacteria -- cell walls with meso-diaminopimelic acid, Example: species (spp) are facultative anaerobes with club-shaped bacilli and include obligate parasites found in the mucous membranes of mammals. C. diphtheriae causes diphtheria. Example: Nocardia fragmenting filaments can be opportunistic pathogens on humans and other animals Example: finely divided filaments form a mycelium lacking aerial hyphae; Actinoplanes is a saprobe in soil feeding on decaying plant material. Example: species have slender rods; are aerobic to microaerophilic but slow-growing; free-living saprobic or pathogenic, waxy cell walls. Mycobacterium tuberculosis cause of tuberculosis in humans, dairy cows, etc. Mycobacterium leprae cause of leprosy Class Streptomycetes -- cell walls with meso- or LL-diaminopimelic acid but no arabinose, galactose or xylose; filamentous growth pattern with aerial hyphae and (exo)spores; aerobes with mycothiol but lack phosphatidylethanolamine. Example: Streptomyces species are sources for antibiotics Example: species fix nitrogen in symbiosis with non-legume plants such as trees, bitterbrush and bayberry trees.

Section 4: Archaebacteria () Key

Archaebacteria Kingdom (or Superphylum) -- prenyl (multiple isoprenoid units) ether linkages in membrane lipids; no muramic acid or peptidoglycan in cell walls; several RNA polymerases; protein-spliced tRNA introns division or phylum -- cell walls of varied compositions Eurytherma superclass -- ancestrally with cell walls of glycoprotein or protein; largest RNA polymerase subunit b unsplit; histones present; tetra-ether lipids in cytoplasmic membrane; mostly hyperthermophiles or thermophiles. Class Protoarchaea [class *] -- (proto is Greek for first) first because these members appear to retain the proposed ancestral archaebacterial traits of hyperthermophily, core histones and sulfur reduction. Examples: Paleococcus, Pyrococcus, Thermococcus Class Picrophilea [class *] -- hyperacidophiles; with membrane glycolipids and DNA gyrase but lacking histones, reverse gyrase and methanogenesis; Examples: , or - grows on burning coal refuse piles. Neobacteria superclass -- cell walls of varied composition; largest RNA polymerase subunit b split into two proteins; core histones present; may have tetra-ether lipids in cytoplasmic membrane; mostly mesophiles Class Methanothermea -- with pseudomurein in cell walls. Methanogens are found in the rumens of ruminant animals (cattle, sheep, goats, deer, camel, etc), termite guts, anaerobic protozoa, and in anaerobic sludge digesters of sewage treatment plants where they produce substantial amounts of . Methane is a greenhouse gas. Examples: – Methanobacterium Examples: – Example: Methanococcales –Methanococcus Example: Methanopyrales -- Class Archaeoglobea -- sulfate or nitrate-reducing hyperthermophiles with glycoprotein cell walls; membranes with tetra-ether lipids; both reverse and DNA gyrases present Example: Archaeoglobus spp Class Halomebacteria -- (hals is Greek for salt) cell walls often with complex carbohydrates; bi-ether plasma membrane lipids; DNA gyrase present but lack reverse gyrase; Example: Methanosarcinales (Methanosarcina) mesophilic methanogens somewhat halophilic (salt loving) in the placed in class Example: Halobacteriales (Halobacterium rod-shaped), Halococcus, etc, halophilic with high salt (minimum 1.5 M to an optimum of 3 to 4 M NaCl, or 9 to 27% salt) requirement. division or phylum -- (kren is Greek for spring or fountain) sulfur-reducing respiration with glycoprotein or protein cell walls; membranes with tetra-ether lipids Class Crenarchaeota -- hyperthermophilic. Example: -- an organotroph (chemoheterotroph) that uses sulfur respiration or fermentation, Example: Sulfolobus hyperacidophiles takes sulfide to sulfuric acid (chemolithoautotroph) or as an organotroph Example: – short to very long rigid rod-shaped which takes elemental hydrogen and sulfur to hydrogen sulfide Class Cenarchaeota -- (kainos is Greek for recent or young) mesophiles or psychrophiles derived from the crenarchaeotes above Example: Cenarchaeum

Section 5. Protozoa Key

Protozoa Kingdom -- endomembrane system, cytoskeleton, cilia or flagella, nucleus, mitosis, sex. Gymnomyxa subkingdom -- ("naked slime") soft cell cortex, often with , reticulopodia or axopodia; radiating centrosomal microtubules (somewhat like the asters in whitefish blastula mitosis); unikont cilia or flagella but not with 3 asymmetrical ciliary microtubular roots; no localized cytostome (cell ) for phagocytosis Sarcomastigota infrakingdom -- no reticulopodia, axopodia or filopodia; locomotion often by ; if cilia (or flagella) present, unikont ("one oar") phylum -- mitochondrial cristae typically flat. Choanocyte unit cell is the trophic (feeding-stage) with single surrounded by collar of microvilli. The flagellum position is termed (flagellum positioned in the posterior of cell). Example: Monosiga is unicellular; Codosiga is colonial, and Proterospongia approaches multicellularity. Example: Grantia #1 phylum -- mt cristae tubular when mitochondria present. Unit cell is anterokont (flagellum placed to the anterior of cell). subphylum -- mainly aciliate and lacking cone of microtubules connecting kinetid to nucleus. Example: proteus #2, Acanthamoeba subphylum -- mostly (flagellate), at least in part of life cycle; microtubular cone Infraphylum -- independently flagella; aerobic; unicellular or multicellular aerial fruiting bodies bearing 1 to many spores with chitin or cellulose cell walls; movement and phagocytosis by pseudopodia Class Myxogastrea -- plasmodial (acellular) slime molds are large multinucleate protoplasmic masses that creep along the substrate while feeding before putting up sporangia. Example: Physarum, Stemonitis, Arcyria - #3 Class Dictyostelea -- cellular slime molds are unicellular amoebae that aggregate into slug-like forms before sporulation. Example: Dictyostelium. Infraphylum Archaeamoebae -- unikont flagella; anaerobic, mitochondria secondarily absent; no aerial fruiting bodies; motile via pseudopodia; cilia nonfunctional, if present. Class Archaeamoebae -- no cysts; cilia non-functional. Examples: or amoebae Class Entamoebea -- cysts form; no cilia Example: Entamoeba histolytica #4-- amoebic is caused by drinking polluted water or eating fresh vegetables and fruits irrigated with untreated human sewage. infrakingdom -- reticulopodia, axopodia or filose pseudopodia (filopodia) commonly present; no locomotion by lobopodia; cilia or flagella bikont ("two oars"); mt cristae tubular, though some may be secondarily flattened; extrusomes, if present, often kinetocysts phylum -- filopodia or plasmodial; may have kinetocyst extrusomes Reticulofilosa subphylum -- chloroplasts due to secondary involving a green alga Example: Chlorarachnion subphylum -- plasmodial endoparasites of eukaryotes. Example: Plasmodiophora brassicae causes club root of cabbage. phylum -- reticulopodia or axopodia; no kinetocyst extrusomes Class -- pseudopodia stiffened into reticulopodia by randomly arranged microtubules; tests (shells) of CaCO3 or limestone; phagotrophic; benthic. Form major deposits of limestone or chalk. They sequester a great deal of carbon in the global carbon cycle. #5 Class -- pseudopodia stiffened into axopodia by regular arrays of microtubules; tests often of glass (silica); beautiful forms; phagotrophic; mostly planktonic (floating in the water currents near the surface). #6 phylum -- axopodia; tests of silica; beautiful forms; kinetocyst extrusomes in some Centrohelea subphylum -- flat mt cristae; axopodia radiate from centrosome Nucleohelea subphylum -- tubular mt cristae; axopodia radiate from nuclear envelope; may belong under another phylum ("corticates") subkingdom -- semi-rigid cell cortex strengthened by microtubules, typically as 3 (or 4) distinct, asymmetrical ciliary roots of parallel bands of microtubules instead of asters; ancestrally bikont cilia or flagella; simple groove or pocket to more complex cytostome for prey ingestion supported by two posterior microtubular roots infrakingdom -- ancestrally with one anterior / dorsal ciliary microtubular root and two ventral roots; additional cortical microtubules; no cortical alveoli [Superphylum Loukozoa -- simple feeding grooves; biciliate or tetraciliate; mitochondria (tubular cristae) or hydrogenosomes [Loukozoa phylum -- Oxymonadida, ; Jakobea, ] Superphylum -- mt cristae ancestrally discoid (flat disks attached to inner membrane by a short stalk); ancestrally biciliate with subparallel centrioles connected by striated fibers; cytostome supported by microtubular band phylum -- typically tetrakont ("four oars"); no Golgi Complex, ie Golgi vesicles unstacked; mitochondria present, or rarely hydrogenosomes; most commonly unicellular or amoeboflagellates. Example: fowleri is a pathogen in domesticated birds Example: Acrasida is a cellular ; Examples: Lyromonads, , Heterolobosea. phylum -- typically bikont; Golgi vesicles stacked (Golgi Complex); mitochondria; chloroplasts derived from secondary symbiogenesis with a green alga but may be secondarily absent or reduced and modified Euglenoida subphylum -- no kinetoplasts; photosynthetic and/or heterotrophic; red eyespots; 1 large, 1 small sensory flagellum; glycoprotein pellicle; peroxisomes are not glyoxysomes Example: #7 is photosynthetic and heterotrophic; commonly found in nutrient-rich (eutrophic) waters. Example: Trachelomonas is a tight-fitting lorica or glass shell; Example: Astasia is an obligate heterotroph. Kinetoplasta subphylum -- 1 or more kinetoplasts (mt with large numbers of plasmid-like DNA mini-circles and maxi-circles and associated with enzymes to facilitate of host); peroxisomes are glyoxysomes; 1 or 2 flagella along plasma membrane margin Examples: gambiense - African sleeping sickness vectored by the Tsetse fly. -- is carried by triatomine bugs #8 Superphylum -- tetrakont with 3 subparallel anterior cilia and 1 posterior ; no mitochondria Metamonada phylum -- Golgi vesicles unstacked; intranuclear spindle (closed mitosis). Examples: and (binucleate). Example: , a common contaminant of ponds, lakes and streams causes Hiker's diarrhea. It looks like a balloon with streamers (flagella) and two large eyes in a clown's face (sucker discs and 2 visible nuclei).] #9 Parabasalia phylum -- Golgi vesicles stacked into Golgi Complex attached to the ciliary root including 4 centrioles (parabasal body); extranuclear spindle Examples: trichomonads and hypermastigotes. [ #10 or Lophomonas are endosymbionts in the gut of termites or wood-eating cockroaches. Example: vaginalis #11 - STD infects both cattle and humans. In cattle it reduces fertility and calf survival. In humans it used to be a major cause of blindness in infants. Example: causes blackhead in turkeys with earhworm or cecal worm accessory hosts. Alveolata infrakingdom -- ancestrally bikont; cortical alveoli (large cortical membrane-bound cisternae or sacs); ancestral symbiogenesis with red alga Dinozoa (Miozoa) phylum -- typically haploid; mononucleate, or if multinucleate then nuclei monomorphic; reduced numbers of flagella; trichocysts common; some photosynthetic and heterotrophic Proteoalveolata subphylum -- usually biflagellate; closed mitosis with intranuclear spindle Example: Colponema presumed similar engulfed a red alga for its symbiogenetic chloroplast which in time developed chlorophyll c. Dinoflagellata (Dinozoa) subphylum -- bikont with 1 transverse and 1 trailing flagellum; closed mitosis with extranuclear spindle; 3, 4 or 5 outer cp membranes; chlorophylls a and c2 from ingesting various chromist algae; ß- carotene, peridinin, and starch stored outside the chloroplast as well as lipids; several different types of eyespots; zygotic meiosis by binary fission; permanently condensed chromosomes with up to 284 chromosomes Example: Zooxanthellae are endosymbionts in corals and anemones producing glycerol to feed them in exchange for carbon dioxide, nitrogen and phosphate nutrients, and site of residence. Example: parasitic pathogens with complex life cycle causing red-tide Example: Gymnodinium and Gonyalaux species which produce which is a protein toxin that blocks sodium channels critical to impulse transmission. Example: Noctiluca and Gonyalaux produce phosphorescence lighting up waves and wakes at night in tropical seas. Example: Ceratium and Peridinium #12 phylum -- cilia or small flagella rarely present in trophic stage usually being restricted to male microgametes, or absent; apical complex of polar rings, micronemes, subcortical microtubules, etc. which facilitate parasitism of host Haematozoa subphylum -- centrioles (basal bodies) with 9 triplets of microtubules Class Haemosporida – Example: Plasmodium falciparum malaria-causing, over 2.7 million deaths a #13 Class Piroplasmida – Example: Babesia bigemina that attacks erythrocytes (red blood cells) in cattle to cause red water or Texas cattle fever. Coccidia (Sporozoa) subphylum -- centrioles reduced to 9 singlets of microtubules Example: Toxoplasma gondii #14- endemic in rodents and some birds, is usually passed to humans by cats, may cause birth defects in human fetuses and sometimes damage in susceptible humans. Example: Eimeria stiedae is a major pathogen in rabbits. Example: can be a serious water system contaminant that causes diarrhea which is very difficult to treat in immuno- suppressed patients such as those with AIDS, transplants, diabetics and the elderly. Gregarina (Sporozoa) subphylum -- centrioles reduced to 9 singlets of microtubules; Example: Monocystis is found in earthworm seminal vesicles. Ciliophora phylum -- multinucleate with polyploid macronucleus (or macronuclei) controlling cell activities and diploid micronucleus involved in sexual reproduction; many mono- or bi- ciliated kinetids (lots of simple or paired cilia); trichocysts common; in anaerobic forms mitochondria missing or replaced by hydrogenosomes; very complex internal organization Example: Paramecium, Didinium, Vorticella, Stentor, Blepharisma, Suctoria are free- living examples. Example: Balantidium coli is hog and human intestinal parasite. #15 and #16.

Section 6. Fungi Key

The kingdom Fungi includes organisms such as molds and mildews, and toadstools, rusts and blights, truffles and yeasts. Fungi are heterotrophic obtaining food by of extracellular enzymes to digest food molecules that are then taken up by the cells via absorption. Some are pathogenic. Most are saprobic decomposing dead organic matter back into raw materials for autotrophs to use. Organisms in this kingdom are classified into phyla based on the spore reproductive structures.

Gametes and zoospores motile with one or two flagella; mostly aquatic

Meiosis is commonly gametic with female meiosis occurring in egg-like sporangia called oogonia; coenocytic hyphae diploid with cellulose cell walls.

Phylum Oomycota • Oomycota are the egg fungi because in this phylum the female spores (eggs) are housed in large, egg-like structures (oogonia) where they are fertilized by male nuclei to produce 2N oospores that develope into diploid coenocytic hyphae with cellulose cell walls. This is gametic meiosis. The male gametes and zoospores are motile with one tinsel flagellum and 1 whiplash flagellum. • Largely aquatic although some forms carry out their life cycles on land under wet, humid conditions. • Commonly saprobic feeding on dead organic matter, but some are pathogenic (causing disease) on plants and animals. • The phylum Oomycota can be classified in the kingdom Chromista. • Examples: o Saprolegnia which is the fuzzy white growth seen on ailing and dead fish in aquaria. o Achlya slides may be used in place of Saprolegnia to better show oogonia. o Phytophera infestans responsible for Potato late in Ireland resulting in the death of more than a million. o Plasmopara viticola Downy mildew of grape has caused severe grape losses in France and California under humid conditions.

Meiosis is commonly zygotic but may be sporic or gametic; coenocytic unicellular or filamentous forms with chitin cell walls.

Phylum • Most are typically haploid reproducing sexually by zygotic meiosis as do the fungi although a few have sporic meiosis, or even perhaps gametic meiosis. • They have chitin cell walls. The rRNA is similar to the fungi. • Chytrids are coenocytic with many unicellular forms bearing rhizoids; some are filamentous. • They have one whiplash flagellum in the gametes and zoospores and centrioles which are not found in the true fungi. • They are aquatic with some saprobic forms feeding; others are parasitic on algae, aquatic , spores, , aquatic plants and animals. • Examples: o Coelomomyces is an obligate parasite on mosquito larvae and other dipterans. o Batrachochytrium dendrobatidis has been implicated in massive frog die-offs in the U. S., Central America and Australia.

No motile gametes or spores bearing flagella; essentially terrestrial Haploid, coenocytic hyphae with chitin cell walls; sporangial walls develop about zygotes which form from fusion of two haploid nuclei from different mating strains of hyphae; meiosis occurs in this zygosporangium which is usually the dormant stage in the life cycle.

Phylum • Zygomycota are the bread molds. • This phylum has large, dark zygosporangia which result whenever two haploid nuclei of different hyphal strains unite to make a zygote. • The zygosporangia appear amongst cottony mats of hyphae of varying colors depending on the spore colors of particular species. • Hyphae are coenocytic with chitinous cell walls. • Many are saprobic as soil or dung fungi • Examples: o Rhizopus stolonifera is the common black bread mold. o Pilobolus is a dung fungus which uses a light-directed water cannon to disperse its spores.

Haploid or dikaryotic, septate hyphae with chitin cell walls

Meiosis is not known to occur (no sexual mechanisms), or rarely occurs.

Phylum Deuteromycota (imperfect fungi) • Many are actually now classified differently. • Examples: o Penicillium molds are useful sources of penicillin antibiotic and cheese flavoring agents. o Aspergillus molds are used to synthesize organic chemicals such as ascorbic acid (vitamin C). Many are either pathogenic or produce harmful byproducts. o Verticillium and Anthracnose species cause wilts and rots in plants. o Candida albicans causes opportunistic yeast infections in man. o Others produce skin infections, ringworm, and athlete's-foot.

Meiosis (a sexual process) occurs in special structures Sac-like asci.

Phylum • The sac fungi -- reproductive structures that contain the spores resemble small sacs or asci (ascus -- singular). • Asci are often borne in cup-shaped fruiting bodies that appear as the "". • Masses of septate (these septae are cross-walls or partitions in the hyphae with large central pores). • Heterokaryotic hyphae with chitinous cell walls form into the mycelia or fruiting bodies of these ascomycetes. • Some lack fruiting bodies being unorganized hyphae or even unicellular. • Yeasts are unicellular fungi. • Examples: o Saccharomyces cerevisiae is the brewer's yeast as well as the baker's yeast. o Taphrina which causes peach curl disease is also in this class. o Edible mushrooms such as the flavorful morels (Morchella), pig's ear (Peziza) and truffles ( Tuberales). o Powdery mildews, Chestnut blight and Dutch Elm disease as well as ergot of rye (Claviceps purpurea which produces an LSD-related compound that causes poisoning of cattle and humans and hallucinations in humans). o The pink bread mold (Neurospora) and the dung mold (Sordaria) o Lichens are symbionts between and ascomycete fungi

Club-like basidia.

Phylum • Bear spores on club-shaped structures called basidia (basidium -- singular). • These are the club fungi, include ‘true mushrooms’ and toadstools. • The fruiting bodies or ascomata of these mushrooms are also compact masses of septate (dolipore septae with membrane caps on small central pores). • Heterokaryotic hyphae forming mycelia. • Cell walls contain chitin. • Examples: o Commercial white button mushrooms (Agaricus bisporus) o The Oriental shiitake mushroom (Lentinula edodes) o Coprinus (shaggy manes or ink caps) are edible basidiomycetes. o The death angel (Amanita) is a toadstool or "chair of death". o Puffballs and bracket or shelf fungi also belong in this phylum. o Smuts and rusts are plant disease-causing agents that are responsible for major and food crop losses. o Russula develope symbiotic relationships with plant roots as ectomycorrhizae in a fashion similar to endomycorrhizae.

Section 7. Plantae Key

Phaeophyta – Brown Algae (typically Kingdom Protista or Chromista) • Largely aquatic organisms lacking waxy cuticle • Chloroplast envelopes with four membranes; • chlorophylls a and c with fucoxanthin pigment; • some filamentous forms but many with tissues and organs; • cold, northern marine waters • algin Examples: Ectocarpus, Fucus, Postelsia, Laminaria, Macrocystis, Nereocystis, and Laminariales

Rhodophyta – • Do not store starch in plastids • Chlorophyll a and sometimes c • Largely aquatic organisms lacking waxy cuticle • Phycobilin pigments aid in deep water photosynthesis • Some appear read • Agar • most forms live in warm marine waters • mostly filamentous forms with complex life cycles but no motile forms Examples: Porphyra, Chondrus crispus, Corallinia, Calliarthon, Gelidium, Polysiphonia

Chlorophyta – Green Algae • Chloroplast envelopes with two membranes • chlorophyll a and carotenoid pigments • chlorophyll a and chlorophyll b • No waxy cuticle • store starch in plastids • found in both marine and freshwater habitats, a few terrestrial forms • much diversity in shapes and life cycles Examples: Chlamydomonas, Volvox, Hydrodictyon, Spirogyra, Cladophora, Ulva, Chara, Coleochaete

Bryophyta • Largely terrestrial organisms with waxy coating, or descended from terrestrial forms • Vascular tissue lacking or primitive; no and phloem. • Store starch in plastids • Chlorophyll a and b

o thallose body or phyllids in ranks of two large, one small; unicellular rhizoids Anthocerophyta – liverworts Examples: Marchantia, Porella o body plan with phyllids in ranks of 3 along the caulids; multicellular rhizoids Bryophyta – Examples: Mnium, Hypnum, Dicranum, Polytrichum, Sphagnum

Lycophyta – Club Mosses • Store starch in plastids • Chlorophyll a and b • Largely terrestrial organisms with waxy coating, or descended from terrestrial forms • Vascular tissues of xylem and phloem • One leaf trace per leaf (microphyll) • no leaf gaps in stele. Examples: Lycopodium,

Pterophyta – Ferns • Store starch in plastids • Chlorophyll a and b • Largely terrestrial organisms with waxy coating, or descended from terrestrial forms • Vascular tissues of xylem and phloem • More than one leaf trace per leaf (megaphyll) • leaf gaps in stele • Sexual reproduction involves spores only; no Examples: Polypodium, Cyrtomium, Davallia, Nephrolepis, Athyrium, Thelypteris, Platycerium, Ophioglossum, Botrychium Also or horsetail (can be classified differently)

Gymnosperms – naked seeds • Store starch in plastids • Chlorophyll a and b • Largely terrestrial organisms with waxy coating, or descended from terrestrial forms • Vascular tissues of xylem and phloem • More than one leaf trace per leaf (megaphyll) • leaf gaps in stele • Sexual reproduction results in formation • Seeds produced in cones, not flowers

Coniferophyta needle-like; cones hard, papery or fleshy; sexes not on separate trees (monoecious). Example: Pinus, Taxus, Juniperus, Abies, Picea, Pseudotsuga, Sequoia, Sequoiadendron

Ginkgophyta Leaves fan-shaped with dichotomous venation; sexes on separate trees (dioecious). Example: biloba

Cycadophyta Few woody trees; mostly shrubs and vines or nonwoody palm-like trees Large, compound pinnate leaves. Examples: Cycas, Zamia

Gnetophyta Few woody trees; mostly shrubs and vines or nonwoody palm-like trees Very reduced megaphyll leaves; green photosynthetic stems. Example:

Angiosperms– flowering plants (boat seeds) Angiospermae, Anthophyta, or Magnoliophyta

• Store starch in plastids • Chlorophyll a and b • Largely terrestrial organisms with waxy coating, or descended from terrestrial forms • Vascular tissues of xylem and phloem • More than one leaf trace per leaf (megaphyll) • leaf gaps in stele • Sexual reproduction results in seed formation • Seeds produced in flowers, not cones

Monocots • One seed leaf • parallel venation • flower parts in 3's • scattered vascular bundles in herbaceous stems Examples: corn, wheat, rice, barley, bamboo and other grasses; onions, lilies, tulips; orchids; palms, and bananas

Dicots • Two seed leaves • netted venation • flower parts in 4's or 5's • vascular bundles in a ring in herbaceous stems Examples: peas, beans, alfalfa, acacia trees, apples, pears, almonds, peaches, apricots, strawberries, raspberries, plums and cherries, maple trees, oak and beech trees, elms, potatoes, tomatoes, eggplant, tobacco, melons, squash; carrots, parsley and parsnip

Section 8. Animalia Key

Colonial, no tissues; asymmetrical to radially symmetrical Phylum Porifera ()

Two or more tissues Diploblastic w/ indeterminate cleavage; ; radially symmetrical w/ ; blind gut Phylum Class Scyphozoa (jelly fish) Class (corals, sea anemones) Class Hydrozoa (hydras, man o’ war) Class Cubozoa (box jellies) Tentacles lacking cnidocytes; complete gut w/ two anal pores Phylum (comb jellies) Triploblastic with w/ determinate cleavage; bilateral symmetry in at least part of life cycle development Grow by adding to size of skeletal elements; use cilia for locomotion No true body cavity, acoelomate, blind gut Phylum Platyhelminthes (flat worms) Coelomate Highly segmented body plan; soft bodied w/ no shell; simple sensory organs and ; closed when present; chitinous bristles Phylum Annelida (segmented worms) Reduced segmentation w/ body plan of foot, mantle and visceral mass; calcium carbonate shell; chitinous radola; feeding organ often present; sensory organs and nervous system may be developed Phylum Class (snails, slugs) Class (clams, oysters, mussels) Class Cephalopoda (squid, octopus) Increase in size by molting cuticle and shedding cuticle and exoskeleton if present, move by other than ciliary locomotion Pseudocoelomate Phylum Nematoda (roundworms) Coelomate No jointed appendages; hydroskeleton only Phylum ( worms) Jointed appendages; chitin exoskeleton Phylum Anthropoda Two pair of branched antennae Subphylum Crustacea (lobsters, crabs, , , barnacles) One pair of unbranched antennae Subphylum One pair of legs per segment Class Chilopodia (centipedes) Two pair of legs per segment Class Diplopoda (millipedes) No antennae Subphylum Class Merostomata (horseshoe crab) Class Pycnogonida (see ) Class Arachnids Order Araneae (spiders) Order Acari(na) (mites, ticks) Order Opiliones (harvestman) Order Solifugae (sunspider) Order Scorpiones (scorpion) Order Pseudoscorpiones Order Thelyphonida (whip scorpion) One pair of unbranched antennae Subphylum Class Insecta (insects) Order Collenbola (snowfleas) Order Thysanuara (Silverfish) Order Odonata (dragonflies, damsel flies) Order Ephemeroptera (mayflies) Order Orthoptera (grasshoppers, locusts, crickets, katydids) Order Blattaria (cockroaches) Order Mantodea (mantids) Order Phasmida (walking sticks) Order Hemiptera (true bugs) Suborder Homoptera (aphids, cicadas) Suborder Heteroptera (bed bug, water strider, squash bug) Order Diptera (flies, mosquitos, gnats, midges) Order Hymenoptera (bees, wasps, ants) Order Lepidoptera (moths, butterflies) Order Coleoptera (beetles, weevils) development Adults with pentaradial symmetry; water vascular system Phylum Echinodermata Class Asteroides (sea stars) Class Echinoidea (sea urchins, sand dollars) Class Ophiuroidea (brittle stars) Class Holothuroidea (sea cucumbers) Class Crinoidea (sea lilies, feather stars) Adults with bilateral symmetry; hollow dorsal nerve cord and cartilaginous notochord; pharyngeal gill slits, and a tail Phylum Chordata No vertebral column and cranial development Notochord, hollow dorsal nerve cord, tail present in larvae but not adults; adults retain and pharyngeal gill slits, chitin or cellulose tunics, no muscle blocks Subphylum Cephalochordata () Notochord, hollow dorsal nerve cord, tail, pharyngeal gill slits, muscle blocks Subphylum Urochordata (, ascidians, sea squirts) Vertebral column and cranial development Subphylum Vertebrata No jaws, retain notochord as adults, medial fins only Class Agnatha Jaws present, do not retain notochord as adults Lateral appendages are fins External gill slits, cartilaginous skeleton, weak jaws, teeth placoid scales, large liver with oil Class Chondrichthyes (sharks, rays, skates, chimareas) No external gill slits (gills covred by bony operculum), typically skeleton bony, jaws well-developed, teeth not placid scales, swim bladder Class Osteichthyes (bony fish: trout, tuna, cod, eels, sturgeons) Tetrapods or descended from tetrapods Eggs and larvae typically aquatic w/ gills, adults usually terrestrial w/ moist glandular skin and weak lungs, three chambered heart Class Amphibia Order Cuadata (newts, salamanders) Order Anura (frogs, toads) Order Gymnophiona (caecilians) Amniotic eggs or derivatives, young and adults typically terrestrial, efficient lungs, four-chambered heart Ectothermic; dry, scaley skin Class Reptilia Order Squamata Suborder Sauria (lizards) Suborder Serpentes (snakes) Order Chelonia (, tortoises) Order Crocodilia (alligators, caymans, crocidiles) Order Rhynchocphalia Endothermic Flow through lungs, feathers, wings Class Aves (birds) Lungs not flow-through, fur, mammary glands Class Mammalia Prototheria (platypuss, echidna) Metatheria (marsupials: kangaroos, wallabies, koala, opossum) Eutheria (placentals: whale, wolf, bat, sloth, hedgehog, armadillo, rabbit, deer, horse, elephant, homid)