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Download Phylogeny of Bacteria, Archaea, and Eukaryotic
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Updated: January 2015 By Jerald D. Hendrix A. B. C. Domain Bacteria Domain Archaea Domain Eucarya The 2nd and subsequent editions of Bergey’s Manual of Systematic Bacteriology divides domain Bacteria into over two dozen phyla, based on cladistic taxonomy. Some of the more notable phyla are described here. Phylum Aquiflexa The earliest “deepest” branch of the Bacteria Contains genera Aquiflex and Hydrogenobacter that can obtain energy from hydrogen via chemolithotrophic pathways Phylum Cyanobacteria Oxygenic photosynthetic bacteria Phylum Chlorobi The “green sulfur bacteria” Anoxygenic photosynthesis Includes genus Chlorobium Phylum Proteobacteria The largest group of gram-negative bacteria Extremely complex group, with over 400 genera and 1300 named species All major nutritional types are represented: phototrophy, heterotrophy, and several types of chemolithotrophy Sometimes called the “purple bacteria,” although very few are purple; the term refers to a hypothetical purple photosynthetic bacterium from which the group is believed to have evolved Phylum Proteobacteria (cont.) Divided into 5 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria Phylum Proteobacteria (cont.) Significant groups and genera include: Photosynthetic genera such as Rhodospirillum (a purple non-sulfur bacterium) and Chromatium (a purple sulfur bacterium) Sulfur chemolithotrophs, genera Thiobacillus and Beggiatoa Nitrogen chemolithotrophs (nitrifying bacteria), genera Nitrobacter and Nitrosomonas Other chemolithotrophs, genera Alcaligenes, Methylobacilllus, Burkholderia Phylum Proteobacteria (cont.) Significant groups and genera include: The family Enterobacteriaceae, the “gram-negative enteric bacteria,” which includes genera Escherichia, Proteus, Enterobacter, Klebsiella, Salmonella, Shigella, Serratia, and others The family Pseudomonadaceae, which includes genus Pseudomonas and related genera Other medically important Proteobacteria include genera Haemophilus, Vibrio, Camphylobacter, Helicobacter, Rickessia, Brucella Phylum Firmicutes “Low G + C gram-positive” bacteria Class Clostridia; includes genera Clostridium and Desulfotomaculatum, and others Class Bacilli; includes genera Bacillus, Lactobacillus, Streptococcus, Lactococcus, Geobacillus, Enterococcus, Listeria, Staphylococcus, and others Phylum Tenericutes One class, Mollicutes Bacteria in this class cannot make peptidoglycan and lack cell walls Includes genera Mycoplasma, Ureaplasma, and others Mollicutes is very close phylogenetically to the low GC Gram-positive bacteria, and has often been included as a class in phylum Firmicutes; however, some idiots insist on placing it in its own phylum Phylum Actinobacteria “High G + C gram-positive” bacteria Includes genera Actinomyces, Streptomyces, Corynebacterium, Micrococcus, Mycobacterium, Propionibacterium Phylum Chlamidiae Small phylum containing the genus Chlamydia Phylum Spirochaetes The spirochaetes Characterized by flexible, helical cells with a modified outer membrane (the outer sheath) and modified flagella (axial filaments) located within the outer sheath Important pathogenic genera include Treponema, Borrelia, and Leptospira Phylum Bacteroidetes Includes genera Bacteroides, Flavobacterium, Flexibacter, and Cytophyga; Flexibacter and Cytophyga are motile by means of “gliding motility” Two major phyla: Phylum Crenarchaeota Originally containing thermophylic and hyperthermophilic sulfur-metabolizing archaea Recently discovered Crenarchaeota are inhibited by sulfur & grow at lower temperatures Phylum Euryarchaeota Contains primarily methanogenic archaea, halophilic archaea, and thermophilic, sulfur-reducing archaea Other phyla have been proposed, predominately of archaea that have been postulated but not cultured: Aigarchaeota, Korarchaeota, Thamarchaeota, Nanoarchaeota Comparison to other domains: http://en.wikipedia.org/wiki/Archaea The domain Eucarya is divided into four kingdoms by most biologists: Kingdom Protista, including the protozoa and algae Kingdom Fungi, the fungi (molds, yeast, and fleshy fungi) Kingdom Animalia, the multicellular animals Kingdom Plantae, the multicellular plants (and the green algae in many schemes) Most of these groups (except probably the fungi) are highly polyphyletic, and there are competing alternate taxonomies to describe the eukaryotes Eukaryotes are believed to have evolved through endosymbiosis events; possibly both primary and secondary endosymbiosis during the origin of certain groups. Organelles that are well established to have originated through endosymbiosis are the mitochondria and chloroplasts. This survey presents several key groups of eukaryotes in the context of their phylogenetic relationships and ecological roles. Selected Protista Diplomonads and parabasalids Unicellular & flagellated Lack mitochondria and chloroplasts Parasites Giardia – a diplomonad; has mitosomes Trichomonas – a parabasalid; parabasal body supports golgi; no mitochndria but has hydrogenosomes; unusually large genome, highly repetitive, lacks introns but may encode around 60,000 genes (almost twice the number of humans) Selected Protista (continued) Euglenozoans Unicellular, flagellated Trypanosoma and Leishmania, two genera of kinetoplastids the kinetoplast is a mass of DNA within their single large mitochondria Trypanosoma includes species of insect-borne parasitic flagellates, including causes of sleeping sickness and Chargas disease Euglena, a euglenid Photosynthetic with chloroplasts; can also live as chemorganotrophs in the darkness and can feed on bacteria via phagocytosis Selected Protista (continued) Alveolates Characterized by alveoli – mebranous sacks located just underneath the plasma membrane; function unknown Ciliates covered with cilia; oral groove; macronuclei and micronuclei, conjugation, many host endosymbionts Paramecium – free-living ciliate Balantidium – parasitic Selected Protista (continued) Alveolates (continued) Dinoflagellates Diverse group of freshwater and marine phototrophic alveolates; part of the plankton Includes Gonyaulax, the “red tide” organism Apicomplexians Once known as the Sporozoa Nonmotile “adult” forms Contain apicoplasts (degenerated nonfunctional chloroplasts) and likely evolved from red-tide dinoflagellates Sexually reproducing (meiosis and chromosome segregation) Different life cycle stages may require different host species Example: Plasmodium, cause of malaria Selected Protista (continued) Stramenopiles Diatoms – another photorophic plantonic group Golden algae (chrysophytes) and brown algae Golden algae are mostly unicellular; some are colonial Brown algae (Fucus) are mostly multicellular; seaweed Oomycetes Slime molds Originally classified as fungi Motile, flagellated sexual spores Includes Phytophthora, cause of the potato blight Selected Protista (continued) Cercozoans and Radiolarians Once classified as amoebas because of pseudopods Cercozoans Chlorarachniophytes: Both freshwater and marine; “amoeba-like;” phototrophic; no test (shell) Foraminifera: Exclusively marine and form symetrical tests of calcium carbonate; may also host algal symbionts Radiolarians Also make calcium tests; typically lobed or spiked; exclusively heterotrophic Selected Protista (continued) Amoebozoa Gymnamoebas – free-living amoebas; unicellular with pseudopod movement; genera Amoeba and Pelomyxa Entamoebas – parasitic, example Entamoeba hystolytica that causes amoebic dysentery Slime molds Once classed as fungi Dictyostelium Life cycle that begins as amoeba that slime together, aggregate, and form multicellular stalks (fruiting bodies) Fungi Basic properties Single celled (yeast) or filamentous (molds; fleshy fungi) Filaments are called hyphae (singular: hypha) Hyphae may be septate or nonseptate (coenocytial) All are heterotrophic chemorganotrophs; none are phototrophic Cell walls contain cellulose and may also contain chitin Fungi (continued) The Chytridiomycetes Probably the deepest branching fungal group, motile sexual spores The Zygomycetes Reproduces asexually by producing haploid spores at the end of stalk-like sporangia Reproduces sexually when gametangia of opposite mating types fuse (plasmogamy) resulting in a dikaryotic sexual spore; when the spore finds favorable conditions, karyogamy and meiosis occurs, forming haploid cells that grow into hyphae Industrially important genera include Mucor, Rhizomucor, and Rhizopus Possibly related phylogenetically to microsporidia and glomeromycetes – two groups of asexually reproducing parasitic fungi Fungi (continued) The Ascomycetes (“Sac fungi”) Reproduce asexually by producing chains of haploid spores at the end of aerial hyphae Reproduce sexually when gametangia of opposite mating types fuse and form a diploid nucleus; meiosis occurs immediately to produce forming haploid ascospores; the ascospores are formed within sacs called asci Important genera include Saccharomyces, Neurospora, Sordaria, Morabella, Tuber, Schizosaccharomyces, Candida, Aspergillus Fungi continued) The Basidiomycetes (“club fungi”) Sexual spores are formed on club-shaped structures called basidia Includes mushrooms and puffballs, Phanerochaete chrysosporium (white rot, used in bioremediation), Cryptococcus (important human pathogen), and smut & rust diseases of plants Red algae and green algae Unicellular, colonial, or simple multicellular Multicellular plants evolved from green algae