Phylogeny of Bacteria, Archaea, and Eukaryotic Microorganisms

Phylogeny of Bacteria, Archaea, and Eukaryotic Microorganisms

PHYLOGENY OF BACTERIA, ARCHAEA, AND EUKARYOTIC MICROORGANISMS Updated: January 2015 By Jerald D. Hendrix Phylogeny of Bacteria, Archaea, and Eukaryotic Microorganisms A. B. C. Domain Bacteria Domain Archaea Domain Eucarya A. Domain Bacteria

The 2nd and subsequent editions of Bergeys 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 A. Domain Bacteria

Phylum Cyanobacteria Oxygenic photosynthetic bacteria Phylum Chlorobi The green sulfur bacteria Anoxygenic photosynthesis Includes genus Chlorobium A. Domain Bacteria 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 A. Domain Bacteria Phylum Proteobacteria (cont.)

Divided into 5 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria A. Domain Bacteria 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 A. Domain Bacteria 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 A. Domain Bacteria 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

A. Domain Bacteria 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

A. Domain Bacteria Phylum Actinobacteria High G + C gram-positive bacteria Includes genera Actinomyces, Streptomyces, Corynebacterium, Micrococcus, Mycobacterium, Propionibacterium Phylum Chlamidiae Small phylum containing the genus Chlamydia A. Domain Bacteria

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 B. Domain Archaea 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, sulfurreducing archaea B. Domain Archaea Other phyla have been proposed, predominately of archaea that have been postulated but not cultured: Aigarchaeota, Korarchaeota, Thamarchae ota, Nanoarchaeota

Comparison to other domains: C. Domain Eucarya 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 C. Domain Eucarya 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. C. Domain Eucarya 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) C. Domain Eucarya

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

C. Domain Eucarya 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

C. Domain Eucarya 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 C. Domain Eucarya 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 C. Domain Eucarya 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 C. Domain Eucarya 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) C. Domain Eucarya 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 C. Domain Eucarya

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 C. Domain Eucarya 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 C. Domain Eucarya 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 C. Domain Eucarya Red algae and green algae Unicellular, colonial, or simple multicellular Multicellular plants evolved from green algae

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