[ppt]phylogeny of bacteria, archaea, and eukaryotic...
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PHYLOGENY OF BACTERIA, ARCHAEA, AND EUKARYOTIC
MICROORGANISMSUpdated: January 2015
By Jerald D. Hendrix
Phylogeny of Bacteria, Archaea, and Eukaryotic MicroorganismsA. Domain BacteriaB. Domain ArchaeaC. Domain Eucarya
A. Domain Bacteria 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
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, sulfur-reducing archaea
B. Domain 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
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