Transcript Phylogeny of Bacteria, Archaea, and Eukaryotic

Updated: January 2015
By Jerald D. Hendrix
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Domain Bacteria
Domain Archaea
Domain Eucarya
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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
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Phylum Cyanobacteria
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Oxygenic photosynthetic bacteria
Phylum Chlorobi
The “green sulfur bacteria”
 Anoxygenic photosynthesis
 Includes genus Chlorobium
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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
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Phylum Proteobacteria (cont.)
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Divided into 5 classes: Alphaproteobacteria,
Betaproteobacteria, Gammaproteobacteria,
Deltaproteobacteria, Epsilonproteobacteria
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Phylum Proteobacteria (cont.)
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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
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Phylum Proteobacteria (cont.)
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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
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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
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Phylum Tenericutes
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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
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Phylum Actinobacteria
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“High G + C gram-positive” bacteria
Includes genera Actinomyces, Streptomyces,
Corynebacterium, Micrococcus, Mycobacterium,
Propionibacterium
Phylum Chlamidiae
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Small phylum containing the genus Chlamydia
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Phylum Spirochaetes
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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
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Includes genera Bacteroides, Flavobacterium,
Flexibacter, and Cytophyga; Flexibacter and Cytophyga
are motile by means of “gliding motility”
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Two major phyla:
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Phylum Crenarchaeota
 Originally containing thermophylic and
hyperthermophilic sulfur-metabolizing archaea
 Recently discovered Crenarchaeota are inhibited by
sulfur & grow at lower temperatures
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Phylum Euryarchaeota
 Contains primarily methanogenic archaea, halophilic
archaea, and thermophilic, sulfur-reducing archaea
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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
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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)
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Most of these groups (except probably the fungi)
are highly polyphyletic, and there are competing
alternate taxonomies to describe the eukaryotes
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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.
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Selected Protista
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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)
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Selected Protista (continued)
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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
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Selected Protista (continued)
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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
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Selected Protista (continued)
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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
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Selected Protista (continued)
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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
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Selected Protista (continued)
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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
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Selected Protista (continued)
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Amoebozoa
 Gymnamoebas – free-living amoebas; unicellular with
pseudopod movement; genera Amoeba and Pelomyxa
 Entamoebas – parasitic, example Entamoeba hystolytica
that causes amoebic dysentery
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Slime molds
 Once classed as fungi
 Dictyostelium
 Life cycle that begins as amoeba that slime together,
aggregate, and form multicellular stalks (fruiting
bodies)
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Fungi
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Basic properties
 Single celled (yeast) or filamentous (molds; fleshy
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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
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Fungi (continued)
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The Chytridiomycetes
 Probably the deepest branching fungal group, motile sexual
spores
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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
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Fungi (continued)
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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
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Fungi continued)
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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
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Red algae and green algae
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Unicellular, colonial, or simple multicellular
Multicellular plants evolved from green algae