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

C. Domain Eucarya Red algae and green algae

Unicellular, colonial, or simple multicellular Multicellular plants evolved from green algae