Bacteria and Archaea

The Prokaryotic Domains

Prokaryotic ComplexityFigure 4.5

Eukaryotic ComplexityFigure 4.7

Prokaryotes

• derived from ancient lineages

• more biomass than all other life combined

• “simple” cellular structure

– no nuclear membrane

– no membrane-bound organelles

– no cytoskeleton

• limited morphological variation

Prokaryotic MorphologiesFigure 27.13

Prokaryotic Morphologies

Figure 27.1

photosynthetic bacteriaFigure 27.7

photosynthetic archaeaFigure 27.20

Prokaryotes• diverse metabolic “strategies”

– photoautotrophy

– chemoheterotrophy

• most bacteria and archaea

– chemoautotrophy

– photoheterotrophy

• energy from light

• carbon from organic compounds

Energy/carbonTable 27.2

Prokaryotes

• in nearly every habitat on Earth– terrestrial– aerobic/anaerobic– marine/freshwater– deep ocean rifts/deep in crust (>2 km)– antarctic ice pack– hot/acidic (>100˚C; pH = 2-3)– salty/alkaline (pH = 11.5)– etc.

Prokaryotes

• a range of growth rates

– generation times

• 10 min

• 1-3 hours

• days - weeks

– suspensions between growth periods

• indefinite

–years, decades, >century, millions?

Prokaryotes

• Some defy taxonomic notions

– get too big

– possess internal membrane systems

– exhibit “eukaryote-like” growth forms

Actinomycete Figure 27.16

MorphologyFigure 27.3

Streptococcus pyogenes Staphylococcus aureusNeisseria gonorrhoeaeDiplococcus

bacterial gas vesiclesFigure 27.4

Prokaryotic Taxonomy• Historically

– morphology

– motility (+/-)

• rolling/gliding

• vertical positioning

• flagella & axial filaments

axial filamentsFigure 27.4

flagella

Figure 27.5

Prokaryotic FlagellumFigure 4.6

Gram’s Stain:

Bacillus subtilisgram positiveFigure 27.6

Gram’s Stain:

E. coligram negative

Figure 27.6

Prokaryotic Taxonomy• Historically

– morphology– motility– reactivity

• Gram’s stain - peptidoglycan cell wall• metabolism

–aerobic/anaerobic–resource utilization–products –inclusion bodies

MycoplasmaFigure 27.17

endospore - resting bodyFigure 27.14

Prokaryotic Taxonomy• Historically

– distinctive features• size

–very large or very small• stress response

–endospore formation• life style

–colonial/parasitic/pathogenic

Chlamydia: obligate intracellular parasiteFigure 27.13

crown gall on geranium

due to Agrobacterium

tumefaciensFigure 27.10

Prokaryotic Taxonomy• Pathogenic requirements

– contact

– entry

– defense evasion

– multiplication

– damage

– infectious transfer

Prokaryotic Taxonomy• Pathogen characteristics

– Invasiveness

– Toxigenicity

• Corynebacterium diphtheriae vs. Bacillus anthracis

• endotoxin vs. exotoxin

–Salmonella vs. Clostridium tetani

Prokaryotic Taxonomy• Koch’s postulates

– Always found in diseased individuals– Grown in pure culture from host inoculant– Cultured organisms causes disease– Newly infected host produces a pure culture

identical to the infective culture

Prokaryotic Taxonomy• Historically

– distinctive features• size

–very large or very small• stress response

–endospore formation• life style

–parasitic/pathogenic• ecological niche

Methanogens & methane using Archaea

• Methanogens release 80-90% of atmospheric methane, a greenhouse gas

• Methane users intercept methane seeping from sub-oceanic deposits

Prokaryotic Taxonomy

• Biofilm production

– on solid surfaces

– mixed colonies

– polysaccharide matrix

– resistant to treatments

Recent Prokaryotic Phylogeny

• Based on rRNA

– evolutionarily ancient

– shared by all organisms

– functionally constrained

– changes slowly with time

– encodes signature sequences

–BUT - yields a different phylogeny than other sequences analyzed

Recent Prokaryotic Phylogeny

• sources of phylogenetic confusion

– Lateral gene transfer

• among members of bacterial species

• among members of different species

• across domains…

– phylogenetic analysis assumes cladogenic evolution

• evolution may have been highly reticulate

Recent Prokaryotic Phylogeny

• sources of phylogenetic confusion

– Mutation

• prokaryotes are haploid

–“recessive” mutations are not masked

• prokaryotes have very little non-coding DNA

• many prokaryotes have very short generation times

Recent Prokaryotic Phylogeny

• rRNA led to three domains

– Archaea: more similar to Eukarya than to Bacteria

– An ancient split between Bacteria and Archaea was followed by a more recent split between Archaea and Eukarya

The Three Domain PhylogenyFigure 27.2

Shared Features of the Three Domains

• plasma membrane

• ribosome structure

• glycolysis

• encode polypeptide sequences in DNA

• replicate DNA semi-conservatively

• transcribe, translate with same genetic code

Table 27.1

some major bacterial groups

Figure 27.8

Bacterial Phylogeny

• Molecular comparisons suggest several higher level groups

– Proteobacteria are highly diversified

• gram negative

• bacteriochlorophyll

• source of mitochondria

• N2-fixers, Rhizobium, Agrobacterium, E. coli, Yersinia, Vibrio, Salmonella, etc.

ProteobacteriaFigure 27.9

Bacterial Phylogeny

• Molecular comparisons suggest several higher level groups

– Proteobacteria are highly diversified

– ancient Cyanobacteria produced oxygen and chloroplasts

• “blue-green algae”

• fix CO2 & N2

• single or colonial - sheets, filaments, balls

Cyanobacteria fix CO2 & N2

Figure 27.11

Cyanobacteria are pond scumFigure 27.11

Bacterial Phylogeny

• Molecular comparisons suggest several higher level groups

– Proteobacteria are highly diversified

– ancient Cyanobacteria produced oxygen and chloroplasts

– Spirochetes have axial filaments

• human parasites & pathogens

• free living in water sediments

Spirochetes have axial filamentsFigure 27.12

Bacterial Phylogeny

• Molecular comparisons suggest several higher level groups

– Proteobacteria are highly diversified

– ancient Cyanobacteria produced oxygen and chloroplasts

– Spirochetes have axial filaments

– Chlamydias have a complex life cycle

• obligate intracellular parasites

Chlamydia Figure 27.13

Bacterial Phylogeny• Molecular comparisons suggest several higher

level groups

– Firmicutes: a diverse (mostly) Gram positive group

• some produce endospores

• some are native flora

–Staphylococcus

Gram + staphylococci

Figure 27.15

Bacterial Phylogeny• Molecular comparisons suggest several higher

level groups

– Firmicutes: a diverse (mostly) Gram positive group

• some produce endospores

• some are native flora

• some are filamentous (actinomycetes)

–Mycobacterium tuberculosis

–Streptomyces spp.

filamentous ActinomyceteFigure 27.16

Bacterial Phylogeny• Molecular comparisons suggest several higher

level groups

– Firmicutes: a diverse (mostly) Gram positive group

• some produce endospores

• some are native flora

• some are filamentous (actinomycetes)

• Mycoplasmas

–small (~0.2 µm), no cell wall, low DNA

Mycoplasma Figure 27.17

unique membrane structureFigure 27.18

unique membrane structureSee page

539

Archaean Phylogeny

• Most known archaea are extremophiles

– many are not

• Archaea cell walls lack peptidoglycan

• Archaea possess unique cell membranes lipids

• Archaea share rRNA signature sequences

• >1/2 of Archaean genes are unlike genes known from Bacteria or Eukaryotes

Archaean Phylogeny

• Crenarchaeota

– most live in hot, acidic habitats

• 70-75˚C; pH 2-3

–Sulfolobus pH = 0.9

–Ferroplasma pH = 0.0

–some maintain internal pH 7.0

a hot, acidic homeFigure 27.19

Archaean Phylogeny

• Crenarchaeota

– most live in hot, acidic habitats

• Euryarchaeota

– Methanogens [CO2 => CH4]

• strict anaerobes in cow guts, rice paddies and hydrothermal vents

• all share rRNA similarities

Archaean Phylogeny

• Crenarchaeota

– most live in hot, acidic habitats

• Euryarchaeota

– Methanogens

– extreme halophiles

• e.g. in the Dead Sea

• some use bacteriorhodopsin (retinal), not bacteriochlorophyll

Archaean Phylogeny

• Crenarchaeota

– most live in hot, acidic habitats

• Euryarchaeota

– Methanogens

– extreme halophiles

– Thermoplasma

• thermoacidophile, no cell wall

• genome size = Mycoplasmas (1.1 x 106)