Prokaryotes (Domains Bacteria & Archaea)

2/4/15

Prokaryotes
(Domains Bacteria & Archaea)
KEY POINTS

1.ꢀ Decomposers: recycle organic and inorganic molecules in environment; makes them available to other organisms.
2.ꢀ Essential components of symbioses. 3.ꢀ Encompasses the origins of metabolism and metabolic diversity.
4.ꢀ Origin of photosynthesis and formation of atmospheric Oxygen

Humans

ANTIQUITY

Colonization of land

Animals
Origin of solar

system and Earth

•ꢀ >3.5 BILLION years old.
•ꢀ Alone for 2

1
4

billion years

Proterozoic Archaean
Prokaryotes

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3

Multicellular eukaryotes

Single-celled eukaryotes
Atmospheric oxygen

General characteristics

1.ꢀ Small: compare to
10-100µm for eukaryotic cell; single-celled; may form colonies.
2.ꢀ Lack membraneenclosed organelles.
3.ꢀ Cell wall present, but

different from plant cell wall.

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4.ꢀ Occur everywhere, most numerous organisms.

–ꢀ More individuals in a handful of soil then there are people that

have ever lived.

–ꢀ By far more individuals in our gut than eukaryotic cells that are actually us.

5.ꢀ Metabolic diversity established nutritional modes of eukaryotes.

6.ꢀ Important decomposers and recyclers

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6.ꢀ Important decomposers and recyclers

•ꢀ Form the basis of

global nutrient cycles.

7. Symbionts!!!!!!!

•ꢀ Parasites

•ꢀ Pathogenic organisms.
•ꢀ About 1/2 of all human diseases are caused by Bacteria

7. Symbionts!!!!!!!

•ꢀ Parasites

•ꢀ Pathogenic organisms.
•ꢀ Extremely important in agriculture as well.

Pierce’s disease is caused by Xylella fastidiosa, a Gamma Proteobacteria. It causes over $56 million in damage annually in California. That’s with $34 million spent to control it! = $90 million in California alone.

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7. Symbionts!!!!!!!

•ꢀ Commensalists

•ꢀ They are everywhere (really).
•ꢀ There can be 10 million cells per square centimeter of skin.

7. Symbionts!!!!!!!

•ꢀ Mutualists

•ꢀ Eukaryotic life would be impossible without this.

7. Symbionts!!!!!!!

•ꢀ Allows herbivorous
(plant-feeding) animals to digest cellulose and other low-quality plant tissues.
•ꢀ Termites •ꢀ Ungulates “chewing the cud”
•ꢀ Lagomorph coprophagy

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7. Symbionts!!!!!!!

•ꢀ Mealybug endosymbionts with endosymbionts.

7. Symbionts!!!!!!!

•ꢀ Komodo dragons and their
“toxins”.
•ꢀ Hunt large prey and can inflict fairly minor wound.
•ꢀ Prey die fairly quickly from wound.
•ꢀ Infection by highly pathogenic

Pasteurella multocida (Gamma

Proteobacteria).
•ꢀ Prominent in saliva of dragons, but dragons have an anti-

Pasteurella antibody.

TAXONOMY is problematic

•ꢀ Relationships obscured by billions of years of evolution
•ꢀ Also obscured by unique bacterial means of recombination (more later).
•ꢀ Grouped primarily by DNA sequence data.
•ꢀ Immense genetic/genomic diversity.

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Current taxonomy is stabilizing

•ꢀ Note that “Prokaryote” is paraphyletic. Why?
•ꢀ Two Domains:

•ꢀ Archaea: extremophiles

(mostly), ancient, probable progenitors of eukaryotes.

•ꢀ Bacteria: most

commonly-encountered prokaryotes.

Characteristics

•ꢀ Cell Surface •ꢀ Motility •ꢀ Genome •ꢀ Reproduction & Growth •ꢀ Metabolic Diversity •ꢀ Nitrogen Metabolism •ꢀ Oxygen Relationships

Cell Surface

•ꢀ Archaea: plasma

membrane of

ether-lipids

(unique in life).

•ꢀ Bacteria: a sugar

polymer -

peptidoglycan

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Cell Surface

•ꢀ Cell wall is often modified with structures to adhere to substrate.
•ꢀ Many secrete a sticky capsule or adhere by fimbriae (ocasionally called pili).

Motility

•ꢀ ~half the species can move. 1.ꢀ Flagella most common

(different structure from

eukaryote)
2.ꢀ Spiral filaments: spirochetes corkscrew
3.ꢀ Gliding over slimy secretions
(via flagellar motors without filament)

•ꢀ Capable of taxis (photo,

chemo, geo, etc.)

Genome

•ꢀ Small genomes:
~1/1000th DNA content of eukaryotes.
•ꢀ No membrane enclosed nucleus.
•ꢀ DNA concentrated in
‘nucleoid’ region.

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Genome

•ꢀ One major chromosome, double stranded DNA molecule in ring.
•ꢀ Sometimes several small DNA rings of few genes:

plasmids.

–ꢀ Replicate independently of main chromosome.
–ꢀ Permit recombination via

conjugation (later).

–ꢀ Involved in resistance to antibodies/antibiotics.

Genome

•ꢀ Broadly, replication & translation of genetic info like that of eukaryotes; differ in details and simplicity.
•ꢀ Used in first DNA recombinant research.

•ꢀ Genetic recombination: Not like eukaryotes

(e.g. chiasma & crossing over)!!

–ꢀ Transformation –ꢀ Conjugation –ꢀ Transduction

Genome: Recombination via transformation

•ꢀ DNA taken up from the environment

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Genome: Recombination via conjugation

•ꢀ Direct transfer of DNA between cells.
•ꢀ Both plasmids and

portions of bacterial

chromosome.

Genome: Recombination via transduction

•ꢀ Transfer of DNA via

phage viruses.

Reproduction & Growth

•ꢀ Meiosis & Mitosis NOT PRESENT.

•ꢀ Asexual binary fission.

•ꢀ DNA replication can be nearly continuous in ideal conditions (depends on pH, salinity, temperature, etc.)
•ꢀ Generation times as fast as 20 minutes

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Metabolism

Metabolic Diversity

•ꢀ Nutrition:

•ꢀ Requires a source of carbon for

synthesizing organic compounds: either carbon dioxide or living matter.

•ꢀ Requires a source of energy to drive

reactions: either light or chemical.

Metabolic Diversity:^MetabolismSource of Carbon

•ꢀ AUTOTROPHS: Need only carbon

dioxide (CO₂) as carbon source

•ꢀ HETEROTROPHS: Need at least one

organic nutrient as carbon source (e.g. glucose; petroleum)

•ꢀ Both of these present in domain Eucarya as well.

Metabolic Diversity:^MetabolismSource of Energy

•ꢀ PHOTOTROPHS: Need only sunlight as

energy source

•ꢀ CHEMOTROPHS: Derive energy from

oxidation of organic molecules.
•ꢀ Both of these present in domain Eucarya as well.

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Metabolism

Metabolic Diversity: Combined

Energy Source:

Sun

Environment

Photoautotroph

Chemoautotroph

CO₂Organic molecules

Photoheterotroph Chemoheterotroph

Which of these are present in multicellular Eucarya?

Metabolism

Photoautotrophs

•ꢀ Use sun for energy, CO₂for carbon.
•ꢀ Photosynthetic bacteria (e.g. cyanobacteria).
•ꢀ Present in many plants and singlecelled Eucarya

Metabolism

Chemoautotrophs

•ꢀ Oxidize inorganics
(H₂S, NH₃) for energy.
•ꢀ Need only CO₂as carbon source.
•ꢀ Unique to Bacteria and Archaea.

•ꢀ E.g. Methanococcus jannaschii lives on

hydrothermal vents at 2600m below sea level.
•ꢀ Reduces H₂+ CO₂to CH₄+ 2H₂O.

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Metabolism Metabolism Metabolism

Photoheterotrophs

•ꢀ Get enery from light but must obtain carbon in organic form (NOT CO₂).
•ꢀ Unique to Bacteria and Archaea.

•ꢀ E.g. Halobacterium salinarium.

Chemoheterotrophs

•ꢀ Consume organic

molecules for both

energy and carbon.
•ꢀ Common among prokaryotes:

–ꢀ saprobes

(decomposers)

–ꢀ parasites (rely on

living hosts)

•ꢀ Also widespread in Protista, Animalia, Plantae.

Nitrogen metabolism

•ꢀ Nitrogen fixation:

•ꢀ The only* mechanism that makes atmospheric Nitrogen available to other organisms.
•ꢀ Convert N₂into ammonia
(NH₃) which is quickly protonated into ammonium (NH₄⁺).
•ꢀ Essential for multicellular life!

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Oxygen Relationships

•ꢀ Aerobic vs. Anaerobic

•ꢀ Cellular respiration:

–ꢀ Carbohydrates + O₂→CO₂
+ H₂O + energy

•ꢀ Obligate aerobes: use O₂for cellular respiration.
•ꢀ Fermentation:
•ꢀ Facultative anaerobes: use

–ꢀ Carbohydrates →CO₂ethanol + energy
+

O₂if it is present by carry out anaerobic respiration or fermentation in anaerobic environment.
•ꢀ Obligate anaerobes: poisoned by O₂; use anaerobic respiration or fermentation.
•ꢀ Anaerobic respiration:

–ꢀ Carbohydrates + [X] → bicarbonate + [X^-] + energy
–ꢀ Where [X] is a substance other than O₂that accepts electrons such as nitrates or sulfates

Oxygen Relationships

•ꢀ Early life (during the Archaean) was primarily anaerobic.
•ꢀ Evolution of photosynthesis in Cyanobacteria changed all this.

Taxonomy of Prokaryotes

•ꢀ Archaea or Archaebacteria

–ꢀ Methanogens –ꢀ Halophiles –ꢀ Thermophiles

•ꢀ Bacteria or Eubacteria

–ꢀ Protobacteria –ꢀ Chlamyidias –ꢀ Spirochetes –ꢀ Cyanobacteria –ꢀ Gram-positive bacteria

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Archaea or Archaebacteria

•ꢀ Live in extreme environments (extremophiles): sulfur hot springs, deep sea vents, high salt environments.
•ꢀ Lack peptidoglycan, unique plasma membrane of liquids

•ꢀ Likely sister group of

Eukaryotes

•ꢀ Methanogens

–ꢀ Use H₂to reduce CO₂to methane (CH₄).
–ꢀ Chemoautotrophs –ꢀ Anaerobic –ꢀ In swamps, marshes, deep sea vents, important decomposers.

•ꢀ Halophiles

–ꢀ Saline environments. –ꢀ Salinity several times higher than sea water.
–ꢀ Photoheterotrophs

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•ꢀ Thermophiles

–ꢀ 60º-80ºCpH 2-4 optimal
–ꢀ Chemoautotrophs –ꢀ Oxidize HS

Bacteria or Eubacteria

•ꢀ Grouped by molecular systematics.

Proteobacteria

•ꢀ VERY diverse, grouped into five taxa based on DNA sequence data.
•ꢀ Includes most types of metabolism that we’ve discussed.
•ꢀ Includes most of the types of symbioses we’ve discussed
•ꢀ Review the summary in Figure 27.16.

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Gram positive Bacteria:

•ꢀ Simple peptidoglycan cell wall. •ꢀ Rival Proteobacteria in diversity.
•ꢀ Most are free-living decomposers.
•ꢀ Some pathogenic (e.g. strains

of Staphylococcus, Streptococcus, Bacillus anthracis, Clostridium botulinum).

•ꢀ Include the mycoplasms--the only bacteria that lack cell walls

Cyanobacteria:

•ꢀ Photoautotrophs •ꢀ Only prokaryotes with plant-like, O₂-generating photosynthesis.
•ꢀ Present in freshwater and marine environments.
•ꢀ Often colonial--first steps toward multicellularity?

Spirochetes:

•ꢀ Helical •ꢀ Recall motility: move by means of rotating, internal, flagellum-like filaments.
•ꢀ Free-living and parasitic.
•ꢀ Chemoheterotrophs
(like us).

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Chlamydias:

•ꢀ ALL are parasites of animals.
•ꢀ Intercellular. •ꢀ Lack peptidoglycan in the cell wall (are they gram-positive or gram-negative?).
•ꢀ Most common form of STD in USA (urethritis).

Prokaryotes: Summary

•ꢀ You should now have a good sense of prokaryote biology and diversity.
•ꢀ Including roles in metabolism, symbioses, global energy cycles.
•ꢀ Important distinguishing characteristics of cell wall, motility, genome, replication.
•ꢀ General aspects of their systematics.

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