DSU logo BIO 101 Principles of Biology II
Bacteria and Archaea

Prokaryotic organisms comprise two of the three domains of organisms.

•  Archaea

•  Bacteria (sometimes called Eubacteria)

•  Formerly, these two groups were placed in the kingdom Monera.

•  We will look into the differences between the two domains a bit later. But first let's concentrate first on features common to all prokaryotes.

All archaea and bacteria have prokaryotic cells.

•  Prokaryotic cells are fundamentally different from eukaryotic cells.

•  Prokaryotes originated about 2 billion years before eukaryotes.

•  Obviously, prokaryotes should be separated from eukaryotes at a high taxonomic level (domain)

•  Recent molecular evidence suggests that although both archaea and bacteria are prokaryotic, they are different enough to be placed in different domains.

Prokaryotes are simpler in structure than eukaryotes.

•  Most prokaryotes are basically unicellular.

•  In some species cells aggregate into "colonies," but there is rarely any cytoplasmic connection between cells, and usually all cells in the colony are of the same type.

•  Prokaryotic cells have no membrane-bound organelles (such as the nuclei, mitochondria, and chloroplasts that are found in eukaryotic cells).

•  However, photosynthetic bacteria (such as cyanobacteria) have internal membranes similar to the thylakoids of eukaryotes, but these membranes are not enclosed within a chloroplast.

•  DNA is not surrounded by a membrane (no nucleus).

•  The region containing the DNA is called the nucleoid.

•  Prokaryotic DNA is "naked" (without histone proteins)

•  Prokaryotic ribosomes are smaller (70s) than those of eukaryotes.

•  Bacteria look very simple-even when seen with the electron microscope.

TEM of bacterium
A bacterium cell seen with the transmission electron microscope. Note the plasma membrane, cell wall, and nucleoid (the lighter area)

Most prokaryotes have a cell wall (like algae, fungi, and plants).

•  Cell walls of archaea are built mainly of protein.

•  Cell walls of bacteria are built mainly of peptidoglycan.

•  Peptidoglycan is a mesh-like molecule composed of chains of sugars cross-linked by short chains of amino acids.

•  This is very different from the walls of eukaryotes, which are built mainly from polysaccharides.

•  Some bacteria also have a lipopolysaccharide (LPS) layer.

•  The LPS is located outside of the peptidoglycan layer.

•  It is somewhat like the lipid bilayer of the plasma membrane.

•  There are two groups of bacteria based on the cell wall.

•  These groups are distinguished by the reaction of their cells to a purple dye (crystal violet). Called the Gram stain, it was developed by Hans Gram in the 1800s. Two types of bacteria can be identified by their color after the treatment.

•  Gram-positive bacteria

•  Appear purple after staining

•  They retain the purple dye because of their thick peptidoglycan layer and lack of the LPS.

•  Gram-negative bacteria

•  Appear pink after staining

•  They do not retain the purple dye.

•  Their peptidoglycan layer is thin, and they have the LPS.

•  The cell wall is often surrounded by a mucilaginous sheath.

•  This sheath is sometimes so thick that the cells appear to be embedded in a mass of jelly.

Prokaryotes are vitally important ecologically and economically.

•  Prokaryotes are found in virtually every place suitable for life.

•  They are the most numerous of all organisms.

•  Most bacteria are important as decomposers.

•  Cyanobacteria are important producers in aquatic ecosystems.

•  Bacteria carry out reactions that influence the environment, especially with regard to the nitrogen cycle.

•  Some parasitic bacteria cause diseases.

•  Many archaea live in extreme environments

•  Thermophiles - in hot springs

Hot springs
Mammoth hot springs in Yellowstone National Park. The coloration is due to thermophilic bacteria and cyanobacteria
Photograph by John Tiftickjian

•  Halophiles - in very salty conditions

Structure and motility

•  Prokaryotic cells are typically spherical (coccus), rod-shaped (bacillus), or helical (spirillum).

Bacterial cell shapes
Typical shapes of bacterial cells

•  Morphologies

•  Unicellular

•  Daughter cells separate shortly after cell division

•  Colonies

•  Cells remain attached in clumps after cell division

•  This often happens because cells are surrounded by a sticky mucilage sheath (capsule)

•  Filaments

Colonies and filaments
Two cyanobacteria illustrating colony and filamentous morphologies
Micrographs by John Tiftickjian

•  Cells remain attached after division.

•  Cells always divide in the same plane.

•  Cells are joined in long strands.

•  Motility

•  Some species swim by means of flagella.

•  Bacterial flagella are composed of a solid protein rod.

•  Eukaryotic flagella have a complex structure of microtubules.

•  Bacterial flagella are analogous to flagella of eukaryotes (not homologous). Although superficially similar, and they give the cell the ability to move, they are very different structurally.

•  Cyanobacteria never have flagella.

•  Some can move by "gliding" (mostly cyanobacteria)


•  Reproduction is only asexual (no gametes).

•  Unicellular species reproduce by cell division.

•  Cell division is typically by binary fission.

•  No mitosis (there is no nucleus)

•  Chromosomes still must replicate and be separated between the daughter cells, but this works by attachment of chromosomes to the plasma membrane, there is no spindle.

•  Colonies and filaments reproduce by fragmentation.

•  Pieces of a colony or filament make break off and continue to grow, creating new individuals.

•  Some species can exchange genes through conjugation.

•  Cells connect to each other by a pilus.

•  DNA transfers from one cell to the other through the pilus.

•  This is different from true sexual reproduction because gametes are not formed (there is no meiosis).

Nutrition and metabolism

•  Bacteria differ in their requirement for oxygen

•  Obligate anaerobes - killed by oxygen

•  Obligate aerobes - must have oxygen

•  Facultative

•  Can use oxygen when it is present, but can also live anaerobically in oxygen-poor environments.

•  Prokaryotes can obtain energy in a variety of ways

•  Some are heterotrophic (require organic food).

•  Saprobes feed on dead organic matter (decomposers)

•  Parasites feed on living organisms (causing diseases)

•  Some are symbiotic with eukaryotic organisms.

•  Some are autotrophic (make their own food).

•  Chemotrophic bacteria

•  These utilize reactions of inorganic compounds to provide energy to make organic food molecules.

•  Photosynthetic bacteria

•  Cyanobacteria do photosynthesis using chlorophyll a (like algae and plants)
•  This produces oxygen as a byproduct (again, like algae and plants)
•  There are other photosynthetic bacteria that lack chlorophyll a and do not produce oxygen.

•  Many can carry out specialize metabolic pathways such as nitrogen fixation.

•  Nitrogen fixation converts N2 gas from the atmosphere into ammonium (NH4+) ions.

•  Ammonium combines with organic compounds to form amino acids.

•  No eukaryotes can use N2 directly from the atmosphere.

•  Cyanobacteria do this in special cells called heterocysts.

Heterocysts in the cyanobacterium Anabaena
Micrograph by John Tiftickjian

•  Symbiotic relationships

•  Many prokaryotes live symbiotically (mutualism) with eukaryotes

•  Rhizobium lives within roots of certain plants (especially legumes).

•  They live in special root nodules
•  They fix nitrogen which the plant benefits from.
•  They in turn obtain food from the plant.
•  Since oxygen inactivates the nitrogen fixing enzyme, the root nodules act as "anaerobic chambers."

•  Some cyanobacteria partner with fungi to form lichens.

Classification of the prokaryotes is based mainly on chemical traits.

•  Domain Archaea

•  Have very unusual metabolic features

•  Cell walls lack a true peptidoglycan component

•  Membranes contain some unusual lipids (diglycerols)

•  Nucleotide sequences of ribosomal RNA different than for other prokaryotes

•  Grow in exotic environments

•  extremely high salinity - halophiles

•  strongly acidic environments - acidophiles

•  high temperatures - thermophiles

•  Domain Bacteria or Eubacteria (true-bacteria)

•  Proteobacteria

•  Actinobacteria

•  Spirochaetes

•  Cyanobacteria

•  Sometimes called blue-green algae

•  Used in this sense, algae is a common name. Cyanobacteria are not closely related to other algae.

•  All true algae are eukaryotic, classified in the Protista.

•  The blue-greens are special in that they are almost the only prokaryotes that contain chlorophyll a.

•  Because chlorophyll a is found in all algae and all higher plants, it's likely that some ancient cyanobacterium was the ancestor of the chloroplast.

•  Remember that the chloroplast probably evolved through endosymbiosis.

•  Many other groups (see textbook for more examples)

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