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Bacteria and Archaea: The Prokaryotic Domains. TER 26. Nitrogen cycle. Mycobacterium tuberculosis Color-enhanced images shows rod-shaped bacterium responsible for tuberculosis (Raven et al 2002). Endosymbiotic Theory. Structure of a Eukaryotic Animal Cell .

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Bacteria and Archaea:

The Prokaryotic Domains

TER 26

Nitrogen cycle

Mycobacterium tuberculosis Color-enhanced images shows rod-shaped bacterium responsible for tuberculosis (Raven et al 2002)

Endosymbiotic Theory


Structure of a Eukaryotic Animal Cell

Structure of a Prokaryotic Cell

  • Prokaryotic cells have a simple interior organization compared to Eukaryotes.
  • Membrane-enclosed nucleus lacking
  • Membrane-enclosed cytoplasmic organelles lacking
  • Cytoskeleton lacking-support from rigid cell wall

Structure of a Eukaryotic Plant Cell


Lecture Themes

  • origins, evolution and diversity
  • structure and function
  • ecological function and relationships

Genome of the Archaeon Methanococcus jannaschii was sequenced in 1996. Sequencing of M. jannashcii confirmed Carl Woese’s long-standing hypothesis that life traces back to three main lineages, one of which (Archaea) includes prokaryotes that share a more recent common ancestry with eukaryotes than with the prokaryotic “true bacteria”


(Keaton 1993)

Cyanobacteria 10 um dia.

E. coli 1X2 um

Mycoplasma 0.3-0.8 um dia.

Bacteriophage 0.07X 0.2 um

Viroid 0.01 X 0.3 um

Lymphocycte 10 um dia.

Largest known prokaryote is the marine bacterium Thiomargarita namibiensis; bright white cell in upper left, about .75 mm dia., attached to two dead ones. Fruitfly in picture for size comparison.

Paramecium 30X 75 um

Sizes of viruses, bacteria and eukaryotes compared Most bacteria are 1-5 um diameter (most Eukaryotic cells are 10-100 um)

Bacillus on the head of a pin


Raven et al 2002

Spherical coccus(Enterococcus)

Pseudomonas aeruginosa


Spirillum volutans

Rod-shaped bacillus(E. coli)

Bacterial FormThree shapes are especially common among bacteria – spheres, rods and spiralsMost are unicellular, some aggregate transiently, some form permanent aggregations of identical cells;some show division of labor between two or more specialized cell times

Helical spirilla(|Aquaspirillum spirosa)


Scanning electron micrograph of a colony of streptomyces, one of the actinomycetes. The actinomycetes have a much more complicated morphology than most other bacteria. (Keaton and Gould 1993)


Most bacterial cell walls contain peptidoglycan (lacking in Archaea)

  • Gram staining is an important technique for identifying bacterial; cells stain differentially based on structure and composition of walls
  • Pathogenesis is related to cell wall structure and composition
  • Many antibiotics act by preventing formation of cell walls, by inhibiting synthesis of cross-links in peptidoglycan
  • Many prokaryotes produce capsules that function in adherance and protection
  • Many prokaryotes have surface appendages called pili that are function in adherance

Penicillium chrysogenum

Neisseria gonorrhoeae

E. coli

The exterior surfaces of Prokaryotes. Almost all prokaryotes have a cell wall, and in most that wall contains peptidoglycan – polymers of modified sugars that are cross-linked by short polypeptides


Aquaspirillum sinosum

  • Mechanisms of Motility Many bacteria are motile. Fllagellar action is the most common,but not the only mechanism, for generating movement.
  • Prokaryotic flagella
  • Flagella-like helical filaments
  • Growing gelatinous threads
  • Motility Behavior
  • Kinesis
  • Taxis

Spirillum volutans

Borrelia burgdorferi

Lyme disease symptoms, and the disease vector – a tick


0.05 um

1 um

Electron micrograph of E. coli shoing long helical flagella.


Vibrio cholerae (pathogen responsbible for cholera); the unsheathed core visible at top of photo is composed of a single crystal of the protein flagellin.

In intact flagella, core is surrounded by a flexible sheath. Rotary motion of the motor creates a kind of rotary motion when organism swims.

Bacteria swim by rotating their flagella.



  • various specialized membranes, but lacking extensive compartmentalization by internal membranes
  • ribosomes present but differ from eukaryotic ones in size and composition
  • genomes are smaller and simpler than in eukaryotes; one major chromosome and, in some species, plasmids
  • Processes of DNA replicatin and protein translation are generally similar to eukaryotes

plasma membrane


Exensive folded photosynthetic membranes are visisble in Prochloron cell. The single, circular DNA molecule is located in the clear area in the central region of the cell.

The mesosome is an infolding of the plasma membrane serves as a point of attachment for DNA in some bacterial cells

Infoldings of plasma membrane, similar in ways to cristae of mitochondria, function in cellular respiration in aerobic bacteria

Thylakoid membranes of photosynthetic cyanobacteria

Cellular and Genomic Organization The organization of cellular components, including the genome, differs substantially between prokaryotes and eukaryotes


Cell divisionAsexual reproduction by cell division via binary fission

Mechanisms of gene transfer-transformation; genes from environment-conjugation; genes from another prokaryote-transduction genes via a virus

Adaptationshort generation time allows favorable mutations and novel genomes arising from gene transfer to spread quickly in rapidly reprducing

Growth virtual geometric growth while in environments with unlimited resources

Prokaryote Reproduction and Population Growth Prokaryote populations grow and adapt rapidly, through asexual reproduction as well as mechanisms involving gene transfer


Dormancy and Endosporulation Some bacteria form highly resistant spores under harsh environmental conditions

Antibiotic synthesisSome prokaryotes (and protists and fungi) synthesize and release antibiotic chemicals that inhibit growth of other microbes

Sporulating Bacillus cell

Bacillus anthracus

Adaptations to Harsh Environmental Conditions: Some bacteria are capable of dormancy, endosporulation and antibiotic synthesis


Sources: Campbell et al (2002), Freeman (2002), Purves et al (2001)

  • Nutrition; how an organism obtains two resources from the environment;
  • -energy
  • -carbon source to build the organic molecules of cells
  • Phototrophs; use light energy
  • Chemotrophs; obtain energy from chemicals taken from the environment
  • Autotroph; needs only the inorganic compound CO2 as a carbon source
  • Hetertroph: requires at least one organic nutrient for making other organic compounds

Sources: Freeman 2002, Campbell 2002

  • The basic themes of metabolism, among all domains are
  • -extracting usable energy from reduced compounds -using light to produce high-energy electrons-fixing carbon.
  • All organisms have mechanisms for trapping usable energy in ATP; ATP allows cells to do work; there is no life without ATP
  • At one point or another, you have studied these metabolic themes as they occur Eukaryotes and perhaps Prokaryotes; photosynthesis(eg,in green plants and respiration (eg in all Eukaryotes)
  • Prokaryotes show tremendous diversity in metabolic that they have evolved dozens of variations on these most basic themes of metabolism
  • This Prokarotic metabolic diversity is important for two reasons:
  • It explains their ecological diversity; they are found almost everywhere because they exploit such a tremendous variety of molecules as food
  • Global nutrient cycling of (eg nitrogen, phosphorous, sulfur, carbon) is mediated by, exists because, prokaryotes can use them in almost any molecular form

Overview of photosynthesis and respiration


Sources: Freeman 2002, Campbell 2002

Overview of cellular respiration One (very important!!) example of metabolic pathways by which many species obtain energy for generating ATP by oxidizing reduced organic compounds

Highly reduced molecule, glucose, serves as original electron donor (ie, molecule is oxidized) and highly oxidized molecule, oxygen, serves as final electron acceptor

Overview of Photosynthesis

Many prokaryotes generate ATP by employing electron donors and acceptors other than sugars and oxygen, and produce by-products other than water


Source: Freeman (2002), Purves et al (2001)

Some Electron Donors and Acceptors Used by Bacteria and Archaea

Electron Donor Electron Acceptor Product Metabolic Strategy *

H2 or organic compounds SO42- H2S sulfate-reducers

H2 CO2 CH4 methanogens

CH4 O2 CO2 methanotrophs

S or H2S O2 SO42- sulfur bacteria

organic compounds Fe3+ Fe2+ iron-reducers

NH3 O2 NO2- nitrifiers

organic compounds NO3- N2O, NO or N2 denitrifiers (or nitrate reducers)

NO2- O2 NO3- nitrosifiers

* This column gives the name biologists use to identify species that use a particular metabolic strategy

nitrification: oxidation of ammonia to nitrite and nitrate ions

denitrification: reduction of nitrogen-containing ions to form nitrogen gas and other products


Source: Freeman (2002)

  • lateral gene transfer has taken place repeatedly through transformation and viral infection
  • in transfers among bactera and archaea the primary mechanism probably involves loops of mobile DNA (plasmids)
  • swapped genes tend to be those involved in energy and carbon metabolism (not information processing , eg DNA replication, transcription, protein synthesis) – interesting…as metabolic diversity is a hallmark of the Bacteria and Archaea!!

Lateral Gene Transfer. Gray branches show diversification of the three domains. Red branches show movement of genes from species in one part of the tree to species in other parts


Nutritional Diversity among Chemoheterotrophs (most known Prokaryotes)

  • Saprobes; decomposers that absorb nutrients from dead organic matter
  • Parasites; absorb nutrients from body fluids of living hosts
  • Relevance of Oxygen to Metabolism among Bacteria and Archaea
  • Obligate aerobes
  • Facultative anaerobes
  • Obligate anaerobes
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains

Why Three Domains?

General Biology of the Prokaryotes

Prokaryotes in Their Environments

chapter 26 bacteria and archaea the prokaryotic domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains

Prokaryote Phylogeny and Diversity

The Bacteria

The Archaea

why three domains
Why Three Domains?
  • Living organisms can be divided into three domains: Bacteria, Archaea, and Eukarya. The prokaryotic Archaea and Bacteria differ from each other more radically than the Archaea from the Eukarya.
why three domains43
Why Three Domains?
  • Evolutionary relationships of the domains were revealed by rRNA sequences. Their common ancestor lived more than 3 billion years ago, that of the Archaea and Eukarya at least 2 billion years ago. Review Figure 26.2 and Table 26.1
general biology of the prokaryotes
General Biology of the Prokaryotes
  • The prokaryotes are the most numerous organisms on Earth,occupying an enormous variety of habitats.
general biology of the prokaryotes47
General Biology of the Prokaryotes
  • Most prokaryotes are cocci, bacilli, or spiral forms. Some link together to form associations, but very few are truly multicellular.
general biology of the prokaryotes48
General Biology of the Prokaryotes
  • Prokaryotes lack nuclei, membrane-enclosed organelles, and cytoskeletons. Their chromosomes are circular. They often contain plasmids. Some contain internal membrane systems.
general biology of the prokaryotes49
General Biology of the Prokaryotes
  • Many prokaryotes move by means of flagella, gas vesicles, or gliding mechanisms. Prokaryotic flagella rotate.
general biology of the prokaryotes50
General Biology of the Prokaryotes
  • Prokaryotic cell walls differ from those of eukaryotes. Bacterial cell walls generally contain peptidoglycan. Differences in peptidoglycan content result in different reactions to the Gram stain. Review Figure 26.7
general biology of the prokaryotes52
General Biology of the Prokaryotes
  • Prokaryotes reproduce asexually by fission, but also exchange genetic information.
general biology of the prokaryotes53
General Biology of the Prokaryotes
  • Prokaryotes’ metabolic pathways and nutritional modes include obligate and facultative anaerobes, and obligate aerobes. Nutritional types include photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs. Some base energy metabolism on nitrogen- or sulfur-containing ions. Review Figure 26.8 and Table 26.2
Prokaryotes in Their Environments

Some prokaryotes play key roles in global nitrogen and sulfur cycles. Nitrogen fixers, nitrifiers, and denitrifiers do so in the nitrogen cycle. Review Figure 26.10

prokaryotes in their environments
Prokaryotes in Their Environments
  • Photosynthesis by cyanobacteria generated the oxygen gas that permitted the evolution of aerobic respiration and the appearance of present-day eukaryotes.
prokaryotes in their environments60
Prokaryotes in Their Environments
  • Many prokaryotes live in or on other organisms, with neutral, beneficial, or harmful effects.
prokaryotes in their environments61
Prokaryotes in Their Environments
  • A minority of bacteria are pathogens. Some produce endotoxins, which are rarely fatal; others produce often highly toxic exotoxins.
prokaryote phylogeny and diversity
Prokaryote Phylogeny and Diversity
  • Phylogenetic classification of prokaryotes is based on rRNA sequences and other molecular evidence.
prokaryote phylogeny and diversity63
Prokaryote Phylogeny and Diversity
  • Lateral gene transfer among prokaryotes makes it difficult to infer prokaryote phylogeny.
prokaryote phylogeny and diversity64
Prokaryote Phylogeny and Diversity
  • Evolution can proceed rapidly in prokaryotes because they are haploid and can multiply rapidly.
the bacteria
The Bacteria
  • There are far more known bacteria than archaea. One phylogenetic classification of the domain Bacteria groups them into over a dozen groups.
the bacteria66
The Bacteria
  • The most ancient bacteria, like the most ancient archaea, may be thermophiles, suggesting that life originated in a hot environment.
the bacteria67
The Bacteria
  • All four nutritional types occur in the Proteobacteria. Metabolism in different proteobacteria groups has evolved along different lines. Review Figure 26.12
the bacteria69
The Bacteria
  • Cyanobacteria, unlike other bacteria, photosynthesize using the same pathways plants use. Many fix nitrogen.
the bacteria70
The Bacteria
  • Spirochetes move by means of axial filaments.
the bacteria71
The Bacteria
  • Chlamydias are tiny parasites that live within the cells of other organisms.
the bacteria72
The Bacteria
  • Firmicutes are diverse; some produce endospores, resting structures resistant to harsh conditions. Some actinomycetes produce important antibiotics. Actinomycetes grow as branching filaments.
the bacteria73
The Bacteria
  • Mycoplasmas, the tiniest living things, lack conventional cell walls and have very small genomes.
the archaea
The Archaea
  • Archaea cell walls lack peptidoglycan, and their membrane lipids contain branched long-chain hydrocarbons connected to glycerol by ether linkages. Review Figure 26.22
the archaea76
The Archaea
  • The domain Archaea can be divided into two kingdoms: Crenarchaeota and Euryarchaeota.
the archaea77
The Archaea
  • Crenarchaeota are heat-loving and often acid-loving archaea.
the archaea78
The Archaea
  • Methanogens produce methane by reducing carbon dioxide. Some live in the guts of herbivorous animals; some in high-temperature environments on the ocean floor.
the archaea79
The Archaea
  • Extreme halophiles are salt lovers that lend a pinkish color to salty environments; some grow in extremely alkaline environments.
the archaea80
The Archaea
  • Archaea of the genus Thermoplasma lack cell walls, are thermophilic and acidophilic, and have a tiny genome (1,100,000 base pairs).