1. 24
Early Life and the Diversification of Prokaryotes

2. Concept 24.1: Conditions on early Earth made the origin of life possible
Abiotic synthesis of elements into small organic molecules
Joining of these monomers into polymers
Packaging of water with these polymers into protocells, membrane-bound droplets
Origin of self-replicating molecules: RNA first, then DNA
Early Earth probably contained water vapor and chemicals released by volcanic eruptions (nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, and hydrogen)
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3. 1920s, Oparin & Haldane hypothesized that early Earth had a reducing environment
1953, Miller & Urey showed in the lab that the abiotic synthesis of organic molecules in a reducing atmosphere is possible in the lab
Amino acids & RNA nucleotides polymerize when dripped onto hot sand, clay or rock
Then organic compounds can spontaneously assemble into protocells (membrane-bound droplets) that act like cells
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4. Fossil Evidence of Early Life
Many of the oldest bacterial fossils are stromatolites from 3.5 bya
Early prokaryotes: cyanobacteria, a photosynthesizing bacteria
Early cyanobacteria began the release of O2 into Earth’s atmosphere
Surviving prokaryote lineages either avoided or adapted to the newly aerobic environment
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5. Stromatolites
Limestones and related rocks are able to preserve layered structures that record sediment accumulations by microbial communities called stromatolites.
Modern-day stromatolites show microbial communities building the layered structures exhibited by stromatolites in ancient rocks.
Stromatolites: layered structures that record sediment accumulation by microbial communities. Earliest records of life on Earth.

6. Cyanobacteria Found in a range of environments Deserts to open ocean
Spherical, unicellular rods, multicellular balls and filaments
Cyanobacteria can be found in a range of environments, from deserts to open ocean. They include unicellular rods, spherical cells, and multicellular balls and filaments.
Other photosynthetic bacteria (that carry out anoxygenic photosynthesis) can be found in several branches of the whole genome tree, including the purple and green bacteria.

7. Time (billions of years ago)
Figure 24.5
30 m
5 cm
10 m
Stromatolites
Figure 24.5 Appearance in the fossil record of early prokaryote groups
Nonphotosynthetic bacteria
Possible
earliest
appearance
in fossil record
Cyanobacteria 4 3 2 1
Time (billions of years ago)
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8. The First Cells Earth formed 4.6 billion years ago
The oldest fossil organisms are prokaryotes (bacteria) dating back to 3.5 bya ago
Prokaryotes only forms of life for 1 billion years
Prokaryotes are unicellular in the domains Bacteria and Archaea
Some of the earliest prokaryotic cells lived in dense mats; others were free-floating individual cells
Most numerous organisms
They can live in most environments
Including places too acidic, salty, cold, or hot for most other organisms
Some prokaryotes colonize the bodies of other organisms
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9. Tree of Life 26.1 The tree of life has 3 Domains (superkingdoms):
Eukarya
Bacteria
Archae
The tree of life has three domains (superkingdoms): Eukarya, Bacteria, and Archaea.
Bacteria appeared about 3.5 bya (1 by after Earth was formed)
Bacteria were only forms of life for 1 by
Prokaryotes: simple cells that lack a nucleus and lack membrane-bound organelles;
All bacteria; in Domains Bacteria and Archae

10. Bacterial Cell Prokaryotes Asexual/binary fission
1 circular chromosome in nucleoid region
Plasmid: small circular non-necessary DNA
Peptidoglycan cell wall
Penicillins kill this way
Gram stain: distinguishes by cell wall differences
Some bacteria have a capsule: which allows them to stick together
Although a bacterial cell is small, bacteria outnumber eukaryotic cells (on present-day Earth) by several orders of magnitude.
Bacteria are prokaryotes: no membrane-bound nucleus, no energy-producing organelles
asexual (these are defining features of eukaryotic cells). Reproduce asexually by binary fission (which is just bacterial mitosis)
A bacterial cell’s DNA is present as a single circular chromosome, and a bacterial cell can carry additional DNA in the form of plasmids. Since the DNA is not separated from the cytoplasm within a nucleus like in the eukaryotic cell, transcription and translation both occur in the same location, the nucleoid region.
Cellular processes are carried out in the cytoplasm or in the membrane of a bacterial cell by proteins that are free floating or membrane bound.
The bacterial cell is supported by a cell wall made of peptidoglycan, a polymer of sugars and amino acids. This is different than the cell wall of plants (cellulose/fiber) or fungi (chitin). Some antibiotics, like the penicillins, work by preventing the cross-links in peptidoglycan, thus preventing formation of bacterial cell wall, and bacteria dies
Gram stain – stain used to distinguish bacteria by cell wall differences
Gram + - stain blue/purple; have very simple but thick cell walls, lots of peptidoglycan (traps purple dye)
Gram - - stain pink; complex cell walls, but thinner with very little peptidoglycan, More often pathogenic (disease causing)

11. Bacterial capsule Bacterial cell wall Tonsil cell 200 nm Figure 24.8
Figure 24.8 Capsule
200 nm
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12. Figure 24.7
(a) Gram-positive bacteria
(b) Gram-negative bacteria
Carbohydrate portion
of lipopolysaccharide
Peptido-
glycan
layer
Outer
membrane
Cell
wall
Cell
wall
Peptidoglycan
layer
Plasma
membrane
Plasma membrane
Gram-positive
bacteria
Gram-negative
bacteria
Figure 24.7 Gram staining
Gram+: stains blue/purple; very simple but thick peptidoglycan cell walls (picks up stain)
Gram -: stains pink: complex cell walls but thinner; much less peptidoglycan; more often pathogenic (disease causing)
10 mm
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13. 3 Shapes of Bacteria Coccus Bacillus Spirochete 1 mm 1 mm 3 mm
Figure 24.6 The most common shapes of prokaryotes
1 mm
1 mm
3 mm
(a) Spherical
(b) Rod-shaped
(c) Spiral
Coccus
Bacillus
Spirochete
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14. Endospores, and Pili
Some bacteria develop resistant cells called endospores when they lack water or essential nutrients
Some prokaryotes stick to the substrate or each other using hairlike appendages called fimbriae
Pili (or sex pili) are longer than fimbriae and allow prokaryotes to exchange DNA
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15. Motility
In a heterogeneous environment, many bacteria exhibit taxis, the ability to move toward or away from a stimulus
For example, some prokaryotes exhibit chemotaxis, movement toward or away from a chemical stimulus
Many prokaryotes have flagella to facilitate movement
Flagella of bacteria, archaea, and eukaryotes are composed of different proteins and likely evolved independently
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16. Flagellum 20 nm Filament Hook Cell wall Motor Plasma Peptidoglycan
Figure 24.10
Flagellum
20 nm
Filament
Hook
Cell wall
Motor
Figure A prokaryotic flagellum
Plasma
membrane
Peptidoglycan
layer
Rod
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17. Acquiring Energy and Carbon
Sunlight: phototrophs
Chemical compounds: chemotrophs
Carbon
Inorganic molecules, CO2: autotrophs
Organic molecules, glucose: heterotrophs
Photoautotrophs (plants, algae, cyanobacteria; photosynthesis; give off O2; rare in bacteria
Chemoheterotrophs (animals, fungi, many prokaryotes). Most bacteria.
2 subgroups
Saprobes: decomposers that absorb nutrients from dead organic matter
Parasites: absorb nutrients from body fluids of living hosts
Photoheterotrophs (rare microorganisms)
Chemoautotrophs (rare microorganisms)
Organisms have two sources of energy—the sun and chemical compounds; as well as two sources of carbon—CO2 (inorganic molecules) and glucose (organic molecules).
We have considered both photoautotrophs who gain energy from the sun and carbon from CO2 and chemoheterotrophs who gain both carbon and energy from organic molecules in the environment.
Most bacteria are chemoheterotrophs; 2 subgroups
Saprobes- decomposers that absorb nutrients from dead organic matter
parasites – absorb nutrients from body fluids of living hosts
Some microorganisms, known as photoheterotrophs, are capable of using energy from the sun and organic molecules from the environment.
Some microorganisms, known as chemoautotrophs, are capable of using chemical reactions to generate ATP and use inorganic molecules as their carbon source.

18. The Role of Oxygen in Metabolism
Prokaryotic metabolism varies with respect to O2
Obligate aerobes :
Require O2 for cellular respiration
Obligate anaerobes:
Poisoned by O2 and use fermentation or anaerobic respiration, in which substances other than O2 act as electron acceptors
Facultative anaerobes:
Use O2 if it is available, but can survive without it
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19. Concept 24.3: Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes
Prokaryotes have considerable genetic variation
3 factors contribute to this genetic diversity
Rapid reproduction
Mutation
Genetic recombination
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20. Horizontal Gene Transfer
Bacterial genome: small, chromosome 100% DNA, lack introns
Obtain new genes: horizontal gene transfer
most worrisome problem: rapid spread of antibiotic resistance
3 Types of Horizonal Gene Transfer:
Conjugation
Transformation
Transduction (by viruses)
Bacterial genomes are small, chromosome made entirely of DNA (no histone proteins), and lack the noncoding DNA (lack introns)characteristic of eukaryotic chromosomes. Their small size allows them to reproduce rapidly when their local environment is ideal for growth.
Despite their small size, however, their genomes are diverse. This variation is possible because, while most of their genes come from the parent cell, they are also able to obtain new genes by horizontal gene transfer.
Horizontal gene transfer allows bacterial cells to gain beneficial genes from organisms distributed throughout the bacterial domain and beyond.
Bacteria have highly efficient mechanisms for adding and subtracting genes that permit them to evolve and adapt rapidly to local conditions. Perhaps the most widely discussed and worrisome manifestation of horizontal gene transfer is the rapid spread of antibiotic resistance among bacteria (Chapter 48).

21. Conjugation
Some bacteria are able to share genetic information through a process called conjugation.
Here, the bacterial cell synthesizes a thin strand of membrane-bound cytoplasm (sex pili) that connects to other cells. This process can transfer plasmids from one cell to another, allowing a cell to share such genes as antibiotic resistance. Also called “gene swapping” . R plasmids, carry genes that code for resistance to antibiotics. Took only 2 years to develop peicillin resistance.
Also called “gene swapping”; transfers plasmids from one cell to another through sex pili
Allows the sharing of genes such as antibiotic resistance (R plasmid)

22. Transformation Gene transfer with no bridge between them
Genes can also be transferred from one cell to another without any direct bridge between them. If DNA is released into the environment by cell breakdown, it can be taken up by other cells.
Gene transfer with no bridge between them
Dead donor cell releases DNA into environment and taken up by recipient

23. Transduction
A third type of horizontal gene transfer can be found in viruses (called bacteriophages). Here, viruses that have infected bacterial cells can integrate their DNA into the host bacterial cell and persist within the cells as they grow and divide. Before leaving the bacterial host, the viral DNA removes itself, sometimes taking additional host DNA with it, which is then incorporated into the viral DNA.
Virus (called bacteriophages) transfers DNA from a donor to a recipient cell; takes donor/host DNA and incorporates it into viral DNA

24. Diversity of Prokaryotes
Figure 24.18
Diversity of Prokaryotes
Eukarya
Domain
Eukaryotes
Korarchaeotes
Domain Archaea
Euryarchaeotes
Crenarchaeotes
UNIVERSAL
ANCESTOR
Nanoarchaeotes
Proteobacteria
Domain Bacteria
Chlamydias
Figure A simplified phylogeny of prokaryotes
Spirochetes
Cyanobacteria
Gram-positive
bacteria
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25. Domain Bacteria Chlamydias Spirochetes Cyanobacteria
Figure
Domain Bacteria
Chlamydias
Spirochetes
Cyanobacteria
2.5 mm
40 mm
5 mm
Chlamydia (arrows)
(TEM)
Leptospira
(TEM)
Oscillatoria
Gram-positive bacteria
Figure Exploring selected major groups of bacteria (part 2)
5 mm
2 mm
Streptomyces
(SEM)
Mycoplasmas
(SEM)
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26. Domain Bacteria: Proteobacteria
Proteobacteria is a clade of gram-negative bacteria with diverse metabolic and nutritional modes
It has been divided into 5 subgroups (alpha, beta, gamma, delta, and epsilon proteobacteria) based on molecular relationships
i.e. Helicobacter pylori causes stomach ulcers
Salmonella causes food poisoning, and Vibrio cholerae causes cholera
Escherichia coli is a common heterotrophic bacteria that is not normally pathogenic
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27. Domain Bacteria: Chlamydias
Chlamydias are disease-causing parasites that can only live within animal host cells
E.g. Chlamydia trachomatis causes blindness and the sexually transmitted disease, nongonococcal urethritis
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28. Domain Bacteria: Spirochetes
Spirochetes are helical gram-negative heterotrophs
Many species are free-living, but some are parasitic
E.g. Treponema pallidum causes syphilis
Borrelia burgdorferi causes Lyme disease
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29. Domain Bacteria: Cyanobacteria
Cyanobacteria are gram-negative photoautotrophs that generate O2 through plantlike photosynthesis
Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis
Cyanobacteria are common members of the phytoplankton in marine and freshwater communities
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30. Domain Bacteria: Gram-Positive Bacteria
Gram-positive bacteria include
Actinomycetes, many of which are soil decomposers
Streptomyces, which are a source of antibiotics
Bacillus anthracis, the cause of anthrax
Clostridium botulinum, the cause of botulism
Staphylococcus and Streptococcus, which can be pathogenic
Mycoplasmas, which are the smallest known cells and the only bacteria lacking a cell wall
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31. Table 24.2-1 A comparison of the three domains of life (part 1)
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32. Table 24.2-2 A comparison of the three domains of life (part 2)
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33. Domain Archae Unusual physiological properties
Transcription similar to Eukarya
Translation differences
Inhabit harsh environments/extremophiles
Very hot
Very salty
Low pH
Recently found in soil, lakes, oceans
Many Archaea have unusual physiological properties and inhabit extreme environments.
They have been found in acidic water at pH 1 or less, in salty water that precipitates NaCl, and in deep-sea hydrothermal vents where temperatures exceed 100°C. Think they evolved from earliest cells.
They also live in less extreme environments such as soil, lakes, and oceans.

34. Concept 24.5: Prokaryotes play crucial roles in the biosphere
Prokaryotes play a major role in the recycling of chemical elements between the living and nonliving components of ecosystems
For example, some chemoheterotrophic prokaryotes are decomposers, organisms that break down dead organic materials and release mineral nutrients
Some prokaryotes can convert molecules into forms that can be taken up by other organisms
For example, some species can fix atmospheric nitrogen (N2) into forms available to plants
Prokaryotes can also “immobilize” or decrease the availability of plant nutrients
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35. Example of Nitrogen Fixation
Soybean roots have nodules that harbor nitrogen-fixing bacteria.
Mutually beneficial relationship between soybeans and nitrogen-fixing bacteria
One example of nitrogen fixation common to those in farming areas is the rotation of crops, corn and beans, in order to return nitrogen to the soil. However, it is not the soybeans that are fixing the nitrogen; instead, the soybean roots have nodules that harbor nitrogen-fixing bacteria.
Soybeans and the nitrogen-fixing bacteria have acquired a partnership to obtain biologically useful forms of nitrogen.

36. Ecological Interactions
Symbiosis is an ecological relationship in which two species live in close contact: a larger host and smaller symbiont
Prokaryotes often form symbiotic relationships with larger organisms
These symbiotic relationships increase the fitness of one or both organisms
In mutualism, both organisms benefit
In commensalism, one organism benefits while neither harming nor helping the other in any significant way
In parasitism, an organism called a parasite harms but does not kill its host
Parasites that cause disease are called pathogens
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37. Prokaryotes cause about 50% of all human diseases
Figure 24.24
Prokaryotes cause about 50% of all human diseases
For example, Lyme disease is caused by a bacterium carried by ticks
5 mm
Figure Lyme disease
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38. Human Microbiome There are more than 750 bacterial species
in our bodies
Mouths
Colon
Skin
Urogenital tracts
Airways
Numbers of the microbial species that inhabit our bodies vary (750+ have been identified in our mouths and colon, and more on our skin), and the list remains incomplete.
Here, you can see a rough guide to the distribution of the species of bacteria found on or within a healthy human adult that had been sequenced in 2010.

39. Human intestines are home to about 500–1,000 species of bacteria
Humans & Bacteria
Human intestines are home to about 500–1,000 species of bacteria
Many of these are mutualists and break down food that is undigested by our intestines
Pathogenic prokaryotes typically cause disease by releasing exotoxins or endotoxins
Exotoxins are secreted and cause disease even if the prokaryotes that produce them are not present
Endotoxins are released only when bacteria die and their cell walls break down
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40. Figure 24.25
Experimental treatment of human cells with the prokaryotic CRISPR-Cas9 system has shown promising results for the treatment of HIV
Figure CRISPR: opening new avenues of research on treating HIV infection
(a) Control cells
(b) Experimental cells
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41. Some bacteria can be used to make natural, biodegradable plastics
Others have been engineered to produce ethanol from plant sources and agricultural and municipal wastes
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42. Prokaryotes are also used in bioremediation, the use of organisms to remove pollutants from the environment
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