BIF 24: Early Life & the Diversification of Prokaryotes.
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Transcript of BIF 24: Early Life & the Diversification of Prokaryotes.
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BIF 24: Early Life & the Diversification of Prokaryotes
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CONDITIONS ON EARLY EARTH MADE THE ORIGIN OF LIFE POSSIBLE
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Chemical and physical processes on early Earth may have produced very simple cells through a sequence of stages:
1. Abiotic synthesis of small organic molecules2. Joining of these small molecules into
macromolecules3. Packaging of molecules into protocells4. Origin of self-replicating molecules
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Synthesis of Organic Compounds on Early Earth
• Earth formed about 4.6 billion years ago, along with the rest of the solar system
• Bombardment of Earth by rocks and ice likely vaporized water and prevented seas from forming before 4.2 to 3.9 billion years ago
• Earth’s early atmosphere likely contained water vapor and chemicals released by volcanic eruptions (nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, hydrogen, hydrogen sulfide)
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Experiments into the Origin of Life
• In the 1920s, A. I. Oparin and J. B. S. Haldane hypothesized that the early atmosphere was a reducing environment
• In 1953, Stanley Miller and Harold Urey conducted lab experiments that showed that the abiotic synthesis of organic molecules in a reducing atmosphere is possible
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• However, the evidence is not yet convincing that the early atmosphere was in fact reducing
• Instead of forming in the atmosphere, the first organic compounds may have been synthesized near volcanoes or deep-sea vents
• Miller-Urey–type experiments demonstrate that organic molecules could have formed with various possible atmospheres
• Amino acids have also been found in meteorites
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Video: Tubeworms
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Video: Hydrothermal Vent
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Figure 25.2
Mas
s of
am
ino
acid
s (m
g)
Num
ber o
f am
ino
acid
s
20
10
01953 2008
200
100
01953 2008
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Abiotic Synthesis of Macromolecules
• RNA monomers have been produced spontaneously from simple molecules
• Small organic molecules polymerize when they are concentrated on hot sand, clay, or rock
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Protocells
• Replication and metabolism are key properties of life and may have appeared together
• Protocells may have been fluid-filled vesicles with a membrane-like structure
• In water, lipids and other organic molecules can spontaneously form vesicles with a lipid bilayer– Adding clay can increase the rate of vesicle formation– Vesicles exhibit simple reproduction and metabolism and
maintain an internal chemical environment
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Figure 25.3
(a) Self-assembly
Time (minutes)
Precursor molecules plusmontmorillonite clay
Precursor molecules onlyRe
lativ
e tu
rbid
ity,
an in
dex
of v
esic
le n
umbe
r
0
20 m
(b) Reproduction (c) Absorption of RNA
Vesicle boundary
1 m
0
0.2
0.4
4020 60
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Self-Replicating RNA and the Dawn of Natural Selection
• The first genetic material was probably RNA, not DNA• RNA molecules called ribozymes have been found to
catalyze many different reactions– For example, ribozymes can make complementary
copies of short stretches of RNA
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Natural selection has produced self-replicating RNA molecules• RNA molecules that were more stable or replicated
more quickly would have left the most descendent RNA molecules
• The early genetic material might have formed an “RNA world”
• Vesicles with RNA capable of replication would have been protocells
• RNA could have provided the template for DNA, a more stable genetic material
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STRUCTURAL AND FUNCTIONAL ADAPTATIONS CONTRIBUTE TO PROKARYOTIC SUCCESS
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Earth’s first organisms were likely prokaryotes
• Most prokaryotes are unicellular, although some species form colonies
• Most prokaryotic cells are 0.5–5 µm, much smaller than the 10–100 µm of many eukaryotic cells
• Prokaryotic cells have a variety of shapes• The three most common shapes are spheres (cocci),
rods (bacilli), and spirals
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Figure 27.2
(a) Spherical (b) Rod-shaped (c) Spiral
1 m
1 m
3 m
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Cell-Surface Structures
• An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment
• Eukaryote cell walls are made of cellulose or chitin• Bacterial cell walls contain peptidoglycan, a network
of sugar polymers cross-linked by polypeptides• Archaea contain polysaccharides and proteins but
lack peptidoglycan
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Scientists use the Gram stain to classify bacteria by cell wall composition
• Scientists use the Gram stain to classify bacteria by cell wall composition
• Gram-positive bacteria have simpler walls with a large amount of peptidoglycan
• Gram-negative bacteria have less peptidoglycan and an outer membrane that can be toxic
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Figure 27.3a
(a) Gram-positive bacteria: peptidoglycan traps crystal violet.
Peptido-glycanlayer
Cellwall
Plasmamembrane
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Figure 27.3b
OutermembranePeptido-glycanlayer
Plasma membrane
Cellwall
Carbohydrate portionof lipopolysaccharide
(b) Gram-negative bacteria: crystal violet is easily rinsed away, revealing red dye.
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Figure 27.3c
Gram-positivebacteria
10 m
Gram-negativebacteria
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Many antibiotics target peptidoglycan and damage bacterial cell walls• Gram-negative bacteria are more likely to be
antibiotic resistant• A polysaccharide or protein layer called a capsule
covers many prokaryotes
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Figure 27.4
Bacterialcell wall
Bacterialcapsule
Tonsilcell
200 nm
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• Some prokaryotes have fimbriae, which allow them to stick to their substrate or other individuals in a colony
• Pili (or sex pili) are longer than fimbriae and allow prokaryotes to exchange DNA
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Figure 27.5
Fimbriae
1 m
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Motility
• In a heterogeneous environment, many bacteria exhibit taxis, the ability to move toward or away from a stimulus
• Chemotaxis is the movement toward or away from a chemical stimulus
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Video: Oscillatoria
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• Most motile bacteria propel themselves by flagella scattered about the surface or concentrated at one or both ends
• Flagella of bacteria, archaea, and eukaryotes are composed of different proteins and likely evolved independently
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Video: Prokaryotic Flagella (Salmonella typhimurium)
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Flagellum
HookMotor
Filament
RodPeptidoglycanlayer
Plasmamembrane
Cell wall
20 nm
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Evolutionary Origins of Bacterial Flagella
• Bacterial flagella are composed of a motor, hook, and filament
• Many of the flagella’s proteins are modified versions of proteins that perform other tasks in bacteria
• Flagella likely evolved as existing proteins were added to an ancestral secretory system
• This is an example of exaptation, where existing structures take on new functions through descent with modification
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Internal Organization and DNA
• Prokaryotic cells usually lack complex compartmentalization
• Some prokaryotes do have specialized membranes that perform metabolic functions
• These are usually infoldings of the plasma membrane
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Figure 27.7
(a) Aerobic prokaryote (b) Photosynthetic prokaryote
Respiratorymembrane
Thylakoidmembranes
0.2 m 1 m
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The prokaryotic genome has less DNA than the eukaryotic genome• Most of the genome consists of a circular
chromosome• The chromosome is not surrounded by a membrane;
it is located in the nucleoid region • Some species of bacteria also have smaller rings of
DNA called plasmids
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Figure 27.8
Chromosome Plasmids
1 m
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• There are some differences between prokaryotes and eukaryotes in DNA replication, transcription, and translation
• These allow people to use some antibiotics to inhibit bacterial growth without harming themselves
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Reproduction and Adaptation
• Prokaryotes reproduce quickly by binary fission and can divide every 1–3 hours
• Key features of prokaryotic reproduction:– They are small– They reproduce by binary fission– They have short generation times
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• Many prokaryotes form metabolically inactive endospores, which can remain viable in harsh conditions for centuries
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Figure 27.9
Coat
Endospore
0.3 m
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• Their short generation time allows prokaryotes to evolve quickly
– For example, adaptive evolution in a bacterial colony was documented in a lab over 8 years
• Prokaryotes are not “primitive” but are highly evolved
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Figure 27.10
Daily serial transfer
0.1 mL(population sample)
Old tube(discardedaftertransfer)
New tube(9.9 mLgrowthmedium)
EXPERIMENT
RESULTS
1.8
Po
pu
lati
on
gro
wth
rat
e(r
elat
ive
to a
nce
stra
l p
op
ula
tio
n)
1.6
1.4
1.2
1.0
0 5,000 10,000 15,000Generation
20,000
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DIVERSE NUTRITIONAL AND METABOLIC ADAPTATIONS HAVE EVOLVED IN PROKARYOTES
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Prokaryotes can be categorized by how they obtain energy and carbon
• Phototrophs obtain energy from light• Chemotrophs obtain energy from chemicals• Autotrophs require CO2 as a carbon source• Heterotrophs require an organic nutrient to
make organic compounds
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Energy and carbon sources are combined to give four major modes of nutrition:
– Photoautotrophy– Chemoautotrophy– Photoheterotrophy– Chemoheterotrophy
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Table 27.1
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The Role of Oxygen in Metabolism
• Prokaryotic metabolism varies with respect to O2
– Obligate aerobes require O2 for cellular respiration
– Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration
– Facultative anaerobes can survive with or without O2
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Nitrogen Metabolism
• Nitrogen is essential for the production of amino acids and nucleic acids
• Prokaryotes can metabolize nitrogen in a variety of ways
• In nitrogen fixation, some prokaryotes convert atmospheric nitrogen (N2) to ammonia (NH3)
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Metabolic Cooperation
• Cooperation between prokaryotes allows them to use environmental resources they could not use as individual cells
• In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells called heterocysts (or heterocytes) exchange metabolic products
• In some prokaryotic species, metabolic cooperation occurs in surface-coating colonies called biofilms
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Figure 27.14
Photosyntheticcells
Heterocyst
20 m
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RAPID REPRODUCTION, MUTATION, AND GENETIC RECOMBINATION PROMOTE GENETIC DIVERSITY IN PROKARYOTES
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• Three factors contribute to this genetic diversity:– Rapid reproduction– Mutation– Genetic recombination
Prokaryotes have considerable genetic variation
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Rapid Reproduction and Mutation
• Prokaryotes reproduce by binary fission, and offspring cells are generally identical
• Mutation rates during binary fission are low, but because of rapid reproduction, mutations can accumulate rapidly in a population
• High diversity from mutations allows for rapid evolution
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Genetic Recombination
• Genetic recombination, the combining of DNA from two sources, contributes to diversity
• Prokaryotic DNA from different individuals can be brought together by transformation, transduction, and conjugation
• Movement of genes among individuals from different species is called horizontal gene transfer
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Transformation and Transduction
• A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation
• Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria)
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Figure 27.11-1
Donor cell
A B
BA
Phage
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Figure 27.11-2
A
Donor cell
A B
BA
Phage
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Figure 27.11-3
Recipientcell
Recombination
A
A
A B
Donor cell
A B
BA
Phage
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Figure 27.11-4
Recombinant cell
Recipientcell
Recombination
A
A
A B
BA
Donor cell
A B
BA
Phage
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Conjugation and Plasmids
• Conjugation is the process where genetic material is transferred between prokaryotic cells
• In bacteria, the DNA transfer is one way• A donor cell attaches to a recipient by a pilus, pulls it
closer, and transfers DNA• A piece of DNA called the F factor is required for the
production of pili
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Figure 27.12
Sex pilus
1 m
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The F Factor as a Plasmid
• Cells containing the F plasmid function as DNA donors during conjugation
• Cells without the F factor function as DNA recipients during conjugation
• The F factor is transferable during conjugation
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Figure 27.13
F plasmid Bacterial chromosome
F cell(donor)
F cell(recipient)
Matingbridge
Bacterialchromosome
(a) Conjugation and transfer of an F plasmid
Hfr cell(donor)
F cell(recipient)
(b) Conjugation and transfer of part of an Hfr bacterial chromosome
F factor
A
A
A
A
A
A A
F cell
F cell
AA
RecombinantF bacterium
A
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Figure 27.13a-1
F plasmidBacterialchromosome
F cell(donor)
F cell(recipient)
Matingbridge
Bacterialchromosome
(a) Conjugation and transfer of an F plasmid
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Figure 27.13a-2
F plasmidBacterialchromosome
F cell(donor)
F cell(recipient)
Matingbridge
Bacterialchromosome
(a) Conjugation and transfer of an F plasmid
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Figure 27.13a-3
F plasmidBacterialchromosome
F cell(donor)
F cell(recipient)
Matingbridge
Bacterialchromosome
(a) Conjugation and transfer of an F plasmid
F cell
F cell
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The F Factor in the Chromosome
• A cell with the F factor built into its chromosomes functions as a donor during conjugation
• The recipient becomes a recombinant bacterium, with DNA from two different cells
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Figure 27.13b-1
Hfr cell(donor)
F cell(recipient)
(b) Conjugation and transfer of part of an Hfr bacterial chromosome
F factor
A
A
A
A
A
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Figure 27.13b-2
Hfr cell(donor)
F cell(recipient)
(b) Conjugation and transfer of part of an Hfr bacterial chromosome
F factor
A
A AA
A
A
A
A
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Figure 27.13b-3
Hfr cell(donor)
F cell(recipient)
(b) Conjugation and transfer of part of an Hfr bacterial chromosome
F factor AA
RecombinantF bacterium
A
A AA
A
A
A
A
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R Plasmids and Antibiotic Resistance
• R plasmids carry genes for antibiotic resistance• Antibiotics kill sensitive bacteria, but not bacteria
with specific R plasmids• Through natural selection, the fraction of bacteria
with genes for resistance increases in a population exposed to antibiotics
• Antibiotic-resistant strains of bacteria are becoming more common
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PROKARYOTES HAVE RADIATED INTO A DIVERSE SET OF LINEAGES
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An Overview of Prokaryotic Diversity
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The genetic diversity of prokaryotes is immense
• Only 9,800 described species
• As many as 10,000 species in a handful of dirt
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Horizontal gene transfer has played a major role in the evolution of prokaryotes
• Most prokaryotes have a mosaic of genes imported from other species– As much as 75% of a genome may be as a result of
horizontal transfer at some point in evolutionary history
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Bacteria Archaea Eukarya
Nuclear envelope Absent Absent Present
Membrane bound organelles
Absent Absent Present
Peptidoglycan Present Absent Absent
Membrane lipids Unbranched hydrocarbons
Some branched hydrocarbons
Unbranched hydrocarbons
RNA polymerase 1 type Several types Several types
Initiator a.a. for protein synthesis
Formyl-methionine (f-Met)
Methionine (Met) Methionine (Met)
Introns in genes Very rare Present in some genes
Present in many genes
Response to standard antibiotics
Usually inhibited Not inhibited Not inhibited
DNA with histones Absent Present in some Present
Circular chromosome
Present Present Absent
Growth at temps >100° C
No Some species No
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• Some archaea live in extreme environments and are called extremophiles
• Extreme halophiles live in highly saline environments• Extreme thermophiles thrive in very hot
environments
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Figure 27.16
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• Methanogens live in swamps and marshes and produce methane as a waste product
• Methanogens are strict anaerobes and are poisoned by O2
• In recent years, genetic prospecting has revealed many new groups of archaea
• Some of these may offer clues to the early evolution of life on Earth
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Bacteria
• Bacteria include the vast majority of prokaryotes of which most people are aware
• Diverse nutritional types are scattered among the major groups of bacteria
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Proteobacteria
• These gram-negative bacteria include photoautotrophs, chemoautotrophs, and heterotrophs
• Some are anaerobic, and others aerobic
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Figure 27.17-a
Alpha
Beta
Gamma
DeltaProteo-bacteria
Epsilon
Subgroup: Alpha Proteobacteria
Rhizobium (arrows) inside a rootcell of a legume (TEM)
2.5
m
Subgroup: Delta ProteobacteriaSubgroup: Gamma Proteobacteria Subgroup: Epsilon Proteobacteria
Nitrosomonas (colorized TEM)
1
m
Subgroup: Beta Proteobacteria
2
m
30
0
m
Helicobacter pylori (colorized TEM)Fruiting bodies of Chondromycescrocatus, a myxobacterium (SEM)
20
0
m
Thiomargarita namibiensiscontaining sulfur wastes (LM)
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Figure 27.17a
Alpha
Beta
Gamma
Delta
Proteobacteria
Epsilon
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Subgroup: Alpha Proteobacteria
• Many species are closely associated with eukaryotic hosts• Scientists hypothesize that mitochondria evolved from
aerobic alpha proteobacteria through endosymbiosis• Example: Rhizobium, which forms root nodules in
legumes and fixes atmospheric N2
• Example: Agrobacterium, which produces tumors in plants and is used in genetic engineering
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Figure 27.17b
Subgroup: Alpha Proteobacteria
Rhizobium (arrows) inside a rootcell of a legume (TEM)
2.5
m
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Subgroup: Beta Proteobacteria
• Example: the soil bacterium Nitrosomonas, which converts NH4
+ to NO2–
Nitrosomonas (colorized TEM)
1 m
Subgroup: Beta Proteobacteria
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Subgroup: Gamma Proteobacteria
• Examples include sulfur bacteria such as Chromatium and pathogens such as Legionella, Salmonella, and Vibrio cholerae
• Escherichia coli resides in the intestines of many mammals and is not normally pathogenic
Subgroup: Gamma Proteobacteria
200
m
Thiomargarita namibiensiscontaining sulfur wastes (LM)
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Subgroup: Delta Proteobacteria
• Example: the slime-secreting myxobacteria
Subgroup: Delta Proteobacteria
300 m
Fruiting bodies of Chondromycescrocatus, a myxobacterium (SEM)
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Subgroup: Epsilon Proteobacteria
• This group contains many pathogens including Campylobacter, which causes blood poisoning, and Helicobacter pylori, which causes stomach ulcers
Subgroup: Epsilon Proteobacteria
2 m
Helicobacter pylori (colorized TEM)
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Figure 27.17-b
Chlamydias
5 m
Spirochetes
2.5
mLeptospira, a spirochete(colorized TEM)
Gram-Positive Bacteria
2 m
5 m
Hundreds of mycoplasmas coveringa human fibroblast cell (colorized SEM)
Streptomyces, the source of manyantibiotics (SEM)
40 m
Oscillatoria, a filamentouscyanobacterium
Cyanobacteria
Chlamydia (arrows) inside ananimal cell (colorized TEM)
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Chlamydias
• These bacteria are parasites that live within animal cells
• Chlamydia trachomatis causes blindness and nongonococcal urethritis by sexual transmission
Chlamydias
2.5
m
Chlamydia (arrows) inside ananimal cell (colorized TEM)
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Spirochetes
• These bacteria are helical heterotrophs
• Some are parasites, including Treponema pallidum, which causes syphilis, and Borrelia burgdorferi, which causes Lyme disease 5
m
Spirochetes
Leptospira, a spirochete(colorized TEM)
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Cyanobacteria
• These are photoautotrophs that generate O2
• Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis
40 m
Oscillatoria, a filamentouscyanobacterium
Cyanobacteria
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Gram-Positive Bacteria
• Gram-positive bacteria include – Actinomycetes, which decompose soil– Bacillus anthracis, the cause of anthrax– Clostridium botulinum, the cause of botulism– Some Staphylococcus and Streptococcus, which
can be pathogenic– Mycoplasms, the smallest known cells
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Figure 27.17j
Gram-Positive Bacteria
5 m
Streptomyces, the source of manyantibiotics (SEM) 2
mHundreds of mycoplasmas coveringa human fibroblast cell (colorized SEM)
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PROKARYOTES PLAY CRUCIAL ROLES IN THE BIOSPHERE
Prokaryotes are so important that if they were to disappear the prospects for any other life surviving would be dim
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Chemical Recycling
• Prokaryotes play a major role in the recycling of chemical elements between the living and nonliving components of ecosystems
• Chemoheterotrophic prokaryotes function as decomposers, breaking down dead organisms and waste products
• Prokaryotes can sometimes increase the availability of nitrogen, phosphorus, and potassium for plant growth
• Prokaryotes can also “immobilize” or decrease the availability of nutrients
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Figure 27.18
Seedlings grow-ing in the lab
Strain 3Strain 20
Nobacteria
Soil treatment
0.2
0.4
0.6
0.8
1.0
Upt
ake
of K
by
plan
ts (m
g)
Strain 1
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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
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• In mutualism, both symbiotic 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
Ecological Interactions
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Figure 27.19
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• The ecological communities of hydrothermal vents depend on chemoautotrophic bacteria for energy
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PROKARYOTES HAVE BOTH BENEFICIAL AND HARMFUL IMPACTS ON HUMANS
Some prokaryotes are human pathogens, but others have positive interactions with humans
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Mutualistic Bacteria
• Human intestines are home to about 500–1,000 species of bacteria
• Many of these are mutalists and break down food that is undigested by our intestines
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Pathogenic Bacteria
• Prokaryotes cause about half of all human diseases
– For example, Lyme disease is caused by a bacterium and carried by ticks
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Figure 27.20
5 m
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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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Horizontal gene transfer can spread genes associated with virulence• Some pathogenic bacteria are potential weapons of
bioterrorism• Horizontal gene transfer can spread genes associated
with virulence• Some pathogenic bacteria are potential weapons of
bioterrorism
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Prokaryotes in Research and Technology
• Experiments using prokaryotes have led to important advances in DNA technology
– For example, E. coli is used in gene cloning– For example, Agrobacterium tumefaciens is used to
produce transgenic plants• Bacteria can now be used to make natural plastics
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Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from the environment
• Bacteria can be engineered to produce vitamins, antibiotics, and hormones
• Bacteria are also being engineered to produce ethanol from waste biomass