Download Chapter 26: Bacteria and Archaea: the Prokaryotic Domains

Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Lecture Themes
•origins, evolution and diversity
•structure and function
•ecological function and relationships
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
1. Prokaryote Phylogeny
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Genome of the Archaeon
Methanococcus jannaschii was
sequenced in 1996. Sequencing of M.
jannashcii confirmed Carl Woese’s longstanding 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”
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Prokaryotic Structure and Function
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
(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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Raven et al 2002
Spherical coccus
(Enterococcus)
Pseudomonas
aeruginosa
Streptococcus
Spirillum
volutans
Bacterial Form
Rod-shaped bacillus
(E. coli)
Three shapes are especially common among bacteria –
spheres, rods and spirals
Most 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)
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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)
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
•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
Penicillium
chrysogenum
•Many prokaryotes have
surface appendages called pili
that are function in adherance
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 crosslinked by short polypeptides
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Aquaspirillum sinosum
Mechanisms of Motility Many bacteria
are motile. Fllagellar action is the most
common,but not the only mechanism,
for generating movement.
Spirillum volutans
Borrelia burgdorferi
•Prokaryotic flagella
•Flagella-like helical filaments
•Growing gelatinous threads
Motility Behavior
Lyme disease
symptoms, and the
disease vector – a
tick
•Kinesis
•Taxis
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
0.05 um
1 um
Electron micrograph of E. coli
shoing long helical flagella.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
•various specialized
membranes, but lacking
extensive
compartmentalization by
internal membranes
mesosome
plasma
membrane
DNA
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
•ribosomes present but
differ from eukaryotic ones
in size and composition
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.
•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
Thylakoid
membranes of
photosynthetic
cyanobacteria
Cellular and Genomic Organization The organization of cellular components, including
the genome, differs substantially between prokaryotes and eukaryotes
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Cell division
Asexual 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
Adaptation
short 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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Dormancy and
Endosporulation Some
bacteria form highly
resistant spores under
harsh environmental
conditions
Sporulating Bacillus cell
Antibiotic synthesis
Some prokaryotes (and
protists and fungi)
synthesize and release
antibiotic chemicals that
inhibit growth of other
microbes
Bacillus anthracus
Adaptations to Harsh Environmental Conditions: Some bacteria are capable of
dormancy, endosporulation and antibiotic synthesis
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Nutritional and Metabolic Diversity
Sources: Campbell et al (2002), Freeman (2002), Purves et al (2001)
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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 process.in that they have evolved
dozens of variations on these most basic themes of
metabolism
This Prokarotic metabolic diversity is important for
two reasons:
1.It explains their ecological diversity; they are found
almost everywhere because they exploit such a
tremendous variety of molecules as food
2.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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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 nitrogencontaining ions to form
nitrogen gas and other
products
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic 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.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Figure 26.2
Figure 26.2
figure 26-02.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Table 26.1
Table 26.1
table 26-01.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
General Biology of the
Prokaryotes
• The prokaryotes are the most numerous
organisms on Earth,occupying an enormous
variety of habitats.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
General Biology of the
Prokaryotes
• Many prokaryotes move by means of
flagella, gas vesicles, or gliding
mechanisms. Prokaryotic flagella rotate.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Figure 26.7
Figure 26.7
figure 26-07.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
General Biology of the
Prokaryotes
• Prokaryotes reproduce asexually by fission,
but also exchange genetic information.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Figure 26.8
Figure 26.8
figure 26-08.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Table 26.2
Table 26.2
table 26-02.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Figure 26.10
Figure 26.10
figure 26-10.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Prokaryotes in Their
Environments
• Many prokaryotes live in or on other
organisms, with neutral, beneficial, or
harmful effects.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Prokaryotes in Their
Environments
• A minority of bacteria are pathogens. Some
produce endotoxins, which are rarely fatal;
others produce often highly toxic exotoxins.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Prokaryote Phylogeny and
Diversity
• Phylogenetic classification of prokaryotes is
based on rRNA sequences and other
molecular evidence.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Prokaryote Phylogeny and
Diversity
• Lateral gene transfer among prokaryotes
makes it difficult to infer prokaryote
phylogeny.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Prokaryote Phylogeny and
Diversity
• Evolution can proceed rapidly in prokaryotes
because they are haploid and can multiply
rapidly.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• There are far more known bacteria than
archaea. One phylogenetic classification of
the domain Bacteria groups them into over
a dozen groups.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• The most ancient bacteria, like the most
ancient archaea, may be thermophiles,
suggesting that life originated in a hot
environment.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• All four nutritional types occur in the
Proteobacteria. Metabolism in different
proteobacteria groups has evolved along
different lines. Review Figure 26.12
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Figure 26.12
Figure 26.12
figure 26-12.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• Cyanobacteria, unlike other bacteria,
photosynthesize using the same pathways
plants use. Many fix nitrogen.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• Spirochetes move by means of axial
filaments.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• Chlamydias are tiny parasites that live within
the cells of other organisms.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• Firmicutes are diverse; some produce
endospores, resting structures resistant to
harsh conditions. Some actinomycetes
produce important antibiotics.
Actinomycetes grow as branching filaments.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Bacteria
• Mycoplasmas, the tiniest living things, lack
conventional cell walls and have very small
genomes.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
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
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
Figure 26.22
Figure 26.22
figure 26-22.jpg
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Archaea
• The domain Archaea can be divided into two
kingdoms: Crenarchaeota and
Euryarchaeota.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Archaea
• Crenarchaeota are heat-loving and often
acid-loving archaea.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Archaea
• Methanogens produce methane by reducing
carbon dioxide. Some live in the guts of
herbivorous animals; some in hightemperature environments on the ocean
floor.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Archaea
• Extreme halophiles are salt lovers that lend
a pinkish color to salty environments; some
grow in extremely alkaline environments.
Chapter 26: Bacteria and Archaea: the Prokaryotic Domains
The Archaea
• Archaea of the genus Thermoplasma lack
cell walls, are thermophilic and acidophilic,
and have a tiny genome (1,100,000 base
pairs).