BLG144: BIOLOGY II

Chapter 26: Bacteria & Archeae

Week # 4 – Part 1
Department of Chemistry & Biology
Tarushika Vasanthan, PhD
Faculty of Science
Department of Chemistry & Biology

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Introduction to Bacteria and Archaea

• Bacteria and Archaea

• Are two of the three largest branches on the tree of life
• Third major branch (domain) is Eukarya
• Most are unicellular, and all are prokaryotic
• Lack a membrane-bound nucleus

• Bacteria and archaea are distinguished by

• Types of molecules that make up plasma membranes and cell walls
• Machinery they use to transcribe DNA and translate mRNA into proteins
Image retrieved from: https://en.wikipedia.org/wiki/Phylogenetic_tree

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Abundance

• Bacteria and archaea are dominant life-forms (total volume)

• Teaspoon of soil: billions of microbes
• Marine archaea: over 10,000 individuals per mL seawater
• Bacteria and archaea living under the ocean may make up 10 percent of the world’s total mass
of living material
• Bacteria and archaea live almost everywhere, from below Earth’s surface to on Antarctic sea ice
• Entirely new phyla of bacteria and archaea have been recently discovered in the field of
microbiology
• Microbiology is the study of microbes

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Some Prokaryotes Thrive in Extreme Environments

• Extremophiles live in extreme habitats:

• Hydrothermal vents
• pH < 1.0
• 0ºC under Antarctic ice
• Water that is 5–10 times saltier than seawater

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Some Prokaryotes Thrive in Extreme Environments

• Extremophiles are a hot area of research:

• Model organisms in search for extraterrestrial life
• Enzymes that function at extreme temperatures and pressures used in industrial processes

Taq polymerase – enzyme

isolated from Thermus
aquaticus

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Medical Importance

• Thousands of bacterial species living in and on your body,

• Many species protect their host from bacteria that cause disease

• Pathogens are bacteria that cause illness

• Pathogenic forms come from several different taxa.
• Pathogenic bacteria tend to affect tissues at the entry points to the body, such as wounds
or pores in the skin, the respiratory and gastrointestinal tracts, and the urogenital canal.

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Koch’s Postulates

• Koch’s postulates are the causative link between a specific disease and a specific microbe:

1. Microbe present in individuals suffering from the disease and absent from healthy
individuals

2. Microbe must be isolated and grown in pure culture away from host

3. If organisms from pure culture are injected into a healthy experimental animal, disease
symptoms appear

4. Organism isolated the diseased experimental animal, again grown in pure culture, and
demonstrated to be the same as the original organism

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The Germ Theory

• Koch’s experimental results were first test of germ theory of disease

• Infectious diseases spread in three main ways:

1. Passed from person to person

2. Transmitted by bites from insects or animals
3. Acquired by ingesting contaminated food or water, or exposure to microbes in surrounding
environment

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What Makes Some Bacterial Cells Pathogenic?

• Virulence:
• Ability to cause disease
• Heritable, variable trait
• Some species have both pathogenic virulent strains and harmless strains
• Escherichia coli: genomes of pathogenic strains are larger because they have acquired
virulence genes
• E.g., a gene that codes for a protein toxin

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Some Pathogenic Bacteria Produce Resistant Endospores

• Endospores: tough, thick-walled, dormant structures formed during times of environmental

stress
• Contain copy of cell’s DNA, RNA, ribosomes, and enzymes
• Metabolic activity stops and original cell breaks down
• Resistant to high temperatures, UV radiation, and antibiotics
• Resume growth as actively dividing cells in favourable conditions
• Involved in transmitting disease to humans

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The Past, Present, and Future of Antibiotics

• Antibiotics
• Molecules that kill bacteria or stop them from growing
• Produced naturally by some soil bacteria and fungi
• Discovered in 1928; widespread use by 1940s
• Extensive use in late twentieth century in clinics and animal feed led to evolution of drug-
resistant strains of pathogenic bacteria
• Biofilms are bacterial colonies enmeshed in polysaccharide-rich matrix that shield bacteria
from antibiotics

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Role in Bioremediation

• Bioremediation is the use of bacteria and archaea to clean up sites polluted with organic
solvents
• Water pollutants
• Are toxic to eukaryotes
• Do not dissolve in water
• Accumulate in sediments
• Naturally existing populations of bacteria and archaea can grow in spills and degrade toxins
• Bioremediation uses two complementary strategies:
1. Fertilizing contaminated sites to encourage growth of existing bacteria and archaea
2. Seeding, or adding, specific species of bacteria and archaea to contaminated sites

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Role in Bioremediation

• Canadian Forces Station Alert, the world’s most

northern permanent settlement,
• Climate is very harsh
• Soils are cold, dry and nutrient deficient,
• Short growing season for microbes

• Many High Arctic sites, including CFS Alert are

contaminated with weathered diesel fuels and other
hydrocarbons.

• Both fertilization of contaminated soils and seeding

with specific microbe species have proven effective
in increasing degradation of hydrocarbons in the
High Arctic.

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Role in Bioremediation

• Where to find microbes to seed cold, polluted soils?

• Microbes capable of breaking down specific pollutants are most abundant in sites contaminated
by those pollutants, and hydrocarbon contaminated northern sites may be a suitable source of
microbes for bioremediation of those molecules.

• In some heavily polluted sites, nearly all of the soil bacteria are capable of breaking down
hydrocarbons

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What Themes Occur in the Diversification of Bacteria and Archaea?

1. Genetic variation through gene transfer

2. Morphological diversity

3. Metabolic diversity

4. Ecological diversity and global impacts

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Genetic Variation Through Gene Transfer

Lateral Gene Transfer Transformation

• Transformation—when bacteria or archaea
naturally take up DNA from the
environment that has been released by cell
lysis or secreted

• Transduction—viruses pick up DNA from

one prokaryotic cell and transfer it to
another cell

• Conjugation—genetic information
transferred by direct cell-to-cell contact

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Genetic Variation Through Gene Transfer

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Morphological Diversity

• Size—volume of bacterial species ranges from

0.15 µm3 to 200 ´106 µm3
• Shape—filaments, spheres, rods, and chains to spiral
• Motility—flagella and gliding

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Cell-Wall Composition

• Gram stain—dyeing system to examine cell walls

• Gram-positive cells look purple under a microscope
• Cell wall has extensive amount of carbohydrate peptidoglycan
• Gram-negative cells look pink
• Cell wall has a thin layer containing peptidoglycan and outer phospholipid bilayer

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Check Your Understanding

To establish a link between a specific bacterium and a skin disease, researchers have shown
that bacterium was present in sick persons but not in healthy individuals. They isolated the
bacterium in a pure culture and demonstrated that experimental healthy animals injected
with this culture became sick. What other experiment do researchers need to perform to be
absolutely sure that the bacterium is responsible for the disease?

A) Demonstrate that the bacterium belongs to the pathogenic lineage.

B) Demonstrate that the bacterium is not able to live outside of humans or animals.
C) Isolate bacterium from an infected sick animal and demonstrate that it is the same
bacterium as the one used for infection.
D) Demonstrate all of the above.
E) No experiments need to be done, because there are enough data to establish that skin
disease is caused by the investigated bacterium.

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Let’s Take a 10 minute Break :)

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Metabolic Diversity

• All organisms must

• Acquire chemical energy that is used to make ATP
• Obtain carbon compounds that can serve as building blocks for synthesis of cellular
components

• Bacteria and archaea may use one of three sources of energy for ATP production: light, organic
molecules, or inorganic molecules

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Metabolic Diversity

• ATP production in bacteria and archaea:

• Phototrophs—light used to excite electrons

• ATP made by photophosphorylation

• Chemoorganotrophs—oxidize organic molecules with high potential energy

• ATP made by cellular respiration or fermentation pathways

• Chemolithotrophs—oxidize inorganic molecules with high potential energy

• ATP made by cellular respiration

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Metabolic Diversity

• Bacteria and archaea fulfill their second nutritional need—obtaining building-block compounds
with carbon–carbon bonds—in two ways:

• Autotrophs—synthesize building-block compounds from simple starting materials

• Heterotrophs—absorbing building-block compounds from their environment

• The basic chemistry required for photosynthesis, cellular respiration, and fermentation
originated in these lineages

• Evolution of variations on each of the processes allowed prokaryotes to diversify into millions of
species that occupy diverse habitats

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Metabolic Diversity

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Ecological Diversity and Global Impacts

• Bacteria and archaea produce extremely sophisticated enzymes

• As a result, they can live in extreme environments and use toxic compounds as food

• The complex chemistry and abundance of bacteria and archaea make them potent forces for
global change

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The Oxygen Revolution

• No free molecular oxygen existed for first 2.3 billion years of Earth’s history.

• Where did it come from?

• Cyanobacteria
• Lineage of photosynthetic bacteria
• Were first to perform oxygenic photosynthesis
• Were responsible for changing Earth’s atmosphere to one with a high concentration of
oxygen

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The Oxygen Revolution

• Once oxygen was common in the oceans, cells could carry

out aerobic respiration
• Before this, only anaerobic respiration was possible
• Cells had to use compounds other than oxygen as
the final electron acceptor during cellular
respiration

• Oxygen is
• Highly electronegative
• An efficient electron acceptor
• More energy released in ETCs with oxygen as
ultimate acceptor than is released with other
acceptor substances

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Nitrogen Fixation and the Nitrogen Cycle

• All organisms require nitrogen (N) to synthesize

proteins and nucleic acids

• Molecular nitrogen (N2) is abundant in atmosphere,

but most organisms cannot use it directly
• Must obtain N from ammonia (NH3) or nitrate
(NO3−)

• Nitrogen fixation—certain bacteria and archaea are

only organisms capable of converting N2 to NH3
• Nitrogen-fixing bacteria live in close association
with plants (e.g., in root structures called nodules)

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Nitrogen Fixation and the Nitrogen Cycle

• The nitrite (NO2) that some bacteria produce as a by-

product of respiration does not build up in
environment

• Used as an electron acceptor by other species and

converted to molecular nitrate, NO3

• NO3 then converted to N2 by another suite of

bacterial and archaeal species

• Nitrogen cycle—driving the movement of nitrogen

atoms through ecosystems around the globe

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Nitrate Pollution

• Widespread use of NH3 fertilizers causes pollution

• When NH3 is added to soil, much of it is used by bacteria as

food

• These bacteria then release nitrite or nitrate as waste

products

• Nitrates cause pollution in aquatic environments

• In an aquatic ecosystem, nitrates can decrease the oxygen

content, causing anaerobic “dead zones” to develop

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Bacteria

• Bacteria are a monophyletic group

• At least 29 major lineages (phyla)

• Recognized by distinctive morphological characteristics or by phylogenetic analyses of gene

sequence data

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Bacteria—Actinobacteria

• Filamentous, forming branching chains

• Genera Streptomyces and Arthrobacter
• Abundant in soil and are important decomposers
• Some live in association with plant roots and fix nitrogen; others can break down toxins
such as herbicides, nicotine, and caffeine
• Over 3000 distinct antimicrobial compounds have been isolated from Streptomyces

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Bacteria—Chlamydiae

• Least diverse of all major bacterial lineages

• Only 13 species known
• All are spherical and very small
• Live as parasitic endosymbionts (i.e., they live inside of living host cells)

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Bacteria—Cyanobacteria

• Photosynthetic bacteria found as independent cells, chains that form filaments, or colonies
• Very abundant
• Produce much of the oxygen, nitrogen, and organic compounds
• Feed organisms living in the surface waters of freshwater and marine environments

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Bacteria—Firmicutes

• Extremely common in animal intestines

• Live in symbiotic mutualism, aiding the digestive process
• Several species used in agriculture and food processing
• Others cause a variety of human diseases

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Bacteria—Proteobacteria

• Diverse in morphology:
• Some species form stalked cells while others form aggregates of cells organized as spore-
forming fruiting bodies
• Several species cause disease
• Others play key roles in nitrogen cycling

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Bacteria—Spirochaetes (Spirochetes)

• Distinguished by corkscrew shape and flagella

• Flagella contained within the outer sheath, which surrounds the cell
• As a flagellum beats, the cell lashes back and forth, moving forward
• Parasitic, disease-causing species are propelled by this motion into the tissues of their host

• Other spirochete species are extremely common in freshwater and marine habitats

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Archaea

• Live in virtually every habitat, including extreme environments

• The domain is composed of several major phyla

• In addition, there are two other groups:

• Korarchaeota—known only from direct-sequencing studies and have been difficult to grow
in culture
• Nanoarchaeota—represented by only one species

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Archaea-Crenarchaeota

• Also called eocytes

• Found in harsh environments:

• E.g., hot springs of Yellowstone National Park
• Thrive in hot, acidic, and even high-pressure environments

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Archaea—Euryarchaeota

• The root word eury– means “broad”

• Live in every conceivable habitat:
• Some species adapted to high salt habitats
• Other species are adapted to acidic conditions
• Genus Methanopyrus live near hot springs called black smokers that are 2000 m below sea
level

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Archaea—Thaumarchaeota

• Recently recognized, ancient lineage

• Extremely abundant in oceans, estuaries, and terrestrial soils

• Mesophilic (“middle-loving”): grow best at moderate temperatures

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Check Your Understanding

You run an osteology lab, where students are able to study the bone structure of various
species. To produce clean bones, you introduce insects and bacteria to remove all remaining
flesh. Which bacteria would be the best purchase for your lab?

A) Spirochaetes
B) Actinobacteria
C) Chlamydiae
D) Cyanobacteria
E) Proteobacteria

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LEARNING OBJECTIVE

Defend the statement that bacteria and archaea are the most important,
diverse, and abundant organisms on the planet.

Provide examples of the key roles of bacteria in bioremediation, human

health, and ecosystems

Describe how prokaryotes achieve genetic variation.

Explain why lateral gene transfer makes it challenging to determine the

evolutionary relationships among major lineages in Bacteria and Archaea.

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