0 Bacteria and Archaea Chapter 26 Opening Roadmap. - PowerPoint Presentation

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Bacteria and

Archaea

Slide2

Chapter 26 Opening Roadmap.

© 2017 Pearson Education, Inc.

Slide3

Introduction

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

Slide4

Introduction

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

Slide5

Why Do Biologists Study Bacteria and Archaea?

Biological impact

Abundance

Habitat diversity

Extremophiles

Medical importance

Koch’s postulates

Germ theory

Pathogens

Role in bioremediation

Slide6

Biological Impact

Ancient, diverse, abundant, and ubiquitous lineages

Oldest fossils are of 3.5-billion-year-old bacteria

Eukaryotes not in fossil record until 1.7 BY later

10,000 species named and described, but hundreds of thousands likely exist

~1000

microbes

(microscopic organisms) in human large intestine

~700

microbes

in human mouth

Slide7

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

Slide8

Habitat Diversity

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

Slide9

Some Prokaryotes Thrive in Extreme Environments

Extremophiles live in extreme habitats:Hydrothermal vents pH < 1.00ºC under Antarctic iceWater that is 5–10 times saltier than seawater

Slide10

Some Prokaryotes Thrive in Extreme Environments

Extremophiles

are a

hot area of research:

May help explain how life on Earth began

Model organisms in search for extraterrestrial life

Enzymes that function at extreme temperatures and pressures used in industrial processes

Slide11

Medical Importance

Pathogens

are

bacteria that cause illness:

Slide12

Koch’s Postulates

Koch’

s postulates

are the

causative link between a specific disease and

a

specific microbe:

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

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

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

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

organism

Slide13

The Germ Theory

Koch’

s experimental results were first test of

germ theory of disease

:

Pattern component is that some diseases are infectious

Process responsible for pattern is transmission and growth of certain bacteria and viruses

Slide14

The Germ Theory

Infectious diseases

 spread in three main ways: 

Passed from person to person

Transmitted by bites from insects or animals

Acquired by ingesting contaminated food or water, or exposure to microbes in surrounding environment

Slide15

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 larger because they have acquired virulence genes

E.g., a gene that codes for a protein

toxin

Slide16

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 favorable conditions

Involved in transmitting

disease to humans

Slide17

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 (see Chapter 22)

Biofilms

are

bacterial colonies enmeshed in polysaccharide-rich matrix

that

shield bacteria from antibiotics

Slide18

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

Slide19

Role in Bioremediation

Bioremediation uses two complementary strategies:

Fertilizing contaminated sites to encourage growth of existing bacteria and

archaea

​

Seeding

, or adding, specific species of bacteria and

archaea

to contaminated sites

Slide20

How Do Biologists Study Bacteria and Archaea?

Enrichment cultures

Metagenomics

Investigating human

microbiome

Molecular

phylogenetics

Slide21

Using Enrichment Cultures

Most described species discovered in controlled conditions in a laboratory

Enrichment cultures

isolate large populations of cells that grow under specific conditions

Led to discovery of

thermophiles

(“heat-lovers”)

Slide22

Figure 26.3

Can bacteria live a mile below Earth’s

surface?

Bacteria are capable of cellular respiration deepbelow Earth’s surface by using H2 as an electron donor and Fe3+ asan electron acceptor.

Bacteria from this environment are not capableof using H2 as an electron donor and Fe3+ as an electron acceptor.

H2

Fe3+

1. Prepare enrichment culture abundant inH2 and Fe3+; raise temperatures above 45ºC.

Heat

2. Add rock and fluid samples extracted fromdrilling operations at depths of about 1000 mbelow Earth’s surface.

Rock and fluid samples

Black, magnetic grains of magnetite (Fe3O4) willaccumulate because Fe3+ is reduced by growing cells and shed asa waste product. Cells will be visible.

No magnetite will appear. Nocells will grow.

Cells are visible, and magnetite is detectable.

At least one bacterial species that can live deep belowEarth’s surface grew in this enrichment culture. Different cultureconditions might result in the enrichment of different species presentin the same sample.

1 µm

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Slide23

Using Metagenomics

Metagenomics

, or

environmental sequencing

Identify species and biochemical pathways by comparing DNA sequences with those of known genes

Rapidly identify and characterize organisms never seen

Used in combination with

direct sequencing

(isolating and sequencing a specific gene from organisms found in a particular habitat) to understand prokaryotic diversity

Slide24

Figure 26.4

1. Collect samples

from an environmentcontaining a mixedcommunity ofunknown organismsand extract DNA.

2. Generate smallDNA fragments andsequence as manyas possible.

Known:

Sample:

Alignment:

3. Compare thesesequences withthose of knowngenes.

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Slide25

Investigating the Human Microbiome

Microbiome

is

the community of microbes that naturally inhabit the body or parts of the body

Humans harbor a diverse ecosystem of symbiotic prokaryotes

Gut microbiome: 100 trillion bacteria and archaea

Some microbes may make us sick, but we depend on many others to stay healthy

Changes in gut microbiome have been linked to inflammatory bowel disease and obesity

Slide26

Evaluating Molecular Phylogenies

Some of the most useful phylogenetic trees for domains Bacteria and

Archaea

have been based on studies of RNA

Specifically, the RNA molecules found in the small subunit of ribosomes, 16S and 18S RNA

In the late 1960s, Carl

Woese

and colleagues determined and compared the 16S and 18S RNA molecules from a wide array of species

The results of their comparison comprise the

tree

of life

Slide27

Web Activity: The Tree of Life

Slide28

Evaluating Molecular Phylogenies

Hypothesis:

major division between prokaryotes and eukaryotes

Hypothesis (

Woese’s

data from

rRNA

sequences): major divisions = three domains

Bacteria, Archaea, and Eukarya (most closely related)

Hypothesis (two domains): Bacteria is one domain and rest of life is other

Hypothesis: Archaea form the root of the tree, and Bacteria and Eukarya are more closely related to each other than either is to Archaea

Slide29

Figure 26.5

DOMAIN BACTERIA

Mycoplasma

Firmicutes

Cyanobacteria

Actinobacteria

Spirochaetes

Chlamydiae

Bacteriodetes

ε

-Proteobacteria

δ-Proteobacteria

α-Proteobacteria

β-Proteobacteria

γ-Proteobacteria

DOMAIN ARCHAEA

Thaumarchaeota

Crenarchaeota

Korarchaeota

Euryarchaeota

DOMAIN EUKARYA

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Slide30

What Themes Occur in the Diversification of Bacteria and Archaea?

Genetic variation through gene transfer

Morphological diversity

Metabolic diversity

Ecological diversity and global impacts

Slide31

Genetic Variation through Gene Transfer

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

Slide32

Figure 26.6a

Plasmid

1.

Two bacterial cellscome into contact. Onecell contains a plasmid.

Chromosome

Conjugationtube

2. Copy of plasmid istransferred from donorcell to recipient cellthrough a conjugationtube.

3. Recipient cellcontains plasmid.

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Slide33

Figure 26.6b

1.

Portion of mainchromosome is copiedand transferred throughconjugation tube torecipient cell.

Chromosome

Conjugationtube

2. Transferred portionof chromosomerecombines withchromosome inrecipient cell.

Recombinantchromosome

3. Recipient cellcontains recombinantbacterial chromosome.

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Slide34

Morphological Diversity

Size

—volume of bacterial species ranges from

0.15

µ

m

3

to

200

×

10

6

µ

m

3

Shape

—filaments, spheres, rods, and chains to spiral

Motility

—flagella and gliding

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Figure 26.7

(a

) Size varies.

Most bacteria are about 1 µm indiameter, but some are much larger.

Smallest

(Mycoplasma mycoides)

(b) Shape varies ...

... from rods to spheres to spirals.In some species, cells adhere toform chains.

Rods, chains of spheres(compost bacteria)

(c) Motility varies.

Some bacteria are nonmotile, butswimming and gliding are common.

Swimming(Pseudomonas aeruginosa)

0.3 µm

Comparesizes

100 µm

Largest (Thiomargarita namibiensis)

Spirals (Campylobacter jejuni)

Gliding (Oscillatoria limosa)

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Slide36

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

Slide37

Figure 26.9

(a)

Gram-positive cell wall

Polysaccharides

Cell wall

(b) Gram-negative cell wall

Peptidoglycan

Plasmamembrane

Protein

Protein

Cell wall

Outer

membrane

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Slide38

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

Slide39

Metabolic Diversity

ATP production:

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

Slide40

Metabolic Diversity

Autotrophs

—synthesize building-block compounds from simple starting materials

Heterotrophs

—

absorbing building-block compounds from their environment

Slide41

Table 26.2

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Slide42

Metabolic Diversity

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

Slide43

Producing ATP through Cellular Respiration

Millions of bacterial, archaeal, and eukaryotic species are

chemoorganotrophs

Break down organic compounds to obtain energy to make ATP

Slide44

Producing ATP through Cellular Respiration

Enzymes strip electrons from organic molecules and transfer them to electron carriers

Carriers feed the electrons to an electron transport chain (ETC)

Electrons are stepped down from a high-energy to a low-energy state

Released energy is used to generate a proton gradient across the plasma membrane

Protons flow back across the membrane through ATP synthase enzyme; results in the production of ATP

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Figure 26.10

(a)

Model of electron transport chain (ETC)

Highpotentialenergy

Potential energy of electron

Electrondonor

e–

By donating an electron,electron donorsbecome oxidized

(b) ETC generates proton gradient across plasmamembrane.

INSIDE CELL

OUTSIDE CELL

H+

Componentsof the electrontransport chain

e–

H+

Hydrogen ions arepumped acrossthe plasmamembrane aselectrons movethrough thetransport chain,creating a protongradient used togenerate ATP

H+

H+

H+

H+

H+

H+

H+

Electronacceptor

By accepting anelectron, electronacceptorsbecome reduced

H+

ATP

ATP synthase

Lowpotentialenergy

ATP

is generated bychemiosmosis

Electron transport chain

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Slide46

Producing ATP through Cellular Respiration

In cellular respiration, most eukaryotes

Use organic compounds with high potential energy as the original electron donor

Use oxygen as the final electron acceptor

Produce CO

2

and water as by-products

Bacteria and archaea

Exploit a wide variety of electron donors and acceptors

Produce by-products other than CO

2

and water

Slide47

Table 26.3

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Slide48

Producing ATP via Fermentation

Fermentation

—make ATP without using electron transport chains

Less efficient than cellular respiration

Does not use an outside electron acceptor

Some bacteria and

archaea

use various organic compounds as starting point for fermentation

Clostridium

ferment complex carbohydrates, proteins, purines, or amino acids

Other bacteria ferment lactose

Bacteria in digestive tract ferment carbohydrates

Slide49

Producing ATP via Photophosphorylation

Bacteria and

archaea

can undergo

photophosphorylation

in one of three ways:

​

Bacteriorhodopsin

activated by light

Uses absorbed energy to create a proton gradient

The gradient drives ATP synthesis via chemiosmosis

Slide50

Producing ATP via Photophosphorylation

One bacterium absorbs geothermal radiation for photosynthesis

Pigments absorb light raise electrons to high-energy states (requires a source of electrons)

Energy released as electrons move through electron transport chains generate ATP

Slide51

Producing ATP via Photophosphorylation

Species that use water as a source of electrons carry out

oxygenic photosynthesis

Many phototrophic bacteria use molecules other than water as the electron donor in

anoxygenic

photosynthesis

Slide52

Obtaining Building-Block Compounds

Organisms must obtain building-block molecules containing carbon–carbon bonds

Autotrophs make their own building-block compounds

Some bacteria are

methanotrophs

(“methane-eaters”

): use methane (CH

4

) as their carbon source.

Some

archaea

are

methanogen

:

produce methane as a by-product of cellular respiration.

Heterotrophs consume building-block compounds

Slide53

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

Slide54

The Oxygen Revolution

No free molecular oxygen existed for first

2.3 billion years of Earth’

s history

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

Slide55

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

Slide56

The Oxygen Revolution

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

Slide57

Figure 26.12

Free energy change relative to glucose (kcal/

mol)

Glucose

Glucose

Glucose

e–

Iron

Electrondonor incellularrespiration

When oxygenis used as thefinal electronacceptor, thechange in freeenergy is equalto almost 700kcal/mol

e–

Oxygen

e–

Nitrate

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Slide58

Nitrogen Fixation and the Nitrogen Cycle

All organisms require nitrogen (N) to synthesize proteins and nucleic acids

Molecular nitrogen (N

2

) is abundant in atmosphere, but most organisms cannot use it directly

Must obtain N from ammonia (NH

3

) or nitrate (NO

3

–

)

Nitrogen fixation

—certain bacteria and archaea are only organisms capable of converting N

2

to NH

3

Nitrogen-fixing bacteria live in close association with plants (e.g., in root structures called nodules)

Slide59

Nitrogen Fixation and the Nitrogen Cycle

The nitrite (NO

2

) 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, NO

3

NO

3

then converted to N

2

by another suite of bacterial and

archaeal

species

Nitrogen cycle

—driving the movement of nitrogen atoms through ecosystems around the globe

Slide60

Figure 26.13

N

2in atmosphere

Reductionby bacteria,archaea

Fixation bybacteria, archaea

Organic compoundswith amino groups(–NH2)

Decompositionby bacteria,archaea, fungi

NO3–(nitrate)

PlantsAlgae

NH3 (ammonia)NH4+ (ammonium ions)

Oxidationby bacteria,archaea

NO2–(nitrite)

Oxidationby bacteria,archaea

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Slide61

Nitrate Pollution

Widespread use of NH

3

fertilizers causes pollution

When NH

3

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

Slide62

Figure 26.14

1.

Ammonia (NH3) isintroduced as fertilizer.

NH3

2. Corn uses some ofNH3 to build protein.Soil-dwelling bacteriaand archaea use NH3as an electron donor.

Cellular respiration

3. Nitrate (NO3–),a by-product ofrespiration, entersgroundwater andwashes into rivers.

NO3–

NO3–

4. NO3– from runoffstimulates “blooms”of marine algae andcyanobacteria.

5. When cells thatbloomed eventually die,decomposers such asbacteria and archaeagrow rapidly, using upoxygen (O2).

6. ANOXIC“DEAD ZONE”

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Slide63

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

Slide64

Table 26.4

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Slide65

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

Slide66

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)

Slide67

Bacteria—Cyanobacteria

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

Slide68

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

Slide69

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

Slide70

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

Slide71

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

Slide72

Table 26.5

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Slide73

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

Slide74

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

Slide75

Archaea—Thaumarchaeota

Recently recognized, ancient lineage

Extremely abundant in oceans, estuaries, and terrestrial soils

Mesophilic

(“middle-loving”

): grow best at moderate temperatures