LECTURE PRESENTATIONS

For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION

Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

ENVE 3003/ ENVE 3103

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology – Assist. Prof. Deniz AKGÜL
LAB
• Safety training and exam

• Safety rules in the lab!

• Attendance to lab: 80%

As an Environmental Engineer, in
which areas/processes do you need
Microbiology knowledge?
 Pathogens
• Disinfection
• Wastewater Treatment
– Activated sludge C removal
• Wastewater Treatment
– Biological Nutrient Removal C,N,P removal
• Sludge Digestion
• Composting
• Organic Waste and Leachate Stabilization in
Lanfills
• controlling water and waste quality
– every biological process is based on the action
of microorganisms
 LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION
Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Chapter 1
Microorganisms and
Microbiology
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology – Assist. Prof. Deniz AKGÜL
 I. Introduction to Microbiology
• 1.1 The Science of Microbiology
• 1.2 Microbial Cells
• 1.3 Microorganisms and Their Environments
• 1.4 Evolution and the Extent of Microbial Life
• 1.5 The Impact of Microorganisms on Humans

© 2012 Pearson Education, Inc.

1.1 The Science of Microbiology
• Microbiology revolves around two
themes:
1. Understanding basic life processes
• Microorganisms are excellent
models for understanding cellular
processes in organisms

2. Applying that knowledge to the

benefit of humans
• Microorganisms play important
roles in medicine, agriculture, and
industry

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1.1 The Science of Microbiology
• The Importance of Microorganisms
– Oldest form of life
– Largest mass of living material on Earth
– Carry out major processes for biogeochemical
cycles
– Can live in places unsuitable for other organisms
– Other life forms require microorganisms to survive

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1.2 Microbial Cells
• The Cell
– A dynamic entity that forms the fundamental
unit of life (Figure 1.2)

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 (a) (b) (c)

a) A bacterial community that developed in the depths of a lake, showing cells of various
phototrophic bacteria.

b) A bacterial community in a sewage sludge sample. The sample was stained with a
series of dyes, each of which stained a specific bacterial group.

c) A microbial community scraped from a human tongue.

Figure 1.2 Bacterial cells and some cell structures
Flagella

Nucleoid Membrane Wall

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1.2 Microbial Cells
• Characteristics of Living
Systems

– Metabolism: chemical
transformation of
nutrients

– Reproduction: generation
of two cells from one

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1.2 Microbial Cells
• Characteristics of Living
Systems (Figure 1.3)
– Differentiation: synthesis
of new substances or
structures that modify the
cell (only in some
microorganisms )
– Communication:
generation of, and
response to, chemical
signals (only in some
microorganisms)

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1.2 Microbial Cells
• Characteristics of Living
Systems (Figure 1.4)
– Movement: via self-
propulsion (only in some
microorganisms)

– Evolution: genetic changes

in cells that are transferred
to offspring

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1.2 Microbial Cells
• Functions of the cells as Catalysts and as
Coding Devices

1. Cells carry out chemical reactions

• Enzymes: protein catalysts of the cell that
accelerate chemical reactions

2. Cells store and process information that is eventually

passed on to offspring during reproduction through
DNA and evolution (Figure 1.4)
• Transcription: DNA produces RNA
• Translation: RNA makes protein
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Figure 1.4 The catalytic and genetic functions of the cell

Genetic Catalytic
functions functions

DNA Energy conservation:

ADP + Pi ATP
Replication Transcription Metabolism: generation
of precursors of macro-
molecules (sugars, amino
RNA acids, fatty acids, etc.)
Enzymes: metabolic catalysts
Translation

Proteins

Growth

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1.3 Microorganisms and Their
Environments all living organisms plus
physical and chemical
constituents of their
environment

environment in which a
microbial population lives

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1.3 Microorganisms and Their
Environments
• Diversity and abundances of
microorganisms are controlled
by resources (nutrients) and
environmental conditions (e.g.,
temp, pH, O2)

N
C P
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Figure 1.6 A summary of life on Earth through time and origin of the cellular domains

Mammals Humans
Vascular
plants
Shelly Origin of Earth
invertebrates
Present (4.6 bya)
 20% O2

1 Origin of
4
bya cellular life
bya

O2
Anoxygenic
Algal phototrophic
diversity bacteria
2 3 Anoxic
bya bya Earth

Earth
Modern is slowly
eukaryotes oxygenated Origin of
cyanobacteria

Bacteria
LUCA
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1.4 Evolution and the Extent of
Microbial Life
• The Extent of Microbial Life
– Microorganisms found in almost every
environment imaginable
– Global estimate of 5  1030 cells
• Most microbial cells are found in oceanic and
terrestrial subsurfaces
– Microbial biomass is significant and cells are key
reservoirs of essential nutrients (e.g., C, P, N)

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1.5 The Impact of Microorganisms on
Humans
• Microorganisms can be both
beneficial and harmful to humans
• harmful microorganisms =>infectious
disease agents, or pathogens

• Many more microorganisms are

beneficial than are harmful
• Ex: Nitrogen fixing bacteria => convert
atmospheric nitrogen into fixed N that the
plants use for growth

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Figure 1.8 Death rates for the leading causes of death in the United States: 1900 and today

1900 2000
Influenza and Heart disease
pneumonia
Tuberculosis Cancer
Gastroenteritis Stroke
Heart disease Pulmonary
disease
Stroke Accidents
Kidney disease Diabetes

Accidents Alzheimer’s
disease
Cancer Influenza and
pneumonia
Infant diseases Kidney disease
Diphtheria Septicemia Infectious disease
Nonmicrobial disease
Suicide

0 100 200 0 100 200

Deaths per 100,000 population Deaths per 100,000 population

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1.5 The Impact of Microorganisms on
Humans
• Microorganisms and Agriculture
– Many aspects of agriculture depend on
microbial activities (Figure 1.9)
• Positive impacts
– nitrogen-fixing bacteria
– cellulose-degrading microorganisms in the rumen
– regeneration of nutrients in soil and water
• Negative impacts
– diseases in plants and animals

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Figure 1.9 Microorganisms in modern agriculture

Nitrogen fixing bacteria

N2 + 8H 2NH3 + H2 Soybean
plant

N-cycle S-cycle

Rumen
Grass Cellulose Glucose Microbial fermentation

Fatty acids CO2 + CH4

(Nutrition for animal) (Waste products)

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1.5 The Impact of Microorganisms on
Humans
• Microorganisms and Food
– Negative impacts
• Food spoilage by microorganisms requires
specialized preservation of many foods
– Positive impacts
• Microbial transformations (typically
fermentations) yield
– dairy products (e.g., cheeses, yogurt,
buttermilk)
– other food products (e.g., sauerkraut,
pickles, leavened breads, beer)
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1.5 The Impact of Microorganisms on
Humans
• Microorganisms, Energy, and the Environment

– Microorganisms are important in biofuels production

• Ex: methane, natural gas, ethanol, hydrogen

– The role of microorganisms in cleaning up pollutants

(bioremediation)
• Ex: consume spilled oil, solvents, pesticides, and
other environmentally toxic pollutants

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1.5 The Impact of Microorganisms on
Humans
• Microorganisms and Their Genetic Resources

– Microorganisms can be used for the

production of antibiotics, enzymes, and
various chemicals

– Genetic engineering use microorganisms to

generate products of value to humans, such
as insulin (biotechnology)

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II. Pathways of Discovery in
Microbiology
• 1.6 The Historical Roots of Microbiology
• 1.7 Pasteur and the Defeat of Spontaneous
Generation
• 1.8 Koch, Infectious Disease, and Pure
Culture Microbiology
• 1.9 The Rise of Microbial Diversity
• 1.10 The Modern Era of Microbiology

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1.6 The Historical Roots of Microbiology
• Microbiology began with the microscope
(Figure 1.12a)

Figure 1.12 Early microscopy

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1.6 The Historical Roots of Microbiology
• Robert Hooke (1635–1703): the first to
describe microorganisms
– Illustrated the fruiting structures of molds
(Figure 1.12b)

Figure 1.12 Robert Hooke and early microscopy

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1.7 Pasteur and the Defeat of
Spontaneous Generation
• Louis Pasteur (1822–1895) Spontaneous generation:
– Disproved theory of hypothesis that living
spontaneous generation organisms can originate
(Figure 1.16) from nonliving matter
• Led to the development of
methods for controlling the
growth of microorganisms: Aseptic technique:
aseptic technique using practices and
procedures to prevent
– Developed vaccines for contamination from
anthrax, fowl cholera, and pathogens
rabies

Pasteur’s Experiment

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Figure 1.16a

Steam, forced
out open end

Nonsterile liquid Neck of flask Liquid sterilized

poured into flask drawn out in flame by extensive heating

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Figure 1.16b

Dust and microorganisms

trapped in bend Open end

Long time

Liquid cooled Liquid remains

slowly sterile

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1.8 Koch, Infectious Disease, and the Rise
of Pure Cultures
• Robert Koch (1843–1910)
– Demonstrated the link between microorganisms
and infectious diseases
• Identified causative agents of anthrax and
tuberculosis

– Developed techniques (solid media) for obtaining

pure cultures of microorganisms

Koch’s Postulates

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Figure 1.19
KOCH’S POSTULATES

Diseased Healthy
The Postulates: Tools: animal animal

1. The suspected pathogen Microscopy, Red

must be present in all staining blood Observe
cases of the disease cell blood/tissue Red
and absent from healthy under the blood
Suspected microscope cell
animals.
pathogen

2. The suspected pathogen Laboratory Streak agar plate

No
must be grown in pure culture with sample
from either organisms
culture. diseased or present
Colonies of healthy animal
suspected
pathogen
Inoculate healthy animal with
cells of suspected pathogen

3. Cells from a pure Experimental

culture of the suspected animals
pathogen must cause
Diseased animal
disease in a healthy
animal.
Remove blood or tissue sample
and observe by microscopy

4. The suspected pathogen Laboratory Suspected Laboratory Pure culture

reisolation pathogen culture (must be
must be reisolated and same
shown to be the same and culture
organism
as the original. as before)

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1.10 The Modern Era of Microbiology

• In the 20th century, microbiology developed

in three distinct directions:
– Applied microbiology
– Basic microbiology
– Molecular microbiology

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1.10 The Modern Era of Microbiology
• Applied Microbiology:
– Medical microbiology and immunology

– Agricultural microbiology and industrial

microbiology

– Aquatic microbiology and marine microbiology

– Microbial ecology

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1.10 The Modern Era of Microbiology
• Basic Microbiology
– Microbial systematics
• The science of grouping and classifying
microorganisms
– Microbial physiology
• Study of the nutrients that microorganisms require
for metabolism and growth and the products that
they generate
– Cytology
• Study of cellular structure

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1.10 The Modern Era of Microbiology
• Basic Science Subdisciplines in Microbiology
– Microbial biochemistry
• Study of microbial enzymes and chemical
reactions
– Bacterial genetics
• Study of heredity and variation in bacteria
– Virology
• Study of viruses

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1.10 The Modern Era of Microbiology
• Molecular Microbiology
– Biotechnology
• Manipulation of cellular genomes
• DNA from one organism can be inserted into a
bacterium and the proteins encoded by that DNA
harvested
– Genomics: study of all of the genetic material
(DNA) in living cells
• Transcriptomics: study of RNA patterns
• Proteomics: study of all the proteins produced by
cell(s)
• Metabolomics: study of metabolic expression in cells
© 2012 Pearson Education, Inc.