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Feb 22, 2013 (4 years and 4 months ago)

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Introduction to Microbiology


Course Outcome 1: Ability to use
practical skills in fundamental
microbiological techniques.

The Evolution of Microorganisms and Microbiology

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The Importance of Microorganisms

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most populous and diverse group of organisms


found everywhere on the planet


play a major role in recycling essential elements


source of nutrients and some carry out photosynthesis


benefit society by their production of food, beverages,
antibiotics, and vitamins


some cause disease in plants and animals

Members of the Microbial World

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organisms and acellular entities too small to be clearly seen
by the unaided eye


some < 1 mm, some macroscopic


these organisms are relatively simple in their construction
and lack highly differentiated cells and distinct tissues

Figure 1.1

Type of Microbial Cells

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prokaryotic cells lack a true membrane
-
delimited nucleus


This is not absolute


eukaryotic cells have a membrane
-
enclosed nucleus, are
more complex morphologically, and are usually larger than
prokaryotic cells

Classification Schemes

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three domain system, based on a comparison of ribosomal
RNA, divides microorganisms into


Bacteria
(true bacteria)
,



Archaea



Eukarya (eukaryotes)

Domain

Bacteria

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Usually single
-
celled


Majority have cell wall with peptidoglycan


Most lack a membrane
-
bound nucleus


Ubiquitous and some live in extreme
environments


Cyanobacteria produce amounts of significant
oxygen

Domain

Archaea

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distinguished from
Bacteria

by unique rRNA sequences


lack peptidoglycan in cell walls


have unique membrane lipids


some have unusual metabolic characteristics


many live in extreme environments


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Figure 1.2 Universal Phylogenetic Tree

Domain
Eukarya
-

E
ukaryotic

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protists


generally larger than
Bacteria

and
Archaea


algae


photosynthetic


protozoa


may be motile, “hunters, grazers”


slime molds


two life cycle stages


water molds


devastating disease in plants



fungi


yeast
-

unicellular


mold
-

multicellular

Acellular Infectious Agents

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viruses


smallest of all microbes


requires host cell to replicate


cause range of diseases, some cancers


viroids and virusoids


infectious agents composed of RNA


prions


infectious proteins

Microbial Evolution


definition of life


cells and organization: organisms maintain an internal
order. Simplest unit of organization is the cell.


Energy use and metabolism: to maintain internal
order, energy is needed. Energy utilized in chemical
reactions
-

metabolism.


Response to environmental changes: organisms react
to environmental changes to promote their survival. If
nutrients conc supply low
-

form endospores.



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regulation and homeostasis: regulate cells to maintain
relatively stable internal conditions
-

homeostasis.


growth and development: growth produces more or
larger cells. Development produces organisms with a
defined set of characteristics.


Reproduction: to sustain life
-

organisms must
reproduce


Biological evolution: populations of organisms change
over the course of many generations. Evolution results
in traits that promote survival and reproductive
success. Ie. Evolve to become resistant to antibiotics.


Figure 1.3

Origins of Life


microbial fossils: the 1
st

direct evidence of primitive cellular
life was the discovered in:


Swartkoppie chert


granular silica


3.5 billion years old


fossil record sparse


indirect evidence and scientific method are used
to study origins of life

Figure 1.4: Microfossils of the
Archeon

Apex
Chert

of Australia.

Figure 1.5

Earliest Molecules
-

RNA


original molecule must have fulfilled protein and hereditary
function (Fig 1.6)


ribozymes



RNA molecules that form peptide bonds


perform cellular work and replication


RNA world hypothesis: Capable of storing, copying and expressing
genetic information as well as catalyzing other chemical reactions.


earliest cells may have been RNA surrounded by
liposomes
-

vesicles bounded by a lipid
bilayer
.


A fascinating exp. Performed by Marin
Hanczyc
, Shelly
Fujikawa

and Jack
Szostak

in 2003 showed that clay triggers the formation
of
liposomes

that actually grow and divide (Fig. 1.7).

Figure 1.6

Figure 1.7

Earliest Molecules


RNA
-

2


cellular pool of RNA in modern day cells exists in and is
associated with the ribosome (
rRNA
,
tRNA
, mRNA)


RNA catalytic in protein synthesis


RNA may be precursor to double stranded DNA
-

suggested
that once DNA evolved, it become storage facility for genetic
info
-

more stable structure.


2 other pieces of evidence support the RNA world
hypothesis:


Adenosine 5’
triphosphate

(ATP) is the energy currency
and is a
ribonucleotide


RNA can regulate gene expression


It seems that proteins, DNA and cellular energy can be
traced back to RNA.

Earliest Metabolism


Evolution of metabolism: the evolution of energy
-
conserving
metabolic processes. Early earth was a hot environment that
lacked O2.


Thus, early energy sources under harsh conditions


inorganics
, e.g.,
FeS
; there are heat
-
loving
archael

species capable of
using inorganic molecules as source of energy.


Oxygen
-
releasing photosynthesis


cyanobacteria

evolved 2.5 billion
ya


stromatolites



mineralized layers of microorganisms


The appearance of
cyanobacteria
-
like cells was an important step in
the evolution of life on earth.


The O2 they released ultimately altered earth’s atmosphere to its
current oxygen
-
rich state, allowing evolution of additional energy
capturing strategies such as aerobic respiration.


Figure 1.8 Section of Fossilized Stromatolite
-

layers of material
were formed when mats of cyanobacteria, layered one on top of
each other became mineralized.

Evolution of 3 Domains of Life


universal phylogenetic tree


based on comparisons of small subunit rRNA (SSU rRNA)


aligned rRNA sequences from diverse organisms are compared
and differences counted to derive a value of evolutionary
distance between organisms (Fig 1.9).


The distance from the tip of 1 branch to the tip of another
branch in the tree
-

represents evolutionary distance.


This distance is the measure of relatedness, but not time of
divergence. If the distance along the lines is very long
-

the
organisms are less related.

Figure 1.9

Endosymbiotic Hypothesis


Generally accepted as the origin of mitochondria,
chloroplasts, and hydrogenosomes from
endosymbiont
-

interaction between 2 organisms
in which 1 organism lives inside the other.


Endosymbiotic hypothesis
: proposed that over
time a bacterial endosymbiont of an ancestral
eukaryote lost its ability to live independently,
becoming either mitochondria (bacteria used aerobic
respiration) or chloroplast (endosymbiont was a
photosynthetic bacterium).

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Evidence to support the hypothesis:


mitochondria and chloroplasts


SSU rRNA show bacterial lineage


genome sequences closely related to
Richettsia

and
Prochloron,
respectively


Recently, the endosymbiont hypothesis has been
modified to hydrogen hypothesis



endosymbiont is anaerobic bacterium that
produces H
2

and CO
2


Hydrogenosomes
-

an organelle found in some protists,
produces ATP by a process called fermentation


Evolution of Cellular Microbes


Ancestral bacteria, archaea and eukaryotes possessed genetic
information that could be duplicated, lost or in some way mutated.


mutation of genetic material led to selected traits ie. Death or
sometimes led to new functions and characteristics to evolve.


new genes and genotypes evolved


Eukaryotic species
-

reproducing sexually


Bacteria and archaea
-

HGT


Bacteria

and
Archaea

increase genetic pool by horizontal gene transfer
within the same generation


Over time, new collections of genes arose and many species evolved.

Microbial Species


Species define as a group of interbreeding or potentially
interbreeding natural populations that is reproductively isolated
from other groups.


eukaryotic microbes fit definition of reproducing isolated
populations


Bacteria

and
Archaea

do not reproduce sexually and are referred to
as strains


strain consists of descendents of a single, pure microbial culture


may be
biovars

(strains characterized by
biochemical/physiological),
serovars

(distinctive properties
-

can be detected by antibodies),
morphovars

(morphology),
pathovars

(pathogenic strains distinguished by the plants in
which they cause disease

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Microbial naming: binomial nomenclature


The latinizined, italicized name: 2 parts


The capitalized part
-

generic name (name of genus to
which the microbe is belong to)


Uncapitalized: species epithet



The Golden Age


of

Microbiology


During the ‘
Golden Age of Microbiology
’, scientists and
the blossoming field of microbiology were driven by the
search for answers to the following four questions:


1)
Is
spontaneous generation

of microbial life possible?

2)
What cause fermentation?

3)
What cause disease?

4)
How can we prevent infection and disease?

Is spontaneous generation of microbial
life possible?


The theory of
spontaneous generation

(or
abiogenesis
) proposes
that
living organisms can arise from nonliving matter.


It was proposed by Aristotle (384

322 BC) and was widely accepted
for almost 2000 years, until experiments by Francesco Redi (1626

1697) challenged it.


In the 18th century, British scientist John T. Needham (1713

1781)
conducted experiments suggesting that perhaps spontaneous
generation of microscopic life was indeed possible, but in 1799,
experiments by Italian scientist Lazzaro Spallanzani (1729

1799)
reported results that contradicted Needham’s findings.


The debate continued until experiments by French scientist
Louis
Pasteur

(1822

1895) using swan
-
necked flasks that remained free of
microbes disproved the theory definitively.


Bent the flask neck into S
-
shape which allow air to enter

but prevent the introduction of dust and microbes

As long as the flask remained upright, no microbial growth appeared in the liquid

Conclude : Microbes in the liquid were the progeny of microbes that had been on the
dust particles



The debate over spontaneous generation led in part to the
development of a generalized
scientific method

by which
questions are answered through observations of the
outcomes of carefully controlled experiments
.


It consists of four steps:


1.
A group of observations leads a scientist to ask a question about some
phenomenon.

2.
The scientist generates a hypothesis

a
potential answer

to the
question.

3.
The scientist designs and conducts an experiment to test the
hypothesis.

4.
Based on the observed results of the experiment, the scientist either
accepts, rejects, or modifies the hypothesis.



The scientific method

SCIENTIFIC METHOD

What causes fermentation?


The mid 19th century also saw the birth of the field of
industrial
microbiology
(or
biotechnology
), in which
microbes are
intentionally manipulated to manufacture products
.



Pasteur’s investigations into the cause of fermentation led to the
discovery that yeast can grow with or without oxygen, and that
bacteria ferment grape juice to produce acids, whereas yeast cells
ferment grape juice to produce alcohol.



These discoveries suggested a method to prevent the spoilage of
wine by heating the grape juice just enough to kill contaminating
bacteria, so that it could then be inoculated with yeast.


Experiment by Pasteur that answered the question “What cause fermentation?”


Pasteurization
, the use of heat to kill pathogens and reduce the
number of spoilage microorganisms in food and beverages, is an
industrial application widely used today.



In 1897, experiments by the German scientist Eduard
Buchner (1860

1917) demonstrated the presence of
enzymes
, that
promote chemical reactions such as
fermentation
.



His work began the field of

biochemistry

and the
study of
metabolism
, a term that refers to the sum of
all chemical reactions in an organism.


What cause disease?


Prior to the 1800s, disease was attributed to various factors such
as evil spirits, sin, imbalances in body fluids, and foul vapors.


Pasteur’s discovery that bacteria are responsible for spoiling wine
led to his hypothesis in 1857 that microorganisms are also
responsible for diseases, an idea that came to be known as the
germ theory of disease
.


In direct evidence for the germ theory of disease
-

Joseph Lister
(English surgeon) on prevention of wound infections.


He developed a system of antiseptic surgery designed to prevent
microorganisms from entering wounds.


Microorganisms that cause specific diseases are called
pathogens
.


Today we know that diseases are also caused by genetics,
environmental toxins, and allergic reactions; thus, the germ
theory applies only to
infectious
disease


Investigations into etiology,
the study of the causation of
disease
, were dominated by German physician
Robert Koch

(1843

1910).


Koch initiated careful microbiological laboratory techniques
in his search for disease agents, such as the bacterium
responsible for anthrax.


He and his colleagues were responsible for developing
techniques to isolate bacteria, stain cells, estimate population
size, sterilize growth media, and transfer bacteria between
media.


They also achieved the first photomicrograph of bacteria.


But one of Koch’s greatest achievements was the elaboration,
in his publications on tuberculosis, of a
set of steps that must
be taken to prove the cause of any infectious disease
.



Koch and his colleagues are also responsible for many other
advances in laboratory microbiology, including:



Simple staining techniques for bacterial cells and flagella


The first photomicrograph of bacteria


The first photograph of bacteria in diseased tissue


Techniques for estimating the number of bacteria in a solution
based on the number of colonies that form after inoculation onto
a solid surface


The use of steam to sterilize growth media


The use of Petri dishes to hold solid growth media


Aseptic laboratory techniques such as transferring bacteria
between media using a platinum wire that had been heat
-
sterilized in a flame


Elucidation of bacteria as distinct species



Koch elucidated a series of steps that must be taken to
prove the
cause of any infectious disease
.


These four steps are now known as
Koch’s postulates
:


1.
The suspected causative agent must be found in every case of the
disease and be absent from healthy hosts.

2.
The agent must be isolated and grown outside the host.

3.
When the agent is introduced to a healthy, susceptible host, the
host must get the disease.

4.
The same agent must be reisolated from the diseased experimental
host.


Koch’s postulates applied to
Tuberculosis


How can we prevent infection and
disease?


In the mid
-
19th century, modern principles of hygiene, such as
those involving sewage and water treatment, personal cleanliness,
and pest control, were not widely practiced.



Medical facilities and personnel lacked adequate cleanliness


Semmelweis & handwashing


In approximately 1848, Viennese physician Ignaz Semmelweis
(1818

1865) noticed that women whose births were attended by
medical students died at a rate 20 times higher than those whose
births were attended by midwives in an adjoining wing of the same
hospital or at home.




He hypothesized that “cadaver particles” from the hands of the
medical students caused puerperal fever, and required
medical students to
wash their hands in chlorinated lime
water

before attending births.



Dead from puerperal fever in the subsequent year dropped
from 18.3% to 1.3%.


Lister & antiseptic technique


A few years later, English physician Joseph Lister (1827

1912) advanced the idea of antisepsis in health care settings,
reducing deaths among his patients by two
-
thirds with the use
of phenol. (
spraying wounds, surgical incisions and dressing
with phenol
)

Modern Age

of

Microbiology


Since the early 20th century, microbiologists have worked to
answer new questions in new fields of science :


1)
What are the basic chemical reactions of life?

2)
How do genes work?

3)
What role does microorganisms play in the environment?

4)
What will the future hold?


What are the basic chemical reactions
of life?


Biochemistry
is the study of metabolism (chemical reaction in life)



It began with Pasteur’s work on fermentation and Buchner’s discovery
of enzymes, but was greatly advanced by the proposition of
microbiologists Albert Kluyver (1888

1956) and C. B. van Niel
(1897

1985) that biochemical reactions are shared by all living things,
are few in number, and involve the transfer of electrons and hydrogen
ions.



In adopting this view, scientists could begin to use microbes as model
systems to answer questions about metabolism in other organisms.



Today, biochemical research has many practical applications,
including: the design of herbicides and pesticides; the
diagnosis of illness; the treatment of metabolic diseases; and
the design of drugs to treat various disorders.


How do genes work?


Microbial genetics is the study of inheritance in microorganisms.



Throughout the 20th century, researchers working with microbes made
significant advances in our understanding of how genes work.



For example, they established that a gene’s activity is related to the
function of the specific protein coded by that gene, and they
determined the exact way in which genetic information is translated
into a protein.



Molecular biology

combines aspects of biochemistry, cell biology,
and genetics to explain cell function at the molecular level.



It is particularly concerned with genome sequencing.


Genetic engineering

involves the manipulation of genes in
microbes, plants, and animals for practical applications, such as the
development of pest
-
resistant crops and the treatment of disease.



Gene therapy

is the use of recombinant DNA (DNA composed of
genes from more than one organism) to insert a missing gene or
repair a defective gene in human cells.



What role do microorganisms play in
the environment?


Environmental microbiology

studies the role
microorganisms play in their natural environment.



Microbial communities play an essential role, for example, in the
decay of dead organisms and the recycling of chemicals such as
carbon, nitrogen, and sulfur.



Environmental microbiologists study the microbes and chemical
reactions involved in such biodegradation, as well as the effects of
community
-
based measures to limit the abundance of pathogenic
microbes in the environment, such as sewage treatment, water
purification, and sanitation measures.


What will the future hold?

Among the questions microbiologists are working to answer today are the
following:


• What prevents certain life forms from being grown in the laboratory?

• Can microorganisms be used in ultraminiature technologies such as
computer circuit boards?

• How can an understanding of microbial communities help us understand
communities of larger organisms?

• What can we do at a genetic level to defend against pathogenic
microorganisms?

• How can we reduce the threat of new and re
-
emerging infectious
diseases?


Impact of microorganisms on humans


Microorganisms as Disease Agents


Microorganisms and Agriculture


Microorganisms and Food


Microorganisms, Energy, and the Environment


Microorganisms and the future