Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Environmental Microbiology
Question 1
What can you know from the title of this
course shown above?
Question 2
You must have already been told or leant
something about microorganisms. Tell me
what are they (e. g microorganisms) all what
you have known.
Hints: SARS, cold, hospital,
skin/muscle(肌肉) cut, diarrhea(痢疾)
size, shape…….
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Chapter 1
Introduction
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
What is Microbiology?
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Microbiology is the study of organisms too
small to be clearly seen by the unaided eye
(i.e., microorganisms) and how they are
living/working/surviving.
– Microorganisms include
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Bacteria (细菌)
Archaea (古菌)
Fungi (真菌)
Protozoa (原生动物)
Algae (藻类)
Viruses (病毒)
0.5~2 µm
0.5~2 µm
2~200 µm
mm~cm
20~300 nm
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Beside their small in size, they are:
1. Basically unicellular, their life dose not depend on other cells. It
means that ONE cell is a complete life, which distinguishes from
other multicultural organisms.
2. Diverse in their living habits (adaptation, live almost everywhere
where life is possible
3. High metabolic activities, fast reproduction.
4. more numerous than any other kind of organisms (genetic diversity)
5. global ecosystem depends on their activities
6. influence human society in many ways
Microorganisms are thought to have been living on
the earth for 2.3~4.7 billion years.
How many years have human beings been living on the earth?
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
生物演化时间略表
Origin
Prokaryotes only
Vertebrate脊椎动物
Invertebrate无脊椎动物
Eukaryotes
40亿年
Dinosaurs恐龙
Human
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Microbiology covers
– e.g., microbial morphology
– e.g., microbial physiology
– e.g., microbial genetics
– Microbial taxonomy
– Microbial cytology
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Fields of Microbiology
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Virology = Study of viruses
Bacteriology = Study of bacteria
Phycology = Study of algae
Mycology = Study of fungi
Protozoology = Study of protozoa
Food and dairy microbiology
Agricultural microbiology
Microbial ecology
Medical microbiology
Microbial genetics and molecular biology
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Current system of classification
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Where are virus?
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC

What is Environmental
Microbiology?
Environmental Microbiology covers the same
subjects stated in previous slide, but stresses
on the organisms and their roles in producing
and/or eliminating environmental problems.
– Subject includes
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Biological treatment of wastes (liquid, solid, gaseous)
Biogeochemical roles in element cycling
Microbial transformation of toxic materials in environments
Interactions between them/other organisms
Microorganisms relevant to public health
Tools and technologies to study/know them
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Brief history of Microbiology
See how Microbiology as a science was
developed and think what we can know
from the history.
1 Observation tools
2 Fight against food decay and diseases
3 From laboratory to natural environment
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Antony Van
Leeuwenhock
(1632-1723)
Dutch
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Discovery of Microorganisms
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Antony van Leeuwenhoek (1632-1723)
– Built more than 500 microscopes
– first person to observe and describe
microorganisms accurately
– Known today as the father of
protozoology and bacteriology
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
First microorganism seen
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Golden Age of Microbiology
(1857- 1914)
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Is spontaneous generation of microbial
life exists?
What causes fermentation?
What causes diseases?
How can we prevent infection and
disease?
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Louis Pasteur
(1822-1895)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Louis Pasteur
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Louis Pasteur
– Rejected theory of spontaneous
generation
– demonstrated that alcohol fermentations
and other fermentations were the result of
microbial activity
– developed the process of pasteurization
to preserve wine during storage by
heating wine just enough to kill bacteria
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Pasteur’s experiment with
the swan-necked flask
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Nonsterile liquid poured into flask
Neck of flask drawn out in flame
Liquid sterilized by heating
Liquid cooled slowly
Dust and microorganisms trapeped in bend
Liquid remains sterile for many years
Flask tipped so microorganisms-laden dust
contacts sterile liquid
Microorganisms grow in liquid
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Swannecked
flask
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Tyndall’s Dust-Free Box
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Joseph Lister
(1827-1912)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Joseph Lister (1827-1912)

Developed a system of antiseptic (无菌)
surgery (外科手术) designed to
prevent microorganisms from entering
wounds
– Surgical instruments were heat sterilized
– Phenol prevented wound infection
because it killed bacteria
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Robert Koch
(1843-1910)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Recognition of the Relationship
between Microorganisms and Disease
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Robert Koch (1843-1910)
– established the relationship between
Bacillus anthracis and anthrax
– Announced that cause of tuberculosis(肺
结核) is a rod-shaped bacterium;
Mycobacterium tuberculosis
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
One of Koch’s first micrographs
showing Bacillus anthracis
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Koch’s postulates
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The microorganism must be present in
every case of the disease but absent from
healthy individuals.
The suspected microorganism must be
isolated and grown in a pure culture.
The same disease must result when the
isolated microorganism is inoculated into a
healthy host.
The same microorganism must be isolated
again from the diseased host.
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Development of Techniques for
Studying Microbial Pathogens
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Koch’s work led to discovery or
development of:
– agar
– petridish
– nutrient broth and nutrient agar
– methods for isolating microorganisms
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC

Fannie Hesse suggested the use of
agar as solidifying agent
– Agar was not attacked by bacteria
– Did not melt until reaching a temperature
of 100 0C
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Richard Petri developed the petri dish,
a container for solid culture media that
is currently used in every micro lab all
over the world.
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Charles
Chamberland
(1851-1908)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Charles Chamberland
(1851-1908)
– discovered viruses and their role in
disease
– developed porcelain bacterial filter
– discovered the first viral pathogen,
Tobacco Mosaic Virus TMV
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Other developments…
Immunological studies
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Pasteur and Roux
– discovered that incubation of cultures for
long intervals between transfers caused
pathogens to lose their ability to cause
disease
– Attenuated culture is a vaccine
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Pasteur and his coworkers
– developed vaccines for chicken
cholera(霍乱), anthrax(炭疽), and
rabies(狂犬病)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
More developments…
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Emil von Behring (1854-1917) and
Shibasaburo Kitasato (1852-1931)
– developed antitoxins for diphtheria and tetanus
– evidence for humoral immunity
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Elie Metchnikoff (1845-1916)
– discovered bacteria-engulfing, phagocytic cells
in the blood
– evidence for cellular immunity
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Pure Culture Paradigm (范例)
– extremely important conceptual development in
microbiology
(and in microbial ecology, too)
remove organisms from complex communities
isolate key processes
obtain reproducible results
This method is still used today
Attitude of Koch’s time:
“Work with impure cultures yields nothing but nonsense and
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Penicillium glaucum“ (Oscar Brefield 1881)
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Sir Alexander Fleming (1929), examining exactly such an
impure culture (Staphylococcus culture contaminated by
Penicillium), led to the discovery of penicillin.
Agar petri dish
zone of no bacterial growth,
due to penicillin produced by fungus
Staphylococcus
colonies
Penicillium
contaminant
Interference competition!
classic ecological process
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Sergei Winogradsky
(A Russian microbiologist
1856-1953)
- isolated nitrifying bacteria
- winogradsky column: microbial
communities develop along a
gradient of oxygen tension; method
still used today
- described oxidation of hydrogen
sulfide, sulfur, ferrous iron
Bacteria: central in element
transformations
Founder of soil microbiology
- …all leading to the concept of
chemoautotrophy – deriving energy
from chemical oxidation of
inorganic compounds and carbon
from CO2
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Martinus Beijerinck (1851-1931)
A Dutch microbiologist
“The way I approach
microbiology...can be concisely
stated as the study of microbial
ecology, i.e., of the relation
between environmental
conditions and the special forms
of life corresponding to them”
Founder of the Dutch Delft School
Of Microbiology
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Martinus Beijerinck (1851-1931)
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isolated N fixers and S reducers
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‘microbial ubiquity’: all microorganisms are everywhere;
conditions and resources determine who flourishes
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enrichment culture: growth medium tailored to suit
particular metabolic function
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with Winogradsky, recognized that microbes are the major
players in element transformations
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led to field of global biogeochemistry
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Albert Jan Kluyver (1888-1956)
-student of Beijerinck
-microbial physiology
-comparative approach
-unifying metabolic
features among microbes
-leader of the Dutch school
after Beijerinck
microbial physiology
comparative approach
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Cornelius Bernardus van Niel
(1897-1985)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Cornelius Bernardus van Niel
(1897-1985)
-Isolated purple sulfur bacteria
-Major contribution, chemistry of photosynthesis:
2 H2A + CO2
CH2O + 2 A + H2O
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where A can be Sulfur or Oxygen…
-extended model to photosynthesis in green plants
-oxygen from water, not from CO2
-Also, chemistry of denitrification, definition of prokaryote in 1961
(with R. Stanier)
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Robert E. Hungate
(1908-2004)
-student of van Niel
-methods for isolating anaerobes
-culture methods – select using
natural substrates, rather than
guesses about what organisms
eat
-microbiology of guts of rumen,
termites
AKA “Grampa Bob”
Anaerobic methods
Cows and termites
-ASM president when
“Environmental Microbiology”
and “Microbial Ecology” formally
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recognized
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
double-helix structure of DNA
In 1953 James Watson and
Francis Crick publish a
description of the double-helix
structure of DNA. The paper
acknowledges that the authors
were "stimulated by knowledge
of the unpublished experimental
results of" Maurice Wilkins and
Rosalind Franklin, whose x-ray
crystallography images of DNA
suggested the structure. Franklin
died in 1958; Watson, Crick and
Wilkins are awarded the Nobel
Prize in Physiology or Medicine in
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1962.
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Frederick Sanger developed a method to sequence
DNA in 1977. He and his co-workers Paul Berg and
Walter Gilbert received the Nobel Prize in Chemistry
in 1980
Paul Berg
Walter Gilbert
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Frederick Sanger
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Carl Woese uses ribosomal RNA analysis to
identify a third form of life, the Archea,
whose genetic makeup is distinct from but
related to both Bacteria and Eucaryea.
Archaea
Eukarya
Bacteria
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Kary B. Mullis invented the polymerase chain
reaction (PCR) method in 1983. He and Kary B.
Mullis received The Nobel Prize in Chemistry 1993
Kary B. Mullis
Michael Smith
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Genomic Sequence: Contribution from The
Institute for Genomic Research (TIGR)
The Institute for Genomic Research (TIGR) published the first
full DNA sequence of a free-living organism Haemophilus
influenzae in 1995, which followed up that achievement with a
rapid-fire series of scientific accomplishments, including:
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Deciphering the genome of the smallest bacterial
genome, Mycoplasma genitalium, and investigating the
minimum complement of genes required to support life.
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Sequencing the first complete genome from a
representative of the third domain of life, the Archaea.
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Playing a key role in deciphering the DNA sequence of
Arabidopsis thaliana, the first plant genome completed, as well
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as the sequences of rice and other important crops.
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Genomic Sequence: Contribution from The
Institute for Genomic Research (TIGR)
Deciphering the genome sequences of more than three
dozen human pathogens, including the bacteria that cause
pneumonia (肺炎), cholera(霍乱), syphilis(梅毒), meningitis(脑
膜炎), Lyme disease anthrax(炭疽热) and gingivitis(齿龈炎) as
well as the parasites that cause malaria(疟疾), amoebic
dysentery (阿米巴痢疾), and African Sleeping Sickness (非洲昏
睡病).
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Finding new ways to use genomics as a tool for microbial
forensics (毒物)and demonstrating the potential to use
microarray technology for tumor diagnosis.
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Developing a host of software tools that are widely
disseminated in the scientific community to assemble, annotate
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and compare genomes.
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Other Contributions
1960s: Ronald Atlas, Richard Bartha
- studies of petroleum degradation
- led to new field of bioremediation,
- extended to many other pollutants: DDT,
PCBs, mercury,
selenium, industrial solvents
1970s fuel-shortage:
- shortage in N fertilizer
- sparked interest in the biology of nitrogen 48
fixers
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Current trends in Environmental microbiology:
A. space exploration – microbes in extreme environments
(hot springs, thermal vents, lithosphere)
B. molecular techniques – diversity of microorganisms
(Carl Woese), new methods to assess presence/abundance
of individual species in situ
C. realization that with pure culture/enrichment techniques,
we know somewhere between 1-10% of existing microbial
species – lots to learn!
D. biology of climate change, global biogeochemistry
49
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
In the future
microbiologists will be
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Trying to better understand and control
existing, emerging, and reemerging
infectious diseases
Studying the association between infectious
agents and chronic diseases
Learning more about host defenses and
host-pathogen interactions
Developing new uses for microbes in
industry, agriculture, and environmental
control
50
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
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Still discovering the many microbes
that have not yet been identified and
cultured
Trying to better understand how
microbes interact and communicate
Analyzing and interpreting the everincreasing amount of data from
genome studies
51
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Fields of Microbiology
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Microbial ecology-Environmental
microbiology
Medical microbiology
Microbial genetics and molecular
biology
52
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
Summary of this chapter
1.What is microorganisms, microbiology,
environmental microbiology?
2.Characteristics of microorganisms
3.Three domains of life
4.Scope of microbiology
5.Brief history of microbiology (try to remember a
few important events and heroes involved, e. g.
Louis Pasteur, Robert Koch ……)
6.Future trends of microbiology (molecular)
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Can you image what will be taught in this subject???
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
After Introduction, can
you image what will be
taught in this subject
??? This question
speaks itself why we
say so much in this first
class.
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Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
The End
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