Environmental Microbiology

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Environmental Microbiology

• What can you know from the title of this course
  shown above?
• 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(??) cut, diarrhea(??)
• size, shape.

Question 1
Question 2
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Chapter 1 Introduction
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What is Microbiology?

• 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
• Bacteria (??) 0.52 µm
• Archaea (??) 0.52 µm
• Fungi (??) 2200 µm
• Protozoa (????) mmcm
• Algae (??)
• Viruses (??) 20300 nm

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• Beside their small in size, they are
• 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.
• Diverse in their living habits (adaptation, live
  almost everywhere where life is possible
• High metabolic activities, fast reproduction.
• more numerous than any other kind of organisms
  (genetic diversity)
• global ecosystem depends on their activities
• influence human society in many ways
• Microorganisms are thought to have been living on
  the earth for 2.34.7 billion years.
• How many years have human beings been living on
  the earth?

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????????
Vertebrate????
Invertebrate?????
Origin
Eukaryotes
Prokaryotes only
40??
Dinosaurs??
Human
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Microbiology covers

• e.g., microbial morphology
• e.g., microbial physiology
• e.g., microbial genetics
• Microbial taxonomy
• Microbial cytology

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Fields of Microbiology

• 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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Current system of classification
Where are virus?
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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
• 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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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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Antony Van Leeuwenhock (1632-1723) Dutch
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Discovery of Microorganisms

• 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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First microorganism seen
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Golden Age of Microbiology(1857- 1914)

• Is spontaneous generation of microbial life
  exists?
• What causes fermentation?
• What causes diseases?
• How can we prevent infection and disease?

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Louis Pasteur (1822-1895)
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Louis Pasteur

• 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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Pasteurs experiment with the swan-necked flask

• 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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Swan-necked flask
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Tyndalls Dust-Free Box
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Joseph Lister (1827-1912)
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Joseph Lister (1827-1912)

• Developed a system of antiseptic (??) surgery
  (????) designed to prevent microorganisms from
  entering wounds
• Surgical instruments were heat sterilized
• Phenol prevented wound infection because it
  killed bacteria

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Robert Koch (1843-1910)
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Recognition of the Relationship between
Microorganisms and Disease

• Robert Koch (1843-1910)
• established the relationship between Bacillus
  anthracis and anthrax
• Announced that cause of tuberculosis(???) is a
  rod-shaped bacterium Mycobacterium tuberculosis

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One of Kochs first micrographs showing Bacillus
anthracis
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Kochs postulates

• 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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Development of Techniques for Studying Microbial
Pathogens

• Kochs work led to discovery or development of
• agar
• petridish
• nutrient broth and nutrient agar
• methods for isolating microorganisms

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• 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
• 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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Charles Chamberland (1851-1908)
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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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Other developmentsImmunological studies

• 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
• Pasteur and his coworkers
• developed vaccines for chicken cholera(??),
  anthrax(??), and rabies(???)

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More developments

• Emil von Behring (1854-1917) and Shibasaburo
  Kitasato (1852-1931)
• developed antitoxins for diphtheria and tetanus
• evidence for humoral immunity
• Elie Metchnikoff (1845-1916)
• discovered bacteria-engulfing, phagocytic cells
  in the blood
• evidence for cellular immunity

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Pure Culture Paradigm (??)
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 Kochs time Work with
impure cultures yields nothing but nonsense
and Penicillium glaucum (Oscar Brefield 1881)
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Sir Alexander Fleming (1929), examining exactly
such an impure culture (Staphylococcus culture
contaminated by Penicillium), led to the
discovery of penicillin.
zone of no bacterial growth, due to penicillin
produced by fungus
Agar petri dish Staphylococcus
colonies Penicillium contaminant
Interference competition! classic ecological
process
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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
• - all leading to the concept of chemoautotrophy
  deriving energy from chemical oxidation of
  inorganic compounds and carbon from CO2

Bacteria central in element transformations Found
er of soil microbiology
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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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Martinus Beijerinck (1851-1931)

• isolated N fixers and S reducers
• microbial ubiquity all microorganisms are
  everywhere conditions and resources determine
  who flourishes
• enrichment culture growth medium tailored to
  suit particular metabolic function
• with Winogradsky, recognized that microbes are
  the major players in element transformations
• led to field of global biogeochemistry

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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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Cornelius Bernardus van Niel (1897-1985)
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Cornelius Bernardus van Niel (1897-1985)

• Isolated purple sulfur bacteria
• Major contribution, chemistry of photosynthesis
• 2 H2A CO2 CH2O 2 A H2O
• 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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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
• ASM president when Environmental Microbiology
  and Microbial Ecology formally recognized

AKA Grampa Bob Anaerobic methodsCows and
termites
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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 1962.
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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
Frederick Sanger
Walter Gilbert
Paul Berg
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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.
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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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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 Deciphering the genome of the
smallest bacterial genome, Mycoplasma genitalium,
and investigating the minimum complement of genes
required to support life. Sequencing the first
complete genome from a representative of the
third domain of life, the Archaea. Playing a
key role in deciphering the DNA sequence of
Arabidopsis thaliana, the first plant genome
completed, as well as the sequences of rice and
other important crops.
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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 (??), cholera(??),
syphilis(??), meningitis(???), Lyme disease
anthrax(???) and gingivitis(???) as well as the
parasites that cause malaria(??), amoebic
dysentery (?????), and African Sleeping Sickness
(?????). Finding new ways to use genomics as a
tool for microbial forensics (??)and
demonstrating the potential to use microarray
technology for tumor diagnosis. Developing a
host of software tools that are widely
disseminated in the scientific community to
assemble, annotate and compare genomes.
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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 fixers
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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
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In the future microbiologists will be

• 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

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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 ever-increasing
  amount of data from genome studies

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Fields of Microbiology

• Microbial ecology-Environmental microbiology
• Medical microbiology
• Microbial genetics and molecular biology

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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)

Can you image what will be taught in this
subject???
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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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The End