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					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…….
                                                                   1
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




             Chapter 1   Introduction




                                        2
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             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 (细菌)     0.5~2 µm
                           Archaea (古菌)      0.5~2 µm
                           Fungi (真菌)        2~200 µm
                           Protozoa (原生动物)   mm~cm
                           Algae (藻类)
                           Viruses (病毒)      20~300 nm
                                                               3
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.
                                                                      4
How many years have human beings been living on the earth?
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



                             生物演化时间略表
                                                     Vertebrate脊椎动物
                                              Invertebrate无脊椎动物
       Origin           Prokaryotes only   Eukaryotes          40亿年




                                                        Dinosaurs恐龙

                                                              Human


                                                                  5
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



                                                 6
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




             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
                                                            7
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




   Current system of classification




                                      8
 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
                           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
                                                                                   9
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
                                                  10
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




 Antony Van
 Leeuwenhock
 (1632-1723)
 Dutch


                        11
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             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



                                                           12
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




                        13
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             First microorganism seen




                                        14
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC


             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?


                                                      15
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




 Louis Pasteur
 (1822-1895)




                        16
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




             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

                                                             17
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             Pasteur’s 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
                                                             18
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




 Swan-
 necked
 flask




                        19
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




                        Tyndall’s Dust-Free Box




                                                  20
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




             Joseph Lister
             (1827-1912)




                             21
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


                                                                22
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




       Robert Koch
       (1843-1910)




                        23
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




             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(肺
                   结核) is a rod-shaped bacterium;
                   Mycobacterium tuberculosis

                                                            24
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC

             One of Koch’s first micrographs
             showing Bacillus anthracis




                                               25
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             Koch’s 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.

                                                               26
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC

             Development of Techniques for
             Studying Microbial Pathogens

                Koch‟s work led to discovery or
                 development of:
                  – agar
                  – petridish
                  – nutrient broth and nutrient agar
                  – methods for isolating microorganisms



                                                           27
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
                Richard Petri developed the petri dish,
                 a container for solid culture media that
                 is currently used in every micro lab all
                 over the world.                                28
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




   Charles
   Chamberland
   (1851-1908)




                        29
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



                                                           30
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC

             Other developments…
             Immunological 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(霍乱), anthrax(炭疽), and
                    rabies(狂犬病)
                                                                 31
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             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


                                                                      32
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
     Penicillium glaucum“ (Oscar Brefield 1881)               33
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.
                                          zone of no bacterial growth,
                                          due to penicillin produced by fungus
  Agar petri dish

 Staphylococcus
        colonies

       Penicillium
     contaminant



             Interference competition!
             classic ecological process
                                                                         34
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
                                 - …all leading to the concept of
                                 chemoautotrophy – deriving energy
                                 from chemical oxidation of
                                 inorganic compounds and carbon
  Bacteria: central in element   from CO2
       transformations                                            35
  Founder of soil microbiology
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                       36
              Of Microbiology
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



                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
                                                                  37
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                            38
                comparative approach
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC
                        Cornelius Bernardus van Niel
                                         (1897-1985)




                                                 39
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

  -       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)
                                                                  40
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
                             -ASM president when
                             “Environmental Microbiology”
         AKA “Grampa Bob”    and “Microbial Ecology” formally
         Anaerobic methods
         Cows and termites
                             recognized                  41
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
                              1962.                         42
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




                                                     43

      Paul Berg         Walter Gilbert   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



                                                44
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




                                                         45

                        Kary B. Mullis   Michael Smith
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:
   •     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
                                                              46
   as the sequences of rice and other important crops.
Shixue Yin (Prof Dr)
Microbiology Section

               Genomic Sequence: Contribution from The
CESE, YZU, 225009 PRC



               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).
  •      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.
  •     Developing a host of software tools that are widely
  disseminated in the scientific community to assemble, annotate
                                                             47
  and compare genomes.
Shixue Yin (Prof Dr)
Microbiology Section


                          Other Contributions
CESE, YZU, 225009 PRC




 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
                       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




                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
                                                         51
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC



             Fields of Microbiology

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



                                                    52
Shixue Yin (Prof Dr)
Microbiology Section

                        Summary of this chapter
CESE, YZU, 225009 PRC




 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???
                                                  53
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.                  54
Shixue Yin (Prof Dr)
Microbiology Section
CESE, YZU, 225009 PRC




                        The End



                                  55

				
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