Environmental Microbiology

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Environmental Microbiology Instructor Dr.
I-Cheng Tseng Class hour Mon. 1500 to 1800
PM Class Bio3417 Contact 65535 E-MAIL
icheng_at_mail.ncku.edu.tw Madigan, M., J.
Martinko, and J. Parker, Brock Biology of
Microorganisms.. Maier, R., I. Pepper, and C.
Gerba, Environmental Microbiology. Atlas R. and
R. Bartha, Microbial Ecology. The selected papers
as listed in the course syllabus.
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Environmental Microbiology 1 Introduction and
Historical Perspective
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Environmental Microbiology
Microbiology

• The study of microorganisms

• The study of the interaction of microorganisms
  within an environment.
• The study of microbes in the environment to
  benefit society.

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Microorganisms
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Bacteria are so small Could they be really
important?

• Disease agents
• Agricultural implication
• Food
• Energy production
• Bioremediation
• Biotechnology

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Historical Perspectives of Microbiology
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Early Days in Microbiology (1676- 1930s)
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• Described oxidation of hydrogen sulfide, sulfur,
  ferrous iron
• Isolated nitrifying bacteria
• Winogradsky column microbial communities develop
  along a gradient of oxygen tension method still
  used today
• All leading to concept of chemoautotrophy
  deriving energy from chemical oxidation of
  inorganic compounds and carbon from CO2

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• Isolated N fixers and S reducers
• Enrichment culture growth medium tailored to
  suit particularmetabolic function
• Microbial ubiquity everythingis everywhere,
  the environment selects.
• With Winogradsky, recognized that microbes are
  the major players in element transformations
• Led the field of biogeochemistry
• Characterized distribution, nutrition and
  taxonomy of luminescent bacteria.

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Molecular and General Microbiology (1940s to
1980s)

• James Watson and Francis Crick (1953)
  discovered the structure of DNA.
• Carl Woes (1977) used ribosomal RNA analysis to
  recognize a third form of life, the Archaea,
  whose genetic makeup is distinct from but related
  to both Bacteria and Eucarya.
• Walter Gilbert and Fred Sanger(1977) developed
  methods to determine the exact sequence of DNA.
• Kary Mullic (1986) used a heat stable enzyme
  from Thermus aquaticus to establish PCR.

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Phylogenetic tree of tree domains
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Molecular Microbial Ecology and Genome (since
1986)

• Norman Pace (1986) developed molecular methods
  to investigate uncultivated microorganisms in the
  environment.
• Craig Venter and Hamilton Smith (1995) completed
  the first genome sequence of bacteria.
• Edward Delong (2000) discovered the diversity of
  marine Archaea and developed environmental
  genomic techniques to access the genomes of
  uncultured marine microbes.
• Craig Venter and others (2004) reported a large
  scale of environmental genome sequences from the
  Sargasso Sea.

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Norman Pace (1986) Molecular microbial ecology
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Venter and TIGR (since 1995) Microbial genome

• The first complete genome sequence from a
  microorganism Haemophilus influenzae (1.8 Mbp).
• Since then, more than 300 microbial genomes are
  sequenced or in progress.
• Different groups of marine microbes
  (heterotrophic bacteria, autotrophic bacteria and
  eukaryotic algae) were selected for sequencing.

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Edward DeLong (2000) Environmental genome
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Craig Venter and other (since 2004)
Environmental genome sequencinghttp//www.sorcere
r2expedition.org/version1/HTML/main.htm
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Major Questions in Environmental Microbiology

• Who is there?
• What are they doing there?
• How much are they doing there?