Lecture 6

Question 1

What are 4 methods for studying microbial ecology?

Answer 1

1. Pure culture
2. Microcosms
3. Culture independent
4. Genomics based

Question 2

Describe pure-culture studies

Answer 2

• Method for studying microbial ecology
• Focus on one or a few species in synthetic media
• Growth curves, physiological, genetic, medical studies
• Of limited relevance to study ecological roles of that microbe. Especially as ost microbes cannot be grown in pure culture

Question 3

Describe microcosms?

Answer 3

• natural habitat samples in the lab
• Winogradsky columns
• not pure culture, but kept under controlled conditions
• One can manipulate parameters (i.e. temp, nutrients, radioactive tracers)
• Enrichment for certain organisms i.e. to enrich for N2-fixing bacteria
• Monitor responses with or without manipulations (nutrient consumption, pollutant biodegradation, waste production etc)
• Use molecular biology tools to monitor presence of genes or gene products in populations (genes=> DNA, genes expression => RNA)
• Could attempt to isolate pre cultures from the microcosm

Question 4

Describe culture-independent (in situ) studies

Answer 4

• direct study of complex communities in environmental samples but with no culturing or enrichment

Question 5

What does culture-independent investigate?

Answer 5

• Where the microbes are (detect)
• Which species (or phyla) are present (identify)
• Population sizes and fluctuations (quantify)
• Physiological and ecological functions functions (characterize)

Question 6

What are some culture-independent methods?

Answer 6

• Measurement of gases and other metabolites often using radioactive isotope tracers
• Molecular biological methods
• Microscopy (FISH)
  - Fluorescent in situ hybridization)
  - FISH microscopy to visualize specific cells (CARD-FISH)
• Stable isotope probing (SIP) studies (DNA- SIP)

Question 7

What are some biological techniques used in culture-INdependent studies?

Answer 7

• extraction of nucleic acids (DNA/ RNA )
• identification and/or quantification of phylogenetically-relevant or fucntion genes & gene products (RNA, proteins)
  - PCR, DNA sequencing, qRT-PCR
  - Hybridization-based techniques (blots, arrays, FISH, etc)
• Amplification and seperation of genes via PCR amplication and denaturing gradient gel electrophoresis (DGGE)
• Cloning of amplified genes for further study
• bioinformatics

Question 8

revoir slide 106-107

Answer 8

Woese

Question 9

What is a monera?

Answer 9

• Concept originated by Haeckel in the mid 19th century for microbes that were not protists
• More rencent definition: single-celled procaryotic organisms
  - Generally referred to as bacteria, rarely as eubacteria
  - The concpet of what a bacterium or procaruote was proved impossible to define
• In 1977 Woese proposed that there were 2 types of bacteria; eubacteria and archeabacteria