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Lecture 12

BIOLOGY 2EE3 Lecture Notes - Lecture 12: Extracellular Polymeric Substance, Biofilm, Activated Sludge


Department
Biology
Course Code
BIOLOGY 2EE3
Professor
Turlough Finan
Lecture
12

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Microbial Ecosystems
Culturable: capable of culture
Biofilm: a thin, slimy film of bacteria that adheres to a surface
Enrichment cultures: medium with specific and known qualities that favor growth
of a particular microorganism
Stable isotope probing: technique for tracing fluxes of nutrients in biochemical
cycling by microorganisms
- A substrate is enriched with a heavier stable isotope that is consumed by the
organisms to be studied
Microbial diversity
Aquatic eutrophication: the process by which a body of water becomes enriched in
dissolved nutrients that stimulate growth of aquatic plant life usually resulting in
the depletion of dissolved oxygen
In nature, do microbes exist as pure cultures?
- No!
- Number of culturable microbes is very low
Culturability
- Seawater: 0.001-0.1 %
- Freshwater: 0.25%
- Unpolluted estuarine waters: 0.1-3 %
- Activated sludge: 1-15%
- Sediments: 0.25%
- Soil: 0.3 %
Ecosystems
- Communities described as functional groups
- Microbes (very small) exist in microenvironments
- Conditions can change in microenvironments over short distances
- Success of microbes in a niche depends on ability to obtain nutrients to
produce energy and biomass
Biofilms
- Groups/layers of microbes on a surface that interact with and support each
other
- Found often in nature
- Also of practical importance to humans who want to rid a surface of
microbes
Microbes in the Environment: Biofilms
1) Adhesion by a primary colonizer occurs
2) Cells divide
3) Micro-colony produces exopolysaccharide (EPS)
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4) Introduction of secondary colonizers and growth of the biofilm community
Biofilm
- Begins with attached bacteria forming the primary layer on surface
o Secondary colonizers then join the biofilm
o Together, the microbes secrete exopolysaccharide (EPS)
EPS helps protect the biofilm but also helps form water-filled
channels for transport of nutrients and wastes
Bad Biofilms
- Can grow on medical implantsopportunity for infection
- Biofilms on food-contact surfaces afford pathogens such as E. coli and
Salmonella the opportunity to survive
Enrichment Culture
- Classical and successful method to isolate particular groups of
microorganisms
o The desired microbe may grow slowly and may be rare
o Enrichment methods promote growth of desired microbes over
undesired cells
o Enrichment methods are very useful (biodegradation, etc.)
- Example
o Enrichment for a free-living bacteria that fixes N2
o Sterile mineral salts & mannitol medium (no added nitrogen source)
Add soil sample & incubate
Air added (N2 & O2)
Remove a sample and culture on sample medium containing
agar
Nitrogen fixing colonies appear
Winogradsky Column
- Illustrates enrichment in action
- Different microbes flourish in different areas of column that correspond to
different nutritional microenvironments
o Aerobic water
o Anaerobic water
o Anaerobic sediment
What microbes are present?
- Cultivation-independent techniques
o Direct sequencing (without growing or cloning)
Extract DNA and PCRsequence
Compare to databases of known sequences for identification
o Fluorescent in situ hybridization (FISH)
Labeled oligonucleotide probes bind to specific DNA/RNA in a
mixed population of cellsvisualize cells under microscope
Microcosms (artificial ecosystems)
- Metagenomics
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