Micros- Chapter 22/23

  1. major components of microbial ecology
    biodiversity & microbial activity
  2. Population
    bacteria that derived from a single cell
  3. Guild
    Populations that are metabolic related
  4. Microbial community
    set of guilds
  5. Ecosystem
    Communities of organisms and their natural environment
  6. Biogeochemical Cycle
    Biological and chemically mediated chemical transformation of elements

    "cycling of elements'

    typically by oxidation-reduction rxn
  7. Niche
    growth and function at optimal levels, habitat,

    Physical habitat -determines the niche
  8. Mutualism
    • Mutualism: + / +
    • Commensalism: + / 0
    • Ammensalism: 0 / -
    • Parasitism: + / -
    • Symbiosis: -share the same ecosystem
  9. Polpulation of microbes vs individual microbes
    • Ubiquity - Biodiversity
    • Abundance
    • Metabolic Power - microbial activity
  10. 3 ways to isolate to obtain a pure culture
    • 1. streak - drag to a single colony
    • 2. agar shake - molton agar, double layer- colonies embedded in agar.
    • 3. Liquid Dilution - serially dilute until no growth. also called MPN
  11. MPN
    • Most Probable Number analysis
    • a repeat dilution series
    • used for estimating the number of microorganisms in foods, waster, and other samples
  12. What is the criteria for Purity
    • 1. microscopy - gram stain
    • 2. observation of colony characteristics on plate or shake tubes
    • 3. growth in media in which the culture grows poorly but contaminates grow well.
  13. What are the 2 drawbacks in studying pure cultures?
    • 1. microorganisms will change characteristics to benefit them in a lab setting
    • ex - pathogens lose virilence - may have different antigens
    • 2. microbial communities are too small (3mm)
  14. Winogradsky Column
    • algae & cyanobacteria
    • purple non sulfur bacteria
    • sulfur chemolithotrophs
    • purple & green sulfur bacteria
    • Anoxic decomposition & sulfate reduction

    gradient: O2 to H2S & light gradient
  15. Growth Rates of microorganisms in the lab
    • 1. faster growht than natural habitat because of feeding all the good stuff (food scarce in nature)
    • 2. slower growth, microorganism may need another factor that is unknown.
  16. How do we quantify microbes in a microbial habitat ?
    • 1. PCR and DGGE
    • 2. Metagenomics
    • 3. Staining methods - fluorescence
  17. 1. Viability Staining
    • use 2 dyes:
    • 1. green fluorescening dye - penetrates all cells
    • 2. red dye (Propidium iodide) - penetrates cells that dont have cell membranes (aka dead cells)

    commercial name: BacLight
  18. 2. Fluorescent staining using DAPI or Acridine Orange
    • -stain binds to DNA and strongly fluorescent when exposed to UV lights.
    • -problem: stains both live and dead cells
  19. 3. Fluorescent Antibody Probes
    • -good tracking a specific organisms within a habitat
    • -specific antibody attaches to specific site
    • -good for diagnosing infectious diseases and other lab work :-)
  20. 4. GFP as a cell Tag
    • -insert GFP into the geome and add to the natural population.
    • -tags green (but not always green)
    • -reporter gene - replace gene with GFP
    • -problem: need oxygen
  21. 5. FISH - Fluorescence in situ hybridization
    • -nucleic acid probe
    • -obligonucleotide complementary to a sequence in a targe gene or RNA -hybridize)
    • -hybridized to cells in a natural environment
    • -doesnt kill microbe
    • -can measure gene expression
  22. PCR

    PCR - polymerase chain rxn: artifical amplification of a DNA sequence by repeated cycles of strand separation & replication

    DGGE - denaturing gradient gel eletrophoresis: separating nucelic acid fragments of the same size that differe in base sequence
  23. phylogenetic staining
    ex - red fluorescent dye tag bacillus, green dye tag staph, etc.
  24. Metagenomics
    • the total genetic complement of all cells present in a particular environment
    • -detect as many as genes as possible that encode recognizable proteins & determine the phylogenetic groups to which it belongs to
  25. Measuring microbial activities in nature
    (4 ways)
    • 1. Chemical Assays
    • 2. Radioisotopes
    • 3. Microelectrodes
    • 4. Stable Isotopes
  26. Chemical Assay of microbial activities in nature
    • direct chemical measurements of microbial rxn
    • ex- fate of lactate oxidation by sulfate-reducing bacteria H2S
    • - not good for highly sensitivity
  27. Radioisotopes in microbial activites in nature
    • - good for:
    • 1. when high sensitivity is required
    • 2. turnover rates need to be determined
    • 3. fate of portions of a molecules needs to be followed.
    • problem: some transofrmations might be due to abiotic prcesses
  28. killed cell control
    • -account the abiotic process in radioisotopes
    • -yields proper control in experiment
    • -ex formalin
  29. Microelectrodes in measuring microbial activities in nature
    • -small glass electrodes
    • -measures: pH, Oxygen, N2O, CO2, H2, or H2S
    • ex- shine the light, add electrodes = measures the amount of oxygen being generated
  30. microautoradiography
    • -MAR
    • -method that cells are exposed to a radioisotope and slided - photographic emulsion. darkness-decay =silver grains in the emulsuion
  31. Stable Isotope probing
    a method for characterizing an organism that incorporates a particular substrate by feeding the subsrate in 13C form and then isolating 13C-enriched DNA and analyzing the gene
  32. Isotopic fractionation
    • -one of two stable isotpe methods
    • -discrimination by enzymes against the heavier isotope of various isotpes of C or S, leading to enrichment of the ligher isotopes.
Card Set
Micros- Chapter 22/23
Microbial Ecology & Methods