Microbial Genomics III

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Microbial Genomics III
2011-11-09 04:42:18
PMB 112 midterm2

general microbiology midterm 2
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  1. metagenomics
    • environmental genomics
    • involves sequencing of "all" DNA in a given environment
    • information on community composition
    • information on community and specific microorganism's capabilities
    • discovery of new microbes, new genes
    • microbes don't have to be cultured
    • enabled by high throughput sequencing technologies
  2. old vs. new metagenomics approach
    • community sample approach (old):
    • amplify single gene
    • get single-gene phylogenetic tree - snapshot of most members of the community, identification of novel phenotypes
    • will amplify most 16S sequences, but some are divergent enough that they will not be amplified - phylotypes will be missed because there is a bias in what you will detect based on what you are able to amplify

    • environmental genomics approach (new):
    • restriction digest total DNA and shotgun sequence or sequence directly with high throughput sequencing
    • get partial genomes - total gene pool of the community - identification of all gene categories, discovery of new genes, linking of genes to phylotypes
  3. environmental genome shotgun sequencing of the Sargasso Sea
    Sargasso Sea - well-studied region of global ocean, gulf stream provides physical boundary separating more nutrient rich waters from nutrient poor open ocean, get seasonal mixing resulting in blooms

    in study extracting DNA from samples of the water, using all of sequence data and pulling out homologues of conserved genes found was very phylogenetically diverse and identified previously unknown phylotypes

    • proteorhodopsin-like genes (light-mediated proton pump known from certain proteobacteria) in new phylogenetic lineages of bacteria and many in archae
    • -> suggests light important to these organisms

    • identification of new genes in known organisms - compared prochlorococcus genes in the Sargasso Sea to the known genome of the lab strain, found genomic islands that differed
    • -> concluded the presence of fitness islands which code for proteins responsible for responses to environmental factors
  4. Deepwater Horizon Blowout
    • Deep continued release of oil
    • focus on underwater oil plume
    • used phylochip and geochip to study communities

    • increased cell density and reduced dissolved oxygen at plume depth
    • used phylochip - DNA chip with 16s rRNA sequences, primers can miss novel microbes with sequences that are very different in amplification
    • diversity reduced in plume

    • used GeoChip - microarray chip of oligonucleotides, shows which genes are present, not which are expressed
    • genes from oil plume samples clustered and were well separated from non-plume samples
    • genes involved in oil degradation were more prevalent in oil plume