Metagenomic Analysis of Farm Soil Inoculated With Methyl Parathion

Your purpose is to see how the bacterial populations and their biomarkers change upon exposure to methyl parathion. Then explain what are the goals of the
project. Your hypothesis should have something to do with what you believe methyl parathion will do to the soil samples. I would personally think methyl
parathion would enrich bacterial species that can break it down or at least better tolerate it. At the same time, because other bacterial strains are dying off
and those that can feed on MP are enriched, I would expect to see a higher abundance of MP degradation biomarkers in the second data set.
Be sure you understand and can explain what the pathway is telling you and how you are going to search for relevant biomarkers. A biomarker in this
instance is a gene that could be involved in the MP pathway you have provided. You need to be able to explain how you will use BLAST to search your
metagenomes for these biomarker genes using sequences you obtain from other MP degrading microorganisms. Also, explain why BLAST is necessary. (I.e.
your genome is only partially annotated through MG-RAST. Non-annotated genes could be missed (MG-RAST lists them as hypothetical proteins) and it is
possible that some of those would be biomarkers that you are looking for.) BLAST allows you to sweep the metagenomes for any sequence similar to
possible biomarker sequences. For the presentation, a single gene sequence can be used as a demonstration as shown in these slides, but keep in mind we
are expecting that you will search dozens if not more different gene sequences at every step in the pathway when looking for that particular biomarker.