Objective

The objective for this lab was to extract DNA from our soil samples. Additionally, we calculated the percent composition of the soil in terms of sand, silt, and clay. Also, we analyzed leaves we gathered from our tree to define its genus and species.

Purpose

The purpose for extracting DNA is so we can arrange it to observe how many different species of microorganisms are in that specific soil environment. We calculated the compostion of the soil in order to be able to associate any ciliates we find with that type of soil. We identified the type of tree we got the soil from for this same purpose.

Procedure

At the beginning of lab, we took a few minutes to look in our cultures for ciliates. After that, we carefully observed our leaves and all the different characteristics of them, such as venation, margins, and overall shape. Using guides online and a book, we identified the type of tree from which these leaves originated. Our soil composition test followed. We took our falcon tubes full of the vortexed soil from las week and measured in millimeters the layers of sand, silt , and clay. We then moved on to the actual DNA extraction from our soil samples, where we first measured one gram of soil and one gram of silica beads and ground them in a mortar and pestle until they were a fine powder. We added 2 milliliters of DNA extraction buffer and approximately 10 milligrams of activated charcoal to the mortar and pestle, where we mixed it using a pipette tip. Once we were done mixing, we transferred the contents to a centrifuge tube. The tube was incubated at 65 degrees Celsius for 10 minutes then centrifuged at 12000g for 5 minutes. We transferred the supernatant liquid into a new centrifuge tube then centrifuged that tube as well to be sure that we had no dirt particles in our sample of DNA.

Data

My soil was found to be approximately 68.75% sand, 12.5% silt, and 18.75% clay. This can be classified as sandy loam. I classified my tree as a live oak, or Quercus virginianus. We successfully prepared a sample of DNA using Emely Canas’ sample of soil.

Conclusion

Looking into the cultures I made, I could only see small organisms and not much of what I thought to be a ciliate. Identifying my tree was a little complicated, as not all of my leaves looked the same despite them all being from the same branch. My soil composition was easy enough, as my tube showed clear lines to distinguish between the sand, silt, and clay. The DNA extraction was the longest yet most rewarding part. I am excited to analyze our samples and see how we can use metabarcoding ourselves.

Storage

I was one of the last students to leave the lab because I was finishing the Questions That Matter, so my lab partners did most if the cleaning and storing for me. I did check to make sure the centrifuge was empty and I looked over the microscopes to check that they were all unplugged and covered. My leaves were stored with the rest of the class’s for later use and the mortar and pestle we used were washed in the sink and left our to dry.