Objective:

The main goal of lab today is to learn about metabarcoding and how it relates to science and the scientific process. During lab we aim to review scientific literature to understand current protocols that have already been set in place by other known scientists so that we may concoct one that will optimize our time during lab this semester.

Purpose:

It is important that we fully comprehend the scientific literature that we are reading because the goal of lab is to create our own metabarcoding protocol that we can apply to ciliates. Learning about metabarcoding with help us to further implement a procedure that can help us better understand soil ciliate diversity and why is important.

Procedure:

1.) Obtain a concavity slide, a 10 microliter micropipette, a sample from the Bermuda grass community, and a compound microscope.

2.) Pipette a 10 microliter drop of the Bermuda grass sample on the concavity slide and place under the microscope.

3.) Use a cover slip and vaseline to place on top of the concavity slide in order to use the microscope at its highest power.

4.) Try to focus the microscope to see any ciliates present in the sample.

5.) Draw/Record your observations; if possible try to identify any ciliates you can if found in the sample.

6.) After viewing the ciliates, clean up your lab station and locate the piece of scientific literature that has been assigned to your group, as well as a questions that matter worksheet that will need need to be filled out in order to brainstorm your groups’ presentation.

7.) Converse with your group members about the article and metabarcoding and brainstorm possible protocols.

Data/Observations:

Ciliates Seen-

Scientific Literature-
I learned about environmental DNA sampling and analysis and how you can isolate a single strand of DNA and extract it for a process called Sanger Sequencing. The most common procedure is metabarcoding which uses 18s rDNA which works for Next Gen Sequencing, but is not effective enough to differentiate between interspecies relationships.

Current Storage:

Today during lab we cleaned up our lab stations and did not store anything. We worked on our presentations for lab next week.

Future Goal:

After reading all of this scientific literature, we hope to uncover the best protocols for the metabarcoding process so that we will be able to implement this process on our own in lab. Once we create/find the best protocol we should be able to sequence DNA extracted from the ciliates.

Source Citation:

Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., . . . Vargas, C. D. (2012). CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms. PLoS Biology, 10(11). doi:10.1371/journal.pbio.1001419