Lab Notebook 14: Poster and Abstract
April 25, 2019
Rithvik Baratam
I. Title: Poster and Abstract
II. Rationale:
The purpose of this lab was to collect the metadata of the different samples and revise our poster in preparation for our presentation. By writing an abstract, we hope to prepare ourselves by briefly analyzing the entirety of the project.
III. Materials:
- Computer
IV. Procedure:
- Voted on CILI-CURE Logo that would be used for t-shirts and/or stickers
- Inputted soil metadata on the master spreadsheet. This included:
- New Soil ID: BCM21_8Sp19
- group number: 8
- GPS Location: (-97.1188, 31.5485)
- Tree Species: Ilex vomitoria
- Breast Height Diameter: 67.94 cm
- pH: 7
- Soil Texture: Silty Loam
- Extraction Method: Silica Bead Method
- DNA Concentration: 1115.6 ng/ul
- Approximate Volume: 500 ml
- PCR Read: positive
- Relabelled Soil ID (BCM21_8Sp19) on the sample bag
- Went to the computer lab to work in a group to edit our poster and fix our abstract.
V. Abstract:
Microbial soil diversity is vital to key processes that maintain soil health, through processes such as biogeochemical cycles, energy flow cycles, and food webs. In order to understand these interactions between microbial communities, the identification of unicellular eukaryotes such as ciliates is crucial. The study aims to test a novel, cost-effective protocol that extracts DNA from the soil using a silica bead method. The experiment concerned extraction, isolation, amplification, and analysis of environmental DNA. This form of non-isolated DNA was extracted from the soil in the rhizosphere of an Ilex vomitoria. In this method of DNA extraction, the soil is ground with silica beads, charcoal, and DNA extraction buffer using a mortar and pestle to lyse encysted ciliates. This environmental DNA was then purified. PCR was used to amplify V4 18S rDNA region of pDNA. The test was positive for the presence of pDNA and it was determined that the pDNA had a concentration of 1115.6 ng/µl. The purpose of this study was to propose a new protocol that would serve as a favorable extraction method. The proposed silica-bead method was employed as a cost-effective alternative to lyse encysted ciliates and extract DNA without harming or compromising DNA integrity. Through the use of next-generation sequencing amplified DNA can be analyzed to determine the species and the amount present in the soil sample. The silica-bead method is an easy way to test the soil for the presence of microorganisms using PCR to amplify the DNA with primers. The sequencing of the eDNA will shed light on the microbial diversity found in the rhizosphere of the tree where the sample was collected.
VI. Revised Poster:
Title: Sequencing of Ciliate DNA in Pursuit of Finding Diversity
VII. Conclusion:
Now that we have revised our poster, it is time that we prepare to present our research. Through this process, I hope to better my skills in presenting and creating scientific posters.