Lab 14: Poster Presentation and Abstract Submission 4/26/2019
Madison Ambrose
1106-22
Purpose/Rationale/Objective:
The purpose of this lab was to finalize our groups abstract and poster for the CURE symposium. The objective of this lab was to make edits to our poster as well as document and relabel the original soil samples with the new ID.
Procedure:
- Vote on the CILI-CURE logo and preferred merchandise.
- Fill out the information on the spreadsheet.
- Relabel DNA and soil samples with new ID AHM22_5Sp19.
- Edit the recommendations made by the TA to the poster.
- Edit Abstract drafts with the group.
- Submit Abstract and poster title to QTM 14 assignment.
- Upload abstract and poster to class Drop Box.
Data:
Abstract:
The biodiversity of microorganisms within terrestrial ecosystems is dependent on the viability of the community profile. Soil microbiomes and the influence of eukaryotes within is largely unexplored. The following field experiment analyzes soil collected from the rhizosphere of a Quercus virginiana to attempt to further classify ciliates and understand the diversity of one of the most controversial monophyletic groups, SAR. Metadata regarding soil texture, percent water content, and pH was obtained from each soil sample. The MNH soil sample was identified as sandy loam and KRM and MAA soil samples were identified as sandy clay. The samples were then isolated and eDNA was extracted using silica beads. The eDNA was then cleaned with 80% isopropanol alcohol and primed with an 18S V4 primer to isolate the V4 region of DNA in eukaryotes. The MHK and KRM samples underwent gel electrophoresis to attempt to view bands of DNA and KRM sample was amplified using a polymerase chain reaction (PCR). Results from the PCR amplification were analyzed using the NanoDrop 2000 Spectrophotometer and the MBC C305 UV gel imager. The MNH sample yielded an A260/280 concentration of 1.3 and the KRM sample yielded 1.44, indicating that DNA was present in the sample. Though it was shown that DNA was present, gel electrophoresis images produced no visible bands. These results indicate that soil collected from the rhizosphere surrounding the Quercus virginiana did not contain quantifiable eDNA for eukaryotes, despite ciliates being observed and cultured before soil eDNA was extracted.
Title: Analysis of Soil and eDNA from the Rhizosphere of a Quercus virginiana
Group Members | Section | Group | Soil ID | GPS Location | Tree Species | BHD (cm) |
Madison Ambrose, Megan Hudson, Kelsi Menzie | 22 | 5 | AHM22_5Sp19 |
-97.1203258, 31.5467120 |
Quercus virginiana | 188.4 |
pH | Soil Texture | Extraction Method | DNA concentration | Volume | PCR | Soil Label on Bag | |||||
6.5 | Sandy Clay | Silica Bead | 1.44 | 30ul | – | KRM22S19 |
Poster:
Storage:
Make sure the lab bench is clean, turn in your QTM, submit the abstract, and upload the poster and abstract to the Drop Box.
Conclusion/Interpretation/Future Steps:
This lab allowed us to wrap up the semester by making our final poster edits and prepare for the CURE symposium. By setting our poster aside for a few weeks then returning to it at the end of the semester allowed us to make modifications with a fresh perspective of the experiment. Additionally, due to the practice we had with the Qiime2 program allowed us to have a more mature understanding of the conclusion and discussion section, specifically on the future steps we can take with the experiment we performed. The edits along with recommendations from our TA and LA were very beneficial and allowed us to perfect the poster for the CURE symposium next week. Going forward I am curious to see what the results from the PCR sequencing will tell us about our community profile and if we will find ciliates that have never been identified before. Lastly, although our eDNA sample had negative results course was a valuable learning experience I can aspects of further into my academic career.