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Sheneman, A. C. & Morrow, M. (2024) “The Effect of Wildfire on Soil Bacterial Diversity.” Student Research Symposium at New Paltz University & the Hudson Valley Life Sciences Symposium at New Paltz University. Poster.
Overview
Overview
New Paltz University Research ('22-'23)
Mentor: Prof. Maureen Morrow, Department of Biology at New Paltz University
Summary: Conducted metagenomic analysis, PCR, and 16S sequencing to investigate soil bacterial diversity and isolate extremophiles in wildfire-affected regions.
Methods
Methods
Research Questions
Research Questions
What extremophilic/thermophilic genetic sequences can be identified from metagenomic analysis of bacteria that survive a wildfire? How does soil bacterial diversity differ in samples collected inside and outside the bounds of a wildfire?
Napanoch Wildfire
Napanoch Wildfire
Photos taken August 2022 and November 2023
Soil Sample Collection
Soil Sample Collection
From inside (left) and outside (right) of the range of the wildfire. Surface soil was scraped with a sterile collection tube, stored at 4C for transport and then some samples were stored at -20C and others at -80C. Soil had distinct moisture, texture, and content differences.
Extraction Methods
Extraction Methods
DNA was extracted using a Soil Extraction QAGEN kit. Proteinase K was determined to not significantly increase yield.
Extraction Analysis
Extraction Analysis
The table (below) is based on the quantification and quality of DNA with NanoDrop and Qubit. It is evident that the quality, primarily determined by an 260/280 value between 1.8 and 2.0 is best in unburned samples. Additionally, we encountered issues with the burned samples having expectedly substantially lower DNA yield (ng/ul).
results
results
MWM = Molecular Weight Marker
- = negative control
+ = positive control
N1 and N2 = Not Burned
B1 and B2 = Burned
PCR and Electrophoresis
PCR and Electrophoresis
Polymerase Chain Reaction (PCR) amplification was conducted to amplify 16S genes. The results were analyzed using gel electrophoresis. This procedure was initially conducted using fresh soil collected from outside of the lab and was successful prior to moving to the wildfire samples. However, the low DNA yield, even after attempts to combine and amplify the yield, resulted in no bands present. The accurate Molecular Weight Marker (MWM), negative (-) and positive (+) controls indicate the use of the correct procedure.
Future Work
Future Work
Following the creation and implementation of this procedure, new lab students after my graduation have begun the process of amplifying the DNA quantity and plan to follow my outlined protocol for metagenomic analysis (based on a literature review) to isolate gene sequences and analyze using KBase.
TALKS & CONFERENCES
TALKS & CONFERENCES
View More Information Here: Talks & Conferences
Student Research Symposium and Hudson Valley Life Sciences Group Symposium (HVLSGS)
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