Genomics & Soil Extremophiles

Overview

SUNY New Paltz Research in Biology

Mentor: Dr. Maureen Morrow, Associate Professor Biology SUNY New Paltz

Conferences: Hudson Valley Life Sciences Symposium (2024), & Student Research Symposium at New Paltz (2024) (See abstract and programme here)

Topics: Extremophilic bacteria, genomics, soil bacteria, prescribed forest burns

Conclusions Quantification of DNA yield from extractions is significantly lower in burned soil, which we anticipate will correspond to a decrease in bacteria diversity when further metagenomic analysis is performed.

Highlights

Hudson Valley Life Sciences Symposium and Student Research Symposium Poster (April and May 2024, respectively)

Process Summary

My lab bench with the Zymo sample kit, my soil sample, gloves for sterility measures, and the components of the kit labelled and organized.

Genomic Analysis of Soil Bacteria

Genomic analysis of extremophiles is a leading area in astrobiological research to understand the types of bacteria and life that may be able to survive in and withstand extreme conditions that may be mistakenly labelled uninhabitable. The initial soil samples utilized were samples from the SUNY New Paltz campus, intended to be compared to soil samples from a forest prescribed burn area. The DNA was extracted using a Zymo Research Kit and analyzed.

This project required independent sampling, extracting, analyzing, etc.

The side of the Zymo research box reading: "The important thing is to not stop questioning. Curiosity has its own reason for existing." - Albert Einstein

The Zymo soil DNA extraction kit selected for this project. Designed to extract DNA from soil samples, first the quantity of soil that could be used needed to be determined. This was the goal of my first, one credit, semester working on this project.

The components of the Zymo kit removed from the packaging, organized, and labeled in order of use.

These tubes depict the various stages in the kit usage (from left to right) with some stages absent as it requires transferring and work in the moment. These solutions and tubes allowed for the eventual extraction of DNA (in addition to centrifuging)

Spring 2023 Results

The soil samples were analyzed with DNA extraction to yield high peaks around 260 and 260/280 numbers near the intended goal (the ideal 260/280 number is 1.8-2.0). This can then be PCR amplified to identify strains of bacteria present. This does not include the .75g sample performed.

Spring 2024

For the continuation of this research in 2024, I was one of nine recipients of the Academic Year Undergraduate Research Experience grant from RSCA at SUNY New Paltz.

We performed further assessments, refining our results and obtaining yield values from both the sample stored at -20 degrees Celsius and at -80 degrees Celsius.