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Lane College is a small, liberal arts, Historically Black College in Jackson, TN. The Division of Natural and Physical Sciences provides undergraduate research experiences for students majoring in biology, chemistry, computer science, mathematics, or physics. To increase inclusivity, all students within one of the five majors are encouraged to apply, regardless of GPA, classification, or previous research experience. This eight-week program features a bi-weekly professional development session and a symposium at the end of the program where students present their research findings. During the summer of 2023, seven biology students completed a metagenomics research study with the goal to explore the biodiversity of different local freshwater aquatic environments. The students collected water samples from four local ponds with metadata such as pH, temperature, dissolved oxygen, and GPS coordinates. Initial observations of aquatic life using microscopy and dichotomous keys were made. The DNA was extracted from the samples using ethanol precipitation followed by clean-up with the ZymoBIOMICS DNA Miniprep kit. DNA was amplified using the Nanopore Rapid PCR barcoding kit or the 16S PCR barcoding kit and sequenced with the Nanopore MinION Mk1C. DNA sequences were initially analyzed using the Nanopore Minnow and Epi2Me What's in My Pot Workflows. Each student explored the subsequent data to answer specific research questions about the biodiversity in each environment, such as the impact of pH, dissolved oxygen, whether the pond was static or free flowing, or the presence of different pathogenic or toxic microbes. Overall, they found that while there was some overlap, aquatic organisms varied in the ponds depending on whether the pond was static or free flowing, pH, dissolved oxygen, and location. Some of the students continued these research projects during the fall 2023 semester in the Biology Undergraduate Research course where they refined their research questions and analyzed the data using additional bioinformatics tools available on Galaxy.
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Abstract 1885 Surveillance of Pathogens in Aquatic Environments
Twenty percent (20%) of annual deaths worldwide are attributed to microbial pathogens. Pathogenic illnesses pose major threats to the overall health and safety of humans. These illnesses can result in death, prolonged hospital stays, and increased hospital expenses. The goal of this research is to study the evolution and ecology of microorganisms and surveillance of human pathogens in local the ponds. Surveillance of pathogens can inform the local and global efforts for monitoring and supporting public health measures to fight diseases. Surveillance is the essential tool to inform policies, prevent infections and control responses. Samples were collected from four ponds in Jackson, TN: Lane College, Muse Park, Fairgrounds and Campbell Street Park. DNA was isolated from the water samples using ethanol precipitation followed by the ZymoBIOMICS DNA Miniprep kit. Samples were prepared for the whole genome sequencing by PCR using the Rapid Barcoding and the 16S PCR Barcoding kits from Nanopore to amplify the DNA samples. The metagenomic DNA was sequenced with the Nanopore M1KC MinION sequencer. The reads were then analyzed by the Epi2Me, What's in my pot (WIMP) or 16S Fastq workflows. All four of the ponds are known to have pathogenic in them. The Lane College Pond has Clostridium and Pseudomonas. The Fairgrounds Pond has Bacillus and Legionella. The Campbell Street Pond has Clostridium, Bacillus, Leptospira and Pseudomonas. The Muse Park Pond has Leptospira, Legionella, and Clostridium. Further studies can be done with this project to examine the concept of how pathogens affect microbiomes in an aquatic environment. This work is supported by a grant from the National Science Foundation EES 2011938.
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- Award ID(s):
- 2011938
- PAR ID:
- 10505271
- Publisher / Repository:
- Journal of Biological Chemistry
- Date Published:
- Journal Name:
- Journal of Biological Chemistry
- Volume:
- 300
- Issue:
- S
- ISSN:
- 0021-9258
- Page Range / eLocation ID:
- 106645
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1016/j.jbc.2024.106645
