An Analysis of the Biodiversity of Aquatic Ecosystems Using Metagenomics
Board Location: #156
Discipline: Biological Sciences
Subcategory: Microbiology/Immunology/Virology
Session: 2
Maya Leon - Lane College
Co-Author(s): Nylah Berry, ,Jada Cain, Erykah Pierson, Mar’Kila Holland, C’Mari Hayes, and Paris Tennonall Lane College Students
Microbes are small microorganisms that work together to form communities called microbiomes. Microbiomes are found in aquatic communities associated with bodies of water, the human body, and that of larger animals. Microbiomes in aquatic communities’ impact larger organisms in the water by contributing to the oxygen levels, source nutrients, and possible contaminations. Analyzing microbes helps define the relationship between the organism and its environment. The goal of this project is to explore the microbiomes in local ponds using metagenomics. Metagenomics will allow the specific nucleotide sequences of the organisms to be analyzed. To complete metagenomic sequencing using the Nanopore Mk1C, different DNA extraction methods were used. DNA was isolated from environmental (e) DNA samples were taken from four ponds in Jackson, Tennessee: Campbell Street Pond, Fairgrounds Pond, Lane College and Muse Park.The e-DNA samples were isolated using ZymoBIOMICS DNA Miniprep Kit from Zymogen.Sodium acetate ethanol precipitation resulted in higher DNA concentrations and yields using the ZymoBIOMICS kit in comparison to the other sample preparation methods using the ZymoBIOMICS kits. The Nanopore MinION collected 3.83 million reads from the four local ponds. The sequenced DNA was analyzed using Whats In My Pot quantitative analysis tool from Epi2Me technology. The results of this research demonstrates that standard sodium acetate ethanol precipitation followed by clean-up with ZymoBiomics DNA kit produced the most data. This method is time effective, cost efficient, and increases the reliability of Nanopore sequencing of e-DNA samples. The results from the Nanopore MinION showed biodiversity in the identified microorganisms from all four ponds.
Funder Acknowledgement(s): This work is supported by NSF DUE 1833960 and HRD 2011938 to MVS.
Faculty Advisor: Dr. Candace Carter Dr. Melanie Van Stry Dr. Consuella Davis, cajones@lanecollege.edu
Role: I collected the samples, did an intense analysis of both DNA kits. Loaded the NanoporeMinION flow cells. Analyzed the data.