Regional-scale microbiome analysis of distinct ecosystems: leveraging phylogenetic and functional genes
Alexa Bennett
PhD student, Bioinformatics Data Sciences Program, University of Delaware
Abstract:
Microbial processes drive Earth’s biogeochemical cycles, including the carbon, nitrogen, phosphorus, and sulfur cycles. Freshwater, saltwater, urban, suburban, rural, and agricultural land use comprise distinct ecosystems that should influence microbial processes and diversity. Assessing the diversity within communities has traditionally used rRNA gene amplicon sequencing or bulk metagenomic sequencing. rRNA amplicons allow the detection of rare community members, but predicting function from taxonomy is error-prone. Metagenomics provides vastly more functional information, but only for the most abundant community members, and is cost-prohibitive for high-throughput analyses. We adapted an existing workflow for high-throughput amplicon multiplex sequencing and used primers for 16S rRNA, 18S rRNA, and nine genes encoding key enzymes in carbon, nitrogen, sulfur, phosphorus, and arsenic cycling. The panel was used to examine diverse ecosystems and sample types across Delaware.
Bio:
Alexa Bennett is a Ph.D. candidate in Bioinformatics Data Science. She conducts her research project under the supervision of Dr. Thomas Hanson from the School of Marine Science and Policy. She obtained a Biological Sciences A.A.S., concentration in Biotechnology, from Delaware Technical Community College (DTCC) and a Marine Science B.S., concentration in Marine Biology with a minor in Biochemistry, from the University of Delaware (UD). Her current research is focused on Project WiCCED, Water in the Changing Coastal Environment of Delaware, Microbiome Core, specifically the Delaware Microbiome Project.
