The future of biodiversity assessment: Using environmental DNA and next-generation sequencing to characterize biological communities in the Central Highlands of Arizona
Faculty Mentor Name
Hilary Eaton, Catherine Benson, Matthew Valente
Document Type
Presentation
Location
Jim and Linda Lee Planetarium
Start Date
5-10-2018 3:20 PM
End Date
5-10-2018 3:30 PM
Abstract
Historically ecological surveys require significant man hours in the field, utilizing methods which can stress species being observed. In using environmental DNA (eDNA) gathered from air, soil, and water, traditional methods may be supplemented or reduced in order to more efficiently utilize funding and reduce or eliminate stress on surveyed species. Water was collected in replicates using aseptic technique from two different sites, 60 miles apart, along the Verde River. Samples were vacuum filtered within 24 hours through 0.45 μm cellulose nitrate (CN) filters to collect eDNA. DNA extraction from the filters was performed. The polymerase chain reaction (PCR) was then optimized to target the 16S rRNA mitochondrial gene in vertebrates and samples were sequenced on an Illumina Forenseq FGx Genomics System. The paired-end reads were filtered for quality, assembled, and clustered into operational taxonomic units (OTUs) at 97% genetic similarity using the program USEARCH. The resulting sequence for each OTU was compared to the NCBI nucleotide database using a BLAST search. Results showed that multiple vertebrate taxa were identified including fish, reptiles, amphibians, birds, and mammals, which corresponded correctly to traditional survey data, and led to some new discoveries. A species accumulation curve showed that species richness was captured well with three samples, but would capture one or two additional species with more samples. This technique represents a new, cutting-edge method to characterize biological communities from water samples that is more efficient and more accurate than traditional survey methods.
The future of biodiversity assessment: Using environmental DNA and next-generation sequencing to characterize biological communities in the Central Highlands of Arizona
Jim and Linda Lee Planetarium
Historically ecological surveys require significant man hours in the field, utilizing methods which can stress species being observed. In using environmental DNA (eDNA) gathered from air, soil, and water, traditional methods may be supplemented or reduced in order to more efficiently utilize funding and reduce or eliminate stress on surveyed species. Water was collected in replicates using aseptic technique from two different sites, 60 miles apart, along the Verde River. Samples were vacuum filtered within 24 hours through 0.45 μm cellulose nitrate (CN) filters to collect eDNA. DNA extraction from the filters was performed. The polymerase chain reaction (PCR) was then optimized to target the 16S rRNA mitochondrial gene in vertebrates and samples were sequenced on an Illumina Forenseq FGx Genomics System. The paired-end reads were filtered for quality, assembled, and clustered into operational taxonomic units (OTUs) at 97% genetic similarity using the program USEARCH. The resulting sequence for each OTU was compared to the NCBI nucleotide database using a BLAST search. Results showed that multiple vertebrate taxa were identified including fish, reptiles, amphibians, birds, and mammals, which corresponded correctly to traditional survey data, and led to some new discoveries. A species accumulation curve showed that species richness was captured well with three samples, but would capture one or two additional species with more samples. This technique represents a new, cutting-edge method to characterize biological communities from water samples that is more efficient and more accurate than traditional survey methods.