Abstract Title
DNA Extraction Protocol Optimization for Decades-Old Aquatic Macroinvertebrate Samples
Additional Funding Sources
This research is made possible by Idaho NSF-EPSCoR Program (award OIA-1757324).
Abstract
Stream benthic macroinvertebrate (BMI) communities are a valuable monitoring tool for assessing water quality. The Idaho Department of Environmental Quality’s Beneficial Use Reconnaissance Program (BURP) has collected > 8,600 samples at randomly selected sites throughout the state since 1994 and identified larval specimens to genus using morphology. Specimens were archived for many of the samples and the BURP samples could enhance detection of water quality and climate effects over the past three decades if species can be identified using DNA barcoding. DNA barcodes are a species-specific sequence of nucleotides found on the mitochondrial COI gene. Our objectives are to 1) develop an effective DNA extraction, amplification, and sequencing protocol and 2) to build a DNA barcode library for Idaho BURP BMI specimens. To date, we have modified DNA extraction protocols to optimize the concentration of extracted DNA. Experiments compared extraction yield to the number of elutions and incubation time. We determined two elutions with a twenty-four-hour incubation period provided the best yield. DNA from additional identified vouchers will be amplified using Polymerase Chain Reaction, sequenced, and submitted to the Barcode of Life (BOLD) database. DNA barcode libraries from will improve monitoring of species diversity in BMI samples and should increase the sensitivity of water quality and climate change studies in Idaho.
DNA Extraction Protocol Optimization for Decades-Old Aquatic Macroinvertebrate Samples
Stream benthic macroinvertebrate (BMI) communities are a valuable monitoring tool for assessing water quality. The Idaho Department of Environmental Quality’s Beneficial Use Reconnaissance Program (BURP) has collected > 8,600 samples at randomly selected sites throughout the state since 1994 and identified larval specimens to genus using morphology. Specimens were archived for many of the samples and the BURP samples could enhance detection of water quality and climate effects over the past three decades if species can be identified using DNA barcoding. DNA barcodes are a species-specific sequence of nucleotides found on the mitochondrial COI gene. Our objectives are to 1) develop an effective DNA extraction, amplification, and sequencing protocol and 2) to build a DNA barcode library for Idaho BURP BMI specimens. To date, we have modified DNA extraction protocols to optimize the concentration of extracted DNA. Experiments compared extraction yield to the number of elutions and incubation time. We determined two elutions with a twenty-four-hour incubation period provided the best yield. DNA from additional identified vouchers will be amplified using Polymerase Chain Reaction, sequenced, and submitted to the Barcode of Life (BOLD) database. DNA barcode libraries from will improve monitoring of species diversity in BMI samples and should increase the sensitivity of water quality and climate change studies in Idaho.