Next Generation Sequencing of Amphibian Metagenomic Amplicons (eDNA) - GLKN

Description

This cooperative agreement is working with the Great Lakes - Northern Forest Cooperative Ecosystem Studies Unit - University of Minnesota. This agreement would be funded from GLRI Project Number: 2018-322b. Environmental DNA assessment of amphibian population health and presence in Great Lakes wetlands. Work under this agreement advances DOI Secretary Priority 1a: Utilize science to identify best practices to manage land and water resources and adapt to changes in the environment. Amphibians are a sensitive indicator of the wetland health; looking at the change over time and if the wetlands are improving or declining. The idea of using the DNA for species sampling is a newer technique and will provide the ability to determine if this is useful technique to monitor the species presence. Scientific techniques developed under this agreement will shared throughout the scientific community through reports and scientific papers. The information will be used by NPS and the land management community as whole. Sharing the outcomes from this agreement will allow other parties to reduce costs to understand amphibian species presence and community structure. The cooperator will take PCR amplicon DNA (<550 base pairs) samples prepared by GLKN and use Next Generation Sequencing (NGS) technology and procedures to sequence the amplicons. Cooperator work will involve working with the NPS researcher to develop a library preparation method (sample tagging) from eDNA samples and sequencing the samples. The Cooperator will work with GLKN to determine the specific protocol that accurately and cost-effectively provides the necessary sequence information. GLKN anticipates that this might include using a NexteraTX chemistry or other non-proprietary chemistries for index library preparation and sequencing plate-quantity sample lanes on an Illumina MiSeq machine with 2x300 protocol. Cooperator expertise will be valuable for assessing availability of library preparation protocols. Samples will be submitted in plate-quantity increments to the cooperator. GLKN anticipates up to 10 MiSeq sequencing lanes and associated library preparations during the duration of the agreement. The exact quantity of samples sequenced will be determined by the specific cost of the sequencing procedures that can be completed within the funding scope of the agreement.

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