Development of an Environmental Metagenetics Approach for Monitoring Aquatic Biodiversity
RC-2240
Objective
The researchers will develop a novel and practical method for monitoring the number of species in aquatic environments from water samples. Specifically the researchers will use molecular genetic tools to identify the presence of fish and amphibian species, especially species of management concern (e.g., invasive, threatened, endangered). When traditional monitoring tools for detection of species (e.g., nets, traps, electrofishing) are inefficient, impractical, or lacking, management groups often are left in a state of inaction or without accurate species information. In these cases, rare species are often overlooked, leading to errors in inference about existing species richness and biodiversity for a given body of water. Recently, however, published work shows that the detection of rare species in aquatic systems can be successfully accomplished with molecular genetic detection tools at significantly higher detection probabilities than traditional methods. Such techniques, which rely on genetic material suspended in water, enable improved sensitivity with reduced effort for detecting the presence of rare or elusive species. In this project, the researchers plan to improve and expand current techniques by (1) developing aquatic environmental DNA (eDNA) metagenetic assays for fishes and amphibians using traditional polymerase chain reaction (PCR) and ultrasequencing, validated for selected species with quantitative real time PCR (qPCR); (2) test the assays on artificial aquatic mesocosom-scale assemblages of known species richness and diversity; (3) test the assays in natural environments whose species richness has been thoroughly evaluated by traditional methods; (4) apply the assays to natural environments with unknown species richness at different spatial scales for comparison with traditional methods for estimating species richness; and (5) apply and compare alternative models for estimating species richness and diversity across a variety of aquatic systems.
Technical Approach
To better and more rapidly measure species richness and diversity in aquatic environments, the researchers will develop a series of protocols and techniques using three modern molecular tools, each of which provides more information about species richness and diversity: standard PCR, qPCR, and ultrasequencing (high throughput sequencing of environmental samples targeting homologous gene regions from taxonomic groups of interest). To evaluate the relative sensitivity and cost effectiveness of this approach compared to traditional, non-genetic tools, the researchers will deploy each of them at three spatial scales: controlled mesocosms of known species composition, multiple thoroughly censused natural habitats, and multiple less, well-studied aquatic habitats at two Department of Defense (DoD) installations, Ft. Custer Training Center (Augusta, Michigan) and Marine Corps Base Camp Pendleton (San Diego, California). The DoD facilities provide the opportunity to detect several state and federally threatened and endangered species. Previously published work with standard PCR demonstrates the ability of this tool to detect rare target species, but inferences to date are limited to presence-absence. Ultrasequencing promises to more cost effectively provide estimates of species richness at reduced cost and produce novel information on the relative abundance of species and within-species genetic diversity (i.e., population level information). The researchers will use qPCR to validate that ultrasequencing detects rare as well as abundant species. Finally, the researchers will apply and evaluate multiple theoretical estimators of species richness and use them to guide sampling designs in natural habitats.
Benefits
This project will provide improved and more rapid environmental surveillance tools for quantifying species richness that will be transferred to federal partners for use in aquatic habitats on DoD installations. The multi-tool, multi-scale approach will enable partner agencies to compare and select tools that most effectively achieve their management goals. In the last year of this project, the researchers will transfer the refined tools to relevant local, state, and federal management groups through training demonstrations at military installations. As a result, the researchers will provide critical knowledge to management agencies to (1) enable their choices about which tools to employ, (2) understand the advantages and limitations inherent to these tools, and (3) evaluate whether to build their own capacity to conduct such surveys or rely on the expertise of third parties.
Symposium & Workshop
FY 2013 New Start Project Selections
Points of Contact
Principal Investigator
Dr. David Lodge
University of Notre Dame
Phone: 574-631-6094
Fax: 574-631-7413
Program Manager
Resource Conservation and Climate Change
SERDP and ESTCP
Document Types
- Fact Sheet - Brief project summary with links to related documents and points of contact.
- Final Report - Comprehensive report for every completed SERDP and ESTCP project that contains all technical results.
- Cost & Performance Report - Overview of ESTCP demonstration activities, results, and conclusions, standardized to facilitate implementation decisions.
- Technical Report - Additional interim reports, laboratory reports, demonstration reports, and technology survey reports.
- Guidance - Instructional information on technical topics such as protocols and user’s guides.
- Workshop Report - Summary of workshop discussion and findings.
- Multimedia - On demand videos, animations, and webcasts highlighting featured initiatives or technologies.
- Model/Software - Computer programs and applications available for download.
- Database - Digitally organized collection of data available to search and access.