Advancing the Environmental DNA Toolkit for Ecosystem Monitoring and Management
The emerging field of Environmental DNA (eDNA) analysis allows characterization of species presence and community biodiversity by identifying trace amounts of genetic material left behind as organisms move through their environments. EESC scientists have been using eDNA technologies to detect native and rare species and as community biomonitoring tools.
Project 1: Characterizing aquatic invertebrate communities in the National Capital Region using eDNA metabarcoding
Aquatic invertebrates such as mayflies and caddisflies are important indicators of stream water quality since many of these invertebrates are sensitive to pollution and sedimentation. Natural resource agencies monitor for aquatic invertebrate diversity using tools like kick-netting to better understand stream quality, but some taxa can be missed or not identified below the genus or even family level, especially for larval forms. EESC scientists compared results of sequencing eDNA filtered from the water to traditional kick-netting in regional National Capital Region National Parks including Catoctin Mountain Park, and Rock Creek Park. While the eDNA approach did not perfectly recover the same taxonomic assemblage as kick-netting, the taxa recovered correlated well with known water quality. In other words, eDNA profiles from healthier streams showed more diverse taxonomic assemblages than those collected in poorer quality streams. The eDNA method could become a valuable tool for natural resource agencies to monitor stream communities in a fast and cost-efficient manner.
Collaborators: Robert S. Cornman and Jennifer A. Fike, USGS Fort Collins Science Center; Sara J. Mueller, The Pennsylvania State College
Project 2: Developing an optimized environmental DNA-based method for inventorying wetland amphibian communities.
The C&O Canal National Historical Park (CHOH) protects hundreds of vernal pools, wetlands, and slow-moving streams. Wetlands found in the western reaches of the CHOH host the most diverse amphibian communities throughout the State of Maryland. With conservation threats from pesticide and fertilizer inputs, stormwater runoff, adjacent land development, and climatic changes affecting wetland water levels and disease dynamics, the park must identify feasible means to understand resource condition and trends given the logistical infeasibility of recurring, physical site sampling. This project is developing analytic methods needed to utilize eDNA to detect lentic amphibian and reptile communities from wetlands across CHOH. Results will be compared to acoustic sampling for amphibians.
Collaborators: Andrew Landsman, National Park Service
Project 3: Using Pollinator eDNA to Assess Ecological Resilience of America’s Grasslands
Pollinators, such as bees and butterflies, are integral to our food security and healthy ecosystems as they transport pollen among plants, allowing the plants to reproduce. Scientists from six USGS science centers are collecting DNA left behind by pollinators as they visit flowers and then analyzing that DNA to identify those pollinators. We are testing our methods to detect pollinators at both a broad scale (11 states across the Northwest and Midwest) and with targeted collections for two imperiled species, the Western Bumblebee and Rusty Patched Bumblebee.
Collaborators: David S. Pilliod, Forest and Rangeland Ecosystem Science Center; Muruleedhara (Murulee) N. Byappanahalli, Great Lakes Science Center; Tabitha Graves, Northern Rocky Mountain Science Center; Ralph Grundel, Great Lakes Science Center; Clint Otto, Northern Prairie Wildlife Research Center; Stephen Spear, Upper Midwest Environmental Science Center
Project 4: Assessment of eDNA as a biomonitoring tool for deep-sea biodiversity
eDNA is proving to be a cost-effective means to survey all forms of marine life, from plankton to fishes to whales, from a single water sample. EESC scientists are utilizing eDNA to better understand deep-sea habitats that are difficult to explore and inventory, such as deep-sea coral and cold seep communities in the U.S. Economic Exclusion Zone. Samples are obtained using Remotely Operated Vehicles and Conductivity Temperature Depth rosettes that capture water at desired depths. eDNA analyses provide critical information about species present on the sea floor and those in the water column that link the deepwater food web to more productive surface waters. Coupled with environmental data, the eDNA data will help define water masses, food webs, and offers a detailed glimpse into how these important ecosystems function.
Collaborators: Amanda Demopoulos, Jill Bourque, USGS Wetlands and Aquatic Research Center; Nancy Prouty, USGS Pacific Coastal Marine Science Center, Santiago Herrera and Luke McCartin, Lehigh University; Andrea Quattrini, Chris Meyer, Sarah Tweedt, Allen Collins, Smithsonian Institution.
Using Pollinator Environmental DNA to Assess the Ecological Resilience of America’s Grasslands
The emerging field of Environmental DNA (eDNA) analysis allows characterization of species presence and community biodiversity by identifying trace amounts of genetic material left behind as organisms move through their environments. EESC scientists have been using eDNA technologies to detect native and rare species and as community biomonitoring tools.
Project 1: Characterizing aquatic invertebrate communities in the National Capital Region using eDNA metabarcoding
Aquatic invertebrates such as mayflies and caddisflies are important indicators of stream water quality since many of these invertebrates are sensitive to pollution and sedimentation. Natural resource agencies monitor for aquatic invertebrate diversity using tools like kick-netting to better understand stream quality, but some taxa can be missed or not identified below the genus or even family level, especially for larval forms. EESC scientists compared results of sequencing eDNA filtered from the water to traditional kick-netting in regional National Capital Region National Parks including Catoctin Mountain Park, and Rock Creek Park. While the eDNA approach did not perfectly recover the same taxonomic assemblage as kick-netting, the taxa recovered correlated well with known water quality. In other words, eDNA profiles from healthier streams showed more diverse taxonomic assemblages than those collected in poorer quality streams. The eDNA method could become a valuable tool for natural resource agencies to monitor stream communities in a fast and cost-efficient manner.
Collaborators: Robert S. Cornman and Jennifer A. Fike, USGS Fort Collins Science Center; Sara J. Mueller, The Pennsylvania State College
Project 2: Developing an optimized environmental DNA-based method for inventorying wetland amphibian communities.
The C&O Canal National Historical Park (CHOH) protects hundreds of vernal pools, wetlands, and slow-moving streams. Wetlands found in the western reaches of the CHOH host the most diverse amphibian communities throughout the State of Maryland. With conservation threats from pesticide and fertilizer inputs, stormwater runoff, adjacent land development, and climatic changes affecting wetland water levels and disease dynamics, the park must identify feasible means to understand resource condition and trends given the logistical infeasibility of recurring, physical site sampling. This project is developing analytic methods needed to utilize eDNA to detect lentic amphibian and reptile communities from wetlands across CHOH. Results will be compared to acoustic sampling for amphibians.
Collaborators: Andrew Landsman, National Park Service
Project 3: Using Pollinator eDNA to Assess Ecological Resilience of America’s Grasslands
Pollinators, such as bees and butterflies, are integral to our food security and healthy ecosystems as they transport pollen among plants, allowing the plants to reproduce. Scientists from six USGS science centers are collecting DNA left behind by pollinators as they visit flowers and then analyzing that DNA to identify those pollinators. We are testing our methods to detect pollinators at both a broad scale (11 states across the Northwest and Midwest) and with targeted collections for two imperiled species, the Western Bumblebee and Rusty Patched Bumblebee.
Collaborators: David S. Pilliod, Forest and Rangeland Ecosystem Science Center; Muruleedhara (Murulee) N. Byappanahalli, Great Lakes Science Center; Tabitha Graves, Northern Rocky Mountain Science Center; Ralph Grundel, Great Lakes Science Center; Clint Otto, Northern Prairie Wildlife Research Center; Stephen Spear, Upper Midwest Environmental Science Center
Project 4: Assessment of eDNA as a biomonitoring tool for deep-sea biodiversity
eDNA is proving to be a cost-effective means to survey all forms of marine life, from plankton to fishes to whales, from a single water sample. EESC scientists are utilizing eDNA to better understand deep-sea habitats that are difficult to explore and inventory, such as deep-sea coral and cold seep communities in the U.S. Economic Exclusion Zone. Samples are obtained using Remotely Operated Vehicles and Conductivity Temperature Depth rosettes that capture water at desired depths. eDNA analyses provide critical information about species present on the sea floor and those in the water column that link the deepwater food web to more productive surface waters. Coupled with environmental data, the eDNA data will help define water masses, food webs, and offers a detailed glimpse into how these important ecosystems function.
Collaborators: Amanda Demopoulos, Jill Bourque, USGS Wetlands and Aquatic Research Center; Nancy Prouty, USGS Pacific Coastal Marine Science Center, Santiago Herrera and Luke McCartin, Lehigh University; Andrea Quattrini, Chris Meyer, Sarah Tweedt, Allen Collins, Smithsonian Institution.