In late 2011, the ACRCC funded a study to better understand eDNA. This study is being referred to as the eDNA Calibration Study, or ECALS.
The main purpose of ECALS is to improve the application of eDNA methodology to assess and mange uncertainty. ECALS will investigate alternate sources of Asian carp DNA, improve existing genetic markers and investigate the relationship between the number and distribution of positive eDNA samples with the density of Asian carp populations. The results of this study will allow project managers to better interpret eDNA results, as well as investigate ways to make the eDNA process more efficient (decrease processing time and cost).
The study has a number of specific objectives:
Objective 1. eDNA vector assessment:
Identify potential vectors, or sources, for Asian carp DNA to enter the Chicago Area Waterways (CAWS) without originating from a live, free-swimming bighead or silver carp (or hybrid). Potential vectors include the introduction of tissue and other cell matter containing Asian carp DNA from:
• Movement of carp and carp material via fish-eating birds, particularly eDNA deposits entering the water via bird excrement
• Combined sewer outfalls (specifically in regions of Chicago where Asian carp are sold in markets on the street) as a vector of eDNA
• Fish carcasses that are transported via barges that pass through the electric dispersal barrier.
Objective 2. Develop eDNA markers for improved population inference:
Develop high-fidelity, sensitive genetic markers for detecting the presence of Asian carp DNA and for making broad estimates of Asian carp abundance. Using multiple markers may aid researchers in their ability to estimate Asian carp populations and movement.
Objective 3.1 Increase the efficiency of eDNA processing:
Develop a way to process eDNA samples more efficiently by decreasing processing time and refining the process so it is more sensitive to lower concentrations of eDNA. As a result, eDNA processing time may be reduced from 10 working days to five working days, allowing for much quicker turnaround time for results and more rapid response to new eDNA hits. Also, assess whether different water sampling protocols might improve Asian carp detection probabilities (depth- integrated sampling, new filtering techniques, appropriate volume of water to sample).
Objective 3.2 Determine eDNA assay sensitivity under no flow conditions:
Determine the relationship between Asian carp size, number and behavior on eDNA loading rates (DNA shedding, sloughing), minimum amounts of eDNA required for detection and time to detection, and the rate at which detectable amounts of eDNA fills a volume of water during non-flowing conditions.
Objective 3.3 Determine eDNA assay sensitivity under flowing water conditions:
Determine the rate at which detectable amounts of eDNA fills a volume of water during flowing conditions.
Objective 3.4 Quantify relationships between major environmental factors and eDNA degradation under no flow conditions:
Determine the relationship between environmental factors -- water temperature, light exposure, zooplankton and microbial biomass, pH -- on eDNA degradation rates in no flow systems.
Objective 3.5 Develop guidance on using calibration data to broadly estimate Asian carp abundance under no flow conditions:
Evaluate likely spread of eDNA from source points in no flow systems so that sampling can be planned such that sample points are reasonably expected to represent independent samples (not from same eDNA plume).
Objective 3.6 Develop a hydrodynamic eDNA transport predictive model to characterize fish occurrence:
Models based on fish behavior and CAWS water-flow dynamics will be developed to better understand eDNA behavior in the system. Models will also help identify likely carp population scenarios.
ECALS 2013 Major Milestones
February 2013: Second interim ECALS Report
- Download Report (PDF)
- Download Executive Summary (PDF)
- Download ECALS Second Interim Report Fact Sheet (PDF)
May 2013: Markers
- Part 1 of a report describing the development of a qPCR marker
July 2013: Calibration
- Report describing the relationship between environmental factors on eDNA degradation rates
July 2013: Calibration
- Part 1 of a report describing shedding studies
Aug 2013: Calibration
- Part 2 of a report describing shedding studies
Aug 2013: Markers
- Part 2 of the markers report released in May
Sept 2013: Sediment Studies Report
Dec 2013: Third interim ECALS Report
ECALS 2012 Major Milestones
March: First Interim Report
April: Begin Bird Studies (field and lab)
- A telemetry study on cormorants in the Illinois Waterway down to Peoria to document migratory and foraging behavior, as well as testing the feces for Asian carp DNA. Lab studies will also be conducted to determine the detectable amounts of Asian carp DNA in cormorant and bald eagle feces when they are fed these fish, and also feathers will be sampled to determine if DNA can be carried on the bodies of these birds.
May: Hi-throughput technique Report
- Report documenting the results from studies conducted to decrease the processing time and cost of eDNA samples. We expect a follow up to this report in late October. Download Report (PDF)
August: Storm Sewers Final Report
- The storm sewer experiment in Chinatown where Asian carp contaminated-ice is deposited in a storm sewer then tested for viable eDNA detections in the sewer and river was conducted in June. This experiment was also conducted in November of last year.
- Download the report (PDF)
December: Optimized Sampling Protocol Report
- Experiments to text different methods of sampling and extracting DNA from the river were conducted in June, this is a follow up to an experiment also conducted in 2011. Testing the limits of detection for three different methods including the standard 2L surface sample with filtering, in-field filtering with 10L of water, and finally centrifuging 50mL Falcon tubes. The goal is to determine the most efficient processes that can be used to sample for eDNA, perhaps by giving resource managers options that are standardized to meet their needs.
ECALS Frequently Asked Questions
How is ECALS funded?
ECALS is an interagency study, with USACE, USGS and USFWS participating and is fully funded by the Great Lakes Restoration Initiative.
What is the timeframe of this study?
ECALS is a two year study, with completion expected at the end of 2013. However, the team will be providing interim products frequently.
What is the purpose of ECALS?
The purpose of ECALS is to investigate alternative sources and pathways for eDNA detections beyond a live fish. The study will also examine how environmental variables such as light, temperature and water velocity impact eDNA detections, explore the correlation between the number of positive samples and the strength of the DNA source, develop more efficient eDNA markers to cut the sampling processing time in half and model eDNA transport specific to the Chicago Area Waterway System. The intent is that all entities using eDNA as a monitoring tool, not just the ACRCC, will be able to use this information to refine their own monitoring and management programs.
What will you do with the results?
Results will be provided frequently, and will be shared with the ACRCC, specifically the Monitoring and Rapid Response Work Group. The results will inform current eDNA sampling strategies and will make the sampling more efficient and allow for more informed interpretation by managers for rapid response decisions in the Chicago Area Waterway System.
What is a vector?
When vectors are described vectors, the source of DNA has to also be considered.
A source is a point of entry into the environment where the fate and transport of eDNA goes from being controlled to being uncontrolled. Think of eDNA as a pollutant. A source is defined by a location and a mode of release.
A vector is a mode of transport in the environment. It may be a bird, rainfall runoff, storm or sewer flows, or a barge, etc. For example, barges may transport dead fish or fish slime on the hull. Runoff may carry fertilizer, fishy ice, etc.
For example: Live fish below the electric dispersal barriers are an obvious potential source of eDNA. They release eDNA into the environment. Once released into the environment, the eDNA may move upstream by one of several vectors - bird, barge, recreational boat or fisherman.
What is calibration?
Calibration refers to investigating the suite of parameters that may influence the detection, degradation or persistence of DNA, and defining how those parameters affect these variables. For example, what effect does temperature have on DNA? What effect does flowing or non-flowing water have on the movement of DNA in a system?
Why would Asian carp DNA be found in fertilizers?
Asian carp are used as ingredients in some fertilizer products, which may then be used in the Chicago region and (via runoff as a vector) end up in the water.
What's a storm sewer experiment?
The ECALS Team conducted a storm sewer experiment in late 2011 to investigate the viability of DNA (or, our ability to detect DNA) being transmitted to the river from a storm sewer after being deposited into a storm drain. This was in response to a report from an Illinois DNR biologist who observed ice holding dead Asian carp being dumped directly into a storm sewer in Chicago's Chinatown- an area where we have detected eDNA in the river nearby. The team simulated this event and demonstrated that, indeed, DNA can be deposited to the river by this mechanism. This study will be repeated summer 2012.
What are alternative sampling trials?
Lab filtering of DNA is a time-consuming step of the eDNA sampling process. The teams is investigating alternative sampling protocols to make eDNA sampling more efficient. One way is to minimize, or eliminate, the lab component by conducting field filtering. Using sieve cloth, river water was filtered in the field, enabling the samples to be processed directly. It is assumed that eDNA is attracted to particulate material, and, therefore, extracting the particulate material in the field, the team was able to process those samples for the presence of Asian carp DNA.
What is an eDNA marker?
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify a species. The team is testing water samples for the markers for bighead and silver carp and intends to develop improved markers to decrease processing time.
What is modeling eDNA transport?
The ECALS Team will be investigating the influence of environmental variables, including water velocity and degradation rates, to model how eDNA can be transported, or how it moves, through the Chicago Area Waterway System.
Asian Carp Regional Coordinating Committee