Environmental DNA Surface Sampling Methods in Freshwater Environments

What is aquatic eDNA sampling, and what is it used for? 

eDNA (Environmental DNA) is a non-destructive method of capturing and analyzing shed genetic material left in the water from aquatic species.  

As more industries are required to demonstrate environmental compliance, eDNA sampling can be used in aquatic environments to produce environmental impact assessments, baseline biodiversity surveys, ongoing biodiversity monitoring, and environmental compliance by detecting early threats like pathogens and parasites, and identifying cryptic, threatened and invasive species.  

For these reasons, eDNA is quickly becoming an accepted biodiversity monitoring method across additional sectors, including aquaculture and land management, water utilities, oil and gas, offshore and onshore wind farms, farming, fisheries, shipping, construction and more.  

In freshwater environments like rivers, lakes, streams, canals, wetlands, reservoirs,  ponds and creeks, collecting eDNA field samples can be a challenge due to the remote locations, variety of sampling environments and variety of species. Having the ability to collect eDNA samples in aquatic environments makes it easier to monitor biodiversity with smaller and more compact tools that can easily be carried and used in the field.  

What are the traditional eDNA sampling methods for aquatic environments, and how effective are they? 

To capture data on the presence of aquatic organisms in freshwater, researchers and citizen scientists have developed many different tools to collect environmental DNA (eDNA) in freshwater environments. These methods mostly consist of water grab sampling (manual collection methods), syringe filtration (manual collection method), in-situ filtration methods (like Ocean Diagnostics’ eDNA Surface Sampler), and passive sampling (collecting DNA on materials like filter paper that is submerged in the water and collected later).  

Both water grab and passive sampling present significant challenges and limitations that in-situ filtration alleviates.  

A High-Level Comparison of eDNA Surface Sampling Methods 

Water Grab Sampling 

In this method, water is manually collected in sterile containers and filtered manually in the field or the lab. Often, the samples must be frozen and transported back to the lab quickly to avoid DNA degradation. This method is time-consuming, involves additional filtration equipment, and leaves the samples open to contamination risks. While it provides a cheap alternative to in-situ filtration, it is not scalable and impractical for difficult-to-reach environments due to the extra equipment needed in the field and difficulties transporting water.  

Syringe Sample Filtration 

Using this method, eDNA filters are manually collected using a single-use plastic syringe (generally 50-60mL in size). To perform this method, water is drawn into the syringe from the environment, connected to the inlet of an eDNA filter, and discharged through the filter. This process is repeated 20-100 times, transferring Liters of water from the environment through the eDNA filter using the pressure of the syringe. This quantitative method is inexpensive and easy to perform with any type of end user, however results in the steady use of single use plastics, significantly raises the risk of contamination by having to constantly connect and disconnect the filter, and can be very physically demanding when needed to be repeated many times in the field.  

Passive Sampling 

In Passive Sampling, researchers submerge materials like filter paper, cotton or sponges into the water where they passively collect eDNA over time. The material is then manually retrieved for the transfer of DNA into a preservative solution for later analysis. This method is subject to species bias based on those shedding DNA near the device, open to biofouling and inefficient water flow and is difficult to use objectively without a thorough understanding of flow rates and water conditions around the passive sampler.  

eDNA In-Situ Filtration for Aquatic Surface Water 

In-situ filtration devices provide the most efficient eDNA surface sampling option in aquatic environments. This method typically involves a portable and rechargeable vacuum pump that draws freshwater onto a filter where the eDNA is captured quantitatively. This method enables researchers to filter higher water volumes and capture more diverse and biologically rich data.  

The benefits of in-situ eDNA surface samplers include: 

• Contamination reduction 
• Rapid sampling time 
• Scalable 
• Standardizes sampling protocols 
• Provides a quantitative volume for determining DNA concentration 
• Rechargeable battery options  
• Less manual labour 
• More field samples
   

While some researchers and community scientists build their own hand-driven vacuum systems using peristaltic pumps, current off-the-shelf systems, like Vampire Samplers, can be difficult to use and require the sterilization of pump tubing between sampling events, adding logistical overhead to sampling campaigns.    

What’s the most efficient tool to collect eDNA samples from aquatic surface water?

Rechargeable, portable and in-situ eDNA surface samplers with vacuum pump systems, like Ocean Diagnostics' eDNA Surface Sampler, enable researchers and community scientists to collect more and reliable quantitative samples in any freshwater environment while eliminating sample contamination potential and manual processing. These devices save users time, money and physically demanding labour while collecting more field data and improving environmental assessments and biodiversity monitoring efforts. 

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