Scientists At Work: We Use Environmental DNA To Monitor How Human Activities Affect Life In Rivers And Streams

Today about 1 in 4 freshwater creatures face extinction. Wetlands are disappearing three times faster than forests. Across the globe, water quality is plummeting, polluted by plastic, sewage, mining sludge, industrial and agricultural chemicals and much m

Planet Outlook
September 18, 2021
Scientists At Work: We Use Environmental DNA To Monitor How Human Activities Affect Life In Rivers And Streams

Rivers, lakes and wetlands cover just 1% of the Earth’s surface but are home to nearly 10% of all species, including fish, mammals, birds, insects and crustaceans. But these rich, diverse ecosystems are in free fall. Worldwide, species are declining faster now than at any other time in human history, and fresh waters are losing more species than land or ocean ecosystems.

Today about 1 in 4 freshwater creatures face extinction. Wetlands are disappearing three times faster than forests. Across the globe, water quality is plummeting, polluted by plastic, sewage, mining sludge, industrial and agricultural chemicals and much more.

It’s challenging to study how these stresses are affecting aquatic life. There are many diverse threats, and river networks cover broad geographic regions. Often they run through remote, nearly inaccessible areas. Current techniques for monitoring freshwater species are labor-intensive and costly.

In our work as researchers in ecology, we are testing a new method that can vastly expand biomonitoring: using environmental DNA, or eDNA, in rivers to catalog and count species. Federal and local agencies need this data to restore water quality and save dwindling species from extinction.

 

Traditional methods are slow and expensive


With traditional biomonitoring methods, scientists count individual species and their abundance at just a few sites. For example, one recent study of mountaintop mining impacts on fish in West Virginia sampled just four sites with a team of four researchers.

Collecting and identifying aquatic organisms requires highly skilled ecologists and taxonomists with expertise in a wide variety of freshwater species. For each sample of fish or invertebrates collected in the field, it takes from hours to weeks to identify all of the species. Only wealthy nations can afford this costly process.

Conserving threatened and endangered species and keeping river ecosystems healthy requires monitoring broad areas over time. Sensitive aquatic insects and fish species are the freshwater equivalent of the proverbial canary in a coal mine: If these species are absent, that’s a strong indicator of water quality problems. The cause may be mining, agriculture, urbanization or other sources, as well as dams that block animals’ downstream movements.

 

Free-floating genetic evidence

Innovations in genetic technology have created a powerful, affordable new tool that we are now testing. The process involves extracting eDNA from genetic material floating in the water – skin, scales, feces and single-celled organisms, such as bacteria.

By analysing this genetic information, we can detect a wide range of species. We started considering using eDNA for our research in 2018, after several studies demonstrated its power to monitor single species of interest or groups of organisms in rivers and oceans.

Collecting eDNA is easy: One 4-ounce water sample can capture remnant DNA from thousands of aquatic species. Another benefit is that it doesn’t require killing wildlife for identification.

In the lab, we analyze the DNA from different taxonomic groups one by one: bacteria, algae, fish and macroinvertebrates – organisms that lack backbones and are large enough to see, such as snails, worms and beetles. Many researchers study just one group, but we assess all of them at the same time.

We then match our DNA sequences with freshwater species that are already catalogued in existing databases. In this way, we can chart the distribution and abundance of these organisms within and across rivers.

This process requires just a cheap filter, a syringe and vials, and anyone can do it. Commercial eDNA companies charge less than $200 to extract and sequence a sample.