Environmental DNA and how biodiversity, our health, and the climate are connected

View of a lake in the Eagle River Valley, Municipality of Anchorage, Alaska.View of a lake in the Eagle River Valley, Municipality of Anchorage, Alaska. (Photo: Diego Delso, CC BY-SA 4.0, via Wikimedia Commons)

Learn about my participation in a biodiversity research project gathering environmental DNA samples from 800 lakes around the world.

OKANAGAN VALLEY, British Columbia – Several months ago I read about an ambitious research project to measure biodiversity on the same day all around the world, with the appropriate target sampling date of May 22, the International Day for Biological Diversity.

The goal is to test the potential of a global strategy for monitoring animal and plant diversity by collecting environmental DNA (eDNA) samples from lakes around the world. Plants and animals “shed” their DNA into aquatic or terrestrial environments, providing eDNA evidence of their presence. This research hopes to redefine global strategies for biodiversity monitoring.

Given that it’s been a while since I’ve conducted field research, I was eager to participate. I immediately contacted lead researcher Prof. Dr. Kristy Deiner of ETH Zurich (Eidgenössische Technische Hochschule Zürich) to express my interest, even though my field research experience involved tools to sample water quality, not environmental DNA. My eDNA experience, in fact, was limited to my digital marketing skills helping my esteemed colleague, Dr. Ryan Kelly of the University of Washington’s School of Marine and Environmental Affairs, create the eDNA Collaborative website.

Given the scope of this research, however, the sampling protocol was designed in such a way that previous eDNA sampling experience was not required. The research team cleverly developed a protocol that could be applied by anyone from eDNA researchers to community scientists.

The lake eDNA sampling kit consists of a 3-litre bucket, hand suction pump, filter cartridge, two hoses, several pairs of nitrile gloves, and a 50 ml plastic tube with 25 ml of preservation buffer to preserve the eDNA filter.

The lake eDNA sampling kit consists of a 3-litre bucket, hand suction pump, filter cartridge, two hoses, several pairs of nitrile gloves, and a 50 ml plastic tube with 25 ml of preservation buffer to preserve the eDNA filter. (Photo: ETH Zürich Environmental DNA sampling protocol)

The research team provided the easy-to-assemble sampling kit, step-by-step instructions on how to use it, and produced an instructional video demonstrating how to collect eDNA from the shoreline without contaminating the sample. The kit itself is a new invention developed specifically for this type of lake eDNA sampling.

Biodiversity, our health, and the climate are intertwined

This research is important because biodiversity “is important for healthy and resilient ecosystems and provides a number of ecosystem services that are essential for human well-being,” according to the Millenium Ecosystem Assessment, an interdisciplinary report by the World Resources Institute. Additionally, future plant biodiversity loss could decrease carbon storage in land ecosystems, according to new research.

The United Nations has deemed conserving and restoring natural spaces as essential for limiting greenhouse gas emissions and adapting to climate impacts. Biodiversity loss, in fact, is one of the “big three” the U.N. considers part of the triple planetary crisis, with pollution and climate change the others. Developing a rapid, cost-efficient way to measure global biodiversity, as this research strives to do, would greatly inform environmental policy everywhere.

Related: Only a few degrees of global warming? So what.

The U.N. Environment Programme (UNEP) in 1988 recognized the importance of biodiversity, calling it “a global asset of tremendous value to present and future generations,” which led to the 1993 Convention on Biological Diversity. Similar to the more familiar Intergovernmental Panel on Climate Change, advisory groups of interdisciplinary experts meet regularly to review research and develop strategies to preserve biodiversity.

How lakes were selected for this research

A view to the southwest from the eastern shore of Skaha Lake, in the Okanagan Valley of British Columbia, Canada.

A view to the southwest from the eastern shore of Skaha Lake, in the Okanagan Valley of British Columbia, Canada. (Photo: Fawcett5 at English Wikipedia)

Researchers carefully selected lakes based on their environmental and geographic characteristics. Before being selected to participate, the research team asked me to identify up to three lakes that met the research parameters, restricted by a range of altitude and surface area. In the event all three were selected, I proposed sampling lakes all within relatively close driving distance to one another: Omak Lake in north-central Washington state, and Skaha Lake and Osoyoos Lake just across the border in British Columbia.

The researchers asked me to sample eDNA from Omak Lake. However, as I discovered a little more than a week before May 22, Omak Lake shoreline access is restricted to the region’s Indigenous Tribes.

Respecting Indigenous rights and land management

The scientific community has not always been on its best behavior when conducting research on lands and waters of Indigenous peoples. As recently as 2003, 70 percent of published research about least-developed countries did not include a local research co-author. Avoiding such “parachute science,” happily, is now top of mind in the research community, with fascinating examples of traditional ecological knowledge informing collaborative research. One example in the Pacific Northwest shows the importance of revitalizing Indigenous mariculture practices for food sovereignty and resilience.

Omak Lake is on land managed by the Confederated Tribes of the Colville Reservation, which was established in 1872. And while there are two public access areas on the north end of the lake, I needed permission to access other areas of the shoreline to ensure eDNA samples representative of the lake’s true biodiversity.

Omak Lake (center of th map) on the Colville Indian Reservation in north-central Washington. An estimated 7,692 residents live on the reservation.

Omak Lake (center of the map) on the Colville Indian Reservation in north-central Washington. An estimated 7,692 residents live on the reservation. (Image: Confederated Tribes of the Colville Reservation)

I could have gotten a permit from the Tribe to use a boat to gather samples, but that was not an option for me. And to have sampled only the north end of the lake would have minimized my contribution to the research and provided minimally valuable data. To access other areas of the shoreline without Tribal permission not only would have been trespassing, but indubitably morally reprehensible as well. Given my untimely realization the Tribe managed the lake, I was unable to gain advance permission. So with the approval of the research team I pivoted to Skaha Lake, where I could get public access on the north, east, south, and west shorelines.

Field research is not always weather dependent — and other surprises

For my time gathering eDNA samples May 22 it was a chilly, windy, and rainy day at Skaha Lake, and I needed all of the rain gear I had, including rain pants and rubber boots and hiking boots to navigate the muddy parts of the shoreline. It also presented a good opportunity to dust off my all-weather Rite in the Rain notebook and weatherproof pen.

When in the field, rain or shine, taking detailed notes of the data being collected is the obvious priority, but it’s also always a good idea to make note of simple observations: weather conditions, wildlife sightings, etc. I only saw a few ducks when I was gathering my eDNA samples, but that doesn’t mean the data will limit biodiversity to duck DNA. There are a variety of reasons my wildlife sightings were limited: weather, time of day, animals I may have scared away upon arrival, and who knows why else.

The Okanagan River flows through the lake, and the research protocol identified two important areas where to gather eDNA samples:

  • Near the main rivers or streams flowing into the lake; and,
  • near the lake’s outflow.

The expectation is eDNA may flow into and accumulate in lakes, making the inflows and outflows areas of particular interest to the researchers, potentially providing the best data about a lake’s biodiversity. Fortunately it was easy for me to gather data in those areas.

Skaha Lake as seen in Google Maps. Each dot represents a location where I sampled lake water from the shore. The Okanagan River flows into the lake from the north (top), and the lake outflows at the southern end (bottom). McLean Creek flows into the lake from the eastern slope (right bottom dot).

Skaha Lake as seen in Google Maps. Each dot represents a location where I sampled lake water from the shore. The Okanagan River flows into the lake from the north (top), and the lake outflows at the southern end (bottom). McLean Creek flows into the lake from the eastern slope (right bottom dot). (Image: Google Maps with dots added by George Thomas Jr.)

Preparation is another key facet of field research. I studied a variety of maps showing the topography of the lake’s shoreline, identifying likely places where I could gather samples. In addition to the obvious inflow of the Okanagan River, I also identified creeks that flowed into Skaha Lake. The shoreline near the lake’s outflow also was easily accessible for me.

However, not all of the creeks I saw on the maps existed. They may have been seasonal creeks that have flow only during the spring snow melt, heavy rainfall, or maybe their paths have shifted over time. Also there were a few places where I thought I could get access but it was restricted by private property, or inaccessible due to the terrain.

Collaboration and data governance

The custom filter cartridge and its components are designed to capture eDNA samples as lake water is pumped through it.

The custom filter cartridge and its components are designed to capture eDNA samples as lake water is pumped through it. (Photo: ETH Zürich Environmental DNA sampling protocol)

So what biodiversity data did I collect? I have no idea — not yet. After several hours of filtering lake water at my sampling locations, I removed the filter from the suction pump, inserted it into the tube to preserve the eDNA sample, and shipped everything back to the research team in Zürich. There the team has access to a specially equipped eDNA laboratory with a clean room filled with air filters and over pressurization to prevent external contaminants.

The next steps for the research team will be to process the samples by extracting DNA from the 800 or so filters, test for plant and animal DNA, and share the final results, probably by February, 2025. The global data set then will be publicly available online.

Sign me up

In order to participate in this study I had to agree to a collaboration agreeement detailing all aspects of the global study. The research team expects to share the results by February, 2025.

In order to participate in this study I had to agree to a collaboration agreement detailing all aspects of the global study. The research team expects to share the results by February, 2025.

Albeit only a few hours collaborating in this global study, it was a joy to be back in the field, rain or shine, and now I can add eDNA sampling to my field research skill set. If you’re looking for field research assistance, sign me up!