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CERC eDNA Crew Blog - 2022

By Columbia Environmental Research Center

CERC eDNA Crew Blog - 2022

 

Is environmental DNA a delicious source of nitrogen for microbes?

By Rachelle Beattie

As the use of environmental DNA (eDNA) methods for tracking and monitoring species increases, a better understanding of the factors that impact eDNA persistence and fate in the environment is needed. 

Environmental DNA (eDNA) refers to the total reservoir of DNA in the environment. It  can include DNA from entire organisms such as bacteria or small insects and worms (i.e. organismal DNA) as well as DNA shed from larger organisms1.

chart of common abiotic factors known to influence the decay rate of eDNA
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An overview of common abiotic factors known to influence the decay rate of eDNA in aquatic environments.

Environmental DNA is used to monitor specific invasive or rare species and to identify organisms in a community. However, collecting an environmental sample that contains high quality eDNA is impacted by many biotic and abiotic factors. Understanding how these factors affect the persistence and fate of eDNA is critical for designing environmental monitoring programs.

Most current research focuses on the effects of abiotic factors such as temperature, pH, suspended solids, and sunlight on eDNA persistence in aquatic samples.

However, there is an increasing interest in the role biotic factors, like microorganisms, play in eDNA persistence and fate.

How do microorganisms impact eDNA persistence and decay?

picture of a person collecting water and sediment samples
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Dr. Thea Edwards (CERC) collecting water and sediment samples to cultivate a nitrifying microbial community.

New evidence suggests that faster eDNA decay rates associated with higher temperatures, an abiotic factor, may instead be the result of increased microbial metabolism in warmer environments. Microorganisms are ubiquitous in the environment and provide a range of ecosystem services including decomposition of organic matter, such as eDNA. Although data are limited, some studies show that microorganisms increase the decay rate of eDNA in aquatic samples2,3; however, a lack of sterile controls has made comparisons difficult.

Are microorganisms capable of using eDNA as a nutrient source?

At the Columbia Environmental Research Center, we have successfully cultured and maintained a community of microorganisms from the environment called nitrifiers. Nitrifiers are a special group of microorganisms, mostly bacteria, that convert nitrogen in the form of ammonia into nitrite and nitrate. Nitrate is critical for the growth and development of plants and algae. While nitrogen makes up 78% of our atmosphere, most of this element is unavailable to living organisms without microbial conversion through processes such as nitrification. Nitrifying bacteria are most frequently found soil and water where decomposing organic matter provides an excellent source of ammonia.

 

Although the nitrogen cycle is necessary for life on earth, our understanding of this process has many knowledge gaps. One of those gaps is whether microorganisms involved in the nitrogen cycle can use alternative forms of nitrogen, such as eDNA, as an energy source. Organic nitrogen found in eDNA may be consumed nitrifying microorganisms; however, this hypothesis remains untested. Both the ability of nitrifying microorganisms to use eDNA as a nitrogen source and their impact on the decay rate of eDNA need to be further investigated.

Chart showing the basic overview of the nitrogen cycle
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A basic overview of the nitrogen cycle. Red arrows represent the portions of the nitrogen cycle (decomposition and nitrification) that are performed by our laboratory’s microbial culture.

Study overview:

This summer, we designed a study to test whether our nitrifying microbial community can use eDNA as their only source of nitrogen. Prior to this experiment, our nitrifying community was supplemented with ammonium sulfate as a source of nitrogen and was able to successfully produce nitrate. This success indicated that the microbial community contains an abundance of nitrifying bacteria. A brief overview of the study design is shown below.

chart showing the overview of the experimental design to determine if a nitrifying microbial community
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An overview of the experimental design to determine if a nitrifying microbial community can use organic nitrogen from eDNA as a nutrient source. Each of the three nitrogen treatments (ammonia only, eDNA only, or a combination of ammonia and eDNA) were inoculated with the nitrifying microbial community in the exponential growth phase (right column) or contained no microbial community (sterile controls, left column) for a total of six experimental treatments. The concentration of eDNA was measured at 10 timepoints over 72 hours to determine the rate of eDNA decay in each treatment.

Results from this study will help us better understand the role of microorganisms in the nitrogen cycle as well as answer multiple unknowns that could inform eDNA research including:

  1. The impact of a nitrifying microbial community on the rate of eDNA decay in an artificial aquatic system
  2. The rate of eDNA decay in sterile water with no microbial community present
  3. The capability of a nitrifying microbial community to use eDNA as a sole nitrogen source

References

  1. Rodriguez-Ezpeleta, N., Morissette, O., Bean, C.W., Manu, S., Banerjee, P., Lacoursière-Roussel, A., Beng, K.C., Alter, S.E., Roger, F., Holman, L.E., Stewart, K.A., Monaghan, M.T., Mauvisseau, Q., Mirimin, L., Wangensteen, O.S., Antognazza, C.M., Helyar, S.J., de Boer, H., Monchamp, M.-E., Nijland, R., Abbott, C.L., Doi, H., Barnes, M.A., Leray, M., Hablützel, P.I., and Deiner, K., 2021, Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What's behind the term?” by Pawlowski et al., (2020): Molecular Ecology, v. 30, no. 19, p. 4601-4605. 
  2. Mauvisseau, Q., Harper, L.R., Sander, M., Hanner, R.H., Kleyer, H., and Deiner, K., 2022, The multiple states of environmental DNA and what is known about their persistence in aquatic environments: Environmental Science & Technology, v. 56, no. 9, p. 5322-5333.
  3. Lance, R.F., Klymus, K.E., Richter, C.A., Guan, X., Farrington, H.L., Carr, M.R., Thompson, N., Chapman, D.C., and Baerwaldt, K.L., 2017, Experimental observations on the decay of environmental DNA from bighead and silver carps: Management of Biological Invasions, v. 8, no. 3, p. 343.