Testing for River Fish DNA and RNA in Environmental Samples

Jim Crocker
18th March, 2024

Testing for River Fish DNA and RNA in Environmental Samples

Image Source: Natural Science News, 2024

Key Findings

  • In a Japanese study, nuclear genes in eDNA/eRNA allowed better detection of fish species than mitochondrial genes
  • eRNA showed more variability than eDNA, making it less reliable for estimating fish numbers
  • These insights can improve aquatic species monitoring and conservation efforts
Environmental DNA (eDNA) and RNA (eRNA) are genetic materials shed by organisms into their environment. Scientists can collect these materials from soil, water, or air to monitor and study biodiversity without physically capturing or observing the organisms. This non-invasive approach has become a game-changer in ecology and conservation, offering a cost-effective and sensitive method for detecting species presence and abundance. However, despite its promise, there are still gaps in our understanding of how different genetic targets within eDNA and eRNA analyses perform in real-world applications. In a recent study by the Japan Society for the Promotion of Science[1], researchers conducted an experiment to evaluate the detection sensitivity and reliability of eDNA and eRNA from multiple genetic sources. They focused on a fish species called ayu (Plecoglossus altivelis) in controlled tank conditions. The study aimed to compare how well eDNA and eRNA could be detected and quantified when targeting different genes, including both mitochondrial (often found in many copies within a cell) and nuclear genes (which are typically present in two copies per cell, but can have multi-copy genes). Previous research has shown that eDNA can sometimes yield false positives due to the detection of old DNA that has persisted in the environment[2]. This study sought to understand the performance of eDNA and eRNA analyses by looking at the concentration of genetic material in water samples and the variability between different test replicates. It was found that assays targeting multi-copy nuclear genes were more sensitive than those targeting mitochondrial genes, meaning they could detect lower concentrations of genetic material more reliably. Interestingly, while eDNA and eRNA concentrations were higher for the nuclear gene, the variability in eRNA quantification did not necessarily match that of eDNA. In fact, the variation between replicates was larger for eRNA, suggesting that while eRNA may be useful for detecting the presence of a species, it might not be as reliable for estimating population abundance. This finding is significant because it helps address some of the limitations of eDNA analysis highlighted in earlier studies. For instance, a meta-analysis[3] comparing traditional biodiversity assessment methods with DNA metabarcoding—a technique that uses eDNA to identify species—found that while DNA metabarcoding is consistent with traditional methods for studying fish communities, it may not always align for smaller organisms. The current study adds to this by suggesting that careful selection of genetic targets is crucial for accurate eDNA and eRNA analyses. Moreover, understanding the persistence and degradation of eDNA is essential for interpreting these analyses accurately[4]. The interaction between environmental factors, such as water temperature, and the molecular state of eDNA, such as fragment size and target gene, can influence how long eDNA remains detectable in the environment. The present study contributes to this body of knowledge by comparing the persistence of different types of genetic materials and their respective detection sensitivities. In conclusion, the research provides valuable insights into the application of eDNA and eRNA for biomonitoring. It suggests that nuclear genes, especially those with multiple copies, could enhance the sensitivity of species detection. However, the variability in eRNA quantification highlights the need for careful interpretation when using these methods to estimate species abundance. By refining eDNA and eRNA analysis techniques, we can improve the accuracy and reliability of biomonitoring, which is crucial for the conservation and management of aquatic ecosystems.

EnvironmentGeneticsMarine Biology


Main Study

1) Comparative evaluation for the performance of environmental DNA and RNA analyses targeting mitochondrial and nuclear genes from ayu (Plecoglossus altivelis).

Published 16th March, 2024


Related Studies

2) Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis.


3) Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment.


4) Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses.


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