Biodiv Sci ›› 2023, Vol. 31 ›› Issue (5): 23062.  DOI: 10.17520/biods.2023062

• Reviews • Previous Articles     Next Articles

Application of environmental RNA technology in aquatic biological monitoring

Miao Li1,2,3,4, Chenyang Yao1,2,3,4, Xiaoyong Chen1,2,3,*()   

  1. 1. State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
    2. Southeast Asia biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar
    3. Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Mengla, Yunnan 666303, China
    4. University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2023-02-28 Accepted:2023-04-20 Online:2023-05-20 Published:2023-05-03
  • Contact: * E-mail:


Background & Aims: Biological monitoring is a core component of biodiversity conservation, and an important tool for assessing the progress of conservation efforts. Traditional aquatic monitoring methods are often based on specimen collection and morphological identification, which are time-consuming and ineffective practices. Additionally, these methods are unable to conduct the type of large-scale, continuous ecological surveys that are required for many conservation initiatives. There is therefore an urgent need to find a new approach to monitoring to meet today’s growing biodiversity surveillance needs.
Progresses & Challenges: As molecular biology tools have improved, environmental RNA technology has been introduced into the field of aquatic biomonitoring and applied to species monitoring, biodiversity assessment, and pathogen detection, showing significant potential to meet conservation needs. However, the development of environmental RNA technology is still at the proof-of-concept stage, and there are many technical drawbacks, including limited understanding of environmental RNA ecological processes, the inconsistent application of the technology and, the lack of a transcriptome database that limits its ability to be used in aquatic biomonitoring.
Review Results: In this review, we first give a brief introduction to environmental RNA technology. We then introduce the analysis process of environmental RNA technology and discuss in detail what information should be noted in the sample collection and preservation process, the environmental RNA extraction and cDNA synthesis process, PCR amplification and sequencing, and analysis of results. Next, we present the current status of the application of environmental RNA technology in three areas: species monitoring, biodiversity assessment, and pathogen detection. Further, we also discuss problems associated with environmental RNA technology in practical applications. Finally, we summarize the strengths and weaknesses of environmental RNA technology. We identify two primary advantages of environmental RNA technology: (1) environmental RNA technology can further improve the accuracy of biomonitoring; and (2) environmental RNA technology can reveal additional relevant information, such as the structural composition of populations, the physiological status of organisms, and the health of ecosystems. The shortcomings of environmental RNA technology are as follows: (1) the ecological processes of eRNAs released into the environment are unclear, which may lead to false positive and false negative errors; (2) the application of environmental RNA technology is not standardized, which makes it impossible to compare the results between different studies; and (3) the lack of a transcriptome database will limit the further development of environmental RNA technology in aquatic biomonitoring. In order to make full use of environmental RNA technology, these shortcomings must be addressed as soon as possible.
Going Forward: In the future, in order to properly apply environmental RNA technology in the field of aquatic biomonitoring, researchers should focus on the following aspects in their research: (1) to clarify the ecological processes of environmental RNA in the aquatic environment to reduce the probability of false positive and false negative errors; (2) to develop a standardized analysis process for environmental RNA technology so that the data obtained from aquatic biomonitoring using these approaches are accurate, reproducible and comparable; (3) to continuously improve the transcriptome database so that environmental RNA technology can be used for more biological assessments; and (4) to further expand the application of environmental RNA technology in aquatic biomonitoring, such as the use of environmental RNA technology to conduct research on the physiological conditions of aquatic organisms, population ecology and ecosystem health evaluation.

Key words: environmental RNA, biomonitoring, biodiversity, population monitoring, pathogens