Barcoding Invisible Life: Detection of Arthropods Using Environmental DNA Collected from Plant Runoff -- Kindai University

Osaka [27 June 2023] Researchers design a non-destructive method for harvesting environmental arthropod DNA from water running on plant surfaces

The complete assessment of arthropod species has major implications in conservation, pest control, community ecology, biosecurity, invasive species monitoring, and biodiversity analysis. However, manual surveys that more or less rely on visual techniques are costly, inefficient, and time-consuming. A team of researchers from Japan has recently developed a non-destructive ‘metabarcoding’ method for collecting the environmental DNA of terrestrial arthropod communities from water flowing over plant surfaces, which could revolutionize how we document terrestrial arthropods.

Arthropods are a diverse group of invertebrate animals that include insects, crabs, spiders, and scorpions, among other animals with jointed appendages. Their diversity is typically influenced by the variety of plants with which they interact. The survey of arthropods is crucial for their conservation as well as pest management in agriculture. However, sample-based surveys for the assessment of arthropod communities are expensive and tedious. Moreover, arthropods tend to move quickly, are usually small in size, and may blend with their surroundings effortlessly, making their detection challenging. As a result, rapid and accurate surveys for arthropod detection are much needed.

In a recent study, Associate Professor Kinuyo Yoneya of the Faculty of Agriculture, Kindai University, in collaboration with Masayuki Ushio from Kyoto University and Takeshi Miki from Ryukoku University, has developed a non-destructive method to identify terrestrial arthropod species by collecting environmental DNA (eDNA) samples from water flowing over plant surfaces. Their findings have been published in the journal Scientific Reports on 12 May 2023.

The arthropod eDNA collection method developed by the team, called "plant flow collection," involves spraying water over plant surfaces, with the assumption that the water running over the plant body will gather eDNA left on its surface from arthropod waste or body tissues. This would then produce a sample that could be tested for eDNA the same way scientists test water samples for biomonitoring aquatic ecosystems like rivers and lakes.

To investigate their hypothesis, the researchers cultivated both eggplants and cabbage, utilizing a combination of greenhouse and field environments. Furthermore, specific aphid species were intentionally introduced onto potted eggplants, while other arthropods naturally migrated to the remaining eggplants and cabbages throughout their growth period. After growing the plants for a couple of months, they sprayed distilled or tap water on them and collected the flowing water at the base of the plants using dustpans. The collected water was then used to extract arthropod eDNA, which was next subjected to ‘metabarcoding’—a technique based on the amplification and sequencing of specific DNA regions known as "barcodes" that are unique to different taxa, i.e., groups of organisms, such as a species. Dr. Yoneya explains, “eDNA metabarcoding enables us to estimate species richness in a certain aquatic area. Thus, it could contribute to ecological research and biota monitoring on a large scale and in the long term.”

So, what barcodes did they use to identify the species? The researchers ran a search to tally the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene of the samples, which is commonly used to identify arthropods. Similar DNA stretches helped the team easily identify the corresponding species from the existing arthropod database. Using this technique, they identified more than 64 arthropod groups, of which 7 were visibly identifiable or artificially introduced in the area, while the remaining 57, including 22 species, were not seen in the visual survey.

To scale up this technique, the researchers tested it with both tap water and rainwater. Interestingly, rainwater had more arthropod species than tap water. "This could be due to the influence of aerial arthropod eDNA, longer collection time, and higher recovery for rainwater samples." says Dr. Yoneya, explaining the possible causes of this variation. The team emphasizes that the results obtained using rainwater need to be interpreted with caution.

Effective pest control relies on the accurate identification of various species of pests. The novel eDNA collection method presented in this study can facilitate the early detection of invasive pest species. Besides, it could change the way arthropods are studied in nature, with implications for a wide range of studies. As Dr. Yoneya observes, “This non-destructive eDNA collection method for arthropod surveying has practical applications in conservation, pest control, community ecology, biosecurity, invasive species monitoring, and biodiversity surveys.”

Plaudits to the research team for its groundbreaking innovation!

Reference
Title of original paper: Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Journal: Scientific Reports

DOI:https://doi.org/10.1038/s41598-023-32862-4

Image Title: Identification of arthropod species from environmental DNA (eDNA) samples.

Image Caption: The sequence reads of arthropod species detected from field cabbage eDNA samples using tap water (S10 and S11) or rainwater (S18–20).

Image Credit: Associate Professor Kinuyo Yoneya from Kindai University

Image Source Link to be added in the Image Credit Section of EA form:

License type: CC BY 4.0

About Kindai University
Kindai University was established in 1949 after the merger of Osaka Technical College (founded in 1925) and Osaka Science and Engineering University (founded in 1943). Over the past several decades, the university has transformed into a comprehensive educational organization with an ever-growing reputation. Kindai University has over 2,200 full-time faculty members, 6 campuses, and 18 research centers. As an academic institution offering a broad range of programs from across disciplines, Kindai University strives to impart practical education while nurturing intellectual and emotional capabilities. The university’s academic programs are fully accredited by Japan’s Ministry of Education, Culture, Sports, Science and Technology as well as by the National Institution for Academic Degrees and University Evaluation.

Website: https://www.kindai.ac.jp/english

About Associate Professor Kinuyo Yoneya from Kindai University
Dr. Kinuyo Yoneya works as an Associate Professor and Lecturer at Kindai University’s Department of Agricultural Science/Graduate School of Agriculture. She obtained her Ph.D. from Kyoto University in 2009. Dr. Yoneya has 25 publications to her credit. She primarily works in the area of life science, ecology, and environmental science.

Funding information
This work was supported by JSPS KAKENHI, a Grant-in-Aid for Young Scientists (Grant Number JP 17K15235), and by the Hakubi Project at Kyoto University.