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Learning about eDNA in Iriomote, Japan by Camila Frances Naputo


Last May and October 2022, I had the chance to join the 1st and 3rd International Workshops for Mangrove Biodiversity Studies by eDNA Metabarcoding in Iriomote, Japan. This opportunity came due to my involvement as Research Assistant of the PEER ManCoRe project. One of our research goals is to assess the biodiversity of different mangrove stands in the Philippines using the eDNA technique. Fortunately, the project through our principal investigator, Dr. Severino G. Salmo III, was able to collaborate with Dr. Tadashi Kajita of the Tropical Biosphere Research Center of the University of the Ryukyus. Through Kajita sensei’s eDNA project under the JSPS Core-to-Core Program, I was invited to join the eDNA workshops to capacitate researchers on the eDNA method in studying mangrove ecosystems. It was a fulfilling experience filled with so much learning, networking, and experiencing Southeast Asian cuisine. Before this trip, I had little to no idea what eDNA was and how it could change the game in conducting biodiversity assessments. I vaguely knew that it was DNA material you obtained from the environment (water, soil, and even air) that you could analyze using metabarcoding techniques. My basic understanding of undergraduate genetics did not fail me! I was very intimidated when I met my fellow participants coming from the different Southeast Asian countries who were much more accomplished than me. I thought I wouldn’t be able to catch up with them. But it turns out we were all on the same level of inexperience with this tool but all enthusiastic to learn. 

What did I gain during my trips to Japan?

  • Knowledge about the eDNA metabarcoding method and its application in conducting rapid biodiversity assessments (and other ecological studies) in mangrove ecosystems

  • Information on the status of baseline data on faunal biodiversity of mangrove ecosystems in the Philippines 

  • Experiencing the full extent of using this tool in a well-equipped lab that contains everything you’ll need to conduct the experiment without having to outsource some of the services (particularly the library preparation and Next-Generation Sequencing) 

eDNA metabarcoding, although already being applied in some laboratories in the country (such as the UP Institute of Biology’s DNA Barcoding Lab), has yet to be used in monitoring the faunal diversity of Philippine mangroves. The concern is understandable. This technique poses many challenges in our country’s context. For one, we don’t have many experts on the field so capacitating Filipino researchers by joining international/collaborative workshops such as this is imperative and takes priority. Second, we don’t have enough fully equipped labs to handle this kind of research. In our project’s case, we don’t have a lab equipped for molecular analyses. Third, this monitoring tool is fairly new and is still in the experimental stages. So far, there is no standard way to collect and analyze eDNA. Each method has their own pros and cons. Lastly, we must consider whether these methods are even applicable or useful in the Philippine context. 

When I first came to Iriomote, I was so fascinated by their laboratory. It had everything you will need to do a complete eDNA metabarcoding analysis. From sampling water to getting sequence results, they had it all. The only thing you had to do was conduct field sampling and take your samples to the lab for processing. Additionally, the research station was strategically located in an isolated island that was surrounded by pristine mangroves: a perfect study site. Whenever I came back from both weeks-long workshops in Iriomote, my mind was always overflowing with new exciting information about this emerging tool and I couldn’t wait to try it on our own field sites. Kajita sensei was very generous and gave us some sampling kits to work with. There were other Filipinos who joined the workshop that time--fellow researchers from Mindanao State University. With the knowledge we gained from this productive workshop, I am excited to learn what we’ll be able to achieve for Philippine mangroves. The future is bright for biodiversity monitoring in the Philippines.

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