An open big-data fish biodiversity database called ANEMONE DB* that is focused on environmental DNA (eDNA) survey was launched on June 2 as reported by NYK.
Dr Michio Kondoh, a professor at Tohoku University’s Graduate School of Life Sciences, is in charge of managing the database, with assistance from NYK Line, Kinkai Yusen Ltd., the town of Minamisanriku, and Earthwatch Japan (collectively referred to as “parties”).
Project Outline
| １ | Using eDNA collected from the sea and river waters, ANEMONE DB accumulates survey results on fish living in water areas. This database opened to the public from June 2 and is the world’s first*** compilation of eDNA-specialized biodiversity monitoring data openly released to the public. |
| ２ | Activity plan for widening the sampling range of eDNA and expanding data:
・Seawater sampling on commercial ocean routes of NYK Line and Kinkai Yusen Kaisha Ltd. will be conducted once a month from this summer. ・Earthwatch Japan will conduct surveys by citizen volunteers at 50 locations in fiscal 2022 and 100 locations in fiscal 2023. |
| ３ | In the town of Minamisanriku, fish surveys will be conducted to research the effects of global warming and detect the appearance of southern species in Shizugawa Bay. |
| ４ | Parties will establish the ANEMONE Consortium as the management body to widely educate the public about the utilization of eDNA. |
ANEMONE DB Background
In recent years, while the loss of biodiversity due to human activities have progressed, the international trend of nature positive**** to put the natural environment on a recovery trend has been spreading.
However, it has been a long-standing challenge to establish a method for efficiently investigating a wide range from the conventional method that relies on capture because enormous labour and cost are required to conduct biological surveys to grasp the current state of nature.
Environmental DNA, or eDNA, is an innovative method***** for a biological survey that reveals the types and distribution of living organisms that exist from a bucket of water and its core technology for the fish survey were developed in Japan.
Since 2017, it has been constructed as big data comprising environmental DNA from fish surveys, which have been conducted 4,298 times at 861 locations around Japan by researchers and 200 citizen volunteers.
This database was developed and operated under the supervision of Dr Michio Kondoh, a professor at the Graduate School of Life Sciences at Tohoku University.
The database was opened to the public on June 2 as the result of an accumulation of sufficient data.
ANEMONE DB Outline
| Name | ANEMONE DB
Open to the public from June 2, 2022 Website: https://db.anemone.bio/ |
| Observation network | Environmental DNA observation network in which universities, national research institutes, municipalities, and corporations from all over Japan participate
(Collaboration with University of Tsukuba and Kazusa DNA Research Institute. under the leadership of Dr. Kondoh of Tohoku University) |
| Observation results
(Implemented from 2019) |
Survey locations: 861; number of surveys: 4,298; detected fish species: 885
Of the above, fixed-point observations were conducted at 77 points (55 coasts, 18 rivers, 4 lakes and marshes) |
| Main observation results | The result of the spread of the wide-area ecosystem visualized by the ANEMONE observation network (at the trial stage of ANEMONE DB)
・Due to the effects of global warming, the movement of fish distribution to the north and changes in fisheries ・Successful capture of wide-area fluctuations such as the changing of the distribution of Japan coastal fish species ・Demonstration of the usefulness of high-precision ecosystem big data in fishery resource management |
| Assumed applications | ・Basic data for selecting natural protection areas and confirming the effects of natural regeneration activities for the recovery of biodiversity
・Data for setting up AI to discover new fishing grounds and promote sustainable use of fishery resources ・Basic data used to elucidate the scientific balance of nature |
Recent Activity Plan
The following initiatives for environmental DNA sampling and use of the ANEMONE DB are being planned by businesses and groups that have been taking part in activities since the beginning.
In collaboration with numerous businesses and organisations, the ANEMONE Consortium intends to increase its activities.
<Environmental DNA sampling survey and activity plan for utilization of database>
① NYK Group (NYK Line and Kinkai Yusen Kaisha Ltd.)
Together with Tohoku University and Hokkaido University, NYK Line took seawater from the open sea in 2021 and for the first time successfully detected the DNA of 158 fish species. The NYK Group will keep organising the subsequent research projects and help to broaden the ANEMONE DB data and survey coverage areas.
| Activity category | Seawater sampling along the coast of Japan (acquisition of environmental DNA from ocean seawater) |
| Activity outline | Seawater sampling is performed along the commercial ocean routes of the vessel Mashiu, which conducts a liner service between the Hitachinaka port (Ibaraki prefecture) and the Tomakomai port (Hokkaido). The ship is operated by Kinkai Yusen Kaisha Ltd., and sampled seawater is provided to Hokkaido University. Analysis results are released on the ANEMONE DB. |
| Implementation period | From the summer of 2022, seawater sampling will be conducted once a month. The amount of each sampling will be about 30 liters. |
| Further information | Overview of Mashiu
Gross tonnage: 11,229 T; LOA: 179.90 m; Service speed: 23.0 knots Route: Hitachinaka port – Tomakomai port; Sailing time (one way): about 20 hours |
② Earthwatch Japan
Since 2020, Earthwatch Japan has been delighted to work with scientists and citizen volunteers on environmental DNA sampling studies. Citizens helped identify 632 fish species at 146 locations across Japan during the 2020–2021 period. The number of survey locations will increase from 41 in 2020 to 100 in 2023.
| Activity category | National simultaneous environmental DNA survey by citizen volunteers (acquired environmental DNA from coastal area surveys all over Japan) |
| Activity outline | With the support of Kakaku.com Inc. and academic experts such as Dr. Michio Kondoh, Earthwatch Japan has been conducting continuous surveys since 2020. The institute has also introduced a unique survey kit that allows the general public to easily collect environmental DNA, and many citizen volunteers are participating. |
| Implementation period | In July-August 2022, Earthwatch Japan plans to conduct a simultaneous survey conducted by about 100 citizen volunteers at 50 locations nationwide. The analysis results will be shared with the participants and educational activities will be conducted to deepen the understanding of biodiversity. In 2023, Earthwatch Japan plans to conduct seawater sampling surveys at more than 100 locations. |
| Further information | The national simultaneous environmental DNA survey is conducted with the support of the following academic experts.
Akihide Kasai (professor of Graduate School of Marine Bioresource and Environmental Science at Hokkaido University) Reiji Masuda (professor of Field Science Education and Research Center at Kyoto University) Satoquo Seino (associate professor of Faculty of Engineering at Kyushu University) |
③ Town of Minamisanriku (Miyagi prefecture)
Changes in fish species’ movement as a result of the effects of global warming have started to be documented in Shizugawa Bay, which borders the shore of the town of Minamisanriku, in recent years. In particular, rabbitfish, a species that was formerly found in the south, has migrated north and turned up in Shizugawa Bay. Additionally, there are worries that rabbitfish will sever the growing wakame seaweed from the rest of the ecosystem. The town of Minamisanriku uses the ANEMONE DB as part of a policy to understand the current state of migratory changes and consider mitigation actions.
The town of Minamisanriku is leading the charge in promoting its use because it also thinks that this environmental DNA database from all across Japan can be usefully utilised at nearby fishing grounds.
Establishment of Consortium and Future Activity Policy
The ANEMONE Consortium was started on June 1 to improve ANEMONE DB’s administration system and spread the idea of nature-positive thinking. This consortium will take the lead in educational initiatives in the future, such as seminars to encourage the use of ANEMONE DB and by establishing working groups for exchanging specialist information. The ANEMONE Consortium intends to grow to 100 businesses/organizations by the end of March 2023 through educational initiatives for a variety of industries and citizens.
Outline of ANEMONE Consortium
| Name
Establishment date |
ANEMONE Consortium
Establishment date: June 1, 2022 |
| Representative | Dr. Michio Kondoh, professor, Graduate School of Life Sciences, Tohoku University |
| Headquarter | 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578 Japan
Graduate School of Life Sciences, Tohoku University |
| Common philosophy and purpose | Common Philosophy: Realization of a natural symbiotic society utilizing advanced biodiversity information
Purpose (1): Efforts to achieve Nature Positive Purpose (2): Development and dissemination of environmental DNA technology Purpose (3): Establishing the foundation of ANEMONE DB |
| Initiating members
(in no particular order) 13 companies/groups, 4 individuals |
Tohoku University, Earthwatch Japan, NYK Line, Tohoku Ryokka Kankyohozen Co., Ltd., Kakaku.com, Inc., The Ecological Society of Japan, The Environmental DNA Society, Center for Sustainable Society, Kazusa DNA Research Institute., Japan Long-Term Ecological Research Network (JaLTER),
Japanese Association for Marine Biology (JAMBIO), Kanagawa Environmental Research Center, Town of Minamisanriku, Keigo Nakamura (Japan RiverFront Research Center), Natsuko Kondo (National Institute for Environmental Studies), Jun Nishihiro (Center for Climate Change Adaption, National Institute for Environmental Studies), Masakazu Hori (Japan Fisheries Research and Education Agency) |
* ANEMONE (All Nippon eDNA Monitoring Network) is a network for biodiversity observation using environmental DNA. In the large-scale project research, which gave birth to the main technology of environmental DNA, the development of quantitative monitoring of fish communities and an ecosystem evaluation method based on environmental DNA analysis under the guidance of Dr Michio Kondoh occurred along the national coast in 2017. Since 2019, Tohoku University, the University of Tsukuba, and the Kazusa DNA Research Institute have played a central role and conducted environmental DNA surveys in environments that cover coasts, rivers, and lakes throughout Japan with the cooperation of universities, national research institutes, government agencies, and citizen volunteers. In addition to regular observations at 77 observation stations, from 2020, about 200 citizens participated in the surveys at 146 sites. Since 2017, 4,298 surveys have been conducted, and 885 fish species have been detected.
** Environmental DNA refers to DNA (deoxyribonucleic acid) derived from living organisms that exist in the environment such as water and soil. Organisms leave traces of their DNA in the environment along with dung and mucus. In recent years, technology (environmental DNA technology) for knowing the types of organisms living there by extracting and analyzing biological DNA from water and soil collected in the field has greatly developed. The environmental DNA technology requires far less workload at the survey site than traditional biological survey methods that rely on capture and direct observation. Therefore, environmental DNA technology is attracting attention as an epoch-making method for realizing multi-point and high-frequency biological surveys, which was not easy with conventional survey methods.
*** Research by Professor Kondoh and ANEMONE officials
**** Activities and ways of thinking to increase the natural environment to prevent biodiversity damage
***** The MiFish method (a comprehensive analysis method for fish) used in environmental DNA surveys was
developed in Japan.
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Source: NYK
