Biomonitoring of microscopic animals by massively parallel sequencing

• Project/Area Number: 15K16137
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Environmental impact assessment
• Research Institution: University of the Ryukyus
• Principal Investigator: SAITOH Seikoh 琉球大学, 熱帯生物圏研究センター, 特命研究員 (10623754)
• Research Collaborator: NAKAMORI Taizo 横浜国立大学, 大学院環境情報研究院, 准教授 (50443081) ; AOYAMA Hiroaki 琉球大学, 戦略的研究プロジェクトセンター, 特命助教 (20468078) ; FUJII Saori アムステルダム自由大学, JSPS海外特別研究員 (50648045)
• Project Period (FY): 2015-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: メタバーコーディング / 定量性 / 微小動物 / 土壌動物 / metabarcoding / quantification / Collembola / Soil organism / DNAバーコード / DNA metabarcoding / トビムシ / 小型節足動物 / 環境DNA

Outline of Final Research Achievements

Metabarcoding is a method to assess biodiversity from unsorted specimens or environmental samples based on two technologies, DNA barcoding and massive parallel sequencing. While it has been used to determine which species are present or absent in a sample, metabarcoding has, nonetheless, been poor in quantification of their abundances. We developed a novel protocol for metabarcoding by which a researcher can minimize biases that occur during PCR amplification and obtain a better analytic result by using an internal control material. Our data showed high linearity (R = 0.91-0.99) between normalized read count and number of individuals of a species included in samples. This protocol can be applied to monitoring of small organisms whose abundances, rather than present or absent, are of interest.

Research Products

• [Journal Article] A quantitative protocol for DNA metabarcoding of springtails (Collembola) (2016)
  • Author(s): Saitoh, S., Aoyama, H., Fujii, S., Sunagawa, H., Nagahama, H., Akutsu, M., Shinzato, N., Kaneko, N., Nakamori, T.
  • Journal Title: Genome Volume: 59 Issue: 9 Pages: 705-723
  • DOI: 10.1139/gen-2015-0228
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] 土壌小型節足動物の局所群集の形成過程: 移動分散の制限とハビタットの異質性の寄与を探る (2017)
  • Author(s): 齋藤星耕, 菱拓雄, 武田博清
  • Organizer: 日本生態学会第64回全国大会
  • Place of Presentation: 早稲田大学, 新宿区, 東京都
  • Year and Date: 2017-03-16
• [Presentation] Multiple mitochondrial sequence types from single collembolan specimens: pseudogenes in Collembola? (2016)
  • Author(s): Saitoh, S., Aoyama, H., Fujii, S., Park, S., Yamada, A., Shinzato, N., Kaneko, N., Nakamori, T.
  • Organizer: XIV International Colloquium on Apterygota
  • Place of Presentation: Nara Kasugano International Forum IRAKA, Nara, Japan
  • Year and Date: 2016-08-24
  • Int'l Joint Research
• [Presentation] DNA metabarcoding of springtails (Collembola) (2015)
  • Author(s): Saitoh, S. Aoyama, H., Fujii, S., Sunagawa, H., Nagahama, H., Akutsu, M., Shinzato, N., Kaneko, N., & Nakamori, T.
  • Organizer: 6th International Barcode of Life Conference
  • Place of Presentation: University of Guelph, Guelph, Ontario, Canada
  • Year and Date: 2015-08-18
  • Int'l Joint Research
• [Presentation] トビムシ類のDNAバーコーディングとメタバーコーディング手法の開発 (2015)
  • Author(s): 齋藤星耕, 青山洋昭, 藤井佐織, 砂川春樹, 長濱秀樹, 阿久津雅子, 新里尚也, 金子信博, 中森泰三.
  • Organizer: 日本土壌動物学会第38回大会
  • Place of Presentation: 香川大学
  • Year and Date: 2015-05-23