Ecological Research

, Volume 32, Issue 4, pp 481–493 | Cite as

DNA barcoding of freshwater zooplankton in Lake Kasumigaura, Japan

  • Wataru Makino
  • Natsumi Maruoka
  • Megumi Nakagawa
  • Noriko Takamura
Original Article


Although DNA barcoding is a promising tool for the identification of organisms, it requires the development of a specific reference sequence library for sample application. In the present study we developed a Lake Kasumigaura, Japan, zooplankton DNA barcode library to increase the sensitivity of future zooplankton monitoring for detecting lake ecosystem condition changes. Specifically, the mitochondrial cytochrome c oxidase subunit I (mtCOI) haplotype, i.e., the primary DNA barcode, was examined for each zooplankton taxon. In crustaceans, 37 mtCOI haplotypes were obtained from 99 individuals, representing four and 15 morpho-species of Copepoda and Cladocera, respectively. Comparing these sequences with those in GenBank shows that the lake harbors putative non-indigenous species, such as Daphnia ambigua. In rotifers, 132 mtCOI haplotypes were obtained from 302 individuals, representing 11 genera and one unclassified taxon. The automatic barcode gap discovery (ABGD) algorithm separated these haplotypes into 43 species. Brachionus cf. calyciflorus was divided into five ABGD species, and different ABGD species tended to occur in different seasons. Seasonal ABGD-species succession was also observed within Polyarthra spp. and Synchaeta spp. These seasonal successions were not detected by inspections of external morphology alone. Accepting up to 7% sequence divergence within the same species, mtCOI reference sequences were available in GenBank for three, 13, and 17 species in Copepoda, Cladocera, and Rotifera, respectively. The present results, therefore, reveal the serious shortage of mtCOI reference sequences for rotifers, and underscore the urgency of developing rotifer mtCOI barcode libraries on a global scale.


Biodiversity DNA barcoding Freshwater zooplankton Lake Kasumigaura Zooplankton monitoring programs 



The sampling was conducted as part of the Lake Kasumigaura Long-term Environmental Monitoring Program of the National Institute for Environmental Studies, Japan. Special thanks go to those who participated in the field-work at the lake. The study was supported by grants from the Japan Society for the Promotion of Science (Nos. 15K07211 and 15H02380) and by the Environment Research and Technology Development Fund (4-1602).

Supplementary material

11284_2017_1458_MOESM1_ESM.pdf (591 kb)
Supplementary material 1 (PDF 591 kb)


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Copyright information

© The Ecological Society of Japan 2017

Authors and Affiliations

  1. 1.Graduate School of Life SciencesTohoku UniversitySendaiJapan
  2. 2.Department of BiologyTohoku UniversitySendaiJapan
  3. 3.Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan

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