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DNA barcoding of freshwater zooplankton in Lake Kasumigaura, Japan

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Ecological Research

Abstract

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.

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Acknowledgements

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).

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Authors and Affiliations

  1. Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Sendai, Miyagi, 980-8578, Japan

    Wataru Makino

  2. Department of Biology, Tohoku University, 6-3 Aramaki aza aoba, Sendai, Miyagi, 980-8578, Japan

    Wataru Makino & Natsumi Maruoka

  3. Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan

    Megumi Nakagawa & Noriko Takamura

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  1. Wataru Makino
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  2. Natsumi Maruoka
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Correspondence to Wataru Makino.

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Makino, W., Maruoka, N., Nakagawa, M. et al. DNA barcoding of freshwater zooplankton in Lake Kasumigaura, Japan. Ecol Res 32, 481–493 (2017). https://doi.org/10.1007/s11284-017-1458-z

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