Finding copepod footprints: A protocol for molecular identification of diapausing eggs in lake sediments

Wataru Makino, Hajime Ohtsuki, Jotaro Urabe

    Research output: Contribution to journalArticlepeer-review

    10 Citations (Scopus)

    Abstract

    Even though calanoid copepods produce diapausing eggs that stay alive in lake sediments, these eggs have rarely been used paleolimnologically, as they lack diagnostic morphological features. In this study, we developed a method to identify copepod diapausing eggs in Japan as a clue toward reconstructing past plankton populations. We first determined a 28S ribosomal DNA (rDNA) (i.e., nc28S) regional sequence library (240 bp) of various calanoid copepod species using ethanol-fixed plankton samples collected from across the Japanese archipelago. Then we applied the UltraSHOT method to extract DNA from an individual diapausing egg. Finally, the nc28S region of diapausing eggs collected from various lakes was sequenced and compared with the regional library for species identification. In total, 21 haplotypes of the nc28S region were recovered from planktonic samples of 11 Japanese freshwater calanoid copepod species. Despite the short length of this region, no identical haplotypes were shared among the species analyzed, including the Acanthodiaptomus pacificus complex treated as a species. Even different lineages of A. pacificus could be separated. These results indicate that the nc28S region can be used as a barcode in Japan. A total of 112 diapausing eggs collected from various lakes and ponds was processed, and the nc28S region of each was successfully sequenced. All of these egg sequences matched one or the other of the nc28S haplotypes in the regional library mentioned above. The set of protocols we applied (i.e., preparing a comprehensive regional sequence library and sequencing egg DNA) is thus useful for involving copepod diapausing eggs in paleolimnological studies in lakes. The nc28S region treated in this study has a strong potential to uncover the paleodiversity of copepods, at least in Japan.

    Original languageEnglish
    Pages (from-to)269-282
    Number of pages14
    JournalLimnology
    Volume14
    Issue number3
    DOIs
    Publication statusPublished - 2013 Aug

    Keywords

    • 28S ribosomal DNA
    • Biodiversity
    • Calanoid copepods
    • Diapausing eggs
    • Japanese lakes
    • Molecular identification

    ASJC Scopus subject areas

    • Ecology
    • Aquatic Science
    • Water Science and Technology

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