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Measuring copepod naupliar abundance in a subtropical bay using quantitative PCR

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Abstract

Copepod nauplii are important in plankton food web dynamics, but limited information is available about their ecology due to methodological challenges. Reported here is a new molecular method that was developed, optimized, and tested in laboratory and field samples that uses quantitative PCR (qPCR) to identify and estimate the abundance of nauplii of the planktonic copepod, Parvocalanus crassirostris. The overall approach included collection of bulk zooplankton samples in the field, size fractionation to create artificial cohorts of relatively few developmental stages, obtaining DNA copy number for each size fraction by qPCR amplification of a target gene region, and estimation of the number of animals in each fraction through application of known DNA copy number across developmental stage. Method validation studies found that our qPCR-based approach has comparable accuracy to microscope-based counts of early developmental stages. Naupliar abundance estimates obtained using the two methods on cultured populations were similar; the regression of qPCR estimates on microscope-based counts resulted in a nearly 1:1 ratio (slope = 1.09). The qPCR-based method is superior to traditional identification and quantification methods for nauplii due to its higher taxonomic resolution, sensitive detection over a range of DNA quantities, and relatively high throughput sample processing.

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Acknowledgments

We thank two anonymous reviewers for their thoughtful comments on the manuscript.  We thank K. Groom and numerous student volunteers who helped with field sampling, A. Orcine for assistance with molecular work, and S. Brown and A. Millan for equipment loans and help in the laboratory. This work was supported by a grant/cooperative agreement from the National Oceanic and Atmospheric Administration, Project R/HE-3, which is sponsored by the University of Hawaii Sea Grant College Program, SOEST, under Institutional Grant No. NA09OAR4170060 from NOAA Office of Sea Grant, Department of Commerce. The views expressed herein are those of the author(s) and do not necessarily reflect the views of NOAA or any of its subagencies. UNIHI-SEAGRANT-JC-11-20.

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Authors and Affiliations

  1. Department of Oceanography, School of Ocean and Earth Sciences and Technology, University of Hawaii at Manoa, Honolulu, HI, 96822, USA

    Michelle J. Jungbluth & Erica Goetze

  2. Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, 96822, USA

    Michelle J. Jungbluth & Petra H. Lenz

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  1. Michelle J. Jungbluth
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  2. Erica Goetze
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  3. Petra H. Lenz
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Correspondence to Michelle J. Jungbluth.

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Communicated by S. Uthicke.

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Jungbluth, M.J., Goetze, E. & Lenz, P.H. Measuring copepod naupliar abundance in a subtropical bay using quantitative PCR. Mar Biol 160, 3125–3141 (2013). https://doi.org/10.1007/s00227-013-2300-y

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  • DOI: https://doi.org/10.1007/s00227-013-2300-y

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