Sea cucumber (Apostichopus japonicus) eukaryotic food source composition determined by 18s rDNA barcoding

Abstract

Food source determination of deposit-feeding sea cucumbers is difficult because the majority of organic debris in gut cannot be reliably or accurately identified by conventional microscopic examination. Advanced DNA barcoding is an effective and rapid technique to determine dietary composition of such feeders. In this study, the composition of eukaryotic food sources of the sea cucumber, Apostichopus japonicus, harvested in two bays of an offshore island in winter and spring was surveyed by high-throughput DNA sequencing. The 18s rDNA v4 loci sequences were amplified to provide a total of 616,184 optimized reads and 823 operational taxonomic units. Winter group sequences were assigned to 27.20 +/- 3.63 and 28.40 +/- 2.88 phyla, and those in spring to 25.80 +/- 3.90 and 24.20 +/- 3.11 phyla. Eukaryote richness was higher in winter than in spring, with Dinoflagellata, Bacillariophyceae, Arthropoda, Cercozoa, and Mollusca the dominant phyla in decreasing order of importance. Our results indicated the guts of A. japonicus contained more organic material sourced from the water column than from within the sediments. The profiling table and cluster analysis revealed winter and spring samples clustered separately, indicating significant seasonal differences in eukaryotic composition. Main winter dietary components were Bacillariophyceae, Dinoflagellata, and Streptophyta, whereas those in spring were Bacillariophyceae, Arthropoda, and Mollusca. In any one season, gut contents did not differ significantly between sampling locations. Our study indicates that DNA sequencing can greatly improve the accuracy of diet studies on sea cucumbers.