Rapid determination of marine ecosystem structure using DNA barcode and next generation sequencing

Abstract

Determination of marine ecosystem structure is not an easy task. It takes long time for one to identify each species comprising the ecosystem when it is assessed by morphology-based identification. DNA barcoding in conjunction with the high-throughput next generation sequencing (NGS) technology makes the whole procedure simple, fast and objective. A large number of plankton samples and their species compositions can be determined within a very short time. In the present study, we applied the DNA barcode NGS technology to examine the plankton community in Tong-Yeong, southern coast of Korea. Zooplankton samples were collected by towing vertically a 60um mesh size net in every two weeks from March to July. Genomic DNA was extracted from the bulk sample and PCR of the DNA barcode was carried out with the universal COI primers. NGS of the PCR product resulted in 743 operational taxonomic units (OTUs) which were predominated by Arthropods (27.3%), Molluscs (25.6%), and Annelids (17.5%) with minor contribution by other 12 phyla. Calanus sinicus, a copepod, comprised the zooplankton community as the most dominant species in March and April and became replaced by the larvae of Crassostrea gigas in June and July. A jelly fish, Rathkea octopunctata, appeared in high abundance in March but disappeared in April. On the contrary, larvae of Mytilus galloprovincialis appeared in April and May and became disappeared by the end of Ju-throughput next generation sequencing (NGS) technology makes the whole procedure simple, fast and objective. A large number of plankton samples and their species compositions can be determined within a very short time. In the present study, we applied the DNA barcode NGS technology to examine the plankton community in Tong-Yeong, southern coast of Korea. Zooplankton samples were collected by towing vertically a 60um mesh size net in every two weeks from March to July. Genomic DNA was extracted from the bulk sample and PCR of the DNA barcode was carried out with the universal COI primers. NGS of the PCR product resulted in 743 operational taxonomic units (OTUs) which were predominated by Arthropods (27.3%), Molluscs (25.6%), and Annelids (17.5%) with minor contribution by other 12 phyla. Calanus sinicus, a copepod, comprised the zooplankton community as the most dominant species in March and April and became replaced by the larvae of Crassostrea gigas in June and July. A jelly fish, Rathkea octopunctata, appeared in high abundance in March but disappeared in April. On the contrary, larvae of Mytilus galloprovincialis appeared in April and May and became disappeared by the end of Ju