ena-STUDY-Viale Adriatico 1/n-20-09-2017-14:02:48:349-828
Metabarcoding hake diet
European hake (EH), Merluccius merluccius, is a demersal fish distributed from the NorthSea and Atlantic to the Levantine Sea in the Mediterranean. EH is an important predatorof deep Mediterranean upper shelf slope communities and it is currently characterised bygrowth overexploitation. EH adults feed mainly on fish and squids whereas the young (<16cm) feed on crustaceans. All current EH diet studies relied on the morphologicalidentification of prey remains in stomach content, however this method is labour intensiveand it precludes the identification of strongly digested food. The development of High-Throughput Sequencing (HTS) approaches provide more accurate methods for dietarystudies revealing many consumed species simultaneously (DNA metabarcoding). The aimof this study is to use a HTS approach based on COI amplification, contextually to classicmicroscopic morphological identification, to analyse EH stomach content and to evaluatethe efficiency of the molecular method. HTS sequencing has been carried out on theamplicons obtained by PCR amplification (Leray et al. 2013) of stomach remains and allthe Miseq Illumina paired-end reads have been analysed by using bioinformatic tools(Boyer et al. 2015) for taxonomic assignment. The selected sequences clustered in OCTUs(Operational Clustered Taxonomic Units) and taxonomically assigned, will be used indiversity analyses to compute distance matrices among samples, to compare taxasummaries from different samples, to create networks and perform PCA and PcoAanalysis. Classic microscopic morphological analyses on stomach content remains havebeen carried out contextually to compare the results of the two methods. The molecularapproach has proven a promising method to study marine fish dietary habits. All the datawill be summarized to reconstruct EH trophic dynamics in the Mediterranean Sea.
European hake (EH), Merluccius merluccius, is a demersal fish distributed from the NorthSea and Atlantic to the Levantine Sea in the Mediterranean. EH is an important predatorof deep Mediterranean upper shelf slope communities and it is currently characterised bygrowth overexploitation. EH adults feed mainly on fish and squids whereas the young (<16cm) feed on crustaceans. All current EH diet studies relied on the morphologicalidentification of prey remains in stomach content, however this method is labour intensiveand it precludes the identification of strongly digested food. The development of High-Throughput Sequencing (HTS) approaches provide more accurate methods for dietarystudies revealing many consumed species simultaneously (DNA metabarcoding). The aimof this study is to use a HTS approach based on COI amplification, contextually to classicmicroscopic morphological identification, to analyse EH stomach content and to evaluatethe efficiency of the molecular method. HTS sequencing has been carried out on theamplicons obtained by PCR amplification (Leray et al. 2013) of stomach remains and allthe Miseq Illumina paired-end reads have been analysed by using bioinformatic tools(Boyer et al. 2015) for taxonomic assignment. The selected sequences clustered in OCTUs(Operational Clustered Taxonomic Units) and taxonomically assigned, will be used indiversity analyses to compute distance matrices among samples, to compare taxasummaries from different samples, to create networks and perform PCA and PcoAanalysis. Classic microscopic morphological analyses on stomach content remains havebeen carried out contextually to compare the results of the two methods. The molecularapproach has proven a promising method to study marine fish dietary habits. All the datawill be summarized to reconstruct EH trophic dynamics in the Mediterranean Sea.