Size-based food webs analysis is essential for understanding food web structure and evaluating the effects of human exploitation on food webs. We estimated the predator–prey mass ratio (PPMR) of the pelagic food web in the East China Sea and Sea of Japan by using the relationships between body mass and trophic position. Trophic position was calculated by additive and scaled models based on nitrogen stable isotope ratios (δ15N). The PPMRs based on additive and scaled models were 5032 (95% confidence interval (CI) 2066–15506) and 3430 (95% CI 1463–10083) respectively. The comparatively high PPMRs could reflect low ecosystem transfer efficiency and high metabolic rate.

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A new species of sapphirinid copepod, Sapphirina doliolettae n. sp. was described from the Kuroshio Extension region in the western North Pacific Ocean. The new species is similar to S. nigromaculata and S. scarlata with respect to the following characteristics: 5-segmented antennule, one inner marginal process on caudal rami, and slender endopods with two apical spines on leg 4. However, it can be distinguished from these congeners by a combination of the following characteristics: the relative length of each segment of the antennule and antenna in both sexes, the width of the fourth pedigerous somite in females, the shape of the anterolateral corner of the genital somite in males and terminal process length of 3rd endopodal segment of leg 2 in males. The mitochondrial cytochrome oxidase subunit I sequences of S. doliolettae showed high interspecific variabilities from other Sapphirina species, including S. nigromaculata (20.2%) and S. scarlata (21.6-21.8%).

Seasonal and day–night changes in the vertical distribution and habitat of mesopelagic crustaceans, Gnathophausia longispina and G. elegans were investigated in the East China Sea during four oceanographic cruises carried out between May 2012 and January 2013. The abundance of G. elegans was approximately one-tenth that of G. longispina, although both species appeared throughout the year. The main distribution range of G. longispina was 100–600 m, and G. elegans was 600–700 m. Only G. longispina showed ontogenetic differences in diel vertical migration (ODVM); most individuals inhabited depths of 500–600 m during the day and 100–400 m at night when younger individuals inhabited shallower layers than mature individuals. Overall, both species showed a small overlap in their vertical distribution at around 600-m depth. Vertical segregation of habitat could have facilitated the sympatric biogeographic distribution of these two congeneric species around the West/Central Pacific Ocean.

Background Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16% in total and by 10% per sample. Based on the 28S marker, the number of OTUs associated with a single species increased by 39% in total and by 15% per sample. The improved accuracy of species identification was confirmed by comparing different sequences obtained from the same species. The newly registered sequences had higher similarity values (mean >0.003) than the pre-existing sequences based on both rRNA genes. These OTUs were identified at the species level based on sequences not only present in the Sea of Okhotsk but also in other areas. Discussion The results of the registration of new taxonomically verified sequences and the subsequent comparison of databases based on metabarcoding data of natural zooplankton samples clearly showed an increase in accuracy in species identification. Continuous registration of sequence data covering various environmental conditions is necessary for further improvement of metabarcoding analysis of zooplankton for monitoring marine ecosystems.