Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA.

Environmental DNA (eDNA) is increasingly used to noninvasively monitor aquatic animals in freshwater and coastal areas. However, the use of eDNA in the open ocean (hereafter referred to OceanDNA) is still limited because of the sparse distribution of eDNA in the open ocean. Small pelagic fish have a large biomass and are widely distributed in the open ocean. We tested the performance of two OceanDNA analysis methods-species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers-to determine the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species (Sardinops melanostictus, Engraulis japonicus, Scomber japonicus, Scomber australasicus, Trachurus japonicus, and Cololabis saira) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure. The results from OceanDNA methods were compared to those of net sampling to test for consistency. Then, we compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method; the reason is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, the combined usage of the two methods to monitor quantitative distribution of small pelagic fish species with information of fish community structures was recommended.

Density-dependent attributes of schooling in small pelagic fishes.

Many small pelagic fishes obligately form schools; some of these schools reach remarkable sizes. Although the school is a fundamental and important ecological unit and is the site of biological interactions such as competition and predation, information on schooling processes in the field remains scarce. Here, we examined the quantitative relationships between population density and school size, the number of schools, and other school characteristics (i.e. packing density, volume, and cross-sectional area) in three species of small pelagic fishes: Japanese anchovy Engraulis japonicus, Japanese sardine Sardinops melanostictus, and chub mackerel Scomber japonicus. We found that school size increased almost linearly with population density, whereas the number of schools and other characteristics increased non-linearly with population density, whereby the rate of increase slowed radically as population density increased. These results indicate that, at low population densities, an increase in density causes an increase in both school size and the number of schools, whereas at higher population densities, an increase in density triggers the formation of larger schools rather than more schools. Furthermore, we found that the shapes of the relationships of all school characteristics with population density differed amongst species. Our results indicate that the schooling behaviour of small pelagic fishes is density-dependent, and responses to changes in density are species-specific. Our results provide insight into how biological interactions such as intra- and inter-specific competition and predator-prey interactions mediate the density-dependent processes that underlie the population dynamics and community structure of small pelagic fishes in marine ecosystems.

Morphological differences between larvae and in vitro-cultured adults of Anisakis simplex (sensu stricto) and Anisakis pegreffii (Nematoda: Anisakidae).

Proper identification of Anisakis species infecting host fishes is very important to both human health and fish disease diagnosis. The foremost problem in the identification of Anisakis larvae in fishes is that L3 larvae cannot be easily differentiated morphologically, especially between A. simplex (sensu stricto) (s.s.) (Rudolphi, 1809) and A. pegreffii Campana-Rouget et Biocca, 1955. Instead, molecular means such as allozyme, mitochondrial DNA (mtDNA) cox2 region and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses had been successfully used. In this study, morphological differences of L3 larvae collected from fishes and in vitro-cultured L4 larvae and adult A. simplex (s.s.) and A. pegreffii were evaluated. Anisakis larvae were collected from 7 different host fishes within Japan. Undamaged A. simplex (s.s.) and A. pegreffii collected from Oncorhynchus keta (Walbaum) and Scomber japonicus Houttuyn, respectively, were used for in vitro-culture in order to obtain L4 and adult stages. Species identification was confirmed by PCR-RFLP analysis of the ITS region (ITS1-5.8S-ITS2) of ribosomal DNA and by mtDNA cox2 gene sequencing. Results revealed that L3, L4 and adult stages of A. simplex (s.s.) and A. pegreffii are morphologically distinguishable based on ventriculus length, wherein the former has longer ventriculus (0.90-1.50 mm) than the latter (0.50-0.78 mm). For oesophagus/ventriculus ratio, these two species are distinguishable only during L4 and adult stages. Also, adult male A. simplex (s.s.) and A. pegreffii were found to be distinguishable by differences in the distribution pattern of the caudal papillae, particularly the 3rd pair of distal papillae.