phyloBARCODER: A web tool for phylogenetic classification of eukaryote metabarcodes using custom reference databases.

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (1) species or classification of query sequences and (2) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of non-mitochondrial genes, e.g., ITS or rbcL.

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.

Biogeochemical impacts of flooding discharge with high suspended sediment on coastal seas: a modeling study for a microtidal open bay.

Freshwater, suspended sediment matter (SSM), and nutrients discharged from rivers into the ocean have large impacts on biological production. In particular, during floods, coastal areas are greatly stirred up and large amounts of nutrients are supplied to the sea surface. We investigate the biogeochemical impact of flooding river discharges containing a large amount of SSM by conducting numerical simulations for a specific flooding event of the Yura River, Japan. Parameters are varied over wide ranges of SSM properties and nutrient content in riverine water. Two qualitatively different regimes of the riverine plume, hypopycnal and hyperpycnal, appear within realistic parameter ranges. Compared with the reference case without SSM, the surface salinity (nutrients) within the riverine plume becomes lower (higher) in hypopycnal cases and higher (lower) in hyperpycnal cases within a few days after the flooding discharge. These results suggest the necessity of properly taking into account the effect of SSM in assessing the influence of high river discharges on coastal biogeochemistry. It is the case not only for the specific river and event we are dealing with but also for other flooding events and other rivers and connecting coastal seas.

Vertical fluxes of nutrients enhanced by strong turbulence and phytoplankton bloom around the ocean ridge in the Luzon Strait.

Steep oceanic ridges and tidal currents in the Luzon Strait generate some of the world's strongest turbulent mixing. To evaluate the impacts of the turbulence intensity on the marine ecosystem, we carried out measurements of microstructure turbulence and biogeochemical hydrography along 21°N in the Luzon Strait during the R/V Hakuho Maru cruise, KH-17-5-2, in November 2017. We found a turbulent kinetic energy dissipation rate exceeding O(10-7) W kg-1 and vertical eddy diffusivity exceeding O(10-3) m2 s-1, two orders of magnitude larger than those in the open ocean, above a shallow sub-ridge on the eastern ridge of the Luzon Strait. In addition, a clear chlorophyll a bloom was identified in the surface layer above the sub-ridge from in situ measurements and satellite observations. High values of nitrate (4.7 mmol N m-2 d-1) and phosphate (0.33 mmol P m-2 d-1) fluxes estimated near the base of the surface chlorophyll a bloom strongly suggest that enhanced turbulent mixing promotes nutrient supply to the euphotic zone and generates new production within the surface layer, contributing to the formation of a quasi-permanent local chlorophyll a bloom north of Itbayat Island on the eastern ridge.