Fig 1.
Positions of OceanDNA sampling stations in the Kuroshio Extension area.
The red circles represent stations B01–B09, the green circles represent stations C00–C09, and the plus mark represents the net sampling location. Maps were made in Spyder (Python 3.7) using Natural Earth data. Free vector and raster map data @ naturalearthdata.com. (a) Colors represent current speeds and arrows represent current velocity vectors on the sea surface (5-day mean from May 10 to 14, 2018) from Ocean Surface Current Analysis Real-time data [34] (https://podaac.jpl.nasa.gov/Data hosted and openly shared by the PO.DAAC, without restriction, in accordance with NASA’s Earth Science program Data and Information Policy). (b) The contours and colors represent sea surface temperature (˚C) distribution on May 10, 2018, from GHRSST Level 4 OSTIA Global Foundation Sea Surface Temperature Analysis data [35] (hosted and openly shared by the PO.DAAC, without restriction, in accordance with NASA’s Earth Science program Data and Information Policy).
Fig 2.
OceanDNA detection results of five target fish at station B06 and fish caught in net sampling.
Detection results using (a) qPCR method and (b) MiFish method, and (c) fish biomass data from the net sampling (pelagic trawling, at depth of 0–25 m).
Fig 3.
Detection rate ranking of five target fish based on qPCR data and MiFish data.
Data based on samples collected on the B-line (a) and C-line (b). The ‘detection rate’ is calculated as: detection number / whole sample number of B-line (or C-line). chub/blue mackerel = Scomber japonicus and Scomber australasicus, sardine = Sardinops melanostictus, anchovy = Engraulis japonicus, jack mackerel = Trachurus japonicus, saury = Cololabis saira.
Fig 4.
Comparison tables for Phi-coefficients analysis of detection performance among the five target fish.
(a) chub/blue mackerel (Scomber japonicus and Sc. australasicus), (b) anchovy (Engraulis japonicus), (c) sardine (Sardinops melanostictus), (d) saury (Cololabis saira), (e) pooling (sum data of all five target fish, chub/blue mackerel, sardine, anchovy, saury and jack mackerel), (f) pooling-4 (sum data of (a) to (d)). 0 = absence, 1 = presence.
Table 1.
Coefficients (Phi-coefficient value and Fisher’s exact test) of detection performance among the five target fish.
Fig 5.
Comparison of spatial distribution pattern detected by qPCR and MiFish methods in the B-line vertical section.
(a) Spatial distribution of chub/blue mackerel (Scomber japonicus and Sc. australasicus). (b) Spatial distribution of sardine (Sardinops melanostictus). Plus marks represent the presence detection samples found by the MiFish method and open circles represent the presence detection samples found by the qPCR method. Background colors represent water temperature (˚C).
Fig 6.
Comparison of spatial distribution pattern detected by qPCR and MiFish methods in the C-line vertical section.
(a) Spatial distribution of chub/blue mackerel (Scomber japonicus and Sc. australasicus). (b) Spatial distribution of sardine (Sardinops melanostictus). Plus marks represent the presence detection samples found by the MiFish method and open circles represent the presence detection samples found by the qPCR method. Background colors represent water temperature (˚C).
Fig 7.
Comparison of MiFish presence/absence detection samples based on OceanDNA quantity measured by qPCR.
(a) Result of chub/blue mackerel (Scomber japonicus and Sc. australasicus) and (b) result of sardine (Sardinops melanostictus). The figures were prepared from pooling data of B-line and C-line. Samples in which qPCR did not detect OceanDNA are not included in this figure. Numbers in x axis represent the OceanDNA quantity (copies/μL) measured by qPCR.
Table 2.
Difference of non-target OTU number (average per sample) and chlorophyll-a concentration (average per sample) between MiFish-0/qPCR-1 and MiFish-1/qPCR-1 samples.
Fig 8.
Differences between the detection results of the qPCR and MiFish methods before and after exclusion of samples in which the library preparation failed.
(a) The detection number ratios (qPCR detection number / MiFish detection number) of chub/blue mackerel (Scomber japonicus and Sc. australasicus), anchovy (Engraulis japonicus) and sardine (Sardinops melanostictus). (b) The detection number ratios of pooling and pooling-4 (pooling-4 = sum of chub/blue mackerel, anchovy, sardine and saury, pooling = chub/blue mackerel, sardine, anchovy, saury, and jack mackerel). (c) Phi-coefficient values of pooling and pooling-4. ‘original’ means the data came from all 247 OceanDNA samples, ‘after omitting’ means those samples, in which the library preparation failed, were excluded.
Fig 9.
Pie chart based on read percentages of fish species detected by the MiFish method.
Here, the pie chart was made based on MiFish data from C-line samples that at least one of sardine, chub/blue mackerel and anchovy was detected by the qPCR method, where sardine = Sardinops melanostictus, California headlightfish = Diaphus theta, chub/blue mackerel = Scomber japonicus + Sc. australasicus, eared blacksmelt = Lipolagus ochotensis, silvery lightfish = Maurolicus muelleri, saury = Cololabis saira, splendid alfonsino = Beryx splendens, smalleye squaretail = Tetragonurus cuvieri, spiny lantern fish = Myctophum spinosum.