5:15 PM - 6:45 PM
[AOS13-P04] Assessment of western North Pacific pelagic fish biodiversity using three eDNA meta-barcoding surface-layer sampling techniques: ship-bottom intake, Niskin, and bucket.
Keywords:Environmental DNA (eDNA) metabarcoding, MiFish primer, Fish Biodiversity, Western North Pacific, Ship-bottom intake, Niskin and bucket sampling
Monitoring biodiversity in the expansive open ocean is crucial for sustainable resource use and effective management. Environmental DNA (eDNA) metabarcoding has emerged as a widely accepted tool for biodiversity monitoring, given its ease of application and non-invasive nature. The western North Pacific is characterized by high productivity and biodiversity, making it a crucial region for ongoing biodiversity monitoring. However, because of the complex hydrographic structures, traditional sampling or survey methods often fall short, especially in areas with intrinsic frontal structures that pose challenges for fish diversity assessment. Therefore, eDNA metabarcoding stands out as a promising alternative for portraying the overall scenario of this intricate habitat. Thus, the current study aims to assess the biodiversity of this intricate oceanic area using eDNA meta-barcoding analysis, comparing three surface sampling methods —ship-bottom intake (4.5m via ship faucet), Niskin (5m or 10m by using Niskin bottle with CTD), and bucket (0m by throwing bucket)—to understand their suitability in the open and intricate oceanic environment.
The samples were collected (10L each) and subsequently filtered through Sterivex membranes with a pore size of 0.45 μm. The processed samples were appropriately stored at -25 degree celcius before DNA extraction. The metabarcoding results were segregated into Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs)to identify the fish species using MiFish primers.
Across all three sampling methods, a total of 320 species spanning 134 families were recorded indicating a highly diversified environment of the sampling sites. The frequently detected taxa across all three methods encompass Cololabis saira (Pacific saury), Diaphus garmani (Garman's lanternfish), Diaphus theta (Theta lanternfish), Engraulis japonicus (Japanese anchovy), Maurolicus muelleri (Silvery lightfish), Myctophum asperum (Prickly lanternfish), Sardinops melanostictus/Sardinops sagax (Japanese/South American pilchard), Scomber japonicus/Scomber australasicus (Chub/Blue mackerel), Seriola quinqueradiata (Japanese amberjack), and Trachurus japonicus (Japanese jack mackerel). The detection of these species often overlaps among the three sampling methods. Overall, the southern part of the studied area exhibited higher biodiversity compared to the northern part, possibly influenced by favorable temperature, food availability, and suitable environmental conditions. Alpha biodiversity indices revealed significant differences among the methods, with ship-bottom intake indicating lower biodiversity compared to the other two methods (Kruskal-Wallis test, P<0.05). Non-Metric Multidimensional Scaling (NMDS) results (Stress= 0.19), based on the Jaccard presence/absence index, indicated partial overlap in taxonomic composition among the sampling sites using the three methods, with significant differences observed between ship-bottom intake and bucket samples, and negligible variance between Niskin and both methods (PERMANOVA, P<0.05). However, rarefaction analysis predicted similar taxonomic richness among all three methods. Discrepancies in biodiversity analysis of ship-bottom intake samples can be attributed to specific sampling sites influenced by complex fronts. Furthermore, the variation in biodiversity among methods can be ascribed to factors such as the lighter weight of DNA in certain species, the rate of eDNA release and degradation in specific sites and environmental conditions, and the impact of heat and wind flux. In conclusion, the findings suggest that bucket samples exhibit higher biodiversity, but caution is advised due to potential overestimation resulting from larval and egg DNA. This study not only compares the accuracy of eDNA meta-barcoding sampling methods but also emphasizes the need for species and site-specific considerations in biodiversity monitoring in the open ocean using eDNA meta-barcoding.
The samples were collected (10L each) and subsequently filtered through Sterivex membranes with a pore size of 0.45 μm. The processed samples were appropriately stored at -25 degree celcius before DNA extraction. The metabarcoding results were segregated into Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs)to identify the fish species using MiFish primers.
Across all three sampling methods, a total of 320 species spanning 134 families were recorded indicating a highly diversified environment of the sampling sites. The frequently detected taxa across all three methods encompass Cololabis saira (Pacific saury), Diaphus garmani (Garman's lanternfish), Diaphus theta (Theta lanternfish), Engraulis japonicus (Japanese anchovy), Maurolicus muelleri (Silvery lightfish), Myctophum asperum (Prickly lanternfish), Sardinops melanostictus/Sardinops sagax (Japanese/South American pilchard), Scomber japonicus/Scomber australasicus (Chub/Blue mackerel), Seriola quinqueradiata (Japanese amberjack), and Trachurus japonicus (Japanese jack mackerel). The detection of these species often overlaps among the three sampling methods. Overall, the southern part of the studied area exhibited higher biodiversity compared to the northern part, possibly influenced by favorable temperature, food availability, and suitable environmental conditions. Alpha biodiversity indices revealed significant differences among the methods, with ship-bottom intake indicating lower biodiversity compared to the other two methods (Kruskal-Wallis test, P<0.05). Non-Metric Multidimensional Scaling (NMDS) results (Stress= 0.19), based on the Jaccard presence/absence index, indicated partial overlap in taxonomic composition among the sampling sites using the three methods, with significant differences observed between ship-bottom intake and bucket samples, and negligible variance between Niskin and both methods (PERMANOVA, P<0.05). However, rarefaction analysis predicted similar taxonomic richness among all three methods. Discrepancies in biodiversity analysis of ship-bottom intake samples can be attributed to specific sampling sites influenced by complex fronts. Furthermore, the variation in biodiversity among methods can be ascribed to factors such as the lighter weight of DNA in certain species, the rate of eDNA release and degradation in specific sites and environmental conditions, and the impact of heat and wind flux. In conclusion, the findings suggest that bucket samples exhibit higher biodiversity, but caution is advised due to potential overestimation resulting from larval and egg DNA. This study not only compares the accuracy of eDNA meta-barcoding sampling methods but also emphasizes the need for species and site-specific considerations in biodiversity monitoring in the open ocean using eDNA meta-barcoding.