Fish community survey using environmental DNA in Kurihama Bay, Japan

Homma, Shota 1 ; Hosokawa, Shinya1; Komuro, Takashi2

Published Feb 27, 2025 on Dryad. https://doi.org/10.5061/dryad.2rbnzs7ws

Data files

Feb 27, 2025 version files 470.43 MB

dataset.csv

39.69 KB
habitat.csv

7.73 KB
positive_field_blank.csv

3.60 KB
raw_data.zip

470.37 MB
README.md

4.93 KB
sample_info.csv

5.82 KB

Abstract

Metabarcoding of environmental DNA (eDNA) is becoming practically applied to fish monitoring and conservation surveys in estuaries. However, estuarine bays may be an unsuitable zone to use eDNA metabarcoding because they are affected by eDNA originating from upstream rivers. In this study, the transition of eDNA composition from river to bay was examined to investigate the influence of freshwater sources on the eDNA composition of the downstream bay. Samples were collected in a bay spanning around 1 km and an upstream river under high and low tide within 1 day in November and in January. The samples were analyzed by using eDNA metabarcoding for fish species and species-specific quantitative analysis for the freshwater fish Cyprinus carpio. Our findings reveal that the eDNA of freshwater fishes was drastically diluted in the model estuarine bay. As a result, the relative-read-based composition clearly changed from riverine to marine environments, and the freshwater inflow had little effect on the relative-read-based composition at those sites. However, eDNA from freshwater fishes was widely detected in the bay by species-specific and metabarcoding analysis, suggesting that fresh water may have a more significant impact when focusing on presence/absence-based composition. Our study also found that the transition zone for the concentration of freshwater eDNA fluctuated spatiotemporally with tides, indicating that the degree of influence from the river varies with tide. Therefore, prior measurement of the distribution of freshwater fish eDNA at low tide would help to conservatively determine better sampling sites and design more reliable sampling in estuaries.

Description of the data and file structure

This dataset was collected for research presented in the following paper, which focuses on environmental DNA (eDNA) surveys targeting fish species:

Homma, S., Hosokawa, S., & Komuro, T. (2024). Fish eDNA Composition Along a Gradient of Freshwater eDNA in an Estuarine Bay. Environmental DNA, 7(1), e70061. https://doi.org/10.1002/edn3.70061

In this study, quantified concentrations of Cyprinus carpio's eDNA and the eDNA composition of fish communities were obtained from samples collected from Kurihama Bay and the Hirasaku River in Japan. The dataset includes quantitative PCR results for Cyprinus carpio and metabarcoding results. The dataset contains both raw sequencing output data and processed data used for analysis. Details of the sampling strategy and analysis methods are provided in the paper and supplementary information.

Files and Description

raw_data.zip

metabarcoding_data: This folder contains compressed FASTQ file (.fastq.gz) containing eDNA metabarcoding sequences. Each file is stored in the folder named after the month in which it was collected, such as "01_Nov" and *"*02_Jan". The file names of FASTQ format and the sample names in the manuscript are linked by the column names (Sample and File_name) in the correspondence_table.csv file. These files were processed by using the PMiFish pipeline as described in the manuscript.

qPCR_data: This folder contains the results of quantitative PCR analysis for Cyprinus carpio.

qPCR_Cyprinus_carpio.csv: Quantified DNA concentration (copies/L, qPCR_Carp) for each sample name (Symbol).

qPCR_data.csv: This file includes Ct-values and quantified DNA concentration (copies/L) for all samples.

The columns of Site, Month, Tide are same as sample_info.csv.

The columns of Ct and Quantity are same as qPCR_details_batch[1-5].csv.

Average represents the average of Quantity across four replicates.

The columns of ③ Volume of DNA Solution Used (μL), ④ Volume of DNA Extract (μL), ⑤ Filtration Volume (mL), Qunatity (Copies / L) 【=(②÷③×④)÷⑤×1000】 represent the values as they are.

No. standard curve represents the identifier for each standard curve in qPCR_standard_curve.csv.

qPCR_details_batch[1-5].csv: This file contains the qPCR analysis results for batches 1 to 5. The analysis was performed using the QuantStudio 3 (Thermo Fisher Scientific, Waltham, MA, USA). A detailed description of the variables is provided in Chapter 3 of the manual Export File Formats and Specifications.

qPCR_standard_curve.csv: No. standard curve: Identifier for each standard curve.

Intercept: The y-intercept of the standard curve equation.

R^2: The coefficient of determination.

Slope: The slope of the standard curve.

Efficiency: The PCR amplification efficiency.

dataset.csv: This file includes a species-by-sample matrix with filtered read counts calculated from the metabarcoding results. The column (sample name) matches the column name of Symbol in sample_info.csv.

sample_info.csv: This file contains a basic sample information and associated environmental variables as described below:

Month, Tide, Symobl: Unique sample name (Symbol) collected in Month at Tide condition.
Site, Site2: Names of sampling site. Site2 is a broader classification that does not distinguish depth.
Group1: Grouping variables (R: River, IB: Inner-bay, OB: Outer-bay). Groups 2 and 3 were added for the purpose of supplementary analysis and not related to the reanalysis.
UB: Grouping analysis indicating sampling depth (U: Upper layer, B: Bottom layer).
pair_id: Identifier indicating paired samples under tidal conditions.
Depth_sample: Depth of water sampling (m)
long: Longitude (decimal degrees, E)
lat: Latitude (decimal degrees, N)
Depth: Depth of sampling site (m)
WT: Water Temperature (degree of C)
PSU: Salinity (Practical Salinity* *Unit)
Turb.: Turbidity (FTU)
Chl_a: Chlorophyll a (μg / L)
qPCR_Carp: qPCR result (copies / L).

habitat.csv

This data provides information on the categorization of specie’s habitats used in the analysis. Species are categorized into 6 habitat categories (Fresh, Brackish, Marine, Fresh-Brackish, Brackish-Marine, Fresh-Brackish-Marine) based on the FishBase database, and the habitat_class column indicates the category for each fish species. Details of the categorizing method can be found in the paper.

positive_field_blank.csv

This data provides information on the filtered read counts of positive field blank, labeled BL.H_N samples in November (details are obtained in the Supplementary information in the paper).

Code/Software

The statistical analysis was conducted in R v.4.3.2 as described in the paper. The scripts was available on GitHub.