DOI: 10.5061/dryad.2rbnzs7ws
title: Fish community survey using environmental DNA in Kurihama Bay, Japan

description: 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: # Fish community survey using environmental DNA in Kurihama Bay, Japan ###
 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](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.