Dataset of biodiversity of the Seine nursery over 20 years in a highly disturbed environment

Estuaries are crucial ecosystems where human activities deeply affect numerous ecological functions. The Seine estuary, located on the French coast of the eastern English Channel, is a very dynamic environment where this conflict between the two contrasting backgrounds exists. The Seine watershed is highly disturbed by human activities due to significant industrial development and high population density. The estuary is a historic fishing ground for brown shrimp (Crangon crangon) and various species of flatfish, among which sole (Solea solea) and plaice (Pleutronectes platessa). However, it is a nursery area for fish and plays a crucial role in the life cycle of many demersal and benthic fish and invertebrates.

Here we present a survey dataset of biodiversity in the nursery of the Seine estuary and eastern bay of Seine collected using a beam trawl throughout three periods from 1995 to 2019. IFREMER (the French Institute for the Exploitation of the Sea) implemented scientific cruises on coastal nursery grounds aimed at describing the fish population and give an insight into the ecosystem functioning in these areas. The NOURSEINE survey presented here came to existence in this context. The surveys happen at the start of autumn to maximize the catchability of juvenile fish.  The beam trawl targets mainly benthic and demersal species over a more than 600 square kilometers study area. The dataset includes abundance and densities of 161 species for 634 hauls performed at around 40 stations each year. These data can be used by fishery scientists and ecologists motivated by earlier stage life of commercial species or by the impact of human disturbances, such as harbor developments, on estuarine communities. They can help in understanding how the nursery functions may change through time and potential human disturbances.

Dataset.csv: The data represents the density for the different species encounters in the trawl stations across the 14 years where the NOURSEINE campaign took place.  The table contains 22435 rows and 22 columns. Each row corresponds to the density of a species or individuals of the same size in a given haul, and this separation comes from the sorting operation. After each haul, the content of the trawl is emptied on deck, and a total or partial sorting is carried out depending on the volume and homogeneity of the capture. All species, both fish and benthic, are sorted, identified, counted and weighted. Fishes of commercial value and all others flatfish are measured. Fish’s otoliths are collected on the main commercial fish species (sole, plaice, flounder, dab, pouting, large whiting and European bass) and their age group determined later on in the laboratory. In 1999, the sampling was incomplete for technical reasons, and only commercial invertebrates were sampled (King scallop and lobster).

Sorting the capture can be separated into three different steps (See pdf figure attached):

               1. Total capture weighting: when the hauls are emptied on the deck, the whole capture is distributed in several baskets/box in order to weight it.

               2. Fish and large taxa sorting: All fish and large taxa of invertebrates easily identified (edible crab, common spider crab, large cephalopods) are sorted, identified, numbered, measured (for fish) and weighted (total weight per taxa). Depending on the size of the capture, a subsample might be necessary, and the operation is only performed on it. In case visual identification is too difficult (for instance due to a large mud proportion), the capture may be washed using a 5mm sieve. The weight ratio between the total capture and the subsample form a “division” variable that allows the calculation of the density. Another subsampling may be needed if a taxon has a high abundance. In that case, for practical reasons, only a subsample of the individuals are numbered and measured. The weight ratio between the total abundance and the subsample form a “coefficient” variable that is also used in the calculation of the density.

               3. Benthic fauna sorting: What is left from the second step is weighted before the sorting operation. All taxa constituting benthic fauna are sorted, identified, numbered and weighted (total weight per taxa). Some taxa may be measured (whelk, scallop). Just like step 2, according to the quantity of benthic fauna, a subsample might be necessary before sorting. All observations are manually recorded on fieldwork paper book before being checked and registered on the NOURSEINE database.

All observations are manually recorded on fieldwork paper book before being checked and registered on the NOURSEINE database.

Description of the columns found in the dataset

Year

The year when the sampling event took place. Ranges between 1995 and 2019.

Month

The month when the sampling event took place. Either 08 (August) or 09 (September).

Day

The day of the month when the sampling event took place. Ranges from 01 to 30.

Boat_Engine_kw

Engine power reflecting the boat used for sampling, given in kilowatt. Ranges between 81 and 552.

Gear_Code

Code describing the fishing gear used during the sampling event. “BT2” corresponds to beam trawl 2 meters and “BT3” is beam trawl 3 meters.

Haul_duration

The number of minutes of the haul operation. For 1250 rows, NA values indicate that this information was not available.

Station_Code

A unique number identifying the sampling event. Ranges between 1 and 1299.

Starting_Longitude_decimal

The longitudinal coordinate of the starting point of the fishing operation. Given in decimal in the WGS 84 system.

Ending_Longitude_decimal

The longitudinal coordinate of the ending point of the fishing operation. Given in decimal in the WGS 84 system.

Starting_Latitude_decimal

The latitudinal coordinate of the starting point of the fishing operation. Given in decimal in the WGS 84 system.

Ending_Latitude_decimal

The latitudinal coordinate of the ending point of the fishing operation. Given in decimal in the WGS 84 system.

Sector

The sector of the sampling area where the sampling event took place. The study area is divided in 12 sectors roughly based on bathymetry and distance to the mouth of the estuary and identified by letters from “A” to “M”.

Starting_Depth

The depth registered when the sampling event started. Given in meters, ranges from 2 to 26. For 13 rows, NA values indicate that this information was not available.

Ending_Depth

The depth registered when the sampling event ended. Given in meters, ranges from 2 to 26. For 313 rows, NA values indicate that this information was not available.

Trawled_Distance_m

The distance covered between the starting position and the ending position. Given in meters, ranges from 332 to 3128.

Trawled_Surface_m2

The surface trawled between the starting position and the ending position. Given in square meters, ranges from 963 to 9070.

Scientific_Name

Scientific name of the individuals identified in the haul. All names have been checked on WORMS (last accessed: 11/12/2019).

Number_Measured

The number of individuals measured during the sampling event. Ranges between 1 and 340.

Size

Size recorded during the measure of the individuals’ size. Given in centimeters for all species, except benthic fauna where millimeters are used. Ranges between 1 and 185.

Age_Group

Code giving the age category of a particular individual belongs to. “G0” means the individuals are less than 1 year old and born the year the sampling event took place. “G1” means the individuals are 1 year old and born the year before the sampling event took place. “G2+” means they are 2 years old

Number_in_Haul

The number of individuals counted or estimated in the entire haul (if individuals have not been numbered). Depending on the size of the capture, a subsample might be necessary. Another subsampling may be needed if a species has a high abundance. In that case, for practical reasons, only a subsample of the individuals are numbered and measured. The weight ratio between the total abundance and the subsample form a “coefficient” variable that is also used in the calculation of the density.

Weight_in_Haul

The weight of individuals counted or estimated in the entire haul (if individuals have not been numbered). Given in gram. Depending on the size of the capture, a subsample might be necessary. The weight ratio between the total catch and the subsample form a “division” variable that allows the calculation of the density. Another subsampling may be needed if a species has a high abundance. In that case, for practical reasons, only a subsample of the individuals are numbered and measured. The weight ratio between the total abundance and the subsample form a “coefficient” variable that is also used in the calculation of the density. For 7 rows, NA values indicated that this information was not available.

Subsample

Depending on the size of the capture, a subsample might be performed to estimate abundance and weight. This column indicates “Yes” if the capture has been subsample to identified the taxa and “No” if the taxa as identified on the whole catch.

Division

A number used to calculate the density from the “Number_in_Haul” column. It represents the weight ratio between the total capture and the subsample. It ranges between 1 and 512. When it is equal to one, the species was sorted in the whole capture.

Species_Density

The density calculated in individuals per square meters. Species densities are calculated based on the trawled surface but also taking into account if the haul has been partially sorted or not. The formula to calculate the density of individual per surface unit is:

Density = (Number_in_Haul * Division) / Trawled_Surface_m2

where Division is a factor used to elevate the abundance if the whole haul was not sorted.