README: Ocean deoxygenation caused non-linear responses in the structure and functioning of benthic ecosystems

https://doi.org/10.5061/dryad.6djh9w16w

This dataset includes data from a scientific cruise on board the RV Coriolis II along the Lower Estuary and Gulf of St. Lawrence. A gradient of oxygen concentration exist from the gulf and the head of the lower Saint Lawrence estuary and data was collected at different location along this gradient to assess the effect of bottom waters deoxygenation on the functioning of benthic ecosystem.

Description of the data and file structure

This data set is organized in 23 tabular data files
More information about the sampling procedure and measurement preformed can be found in the method section of the associated publication

CTD cast data

CTD cast data are included in 11 .cnv files. These files contain continuous profile of data recorded during the down and up cast. Data from the down cast was used during this study. File names include cruise ID (MAC20) and a sequential number (001) corresponding to the cast number of the cruise. The metadata of each file includes the date, time and location of the cast. The data includes at least the pressure, temperature (°C), salinity (psu) and oxygen concentration (µM). These files were processed using oce R package (Kelley D, Richards C (2023). oce: Analysis of Oceanographic Data. R package version 1.8-1, https://CRAN.R-project.org/package=oce)

Environmental data

The file "MAC2020_env.txt" (separator = tab; decimal = ",") contain the environmental characteristics of each sampled location. It includes the proportion (%) of sand and mud of the sediment, the sediment loss on ignition (LOI in %) as well as the sediment total nitrogen (N in %), total carbon (C in %), organic carbon (Corg in %) and d¹³C (d13C in &permil). The temperature (Temp in °C), salinity (Sal in psu) and oxygen concentration (Oxy in µM) of bottom waters for each sampled location is also mentioned as well as the depth (Depth in m) of the sampled location.

Porewater profiles

Three data files are related to porewater profiles:
The file "Profiles_merged.csv" (separator = ";", decimal = ",") contains the microprofiles of oxygen concentration. This file includes oxygen concentration (Conc. in µM), the corresponding depth within the sediment (Depth_cm in cm, with 0 corresponding to the sediment water interface and negative values corresponding to the overlying water), station names (Station) and replicate number.
The file "porewater_nut.txt" (separator = tab; decimal = ",") contains the profiles of nutrient concentrations. This file includes the station names (Station), the corresponding depth within the sediment (Depth in cm, with 0 corresponding to the sediment water interface and negative values corresponding to the overlying water), ammonium concentration (NH4 in µM), nitrate concentration (NO3 in µM), nitrite concentration (NO2 in µM) nitrite + nitrate concentration (NOx in µM) and phosphate concentration (PO4 in µM).
The file "DOU_OPD_Fick.txt" (separator = tab; decimal = ",") contains diffusive oxygen uptake by the sediment (DOU in mmol m^-2 d^-1) computed following Fick first law (see section 2.3 of the associated publication). This file includes the station names (Station), the replicate (replicate), the DOU and oxygen penetration depth (OPD in cm).

Macrobenthic community structure

The file "Macrofauna_density.txt" (separator = tab; decimal = ",") includes station names (Station), the size fraction of the macrofauna (Fraction; i.e., 0.5 to 1 mm = 0.5 and > 1 mm = 1), the replicate ID (replicate), species names (Noms_bdd. This column also includes the "DELETE" word at some lines. This correspond to poorly identified species of fragment of organisms), species count (Abundance) and species density (Density_ind_m2 in individuals m^-2)
The file "Macrofaune_traits.txt" (separator = tab; decimal = ",") includes species names (Species), and the affinity of each species for a given functional trait (Sc = scavenger, SurD = surface deposit feeder, SubD = subsurface deposit feeder, F = filtrer feeder, Epi = epifauna, SurfMod = surface modifier, Con = conveyer belt, BioDiff = biodiffuser). See section 2.8 of the associated publication for further details.

Bioturbation

The file "particle_mixing.txt" (separator = tab, decimal = ",") contains the luminophore profiles. It includes the depth (Depth in cm) and the proportion of luminophore (in %) in each replicate. Please note that in this file, the column name represent the station and replicate (e.g. P07_C1 corresponds to the station P07 and replicate 1)
The file "Results_particle_mixing.csv" (separator = ";", decimal = ",") contains the sediment reworking rates. It includes the RMSE of the model (RMSE), the biodiffusion coefficient (Db in cm² y^-1) and the maximum penetration depth of luminophore (MPD in cm)
The file "Profile_Br.txt" (separator = tab; decimal = ",") contains the depth profiles of bromide. It includes depth (Depth in cm), and the concentration of Br^- (in µM) at each station (i.e., each column represents a station).
The file "fitted_irr.csv" (separator = ";", decimal = ",") contains the fitted model of Br^-. It includes the depth within the sediment (Depth in cm), the station names (Station) and the bromide concentration (Br in µM).

Incubation

The file "Data_incubation.txt" (separator = tab, decimal = ",") contains the real time oxygen concentration measured in the overlying water of the sediment core incubation. It includes the station names (Station), the replicate ID (Replicate) the incubation duration (duration_h in hour), the percentage of oxygen as compared to the initial concentration (Saturation_percent in % with the first point of the incubation correspond to 100 %) and the initial oxygen concentration in the overlying water of the incubator (InitialOx_uM in µM). Please note that all sediment cores were characterized by an internal diameter of 10 cm.

The file "OW_height.txt" (separator = tab, decimal = ",") includes the station names (Station), the replicate ID (Replicate) and three consecutive measure of the height of the overlying water (h1, h2 and h3 in cm). Knowing the area of the sediment core (inner diameter = 10 cm) this allow for the estimation of the volume of the overlying water.

Code/Software

Most of the analyses were performed using R software (version 4.2.0). Used packages are details in the associated publication and information can be found in the corresponding vignettes.