DOI: 10.5061/dryad.j3tx95xqz
title: Testing biodiversity-ecosystem function relations in nearshore marine sediments

description: Rapid biodiversity loss is raising concerns about potential declines in
 the functioning of Earth’s ecosystems. Although decades of research
 explore biodiversity-ecosystem function (BEF) relations, empirical BEF
 assessments have lagged behind theoretical advances, particularly in
 marine benthic systems. Here, we incubate intact sediment push cores to
 examine the relationship between macroinfaunal community composition and
 benthic nutrient cycling in three nearshore sub-Arctic sites. First, we
 quantitatively assess potential effects of taxonomic and functional
 diversity, as well as community-weighted trait means, on oxygen and
 nutrient fluxes. Second, we examine fluxes in relation to macrofaunal
 abundance, oxygen consumption (a proxy for total core metabolism), and
 abundance of key functional groups, to test fundamental expectations based
 on ecological theory. We report distinct macrofaunal communities and
 contrasting benthic fluxes among sites, with oxygen and ammonium largely
 driving multivariate inter-site flux differences. Diversity indices and
 community-weighted trait means collectively explained ~76% of the
 variation in multivariate fluxes but provided little insight into the
 mechanistic links between diversity and functioning. In fact, we find that
 total macrofaunal abundance was the key driver of benthic fluxes at our
 sites, rather than functional community composition, which may have
 important implications for coastal conservation planning. Overall, our
 findings emphasize the highly context-dependent nature of BEF
 relationships and highlight the need to improve empirical understanding of
 these patterns in complex, natural ecosystems.
description: # Testing biodiversity-ecosystem function relations in nearshore marine
 sediments Data were collected from three intertidal soft-sediment sites
 around the island of Newfoundland, Canada, using manual sediment push
 cores. Nutrient (ammonium, silicate, phosphate, and combined
 nitrate/nitrite) and oxygen fluxes were measured during 24-hour
 incubations of sealed sediment cores. Cores were then sectioned into depth
 layers (0-2 cm, 2-5 cm, and 5-10 cm), and macrofauna were sieved through a
 500 micron mesh, enumerated, and identified to the lowest possible
 taxonomic level. This dataset includes: 1. Raw abundance data and
 functional trait information, as well as nutrient and oxygen
 concentrations measured in each core;  2. Taxonomic and functional
 diversity indices (including Hill numbers) calculated using common methods
 in the field; 3. Nutrient and oxygen flux rates calculated using common
 methods in the field;  4. Code used to produce the figures, tables, and
 analyses in Clinton et al. (2025). ## Description of the data and file
 structure ### File structure Code: This folder contains all scripts needed
 to produce the figures, tables, and analyses in Clinton et al. (2025).\
 Data: This folder contains raw and processed data (.csv files). ###
 Description of raw data ###### abundances_*by*_*core*.csv A *core* x
 *species* matrix that contains raw abundances for each taxon identified in
 each sediment core. Column headers `Alitta.sp` to  `Tellinidae.indet` are
 taxon names following binomial nomenclature
 (e.g., `.`). The column `core_id` follows the
 format: `__`. Note that enrichment type is unrelated to
 the analysis conducted in Clinton et al. (2025). ######
 CWM_*by*_*core*.csv Contains community-weighted mean trait values for each
 core. For details on how these values were calculated, see Clinton et al.
 (2024). The column `core_id` follows the format: `__`. The 3 possible values for `site` are: `NS` = Newman Sound, `NH` =
 Neddie's Harbour, and `SP` = St. Paul's Bay. All remaining
 columns (`diet_Hb` to `log_body_size_scaled`) contain unitless values
 between 0 and 1. Note that the traits Diet, Feeding guild, and sediment
 reworking are each divided into several modalities, which are denoted in
 the column name using an underscore, as seen below: `Diet`: `_Hb` =
 Herbivore, `_C` = Carnivore, `_Dt` = Detritivore.\ `Feeding guild`: `_Pr`
 = Predator, `_Gr` = Grazer, `_Sc` = Scavenger, `_Ff` = Filter feeder,
 `_SD` = Surface deposit-feeder, `_SSD` = Sub-surface deposit-feeder.\
 `Reworking`: `bd` = Biodiffusor, `sm` = Surficial modifier, `updown` =
 Upward/downward conveyor, `epi` = epipelagic\ `log_body_size_scaled`: Log
 transformed maximum body size (mm), scaled between 0 and 1 ######
 TD_*indices*.csv Contains taxonomic diversity indices for each core. For
 details on how these values were calculated, see Clinton et al. (2024).
 Column names can be interpreted as follows:  `site`: Name of the site at
 which that sediment core was collected. \ `core_id`: Unique identifier for
 each sediment core. Follows the format: `__`.`iet`\
 `shannon`: Shannon-Weiner index\ `simpson`: Simpson's diversity
 index\ `richness`: Taxonomic richness (i.e., the number of unique taxa
 observed within a given core)\ `pielous_evenness`: Pielou's evenness
 index. Value of 1 indicates perfect evenness (i.e., all taxa are equally
 abundant), value of 0 indicates maximum unevenness (one taxon dominates
 completely).  ###### FD_*indices*.csv Contains functional diversity
 indices for each core. For details on how these values were calculated,
 see Clinton et al. (2024). Column names can be interpreted as follows: 
 `Nb_sp`: Number of unique taxa observed within a given core.\
 `Tot_weight`: Number of organisms observed within a given core. \ `FRic`:
 Functional richness \ `FDiv`: Functional divergence\ `FEve`: Functional
 evenness \ `FDis`: Functional dispersion\ `FSpe`: Functional
 specialization\ `FOri`: Functional originality  ######
 functional_groups.csv A *species* x *trait* matrix, which includes trait
 information for each `taxon`. Also outlines the functional group (`FG`) to
 which each taxon was assigned, based on these traits. Each functional
 group and trait is described in detail below. Note: The traits Diet and
 Feeding guild are fuzzy coded (values between 0 and 1) and divided into
 several modalities, which are denoted in the column name using an
 underscore. For example, the trait `diet` has three modalities: `Hb`
 (Herbivore), `C` (Carnivore), and `Dt` (Detritivore). The codes used to
 define each modality are also outlined below: `Diet`: `diet_Hb` =
 Herbivore, `diet_C` = Carnivore, `diet_Dt` = Detritivore.\ `Feeding
 guild`: `_Pr` = Predator, `_Gr` = Grazer, `_Sc` = Scavenger, `_Ff` =
 Filter feeder, `_SD` = Surface deposit-feeder, `_SSD` = Sub-surface
 deposit-feeder.\ `Reworking`: `bd` = Biodiffusor, `sm` = Surficial
 modifier, `updown` = Upward/downward conveyor, `epi` = epipelagic\ `Body
 size`: Values in the body size column are the maximum recorded size (in
 mm) for that taxon.\ `Mobility`: Value between 0 and 1 indicating the
 degree of mobility exhibited by the taxon within the sediment matrix. None
 (value: 0) = Sedentary or only moving within a fixed tube structure. Low
 (value: 0.3) = Limited free movement (e.g., withdraws into sediment when
 disturbed). Moderate (value: 0.6) = Slow movement within the sediment
 matrix via non-permanent burrow formation. High (value: 1) = Freely mobile
 within sediment in a permanent, excavated burrow system. Outlines which
 taxa were assigned to which functional groups \
 `FG`: `free_move_bd_Hb_Dt` = free-moving, biodiffusing
 herbivores/detritivores, `hunters` = free-moving, biodiffusing
 carnivores, `other` = other, `copepod` = small epipelagic copepods
 (referred to as "swimmers" in Supplementary material of Clinton
 et al. 2025), `burrowers` = surficial modifiers with permanent burrow
 systems, `low_mob_sm` = low-mobility surficial
 modifiers,  `snails_and_co` = free-moving surficial
 modifiers, `heads_down` = sub-surface deposit feeding upward
 conveyors,  `heads_up` = surface deposit feeding downward conveyors 
 ###### IncubationData_UnenrichedCores.csv Contains site-level information,
 as well as variables collected during the sediment core incubations.
 Column headers are defined below: `site_name_full`: Collection site. Note
 that Alien Cove refers to Newman Sound \ `site`: Abbreviation for
 collection site. AC = Alien Cove (Newman Sound), SP = St. Paul's, NH
 = Neddie's Harbour\ `lat`: Latitude of collection site.\ `long`:
 Longitude of collection site.\ `substrate`: Categorical description of
 substrate at collection site (sand, mud, or gravel)\ `bottom_temp`: Water
 temperature (degrees Celsius) at the site during collection.\ `salinity`:
 Salinity (ppm) at site during collection.\ `day`: Day on which collection
 occurred.\ `month`: Day on which collection occurred.\ `year`: Year in
 which collection occurred.\ `settlement_time`: Number of hours cores were
 left undisturbed between collection and incubation, to ensure all
 suspended sediment had settled out of the water column. \ `treatment`:
 Category of core (none indicates regular sediment cores, none_bw indicates
 cores that were incubated and contained only bottom water, bottom_water
 indicates oxygen measures taken from the store of replacement bottom water
 collected at each site.\ `core_ID`: Unique identifier for each sediment
 core. Follows the format: `__`. `water_height`:
 Height (cm) of the water overlying sediment in each core. Used to
 calculate total volume. \ `oxy_0h`: Oxygen concentration (μmol/L) in each
 core, measured at the beginning of the incubation (hour zero). \ `oxy_4h`:
 Oxygen concentration (μmol/L) in each core, measured 4 hours into the
 incubation. \ `oxy_8h`: Oxygen concentration (μmol/L) in each core,
 measured 8 hours into the incubation. \ `oxy_12h`: Oxygen concentration
 (μmol/L) in each core, measured 12 hours into the incubation. \ `oxy_16h`:
 Oxygen concentration (μmol/L) in each core, measured 16 hours into the
 incubation. \ `oxy_20h`: Oxygen concentration (μmol/L) in each core,
 measured 20 hours into the incubation. \ `oxy_24h`: Oxygen concentration
 (μmol/L) in each core, measured 24 hours into the incubation. ######
 NutrientData_UnenrichedCores.csv Contains duplicate measurements of
 nutrient concentrations (mmol m ^-3^) for each `core_id`, at each `time`
 point in the incubation (start: 0h, mid: 12h, end: 24h). Nutrient
 concentration columns follow the format:
 `_`. ### Code #####
 000-study-site-map.R Generates components of the study site map (Fig. 1)
 in Clinton et al. * Figure outputs: study_sites_map.tiff,
 NorthAmerica_inset_map.tiff ##### 001-nutrients-and-oxygen-data-setup.R
 Script used to clean nutrient and oxygen data, and join them into one data
 frame. * Input: `IncubationData_UnenrichedCores.csv`,
 `NutrientData_UnenrichedCores.csv` * Processed data outputs:
 `Oxygen_and_Nutrient_concentrations_raw.csv` #####
 002-nutrients-and-oxygen-apply-corrections.R Applies corrections to
 nutrient and oxygen values, required to account for the nutrients and
 oxygen added via bottom water additions during incubations. Then,
 calculates flux rates in units of mmol/m^2^/day and umol/m^2^/day for each
 of the 4 nutrients and for oxygen. * Input:
 `Oxygen_and_Nutrient_concentrations_raw.csv` * Processed data outputs:
 `Oxygen_and_Nutrient_concentrations_corrected.csv`,
 `Oxygen_and_Nutrient_FluxRates_AllCores.csv`,
 `Mean_Oxygen_and_Nutrient_FluxRates_AllCores.csv` #####
 003-nutrients-and-oxygen-plots.R Creates a plot of oxygen consumption in
 each core and bar plots of nutrient flux rates. * Input:
 `Oxygen_and_Nutrient_concentrations_corrected.csv`,
 `Oxygen_and_Nutrient_FluxRates_AllCores.csv`,
 `Mean_Oxygen_and_Nutrient_FluxRates_AllCores.csv` * Figure output:
 `OxygenConsumption_AllSites.tiff`,
 `Nutrient_FluxRates_AllSites_ByCore.tiff`,
 `Nutrient_FluxRates_AllSites.tiff` #####
 004-nutrients-and-oxygen-site-comparisons.R Tests for differences in flux
 rates among sites using univariate (GLS) and multivariate (PERMANOVA,
 nMDS) analyses. * Input: `Oxygen_and_Nutrient_FluxRates_AllCores.csv` *
 Figure output: `spiderplot_nutrient_fluxes.tiff` #####
 005-community-diversity-data-setup.R Script used to clean community
 composition data and join them into one data frame. Includes taxonomic and
 functional diversity indices, community-weighted trait means, and
 functional group abundances. * Input: `functional_groups.csv`,
 `abundances_by_core.csv`, `Oxygen_and_Nutrient_FluxRates_AllCores.csv`,
 `TD_indices.csv`, `FD_indices.csv`, `CWM_by_core.csv` * Processed data
 output: `All_Explanatory_and_Response_Variables.csv` #####
 006-hill-numbers.R Estimates the first three Hill numbers (q = 0, 1, 2)
 following Chao et al. (2014). * Input:
 `abundances_by_core_for_calculation_of_indices.csv` * Processed data
 output: `Hill_numbers.csv` #####
 007-diversity-and-fluxes-multivariate-analysis.R Performs Redundancy
 Analyses (RDAs) on multivariate benthic fluxes as a function of diversity
 indices, CWMs, and Hill numbers. Variation partitioning describes the
 portion of variance explained by each set of explanatory variables. *
 Input: `All_Explanatory_and_Response_Variables.csv`,  `Hill_numbers.csv` *
 Figure outputs: `RDA_Indices_ggvegan_plot.tiff`,
 `RDA_CWMs_ggvegan_plot.tiff` ##### 008-mechanistic-links-FGs-and-fluxes.R
 Uses Generalized Additive Models (GAMs) to explore potential drivers of
 ammonium and oxygen flux. Produces supplementary plots of the
 relationships between NH~4~^+^ flux, O~2~ flux, and total macrofaunal
 abundance. * Input: `All_Explanatory_and_Response_Variables.csv` * Figure
 outputs: `Oxygen_flux_vs_macrofaunal_abundance.tiff`,
 `Ammonium_flux_vs_macrofaunal_abundance.tiff`,
 `Ammonium_flux_vs_oxygen_uptake.tiff` ## References Clinton ME, Snelgrove
 PVR, Bates AE (2025). Testing biodiversity-ecosystem function relations in
 nearshore marine sediments. Estuarine, Coastal and Shelf Science. Clinton
 ME, Snelgrove PVR, Bates AE (2024). Macrofaunal diversity patterns in
 coastal marine sediments: Re-examining common metrics and methods. Mar
 Ecol Prog Ser 735:1-26.