Diverging carbonate budgets following tropicalisation of temperate reefs

Full description

Climate-driven shifts in habitat-forming species abundance and distributions are transforming how ecosystems produce and cycle carbon, nutrients, and energy. Temperate kelp forests are increasingly being replaced by tropical or warm-affinity habitat-forming species like turf seaweeds and corals, i.e., “tropicalised”. These changes can have cascading effects on associated species such as calcifying organisms, which contribute to sediment generation and carbon cycling via the production of calcium carbonate. This study quantified carbonate production and erosion across a temperate kelp forest and three tropicalised reef states following the 2011 marine heat wave: kelp-turf mix, warmer-affinity seaweeds, and coral-turf dominance. Results show gross carbonate production was highest in coral-turf reefs (1.85 ± 0.65 kg m⁻² yr⁻¹), lowest in warmer-affinity seaweed reefs (0.04 ± 0.02 kg m⁻² yr⁻¹), and intermediate in temperate kelp forests (0.60 ± 0.19 kg m⁻² yr⁻¹). These differences were linked to the abundance of corals in the coral-turf state and scarce calcifying algae in the warmer-affinity seaweed state. Bioerosion played a moderate role in the overall budget, but the dominant bioeroders differed between habitats: urchins in temperate reefs contributed 80% less than parrotfishes in tropicalised reefs. Overall, tropicalisation can either increase or decrease carbonate availability, depending on the dominant habitat-formers. These shifts may significantly impact inorganic carbon cycling and the structural and functional integrity of coastal reef ecosystems. # Diverging carbonate budgets following tropicalisation of temperate reefs Dataset DOI: [10.5061/dryad.83bk3jb68](https://doi.org/10.5061/dryad.83bk3jb68) ## Description of the data and file structure * This script analyses data from the study: * "Diverging carbonate budgets following tropicalisation of temperate reefs" * The analysis quantifies changes in benthic community structure, calcification, and bioerosion across a temperate-to-tropical transition. Analyses and figures correspond to: * Tropicalisation states (Figure 2) * Community % cover by organism (Figure 3) * Carbonate production and bioerosion (Figure 4) ### Files and variables #### File: Photo_quadrat_data_RSPB-2025-2578.csv **Description**: Photo-habitat quadrat analyses across sites * *Photo*: Photo_quadrat identifier * *Site*: Study site * *Transect*: Replicate transect * *Functional_Group*: Benthic functional group * *Count:* Each row = one random point on image #### File: Calcifier_data_RSPB-2025-2578.csv **Description**: Percent cover and carbonate production of calcifiers * *Scenario*: Tropicalisation states (turf/coral, temperate seaweeds, transition stage, warmer-affinity seaweeds) * *Site*: Study site * *Transect*: Replicate * *Morph*: Calcifiers category (CCA, articulated macroalgae, *Acropora* branching, *Acropora* plating, massive corals, encrusting corals, *Turbinaria*, other branching) * *Organism*: Calcifier class (Corals, CCA, or articulated macroalgae)  * *Production_kg.m.2.yr.1*: Carbonate production (kg.m ^-2^.year ^-1^) * *Perc_cover*: Calcifier percent cover (%) #### File: Bioeroder_data_RSPB-2025-2578.csv **Description**: Parrotfish and urchin bioerosion  * *Scenario*: Tropicalisation scenarios (turf/coral, temperate seaweeds, transition stage, warmer-affinity seaweeds) * *Site*: Study site * *Organism*: Bioeroders (Urchins or parrotfish) * *Prod_orga_site*: Mean bioerosion (kg.m ^-2^.year ^-1^) * *sd_site*: Standard deviation of the mean bioerosion at the site level * *n*: Number of transects * *se*: Standard error of the mean bioerosion at the site level #### File: RSPB-2025-2578_Script.R **Description:** R script used to perform all analyses and generate figures. ###### ***Software / Session Information*** R version: 4.4.1 (2024-06-14) Required R packages: patchwork (1.2.0), emmeans (1.10.3), mvabund (4.2.1), vegan (2.6-6.1), tidyverse (2.0.0), dplyr (1.1.4), glmmTMB (1.1.9), DHARMa (0.4.6), ggplot2 (3.5.1) ###### **How to reproduce the analysis** 1. Download all data files and the R script. 2. Place `.csv` files in the same folder as the script. 3. Open **R** or **RStudio**. 4. Install required packages if not already installed. 5. Run `RSPB-2025-2578_Script.R` top-to-bottom. All figures and statistical outputs in the manuscript will be reproduced.

Notes

Associated Persons
Océane Attlan (Creator)