Diverging carbonate budgets following tropicalisation of temperate reefs

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.