Authors: J. Carlot, S. Comeau, A. Chiarore, A. Mirasole, S. Alliouane, F. Micheli, C. L. Hurd, J.-P. Gattuso, N. Teixidó
Abstract: Ocean acidification (OA) driven by increasing atmospheric CO₂ is altering marine biodiversity. However, impacts of OA on ecosystem functioning at the community level, including calcification, primary production, and nutrient uptake, remain largely unknown. Here, we conducted community transplant experiments at natural CO₂ vents to assess how declining pH affects marine community species composition, biomass, and key ecosystem processes over time. Our results indicate that community shifts caused by declining pH lead to decreased biomass and calcification rates, while photosynthesis and nutrient uptake rates increased. By leveraging OA field model systems and in situ measurements of ecosystem functioning, this study provides critical insights into how OA-induced biodiversity loss reshapes the structure and functioning of temperate marine coastal ecosystems.
Data availability. The raw observational data underlying this study are subject to a temporary embargo, as they form part of the ongoing Beatriu de Pinós grant (2024BP00106; expected completion: 31 August 2027). To ensure full reproducibility, we provide the complete processed datasets, model outputs, and fully annotated analysis code used to generate all results, tables, and figures in the manuscript. Upon completion of the grant, the raw data will be made publicly available in this repository.
Figure reproducibility. All figures and figure panels presented in the manuscript were graphically post-processed for publication purposes. As a result, figures generated directly from the provided code may differ slightly in layout or formatting from those shown in the published article. However, the code reproduces all figures in their analytical (raw) form and fully replicates the underlying results.
Repository structure.
📁 Data is the folder where you might find the data needed to reproduce the figures.
• Figure 1 • Figure 2 • Figure 3 • Figure 4 •
📁 R_Script hosts the scripts used for the current analyses.
The analysis scripts are indexed and correspond to the different phases of the project conducted over the past two years. Once the raw data are released, these scripts will serve as the complete processing and analysis pipeline, from raw measurements to final results.
Each script is documented and linked below:
- 0. Titration_alkalinity.R: Quantifies total alkalinity (AT) from processed titration samples.
- 1. Quality_Check_O2_Sensors.R: Formats and performs quality control on oxygen data obtained from sensors.
- 2. MiniDots.R : Extracts oxygen data to estimate dark respiration (DR) and gross photosynthetic rates (GP) of the samples.
- 3. Alkalinity.R: Converts changes in total alkalinity into calcification rates.
- 4. PI_Photo.R: Derives the relationships between calcification rate (CR), dark respiration (DR), gross photosynthesis (GP), and irradiance (photosynthesis–irradiance curves).
- 5. PAR_profiles.R: Extracts light (PAR) profiles recorded during incubation experiments.
- 6. Vizualisation.R: Visualizes the three pH conditions across the three study sites (Figure 1).
- 7. Nutrients.R: Extracts and processes nutrient uptake data.
- 8. Covers_communities.R: Quantifies community cover on experimental tiles across different sampling times.
- 9. Biomass_communities.R: Estimates community biomass on experimental tiles across sampling times (Figure 2).
- 10. Conditions_T0.R: Defines initial (pre-experimental) conditions (Table 1).
- 11. Changes_communities.R: Quantifies temporal changes in ecosystem functions.
- 12. Long-term.R: Assesses long-term functional changes on historical tiles (Figure 4).
- 13. Review.R: Addresses reviewer comments from Round 1, including the generation of the revised Figure 3.
As the raw observational data are not yet publicly available, the following scripts correspond to the figures in the manuscript and currently work with the processed data:
• Figure 1 • Figure 2 • Figure 3 • Figure 4 •
📁 Outputs hosts the main figures.
• Figure 1 • Figure 2 • Figure 3 • Figure 4 •
System informations
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.3 (2025-02-28)
os macOS 26.2
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Madrid
date 2026-02-15
rstudio 2026.01.0+392 Apple Blossom (desktop)
pandoc NA
quarto 1.8.25 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [1] CRAN (R 4.4.1)
backports 1.5.0 2024-05-23 [1] CRAN (R 4.4.1)
bayesplot 1.11.1 2024-02-15 [1] CRAN (R 4.4.0)
bridgesampling 1.1-2 2021-04-16 [1] CRAN (R 4.4.0)
brms * 2.22.0 2024-09-23 [1] CRAN (R 4.4.1)
Brobdingnag 1.2-9 2022-10-19 [1] CRAN (R 4.4.0)
callr 3.7.6 2024-03-25 [1] CRAN (R 4.4.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.4.0)
checkmate 2.3.2 2024-07-29 [1] CRAN (R 4.4.0)
cli 3.6.5 2025-04-23 [1] CRAN (R 4.4.1)
coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.4.1)
codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.3)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.4.1)
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.1)
curl 7.0.0 2025-08-19 [1] CRAN (R 4.4.1)
distributional 0.5.0 2024-09-17 [1] CRAN (R 4.4.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
emmeans 1.10.7 2025-01-31 [1] CRAN (R 4.4.1)
estimability 1.5.1 2024-05-12 [1] CRAN (R 4.4.1)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.1)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0)
generics 0.1.4 2025-05-09 [1] CRAN (R 4.4.1)
ggplot2 * 4.0.0 2025-09-11 [1] CRAN (R 4.4.1)
ggridges * 0.5.6 2024-01-23 [1] CRAN (R 4.4.0)
glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.1)
gtable 0.3.6 2024-10-25 [1] CRAN (R 4.4.1)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
inline 0.3.21 2025-01-09 [1] CRAN (R 4.4.1)
jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.4.1)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.4.1)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.3)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.1)
loo 2.8.0 2024-07-03 [1] CRAN (R 4.4.0)
lubridate * 1.9.4 2024-12-08 [1] CRAN (R 4.4.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.1)
Matrix 1.7-2 2025-01-23 [1] CRAN (R 4.4.3)
matrixStats 1.5.0 2025-01-07 [1] CRAN (R 4.4.1)
mvtnorm 1.3-3 2025-01-10 [1] CRAN (R 4.4.1)
nlme 3.1-167 2025-01-27 [1] CRAN (R 4.4.3)
patchwork * 1.3.0 2024-09-16 [1] CRAN (R 4.4.1)
pillar 1.10.2 2025-04-05 [1] CRAN (R 4.4.1)
pkgbuild 1.4.7 2025-03-24 [1] CRAN (R 4.4.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.1)
posterior 1.6.1 2025-02-27 [1] CRAN (R 4.4.1)
processx 3.8.6 2025-02-21 [1] CRAN (R 4.4.1)
ps 1.9.1 2025-04-12 [1] CRAN (R 4.4.1)
purrr * 1.0.4 2025-02-05 [1] CRAN (R 4.4.1)
QuickJSR 1.7.0 2025-03-31 [1] CRAN (R 4.4.1)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.4.1)
ragg 1.3.3 2024-09-11 [1] CRAN (R 4.4.1)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.1)
Rcpp * 1.1.0 2025-07-02 [1] CRAN (R 4.4.1)
RcppParallel 5.1.10 2025-01-24 [1] CRAN (R 4.4.1)
readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0)
readxl * 1.4.4 2025-02-27 [1] CRAN (R 4.4.1)
rJava 1.0-11 2024-01-26 [1] CRAN (R 4.4.1)
rlang 1.1.6 2025-04-11 [1] CRAN (R 4.4.1)
rstan 2.32.7 2025-03-10 [1] CRAN (R 4.4.1)
rstantools 2.4.0 2024-01-31 [1] CRAN (R 4.4.1)
rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.4.1)
S7 0.2.0 2024-11-07 [1] CRAN (R 4.4.1)
scales 1.4.0 2025-04-24 [1] CRAN (R 4.4.1)
sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.4.1)
StanHeaders 2.32.10 2024-07-15 [1] CRAN (R 4.4.1)
stringi 1.8.7 2025-03-27 [1] CRAN (R 4.4.1)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
systemfonts 1.3.1 2025-10-01 [1] CRAN (R 4.4.1)
tensorA 0.36.2.1 2023-12-13 [1] CRAN (R 4.4.1)
textshaping 1.0.0 2025-01-20 [1] CRAN (R 4.4.1)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.1)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.0)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.1)
tzdb 0.5.0 2025-03-15 [1] CRAN (R 4.4.1)
utf8 1.2.5 2025-05-01 [1] CRAN (R 4.4.1)
V8 6.0.1 2025-02-02 [1] CRAN (R 4.4.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
xlsx 0.6.5 2020-11-10 [1] CRAN (R 4.4.0)
xlsxjars 0.6.1 2014-08-22 [1] CRAN (R 4.4.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.1)
[1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
* ── Packages attached to the search path.
Author contributions: All authors have agreed to the submission of this manuscript and take responsibility for the integrity, accuracy, and ethics of the work. J.C. and N.T. are responsible for the overall integrity of the manuscript. All authors made substantial intellectual contributions and meet the authorship criteria of Ecology Letters. Conceptualization: J.C., S.C., J-P.G. and N.T. Data curation: J.C., A.C., A.M., S.A. and N.T. Formal analysis: J.C. Investigation: J.C., A.C., A.M. and N.T. Writing (first draft): J.C. Writing (review and editing): J.C., S.C., A.C., A.M., S.A., C.L.H., F.M., J-P.G. and N.T. Funding: J.C & N.T. The authors declare no competing interests.