Data and scripts for the manuscript "Invasive macroalgae shape chemical and microbial waterscapes on coral reefs" Reefwater microbiome and metabolome analysis Microbiome : seqtab.no1.rds, taxa_NS.rds and reefwater_sampleMetadata.csv. To use with script "reefwater microbiome analysis.R" Metabolome : reefwater_posMZmine_wblanksQC.csv (MS1 feature intensities) and eaux_pos.sampleMetadata.csv. To use with script " reefwater metabolome_posMS analysis.R" Multiomic : "multiomic_processed data". To use with script "multiomic_reefwater_DIABLO.R" Algal metabolites diffusion and molecular network analysis Venn Diagrams, Compounds polarity: endosurf_posMZmine_MS1_quant.csv (MS1 feature peak intensities). To use with script "algal metabolites MS1.R" Discriminant features, Molecular network analysis and annotations in positive ionization mode: endosurf_posMZmine_GNPS_wblanksQC_gap_quant.csv (MS1 features with MS2 peak intensities),endosurf_sw_pos_fbmnextra_gap.csv (FBMN output), sirius_classif_pos.xlsx, sirius_compID_pos.xlsx. To use with script "algal metabolites MS2_FBMN.R" Discriminant features, Molecular network analysis and annotations in negative ionization mode: endosurf_sw_neg_quant_table.csv, endosurf_sw_neg_fbmn.csv, sirius_classif_neg.csv, sirius_compID_neg.csv. To use with script "algal metabolites MS2_FBMN_neg".R

Over the past decades, human impacts have changed the structure of tropical benthic reef communities towards coral depletion and macroalgal proliferation. However, how these changes have modified chemical and microbial waterscapes is poorly known. Here, we assessed how the experimental removal of macroalgal assemblages influences the chemical and microbial composition of two reef boundary layers, the benthic and the momentum. Chemical and microbial waterscapes were spatially structured, both horizontally and vertically, according to macroalgal dominance and boundary layers. Microbes associated with reef degradation were enriched in the boundary layers surrounding macroalgal-dominated substrata. Dominant macroalgae were surrounded by a distinct chemical pool of diverse lipid classes (e.g., diterpenoids and glycerolipids) and labile organic matter (e.g., organooxygen compounds), which diffused from algal tissues to boundary layers according to their polarity. Finally, our results highlighted strong co-variations between specific algal-derived metabolites and planktonic microbes, giving insight into their roles in coral reef functioning and resilience.