Contact- and water-mediated interactions with an allelopathic macroalga drive distinct coral microbiome and metabolome

In this study, we investigated the competitive effects of the macroalga Dictyota bartayresiana on the coral Pocillopora acuta in the lagoon of Mo‘orea, French Polynesia. By means of a manipulative field experiment, we tested the effects of interaction type (direct contact and close proximity) and prevailing water current (up and downstream of the alga) on the microbiome and metabolome composition of the coral holobiont and its associated near-surface seawater. In addition, we explored whether the effects on the coral microbiome and metabolome vary within colonies by comparing apex and side fragments. Coral holobionts were exposed to the treatment for 3 months between October and December 2020. Microbiome investigated from 16S rRNA samplicon sequencing on a NovaSeq 6000 Metabolome by untargeted metabolomics (LC-MS/MS) on a Q-Exactive Plus Orbitrap in positive ionization mode Description of the data and file structure The repository is stuctured into two groups : data --> with raw and processed/summary data, separated into three folders for microbiome (micro), metabolomic (metab) and multiomic data. scripts --> analytical scripts and figures compilation (figures.R) For microbiome analysis : Raw data : seqtab.rds --> raw ASV abundance table taxa_NS.rds --> taxonomy table sampleMetadata.csv --> metadata file Processed data : ps.filt.rds --> clean phyloseq object readily usable for analysis raw_asv_count.xlsx --> ASV counts across samples with their taxonomy vip_blast_seq.xlsx --> amplicon sequences for BLAST search ASVsampleGroup_trmt_meanprop.xlsx --> mean relative abundances of ASVs across groups for Cytoscape Script --> coral_microbiome_final.Rmd For metabolome analysis : Raw data : coralendosw_pos_fbmn.xlsx --> FBMN data with molecular networks and putative classification siriusclass_coral_pos_xlsx --> Putative classification of metabolites from SIRIUS siriusform_coral_pos_xlsx --> Putative molecular formulas from SIRIUS Processed data : ms1_pos_df.csv --> Peak areas of MS1 features after filtration, readily usable ms2_pos_df.csv --> Peak areas of MS1 features with consensus MS2 fragmentation spectra after filtration, readily usable MS_sampleGroup_trmt_meanprop.xlsx --> mean relative abundances of metabolites for Cytoscape network visualizations Script --> coral_metabolome_final.Rmd For multiomic analysis : Processed data : endo_df_corr.xlsx --> microbiome data msendo_corr.xlsx --> metabolome data Script --> coral_multiomic_clean.Rmd For current data and windrose plot Data --> current_Papetoai_20250415-20250417_002 Script --> script_windrose.R Code/Software Scripts coded on R version 4.2.3