Published January 15, 2024 | Version v2
Dataset Open

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

Authors/Creators

  • 1. ROR icon Centre de Recherches Insulaires et Observatoire de l'Environnement

Contributors

Supervisor:

  • 1. Ecole Pratique des Hautes Etudes
  • 2. ROR icon Centre de Recherches Insulaires et Observatoire de l'Environnement

Description

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

Files

Coral multi-omic response to macroalgal competition.zip

Files (13.1 MB)

Additional details

Funding

Agence Nationale de la Recherche
CoralMates - Uncovering unseen players of coral recruitment for reef conservation ANR-18-CE02-0009
École Pratique des Hautes Études
PhD scholarship

Dates

Created
2024-01-15