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本研究于法属波利尼西亚莫雷阿岛（Mo‘orea）泻湖开展，旨在探究大型海藻（macroalga）*Dictyota bartayresiana*对珊瑚*Pocillopora acuta*的竞争效应。本研究通过控制性野外实验，测试了互作类型（直接接触与近距离毗邻）及主导水流（海藻上游与下游区域）对珊瑚共生体（holobiont）及其关联近表层海水的微生物组与代谢组组成的影响。此外，本研究通过对比珊瑚群体的顶端与侧边断枝，探究了珊瑚群体内部不同位置对微生物组与代谢组的效应差异。所有珊瑚共生体于2020年10月至12月间接受为期3个月的实验处理。 微生物组数据通过NovaSeq 6000平台的16S rRNA扩增子测序（16S rRNA amplicon sequencing）获得；代谢组数据则通过Q-Exactive Plus Orbitrap质谱仪在正离子模式下开展非靶向代谢组学（untargeted metabolomics）分析（LC-MS/MS）获得。 ### 数据与文件结构说明 本数据集仓库结构化分为两组： - data文件夹：存放原始与处理后/汇总数据，进一步分为微生物组（micro）、代谢组（metab）与多组学（multiomic）三个子文件夹。 - scripts文件夹：存放分析脚本与图片合成代码（figures.R）。 #### 微生物组分析 ##### 原始数据 - seqtab.rds：原始扩增子序列变体（Amplicon Sequence Variant, ASV）丰度表 - taxa_NS.rds：分类学表 - sampleMetadata.csv：元数据文件 ##### 处理后数据 - ps.filt.rds：可直接用于分析的标准化phyloseq对象 - raw_asv_count.xlsx：各样本ASV计数及其分类学注释信息 - vip_blast_seq.xlsx：用于BLAST比对搜索的扩增子序列 - ASVsampleGroup_trmt_meanprop.xlsx：各组ASV平均相对丰度表，用于Cytoscape可视化 分析脚本：coral_microbiome_final.Rmd #### 代谢组分析 ##### 原始数据 - coralendosw_pos_fbmn.xlsx：包含分子网络与推定注释的基于特征的分子网络（Feature-Based Molecular Networking, FBMN）数据 - siriusclass_coral_pos.xlsx：通过SIRIUS软件获得的代谢物推定注释分类结果 - siriusform_coral_pos.xlsx：通过SIRIUS软件获得的代谢物推定分子式 ##### 处理后数据 - ms1_pos_df.csv：过滤后可直接用于分析的MS1特征峰峰面积数据 - ms2_pos_df.csv：过滤后可直接用于分析的整合MS2碎裂谱的MS1特征峰峰面积数据 - MS_sampleGroup_trmt_meanprop.xlsx：各组代谢物平均相对丰度表，用于Cytoscape网络可视化 分析脚本：coral_metabolome_final.Rmd #### 多组学分析 ##### 处理后数据 - endo_df_corr.xlsx：微生物组数据 - msendo_corr.xlsx：代谢组数据 分析脚本：coral_multiomic_clean.Rmd #### 水流数据与风玫瑰图 - 数据文件：current_Papetoai_20250415-20250417_002 - 分析脚本：script_windrose.R ### 代码与软件 所有分析脚本均基于R 4.2.3版本编写。