Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts

Four species of marine sponges were collected from Davies Reef at 4 - 9m depths. Four biological replicates of each of Carteriospongia foliascens, Cliona orientalis, Coscinoderma matthewsi, Ircinia ramosa, Pericharax heteroaphis, and Stylissa flabelliformis were placed into separated plastic bags filled with seawater and brought to the surface. Following collection, part of the tissue from each specimen was immediately preserved in 70% ethanol for species classification and the remaining tissue was snap-frozen in liquid nitrogen. Following sample preparation the LC-MS/MS spectrometry data were processed and annotated following the EMP method Computational methods for Release 2 and the EMP Multi-omics project (EMP500). Available from: https://github.com/biocore/emp/blob/master/methods/methods_release2.md.The mass spectra and the spectral matching results are accessible with the Metabolomics USI interface using the GNPS job ID and the corresponding MF id (e.g., X4151 corresponds to the scan/cluster number 4151). The computational annotations of putative small peptides, which can be classified as level 2/3 annotation (putative/partial structure) based on MSI standards [59], were performed using the DEREPLICATOR algorithm v.1.2.8Mass spectrometry data were deposited on the MassIVE public repository under the accession MSV000083475. See Zhang et al. 2022 for futher details.

本研究从戴维斯礁（Davies Reef）4~9米水深处采集了6种海洋海绵，分别为叶状卡特海绵（Carteriospongia foliascens）、东方穿孔海绵（Cliona orientalis）、马修斯壳海绵（Coscinoderma matthewsi）、分支海绵（Ircinia ramosa）、异口围皮海绵（Pericharax heteroaphis）及扇形斯氏海绵（Stylissa flabelliformis），每个物种设置4个生物学重复样本。将各重复样本置于装有天然海水的独立密封塑料袋中，运回海面。
样本抵达后，立即取每个样本的部分组织置于70%乙醇中保存，用于后续物种分类鉴定；剩余组织则通过液氮快速冷冻保存。
样本制备完成后，参照地球微生物组计划（Earth Microbiome Project, EMP）第二版计算方法及EMP多组学项目（EMP500）的标准流程，对液相色谱-串联质谱（Liquid Chromatography-Tandem Mass Spectrometry, LC-MS/MS）数据进行处理与注释。相关方法文档可通过以下链接获取：https://github.com/biocore/emp/blob/master/methods/methods_release2.md。
质谱数据及谱图匹配结果可通过代谢组学USI（Metabolomics USI）界面，结合全球天然产物社交分子网络（Global Natural Products Social Molecular Networking, GNPS）任务ID及对应的MF ID进行检索查询，例如X4151对应扫描/聚类编号4151。
基于代谢组学标准倡议（Metabolomics Standards Initiative, MSI）标准[59]，可将注释结果划分为2/3级注释（推定结构/部分结构）；本研究使用DEREPLICATOR v1.2.8算法完成潜在小肽的计算注释。所有质谱数据已上传至公共数据库MassIVE，登录编号为MSV000083475。
更多详细信息可参考Zhang等人2022年发表的相关研究。