Water mass specific genes dominate the Southern Ocean microbiome

These data correspond to co-abundant groups of AGNOSTOS clusters (CAGs) catalogs, annotations and abundance matrices obtained from 218 metagenomes sampled during the Antarctic Circumpolar Expedition (ACE). The methodology and results obtained using these data are presented in the study entitled Water mass specific genes dominate the Southern Ocean microbiome, by Faure et al. (2025).Here is a description of each catalog/dataset :Metadata_CTD_ACE_clean: Environmental metadata for CTD samples.Metadata_UDW_ACE_clean: Environmental metadata for UDW samples.Metadata_GeneMat_KNNimputed.rds: Environmental data for metagenomics samples, after imputation of missing values.CAGs_T60MAX_FL_RSquared10.txt: Catalog of CAGs, linking every env-AGC (AGC with random forest R-squared above 10%, see the study for more details) from the small size fraction to its CAG.CAGs_T60MAX_ATT_RSquared15.txt: Catalog of CAGs, linking every env-AGC (AGC with random forest R-squared above 15%, see the study for more details) from the large size fraction to its CAG.GM_CAGs_T60MAXGQ_transposed_NZVuniquecut20_FL_RSquared10.tsv.gz: CAG-level matrix of coverage, focusing on CAGs from the free-living size fraction (0.2-3 and 0.2-40 µm). CAG = cluster of co-abundant AGNOSTOS gene clusters, please refer to Faure et al. for methods details on the clustering. In this matrix, each line corresponds to one sample and each column corresponds to on CAG, as identified in the Annotation matrix. Cells contain the sum of AGNOSTOS cluster-level coverage values for each CAG.GM_CAGs_T60MAXGQ_transposed_NZVuniquecut20_ATT_RSquared15.tsv.gz: CAG-level matrix of coverage, focusing on CAGs from the >3µm size-fraction. In this matrix, each line corresponds to one sample and each column corresponds to on CAG, as identified in the Annotation matrix. Cells contain the sum of AGNOSTOS cluster-level coverage values for each CAG.FuncEnrich.tar.gz: Folder containing functional enrichment tests outputs for each CAG of interest discussed in Faure et al. (please refer to the study for more details on the methodology).TaxoCags_UniRef90.tar.gz: Folder containing taxonomic annotations of CAGs of interest discussed in Faure et al. based on Uniref90 using MMSeqs2, please refer to the study for more details on the methodology.TaxoCags_GTDB.tar.gz: Folder containing taxonomic annotations of CAGs of interest discussed in Faure et al. based on GTDB using Kraken2, please refer to the study for more details on the methodology.Annotations_SAR11_CAGs.tar: Folder containing annotations specific to the three SAR11-related CAGs displayed in our study, including FeGenie outputs.Other relevant files for our study can all be found on Zenodo under DOI 10.5281/zenodo.14181291