Trichodesmium metagenome file for protein identification (Anderson et al., 2025)

Supplementary dataset, supplementary tables, and supplementary figures for Anderson et al. (2025), 'Trichodesmium protein abundance patterns reflect the influence of resource availability across ocean regions'. Supplementary dataset: Three metagenomes sequenced from picked Trichodesmium colonies in the North Atlantic, North Pacific, and South Pacific ocean basins were combined into this reference metagenome. Reference was concatenated by Dr. Kyle Frischkorn. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifier PXD057942 and doi: 10.6019/PXD057942. 'all_3_t_metaG.faa' -- fasta file containing all 3 concatenated metagenomes (translated contigs) '3_metag_kegg.txt' -- text file containing KEGG KO annotations of contigs Supplementary tables: 'Supplementary_Tables.xlsx' Table S1: Sample metadata. Table S2: Sampling details and citations for metagenomes used to build the metagenome reference database. Table S3: Protein spectral counts and UniProt and KEGG annotations. Table S4: Marker protein list with UniProt and Tery IDs, literature citations, and putative functions. Table S5: List of putative Fe-P co-stress markers (Fig. S2) which were upregulated in Trichodesmium IMS101 under Fe-P co-stress culture relative to replete conditions (Walworth et al., 2016, Supplemental Data 3) and which were detected in all three ocean regions in this study. Table S6: P and Fe stress signals by sample (Fig. 4). Table S7: KEGG submodule designations of KEGG-annotated Trichodesmium protein spectra used to generate heatmap (Fig. 2b). KEGG submodule designation is detailed in SI methods. Supplementary figures: 'Figure_S1.pdf'; Figure S1: Correspondence analysis of spectral counts of only Trichodesmium proteins detected in all three regions. Explanatory variables are included based on significance determined from vector analysis. DIP and dFe values are co-located with metaproteome samples except for North Atlantic dFe values, which were calculated as an average of past transect data (Table S1; see Rouco et al. (2018)). 'Figure_S2.pdf'; Figure S2: Putative Fe-P co-stress signal metric displayed at the regional level. Putative Fe-P co-stress marker proteins (Table S5) were determined to be upregulated in T. erythraeum IMS101 under Fe-P co-stress relative to replete conditions, and were not regulated by either Fe or P single stress relative to replete conditions (Walworth et al, 2016). Differences between regions were not significant (P>0.05) based on Kolmogorov-Smirnov testing. 'Figure_S3.pdf'; Figure S3: Pearson correlations of spectral counts (Table S3) of (A) P stress marker proteins (Table S4) and NifH spectral counts and (B) Fe stress marker proteins (Table S4) and NifH spectral counts across all samples. Significance (P<0.05) is denoted by asterisks. Only stress marker proteins detected in all three ocean regions studied here and used in the stress signal analysis are included in the correlation. Code for figures, intermediate data products, and statistics for (Anderson et al., in process) is available on GitHub and uses the Supplementary tables here.