{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/muestrasProteomicayOTUSagostocopia.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/checksum.txt"],"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/PUASquantify3replicasmsf.msf"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Control_CC_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/DD15_PT_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Control_PT_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix15_CC_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix500_PT_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix500_CC_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix500_CC_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Control_CC_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Control_PT_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/DD15_PT_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix15_PT_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/DD15_CC_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Control_CC_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix500_CC_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix500_PT_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Control_PT_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix15_CC_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix15_PT_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/DD15_CC_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/DD15_PT_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix500_PT_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix15_CC_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/DD15_CC_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/Mix15_PT_1.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/todas_medium.fasta"],"Mztab":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075100/PUAS_quantify3replicasmsf.mzTab"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["franciscojavier.fernandez@gm.uca.es"],"submitter":["ALMUDENA ESCOBAR NIÑO"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["polyunsaturated aldehydes","phycosphere","Proteomics","Diatom-bacteria interactions; microbial ecology; polyunsaturated aldehydes; phycosphere","Diatom-bacteria interactions","microbial ecology"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075100"],"sample_protocol":["Extraction of proteins was performed by means of ultrasonication with Ultrasonic homogenizer Vibra cell 75185 (Sonics & Materials, Inc., distributed by Cole‑Parmer, United States). A 2 mL mixture of bacterial suspension and lysis buffer (1:1 ratio; Tris 0.2 M, 8% SDS, 80 mM DTT, and Pierce Protease Inhibitor Mini Tablets, EDTA-free, Thermo A32955) was subjected to ultrasonication in three cycles of 20 s each at 75% amplitude, 130 W, and 20 Hz, with samples kept on ice to prevent overheating. Sam-ples were transferred into 15 ml falcon tubes and centrifuged at 15,000 g for 5 min. The supernatant (protein extract) was pipetted into fresh tubes, mixed with 4 volumes of cold acetone and stored at -80˚C overnight. Protein pellet was obtained by centrifuging samples at 15,000 g for 10 min. Protein pellet was resuspended in 0.2 mL of denaturing buffer (8 M urea, 100 mM Tris-HCl pH 8.5, 5 mM DTT). Protein concentrations were determined using the Qubit Protein Assay kit (Thermo Scientific™, USA) following the manufacturer’s instructions).  Protein digestion was performed using the small-scale FASP protocol described by 29Escobar-Nino et al. (2023). Briefly, the protein pellet was reduced for 30 min at room temperature in denaturing buffer. An aliquot of 50 μg protein, diluted in UA buffer (8 M urea, 100 mM Tris-HCl pH 8.5), was added to a 30 kDa cutoff filter (Vivacon 500, VN01H22; Sartorius, Germany) and centrifuged at 14,000 g for 10 min. The filter was washed with 450 μL UA buffer at 14,000 g for 10 min. Proteins were alkylated for 30 min in the dark with 100 μL CAA solution (55 mM chloroacetamide, 8 M urea, 100 mM Tris-HCl pH 8.5). After centrifugation at 14,000 g for 10 min, the filter was washed twice with 450 μL UA buffer. Protein digestion was carried out with 0.5 μg trypsin (Pierce Trypsin MS-Grade, 90057, Thermo Scientific, USA) in 450 μL dilution solution (100 mM Tris-HCl pH 8.5, 1 mM CaCl₂) at 37 °C overnight. Peptides were col-lected by centrifuging the filter at 14,000 g for 10 min and acidified with 20% TFA (fi-nal concentration 0.5%). Digested Peptide were desalted using C18 solid-phase extraction columns (Pierce 89873, Thermo Scientific™, Waltham, USA) according to the manufacturer’s instruc-tions. Eluted peptides were dried in a vacuum concentrator (Vacufuge Vacuum Con-centrator 5301 Centrifuge; Eppendorf, Germany) for 40 min. The peptide pellet was resuspended in 25 μL solubilization buffer (0.1% formic acid / 0.02% DDM [n-dodecyl β-D-maltoside]), and peptide concentration was measured using a Nanodrop 2000 (Thermo Scientific™, Waltham, USA). Finally, the peptide solution was diluted to 0.5 μg μL-1, and 2 μL were used for LC-MS analysis. Peptides solution were separated using a Vanquish Neo liquid chromatography system (Thermo Scientific, USA) with a PepMap RSLC C18 column (2 µm, 100 Å, 75 µm inner diameter, 50 cm) (Thermo Scientific, USA). Peptides were separated on a. Peptides were loaded onto the column and eluted over 43 minutes using a segmented linear gradient from 1% to 97.5% of solvent B (0 min: 1% B; 0–10 min: 20% B; 10–20 min: 22.5% B; 20–35 min: 45% B; 35–36.1 min: 97.5% B; 36.1-43 min: 97.5% B) (sol-vent A: 0.1% Formic Acid; solvent B: 80% Acetonitrile, 0.1% Formic Acid) at a flow rate of 300 nL min-1. Mass spectra were acquired by an Orbitrap Exploris 240 mass spectrometer (Thermo Scientific, USA) in data-dependent acquisition (DDA) mode using a TOP15 method. MS spectra were obtained in the Orbitrap Exploris 240 analyzer (Thermo Sci-entific, USA) in full-scan mode, with a mass range of 350–1500 m/z, a resolution of 120,000 FWHM, an AGC target of 300%, and a maximum injection time of 60 ms. Pre-cursors were selected with an isolation window of 1.6 m/z. HCD fragmentation was performed with a normalized collision energy of 30%. MS/MS spectra were acquired with a standard AGC target at a resolution of 15,000 FWHM, a maximum injection time of 30 ms, and a fixed first mass of m/z 100. Peptides with a charge state of +1, greater than +6, or with unassigned charge were excluded from MS2 fragmentation. A dynamic exclusion of 30 s prevented repeated selection of precursors."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["A custom bacterial protein sequence database was generated using a two-step sequential reduction strategy. In the first search, raw mass spectrometry data were processed with Proteome Discoverer (v3.1.1.93). MS/MS spectra were analyzed in sets of ten using the Sequest search engine against UniProtKB protein databases (downloaded March 24, 2025) corresponding to bacterial groups previously identified by OTU analyses, including Actinomycetes, Alphaproteobacteria, Bdellovibrionales, Candidatus Kaiserbacteriota, Cyanobacteriota, Gammaproteobacteria, Bacteroidia, Pirellulaceae, Cytophagales, Acidimicrobiia, Sphingobacteriales, Verrucomicrobiales, Flavobacteriales, Planctomycetota, Bacillales, Lactobacillales, Balneolales, Fusobacteriales, Saccharimonadales, Chlamydiales, and Parcubacteria. Proteomes of Thalassiosira oceanica and Thalassiosira pseudonana were also included to exclude proteins derived from the culture medium.  Trypsin was set as the digestion enzyme with a minimum peptide length of six amino acids. Variable modifications included methionine oxidation, N-terminal protein acetylation, and methionine loss, while carbamidomethylation of cysteine was set as a fixed modification. Peptide scores were recalibrated using the Percolator node with a target/decoy strategy to estimate identification probabilities and control the false discovery rate (FDR). In this consensus workflow, peptides with FDR < 5% were accepted, proteins required at least one identified peptide, and all peptides were considered regardless of peptide-spectrum match (PSM) number. Shared peptides were retained for all matching proteins rather than assigned only to the highest-scoring protein. Resulting FASTA files from each taxonomic group were merged using the “Compile Fasta Database” tool to generate a taxon-specific database. This database was used in a second search under the same parameters, increasing peptide identification confidence to medium (FDR ≤ 5%).  FASTA files generated for bacterial and diatom proteins in the second step were used for the final search together with a contaminant database.  Protein identification and label-free quantification were performed in Proteome Discoverer 3.1.1.93 using the Processing Workflow PWF_Hybrid_Precursor_Quant_and_LFQ_MPS_SequestHP_Percolator and the Consensus Workflow CWF_Comprehensive_Enhanced_Annotation_LFQ_and_Precursor_Quan. Raw files were calibrated with the Spectrum File RC node and features detected using the Minora Feature Detector. Digestion and modification settings were as described above. Peptides were retained at FDR ≤ 1%. Quantification was conducted with the Precursor Ion Quantifier node, considering unique and razor peptides, with precursor abundance based on intensity. Only features detected in 100% of replicates were included. Protein abundances were calculated by summing peptide abundances and normalized to total peptide abundance per sample.  Differential abundance was assessed using background-based t-tests. Adjusted p-values were calculated using the Benjamini–Hochberg procedure to control FDR, and significance was set at adjusted p ≤ 0.05. Databases used for identification included those generated in the reduction step and a list of common contaminants from The Global Proteome Machine (TheGPM).  Exclusive proteins were defined as those detected in all three biological replicates of one condition and absent in all replicates of the compared condition. Absent proteins were those undetected in one condition but present in all replicates of the other. Proteins were considered upregulated when the abundance ratio was ≥ 2 and downregulated when ≤ 0.5.  Finally, functional annotation was performed using OmicsBox v3.0.29, including BLAST searches, Gene Ontology mapping and annotation, UniProt annotation, and KEGG and BRITE classification."],"omics_type":["Proteomics"],"labhead":["Francisco Javier Fernández Acero"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["University of Cádiz/IVAGRO"],"species":["Bacteria"],"publication":["10.3389/FMICB.2026.1838042"],"submitter_mail":["almudena.escobar@uca.es"],"submitter_affiliation":["University of Cadiz"],"submitter_country":["Spain"],"doi":["10.6019/PXD075100"],"additional_accession":[]},"is_claimable":false,"name":"Polyunsaturated aldehydes induce distinct proteomic responses in two diatom-associated bacterial communities","description":"Diatom-derived polyunsaturated aldehydes (PUAs) significantly influence marine bacterial dy-namics, yet the underlying proteomic mechanisms remain elusive. We employed high-resolution comparative proteomics to decipher the functional reprogramming of two bacterial communi-ties—one naturally associated with a PUA-producing diatom (N-community) and another with a non-PUA producer (I-community)—under ecologically relevant PUA exposure. While growth rates and cell densities remained unaffected, indicating an absence of acute toxicity, proteomics revealed pronounced community-specific reorganization. N-communities displayed stable, regula-tion-oriented adjustments consistent with physiological accommodation, whereas I-communities exhibited dose-dependent stress responses, shifting toward protein repair and antioxidant defense. Our findings demonstrate that PUAs trigger profound proteomic reprogramming conditioned by the communities' prior ecological history. This functional divergence provides a molecular basis for understanding bacterial fitness and succession during diatom blooms, where PUA-mediated in-teractions could act as a selective filter shaping the phycosphere's microbial landscape. Polyunsaturated aldehydes (PUA) produced by diatoms have been proposed to exert a wide range of effects on marine bacteria, from inhibitory or stress-inducing responses to neutral or potentially beneficial effects. However, the bacterial proteomic responses remain elusive. Here, we employed a high-resolution comparative proteomic approach to decipher the functional reprogramming of two distinct bacterial communities under ecologically relevant PUA exposure. One community was composed by bacteria naturally associated with a PUA-producing diatom (N- communy and, a second community associated with a non-PUA-producing diatom (I-community). Bacterial growth rates and final cell densities were not significantly affected by any treatment, indicating the absence of toxic effects even at high PUA concentrations. Dissolved organic carbon consumption did not provide evidence that PUA was the relevant carbon source. Interestingly, comparative proteomic analyses revealed pronounced community-specific reorganization in response to PUA expo-sure.Our results show that PUAs trigger a profound proteomic reprogramming rather than a simple stress response. While I-community prioritized antioxidant defense and protein repair, N-community showed a metabolic shift towards energy conservation. These findings suggest that the metabolic history of bacterial assemblages determines their success in the phycosphere, providing a molecular basis for microbial succession during diatom blooms.","dates":{"publication":"2026-06-04","submission":"2026-03-02"},"accession":"PXD075100","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:260201","NEWT:35554","NCBITaxon:12939","NEWT:32046","NEWT:544496","NEWT:59529","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:10245","NEWT:55153","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:351581","NEWT:43186","NEWT:428146","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:661410","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:1401257","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7719","NEWT:7959","NEWT:2261","NEWT:868565","NEWT:94323","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:192875","NEWT:1214915","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:284218","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:5763","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NEWT:5757","NEWT:68415","NCBITaxon:4563","NEWT:5755","NEWT:44688","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:347256","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:145458","NEWT:633149","NEWT:1149786","NEWT:10239","NEWT:68895","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:72901","NEWT:213863","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1235816","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:1772","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:11988","NEWT:284812","NEWT:8175","NEWT:400667","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:459758","NEWT:3702","NEWT:1245466","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:586722","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:274","NEWT:7070","NCBITaxon:287","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1303443","NEWT:9483","NEWT:333760","NEWT:34607","NEWT:56636","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:81077","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NEWT:34613","NCBITaxon:4932","NEWT:109760","NEWT:29031","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:886559","NEWT:3750","NEWT:55521","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:1130798","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:561007","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:203696","NEWT:472","NEWT:352472","NEWT:97441","NEWT:1071661","NEWT:1202531","NEWT:1202532","NEWT:360094","NEWT:1408223","NEWT:470","NEWT:1408224","NEWT:41364","NEWT:5911","NEWT:1313","NEWT:1218097","NEWT:1080348","NCBITaxon:50557","NEWT:1314","NEWT:39251","NEWT:39491","NEWT:212142","NCBITaxon:5811","NEWT:29491","NEWT:101841","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:688333","NEWT:215402","NCBITaxon:548681","NEWT:318586","NCBITaxon:5820","NEWT:1547","NEWT:272634","NEWT:198107","NEWT:9031","NEWT:27292","NEWT:1872122","NEWT:1308","NEWT:7091","NEWT:1034015","NEWT:760568","NEWT:141262","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:3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