#METABOLOMICS WORKBENCH uchimiya_20231029_183756 DATATRACK_ID:4427 STUDY_ID:ST002954 ANALYSIS_ID:AN004851 VERSION 1 CREATED_ON 11-07-2023 #PROJECT PR:PROJECT_TITLE Metabolite flux from temperature-acclimated diatom strains PR:PROJECT_SUMMARY The temperature increase occurring in the surface ocean has fundamental PR:PROJECT_SUMMARY implications for physiological rates and processes of marine microbes. Here we PR:PROJECT_SUMMARY asked whether the temperature at which a marine diatom strain is acclimated PR:PROJECT_SUMMARY affects carbon transfer to a co-cultured heterotrophic bacterium. Model systems PR:PROJECT_SUMMARY were established in which the diatom Thalassiosira pseudonana was acclimated for PR:PROJECT_SUMMARY three months at temperatures below (14°C), equal to (20°C), and above (28°C) PR:PROJECT_SUMMARY the temperature of optimal growth, and then inoculated with the heterotrophic PR:PROJECT_SUMMARY bacterium Ruegeria pomeroyi. This Project contains results obtained from main PR:PROJECT_SUMMARY and drawdown experiments. PR:INSTITUTE University of Georgia PR:LAST_NAME Uchimiya PR:FIRST_NAME Mario PR:ADDRESS 315 Riverbend Rd, Athens, GA, 30602, USA PR:EMAIL mario.uchimiya@uga.edu PR:PHONE (706) 542-8387 PR:PROJECT_COMMENTS See also Metabolomics Workbench_UGA_temp_Oct2023_drawdown.docx for details about PR:PROJECT_COMMENTS this deposition. PR:DOI http://dx.doi.org/10.21228/M88B0T #STUDY ST:STUDY_TITLE Metabolite flux from temperature-acclimated diatom strains (drawdown experiment) ST:STUDY_SUMMARY The temperature increase occurring in the surface ocean has fundamental ST:STUDY_SUMMARY implications for physiological rates and processes of marine microbes. Here we ST:STUDY_SUMMARY asked whether the temperature at which a marine diatom strain is acclimated ST:STUDY_SUMMARY affects carbon transfer to a co-cultured heterotrophic bacterium. Model systems ST:STUDY_SUMMARY were established in which the diatom Thalassiosira pseudonana was acclimated for ST:STUDY_SUMMARY three months at temperatures below (14°C), equal to (20°C), and above (28°C) ST:STUDY_SUMMARY the temperature of optimal growth, and then inoculated with the heterotrophic ST:STUDY_SUMMARY bacterium Ruegeria pomeroyi. This deposition is for results obtained from a ST:STUDY_SUMMARY drawdown experiment of phytoplankton metabolites using R. pomeroyi conducted ST:STUDY_SUMMARY during this study. ST:INSTITUTE University of Georgia ST:LABORATORY Moran Lab, Edison Lab ST:LAST_NAME Uchimiya ST:FIRST_NAME Mario ST:ADDRESS 315 Riverbend Rd, Athens, GA, 30602, USA ST:EMAIL mario.uchimiya@uga.edu ST:PHONE (706) 542-8387 ST:SUBMIT_DATE 2023-10-29 #SUBJECT SU:SUBJECT_TYPE Plant SU:SUBJECT_SPECIES Thalassiosira pseudonana SU:TAXONOMY_ID 296543 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T0_1 Temperature:14 | Time point:0 RAW_FILE_NAME=114; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=14°C T0; Biological replicate=1 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T0_2 Temperature:14 | Time point:0 RAW_FILE_NAME=116; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=14°C T0; Biological replicate=2 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T0_3 Temperature:14 | Time point:0 RAW_FILE_NAME=103; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=14°C T0; Biological replicate=3 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T0_4 Temperature:14 | Time point:0 RAW_FILE_NAME=117; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=14°C T0; Biological replicate=4 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T10_1 Temperature:14 | Time point:10 RAW_FILE_NAME=120; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=14°C T10; Biological replicate=1 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T10_2 Temperature:14 | Time point:10 RAW_FILE_NAME=108; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=14°C T10; Biological replicate=2 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T10_3 Temperature:14 | Time point:10 RAW_FILE_NAME=113; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=14°C T10; Biological replicate=3 SUBJECT_SAMPLE_FACTORS Drawdown experiment 14_T10_4 Temperature:14 | Time point:10 RAW_FILE_NAME=104; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=14°C T10; Biological replicate=4 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T0_1 Temperature:20 | Time point:0 RAW_FILE_NAME=110; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=20°C T0; Biological replicate=1 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T0_2 Temperature:20 | Time point:0 RAW_FILE_NAME=102; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=20°C T0; Biological replicate=2 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T0_3 Temperature:20 | Time point:0 RAW_FILE_NAME=106; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=20°C T0; Biological replicate=3 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T0_4 Temperature:20 | Time point:0 RAW_FILE_NAME=109; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=20°C T0; Biological replicate=4 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T10_1 Temperature:20 | Time point:10 RAW_FILE_NAME=107; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=20°C T10; Biological replicate=1 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T10_2 Temperature:20 | Time point:10 RAW_FILE_NAME=118; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=20°C T10; Biological replicate=2 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T10_3 Temperature:20 | Time point:10 RAW_FILE_NAME=112; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=20°C T10; Biological replicate=3 SUBJECT_SAMPLE_FACTORS Drawdown experiment 20_T10_4 Temperature:20 | Time point:10 RAW_FILE_NAME=122; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=20°C T10; Biological replicate=4 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T0_1 Temperature:28 | Time point:0 RAW_FILE_NAME=121; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=28°C T0; Biological replicate=1 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T0_2 Temperature:28 | Time point:0 RAW_FILE_NAME=123; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=28°C T0; Biological replicate=2 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T0_3 Temperature:28 | Time point:0 RAW_FILE_NAME=105; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=28°C T0; Biological replicate=3 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T0_4 Temperature:28 | Time point:0 RAW_FILE_NAME=124; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, at inoculation of bacteria; Sample descritpion=28°C T0; Biological replicate=4 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T10_1 Temperature:28 | Time point:10 RAW_FILE_NAME=111; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=28°C T10; Biological replicate=1 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T10_3 Temperature:28 | Time point:10 RAW_FILE_NAME=115; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=28°C T10; Biological replicate=3 SUBJECT_SAMPLE_FACTORS Drawdown experiment 28_T10_4 Temperature:28 | Time point:10 RAW_FILE_NAME=119; Dataset type=Endometabolome; Organism=Filtered lysate from phytoplankton, marine diatom, Thalassiosira pseudonana CCMP1335, after 10 h of inoculation with bacteria; Sample descritpion=28°C T10; Biological replicate=4 #COLLECTION CO:COLLECTION_SUMMARY 1 mL of subsamples were collected in 1.5-mL tubes at the incubation periods of 0 CO:COLLECTION_SUMMARY and 10 hours for NMR analyses. CO:COLLECTION_PROTOCOL_FILENAME 2_Collection protocol_UGA_temp_Oct2023_drawdown.docx CO:SAMPLE_TYPE Algae CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Axenic cultures (1 L in L1 media, 35 ppt) of the diatom Thalassiosira pseudonana TR:TREATMENT_SUMMARY CCMP1335 were grown at different temperatures of 14, 20, and 28°C under 120 TR:TREATMENT_SUMMARY µmol photons m-2 s-1 (ULM-500 Light Meter, Walz) and a 16:8 h light:dark cycle TR:TREATMENT_SUMMARY (four replicates for each treatment). They were harvested in late exponential TR:TREATMENT_SUMMARY growth phase by filtration onto 2.0 µm Isopore filters (1 L) and stored at TR:TREATMENT_SUMMARY -20°C for later experimentation. Diatom cells were rinsed from filters into 10 TR:TREATMENT_SUMMARY mL sterile L1 media, sonicated to lyse cells for 20 min, and passed through a TR:TREATMENT_SUMMARY pre-combusted GF/F filter. R. pomeroyi was inoculated into 2.7 mL of the TR:TREATMENT_SUMMARY endometabolome samples (3 x 107 cells mL-1) and grown for 10 h. TR:TREATMENT_PROTOCOL_FILENAME 3_Treatment protocol_UGA_temp_Oct2023_drawdown.docx #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 540-µL of subsamples were mixed with 60-µL of a phosphate buffer (30 mmol L-1 SP:SAMPLEPREP_SUMMARY phosphate in deuterated water; pH 7.4; 1 mmol L-1 internal standard SP:SAMPLEPREP_SUMMARY 2,2-dimethyl-2-silapentane-5-sulfonate) and transferred to NMR tubes. One SP:SAMPLEPREP_SUMMARY media-blank sample was also included. SP:SAMPLEPREP_PROTOCOL_FILENAME 4_Sample preparation protocol_UGA_temp_Oct2023_drawdown.docx #CHROMATOGRAPHY #ANALYSIS AN:ANALYSIS_TYPE NMR AN:ANALYSIS_PROTOCOL_FILE 5_Analysis protocol_UGA_temp_Oct2023_drawdown.docx AN:SOFTWARE_VERSION TopSpin version 3.5 #NMR NM:INSTRUMENT_NAME AVANCE III HD instrument (Bruker) NM:INSTRUMENT_TYPE FT-NMR NM:NMR_EXPERIMENT_TYPE 2D-1H-13C NM:SPECTROMETER_FREQUENCY 600 MHz #NMR_METABOLITE_DATA NMR_METABOLITE_DATA:UNITS Intensity NMR_METABOLITE_DATA_START Samples 14_T0_1 14_T0_2 14_T0_3 14_T0_4 14_T10_1 14_T10_2 14_T10_3 14_T10_4 20_T0_1 20_T0_2 20_T0_3 20_T0_4 20_T10_1 20_T10_2 20_T10_3 20_T10_4 28_T0_1 28_T0_2 28_T0_3 28_T0_4 28_T10_1 28_T10_3 28_T10_4 Factors Temperature:14 | Time point:0 Temperature:14 | Time point:0 Temperature:14 | Time point:0 Temperature:14 | Time point:0 Temperature:14 | Time point:10 Temperature:14 | Time point:10 Temperature:14 | Time point:10 Temperature:14 | Time point:10 Temperature:20 | Time point:0 Temperature:20 | Time point:0 Temperature:20 | Time point:0 Temperature:20 | Time point:0 Temperature:20 | Time point:10 Temperature:20 | Time point:10 Temperature:20 | Time point:10 Temperature:20 | Time point:10 Temperature:28 | Time point:0 Temperature:28 | Time point:0 Temperature:28 | Time point:0 Temperature:28 | Time point:0 Temperature:28 | Time point:10 Temperature:28 | Time point:10 Temperature:28 | Time point:10 Ala 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Asp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 beta-1_3-glucan 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Betaine 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Choline 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 DHPS 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 DMSP 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 G3P 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Gln 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Glu 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Gly 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Homarine 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Ile 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 leucine 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Lys 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Pro 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 NMR_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name pubchem_id inchi_key kegg_id other_id other_id_type ri ri_type moverz_quant Ala 5950 Asp 5960 beta-1,3-glucan Betaine 247 Choline 305 DHPS DMSP G3P 439162 Gln 5961 Glu 33032 Gly 750 Homarine 3620 Ile 6306 leucine 6106 Lys 5962 Pro 145742 METABOLITES_END #END