{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001372","ANALYSIS_ID":"AN002290","VERSION":"1","CREATED_ON":"May 5, 2020, 1:21 pm"},

"PROJECT":{"PROJECT_TITLE":"Patterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: North Pacific Subtropical Gyre depth profile","PROJECT_TYPE":"Marine Metabolomics","PROJECT_SUMMARY":"In the surface ocean, carbon is fixed by phytoplankton and respired by the entire marine community at an astonishingly high rate. At any point in time, the difference between these two processes yields a carbon pool in surface particles that is a combination of both freshly fixed and partially degraded material. On a molecular level, we have a limited knowledge of the small molecules, or metabolites, within this pool. Specific metabolites have been shown to be responsible for fueling respiration, maintaining organismal interactions, and transferring energy throughout the microbial community. Metabolomics, or the direct observation and quantification of the small molecules that are the result of cellular activity, provides an important lens through which we can begin to assess the standing stocks of small compounds that likely fuel a great deal of heterotrophic activity in the surface ocean. Here we describe community metabolomes of particulate material into the North Pacific Ocean and compare the metabolomes to a variety of phytoplankton grown in the lab. Using both targeted and untargeted metabolomics, we identify metabolites in the particulate carbon pool and explore their latitudinal and phylogenetic distributions. This analysis reveals several compounds that have not been previously recognized as abundant components of the marine organic carbon pool. We found that the community metabolome showed distinct differences between the regimes that likely reflects the phytoplankton community present. The community metabolome in surface waters of the subtropical domain was remarkably consistent even when sampled weeks apart, while the northern regions showed a patichier and less reproducible community metabolome. Some individual compounds showed distinct patterns between oceanographic regimes, including homarine, an abundant molecule that can contribute up to 4% of the total particulate carbon pool in marine surface waters. Glutamic acid and glutamine showed opposite patterns in the oceanographic regimes, suggesting differences in community-level nitrogen assimilation in these different regimes. Overall, this study offers a new perspective into particulate carbon composition in oceanographic research, reveals important carbon pools that may fuel the microbial loop, and suggests an altered community-level nitrogen assimilation capacity over the North Pacific transition zone.","INSTITUTE":"University of Washington","DEPARTMENT":"School of Oceanography","LABORATORY":"Ingalls Lab","LAST_NAME":"Heal","FIRST_NAME":"Katherine","ADDRESS":"1501 NE Boat Street, Marine Science Building, Room G, Seattle, WA, 98195, USA","EMAIL":"kheal@uw.edu","PHONE":"612-616-4840"},

"STUDY":{"STUDY_TITLE":"Patterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: North Pacific Subtropical Gyre depth profile","STUDY_TYPE":"Marine metabolomics depth profile","STUDY_SUMMARY":"In the surface ocean, carbon is fixed by phytoplankton and respired by the entire marine community at an astonishingly high rate. At any point in time, the difference between these two processes yields a carbon pool in surface particles that is a combination of both freshly fixed and partially degraded material. On a molecular level, we have a limited knowledge of the small molecules, or metabolites, within this pool. Specific metabolites have been shown to be responsible for fueling respiration, maintaining organismal interactions, and transferring energy throughout the microbial community. Metabolomics, or the direct observation and quantification of the small molecules that are the result of cellular activity, provides an important lens through which we can begin to assess the standing stocks of small compounds that likely fuel a great deal of heterotrophic activity in the surface ocean. Here we describe community metabolomes of particulate material into the North Pacific Ocean and compare the metabolomes to a variety of phytoplankton grown in the lab. Using both targeted and untargeted metabolomics, we identify metabolites in the particulate carbon pool and explore their latitudinal and phylogenetic distributions. This analysis reveals several compounds that have not been previously recognized as abundant components of the marine organic carbon pool. We found that the community metabolome showed distinct differences between the regimes that likely reflects the phytoplankton community present. The community metabolome in surface waters of the subtropical domain was remarkably consistent even when sampled weeks apart, while the northern regions showed a patichier and less reproducible community metabolome. Some individual compounds showed distinct patterns between oceanographic regimes, including homarine, an abundant molecule that can contribute up to 4% of the total particulate carbon pool in marine surface waters. Glutamic acid and glutamine showed opposite patterns in the oceanographic regimes, suggesting differences in community-level nitrogen assimilation in these different regimes. Overall, this study offers a new perspective into particulate carbon composition in oceanographic research, reveals important carbon pools that may fuel the microbial loop, and suggests an altered community-level nitrogen assimilation capacity over the North Pacific transition zone.","INSTITUTE":"University of Washington","DEPARTMENT":"School of Oceanography","LABORATORY":"Ingalls Lab","LAST_NAME":"Heal","FIRST_NAME":"Katherine","ADDRESS":"1501 NE Boat Street, Marine Science Building, Room G","EMAIL":"kheal@uw.edu","PHONE":"612-616-4840"},

"SUBJECT":{"SUBJECT_TYPE":"Other","SUBJECT_SPECIES":"Natural mixed marine microbial community"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"FilterA",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"A","Type":"Blk","RAW_FILE_NAME":"170410_Blk_FilterBlk_A;170410_Blk_FilterBlk_A;170413_Blk_FilterBlk_A"}
},
{
"Subject ID":"-",
"Sample ID":"FilterB",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"B","Type":"Blk","RAW_FILE_NAME":"170410_Blk_FilterBlk_B;170410_Blk_FilterBlk_B;170413_Blk_FilterBlk_B"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-15m_A",
"Factors":{"Depth_m":"15","Vol_L":"10.7"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"A","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-15m_A;170410_Smp_KM1513-15m_A;170413_Smp_KM1513-15m_A"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-15m_B",
"Factors":{"Depth_m":"15","Vol_L":"10.7"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"B","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-15m_B;170410_Smp_KM1513-15m_B;170413_Smp_KM1513-15m_B"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-15m_C",
"Factors":{"Depth_m":"15","Vol_L":"10.7"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"C","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-15m_C;170410_Smp_KM1513-15m_C;170413_Smp_KM1513-15m_C"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-45m_A",
"Factors":{"Depth_m":"45","Vol_L":"9"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"A","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-45m_A;170410_Smp_KM1513-45m_A;170413_Smp_KM1513-45m_A"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-45m_B",
"Factors":{"Depth_m":"45","Vol_L":"9"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"B","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-45m_B;170410_Smp_KM1513-45m_B;170413_Smp_KM1513-45m_B"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-45m_C",
"Factors":{"Depth_m":"45","Vol_L":"9"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"C","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-45m_C;170410_Smp_KM1513-45m_C;170413_Smp_KM1513-45m_C"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-75m_A",
"Factors":{"Depth_m":"75","Vol_L":"12.7"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"A","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-75m_A;170410_Smp_KM1513-75m_A;170413_Smp_KM1513-75m_A"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-75m_B",
"Factors":{"Depth_m":"75","Vol_L":"12.7"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"B","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-75m_B;170410_Smp_KM1513-75m_B;170413_Smp_KM1513-75m_B"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-75m_C",
"Factors":{"Depth_m":"75","Vol_L":"12.7"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"C","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-75m_C;170410_Smp_KM1513-75m_C;170413_Smp_KM1513-75m_C"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-125m_A",
"Factors":{"Depth_m":"125","Vol_L":"12.17"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"A","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-125m_A;170410_Smp_KM1513-125m_A;170413_Smp_KM1513-125m_A"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-125m_B",
"Factors":{"Depth_m":"125","Vol_L":"12.17"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"B","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-125m_B;170410_Smp_KM1513-125m_B;170413_Smp_KM1513-125m_B"}
},
{
"Subject ID":"-",
"Sample ID":"KM1513-125m_C",
"Factors":{"Depth_m":"125","Vol_L":"12.17"},
"Additional sample data":{"Latitude":"24.5548","Longitude":"-156.3298","UTC":"2015-07-31T19;54;20","Replicate":"C","Type":"Smp","RAW_FILE_NAME":"170410_Smp_KM1513-125m_C;170410_Smp_KM1513-125m_C;170413_Smp_KM1513-125m_C"}
},
{
"Subject ID":"-",
"Sample ID":"April11AqExtractsHalf_1",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"1","Type":"Pool","RAW_FILE_NAME":"170410_Poo_April11AqExtractsHalf_1;170410_Poo_April11AqExtractsHalf_1;170413_Poo_April11AqExtractsHalf_1"}
},
{
"Subject ID":"-",
"Sample ID":"April11AqExtractsHalf_2",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"2","Type":"Pool","RAW_FILE_NAME":"170410_Poo_April11AqExtractsHalf_2;170410_Poo_April11AqExtractsHalf_2;170413_Poo_April11AqExtractsHalf_2"}
},
{
"Subject ID":"-",
"Sample ID":"April11AqExtractsHalf_3",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"3","Type":"Pool","RAW_FILE_NAME":"170410_Poo_April11AqExtractsHalf_3;170410_Poo_April11AqExtractsHalf_3;170413_Poo_April11AqExtractsHalf_3"}
},
{
"Subject ID":"-",
"Sample ID":"April11AqExtractsFull_1",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"1","Type":"Pool","RAW_FILE_NAME":"170410_Poo_April11AqExtractsFull_1;170410_Poo_April11AqExtractsFull_1;170413_Poo_April11AqExtractsFull_1"}
},
{
"Subject ID":"-",
"Sample ID":"April11AqExtractsFull_2",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"2","Type":"Pool","RAW_FILE_NAME":"170410_Poo_April11AqExtractsFull_2;170410_Poo_April11AqExtractsFull_2;170413_Poo_April11AqExtractsFull_2"}
},
{
"Subject ID":"-",
"Sample ID":"April11AqExtractsFull_3",
"Factors":{"Depth_m":"NA","Vol_L":"NA"},
"Additional sample data":{"Latitude":"NA","Longitude":"NA","UTC":"NA","Replicate":"3","Type":"Pool","RAW_FILE_NAME":"170410_Poo_April11AqExtractsFull_3;170410_Poo_April11AqExtractsFull_3;170413_Poo_April11AqExtractsFull_3"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Samples for particulate metabolites were collected from different water depths by niskin bottles attached to a conductivity, temperature, depth array (CTD). Metabolite samples were filtered onto 142 mm 0.2 µm Durapore filters using peristaltic, polycarbonate filter holders, and Masterflex PharMed BPT tubing (Cole-Parmer). Filters were quenched in liquid nitrogen immediately after filtration and stored at -80°C until extraction. Each sample was 30-40 L filtered seawater; each filter was split into three equal parts for triplicate extractions. A blank PTFE filter was extracted alongside samples as a methodological blank.","SAMPLE_TYPE":"Suspended Marine Particulate Matter","STORAGE_CONDITIONS":"Described in summary"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment - this was a study of the natural marine microbial population at different depths in the North Pacific Subtropical Gyre."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, filters were cut up and put into 15 mL teflon centrifuge tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added along with ~2 mL of cold aqueous solvent (50:50 methanol:water) and ~3 mL of cold organic solvent (dichloromethane). The samples were shaken on a FastPrep-24 Homogenizer for 30 seconds and chilled in a -20 °C freezer repeatedly for three cycles of bead-beating and a total of 30 minutes of chilling. The organic and aqueous layers were separated by spinning samples in a centrifuge at 4,300 rpm for 2 minutes at 4 °C. The aqueous layer was removed to a new glass centrifuge tube. The remaining organic fraction was rinsed three more times with additions of 1 to 2 mL of 50:50 methanol:water. All aqueous rinses were combined for each sample and dried down under N2 gas. The remaining organic layer was transferred into a clean glass centrifuge tube and the remaining bead beating tube was rinsed two more times with cold organic solvent. The combined organic rinses were centrifuged, transferred to a new tube, and dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of water. Dried organic fractions were re-dissolved in 380 µL of 1:1 water:acetonitrile. 20 µL of isotope-labeled injection standards in water were added to both fractions. Blank filters were extracted alongside samples as methodological blanks.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"Bligh-Dyer","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"See attached summary","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity I-Class","COLUMN_NAME":"Waters Acquity UPLC HSS Cyano (100 x 2.1mm, 1.8um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"See attached protocol","MS_RESULTS_FILE":"ST001372_AN002290_Results.txt UNITS:Adjusted and normalized peak areas Has m/z:Yes Has RT:Yes RT units:Seconds"}

}