The following repo hosts information and code generated on behalf of the Center for Chemical Currencies of a Microbial Planet's DeepDOM Data Integration Project.
Deep Dissolved Organic Matter (DOM) otherwise known as DeepDOM is the name for a cruise (deployment KN210-04, https://www.bco-dmo.org/deployment/59057) that was conducted across the Western Atlantic Ocean (starting at Montevideo, Uruguay and ending at Bridgetown, Barbados) in 2013. Here is the cruise report for the DeepDOM cruise: KN210-04 cruise report.pdf
The science objectives of this cruise included:
- Characterizing deep ocean dissolved organic matter in water masses of the western Atlantic Ocean.
- Characterizing microbial community at select sampling stations and depths.
- Characterizing metabolic capabilities of surface, mesopelagic, and bathypelagic microbial consortia vis-a-vis the degradation of organic matter from each zone.
- Examining metabolic and phylogenetic links between microbes in different marine zones (surface, meso-pelagic and bathypelagic depths).
Seawater samples were collected using the following methods to investigate the science objectives shown above:
- Collecting discrete water samples using Niskin-bottles.
- Collecting microbial communities from these water samples, by in-situ pumping, or by net-traps and net-tows.
- Conducting incubation experiments in lab and on deck.
- Conducting mass spectrometry and flow cytometry underway, using the vessel's seawater intake.
The purpose of this README file is to provide links to all the relevant metadata and data files in one location to aid training, exploration, and integration efforts for the the C-CoMP DeepDOM Data Integration exercise. The datasets are presented below:
Data description and summary: This data table contains a record of measurements collected by CTD sensors over the course of the cruise. Header fields include: station #, date, lat, lon, depth, pressure, temperature, salinity, O2 concentrations, density, turbidity, par, spar. 74 discrete casts were conducted at 23 separate stations. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
BCO-DMO Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/481167
Data description and summary: The cruise event log includes metadata about all sample collections or 'events' that took place during the cruise. Header fields include: instrument, action, station, cast #, lat, lon, seafloor, author, and comment. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
Cruise Event Data Table: http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/Deep_Atlantic_DOM/event_log.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/Deep_Atlantic_DOM/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/Deep_Atlantic_DOM/event_log%7D
BCO-DMO Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/456062
Data description and summary: This dataset includes 20 microbial metaproteomes from DeepDOM Station 2 that were collected at 10 depths. Samples were collected by McLane Pump and filtered onto GFF as well as GF75 glass filters and frozen at -80C until analysis (one GFF and one GF75 filter per depth). See the PRIDE project webpage (https://www.ebi.ac.uk/pride/archive/projects/PXD034035) and BCO-DMO dataset (https://www.bco-dmo.org/dataset/875622) for more method details. File name identifiers include DeepDOM station (st2), size fraction (GFF or GF75), and depth (e.g. 507 meters). Lead PI: Mak Saito, Woods Hole Oceanographic Institution
Processed data is underway, but raw data is available at PRIDE under the accession number: PXD034035 and is linked at BCO-DMO. The PRIDE FTP download page is here: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD034035
Data description and summary: Inorganic and organic nurient concentrations were measured in seawater collected from Niskin bottles. Measurements include phosphate, nitrate+nitrite, silicate, nitrite, ammonium, non-purgeable organic carbon, and total nitrogen concentrations. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
DeepDOM Nutrient Data Table: DeepDOM_nutrients.txt
BCO-DMO Nutrient Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/473302
Data description and summary: This dataset contains dissolved metabolite abundances from seawater samples collected during the R/V Knorr cruise KN210-04 between 29 Mar 2013 and 06 May 2013 along the eastern coast of South America. Sample depth, lat, lon, station, time, and cast are from CTD profiles are also included in this dataset. Targeted Metabolites have been corrected for extraction efficiency, but detection limits for the instrument (TSQ) need to be considered during data analysis. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
DeepDOM Targeted Metabolite Abundances (Dissolved) Data Table:DeepDOM_metabolites_dissolved.txt
BCO-DMO DeepDOM Targeted Metabolite Abundances (Dissolved) Data Table Link: http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/Deep_Atlantic_DOM/metabolites_dissolved.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/Deep_Atlantic_DOM/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/Deep_Atlantic_DOM/metabolites_dissolved%7D
BCO-DMO DeepDOM Targeted Metabolite Abundances (Dissolved) Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/700032
Raw files are available at the MetaboLights repository under study MTBLS1752: https://www.ebi.ac.uk/metabolights/MTBLS1752/files and are indicated with the key word 'exometabolome'
Data description and summary: This dataset contains particulate metabolite abundances from seawater samples collected during the R/V Knorr cruise KN210-04 between 29 Mar 2013 and 06 May 2013 along the eastern coast of South America. Sample depth, lat, lon, station, time, and cast are from CTD profiles are also included in this dataset. Some of these data are published Kujawinski et al., 2017. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
DeepDOM Targeted Metabolite Abundances (Particulate) Data Table: DeepDOMmetabolites_particulate.txt
BCO-DMO DeepDOM Targeted Metabolite Abundances (Particulate) Data Table Link: http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/Deep_Atlantic_DOM/metabolites_particulate.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/Deep_Atlantic_DOM/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/Deep_Atlantic_DOM/metabolites_particulate%7D
BCO-DMO DeepDOM Targeted Metabolite Abundances (Particulate) Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/700045
Raw files are available at the MetaboLights repository under study MTBLS1752: https://www.ebi.ac.uk/metabolights/MTBLS1752/files and are indicated with the key word 'endometabolome'
Data description and summary: This dataset includes 25 samples collected from various depths across 4 stations (2,7,15,23) that were measured using untargeted metabolomics in negative ionization mode using 7 T FT-ICR mass spectrometer (both direct infusion and liquid chromatography in some cases). See Longnecker et al. 2020 (doi: https://doi.org/10.1002/lol2.10149) for more information. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
The data are available on MetaboLights using the study numbers MTBLS1024 (https://www.ebi.ac.uk/metabolights/MTBLS1024/files) and MTBLS6735 (https://www.ebi.ac.uk/metabolights/MTBLS6735/files).
Data Description and summary: Holm et al. 2022 includes 104 (100 samples + 4 blanks) samples collected during the DeepDOM cruise. Lipids were extracted from 0.22 um pore-sized membranes and analyzed using high performance liquid chromotagraphy coupled with electrospray ionization high-resolution accurate-mass spectrometry. See Holm et al. 2022 for more methods and results. Lead PI: Benjamin Van Mooy, Woods Hole Oceanographic Institution
The data are available on MetaboLights using the study number MTBLS2838 (https://www.ebi.ac.uk/metabolights/MTBLS2838/descriptors) and DeepDOM samples include the identifier KN210_4 in the second field of the sample names.
Data description and summary: This dataset contains the concentration of total organic sulfur in seawater from samples collected during the R/V Knorr cruise KN210-04 between 29 Mar 2013 and 06 May 2013 along the eastern coast of South America. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
DeepDOM Organic Sulfur Concentrations Data Table: DeepDOM_TOS.txt
BCO-DMO DeepDOM Organic Sulfur Concentrations Data Table Link: http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/Deep_Atlantic_DOM/TOS.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/Deep_Atlantic_DOM/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/Deep_Atlantic_DOM/TOS%7D
BCO-DMO DeepDOM Organic Sulfur Concentrations Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/745542
Data description and summary: Viral and bacterial counts from filtered water, stained with SYBR Green and counted using epifluorescent microscopy. Duplicates were collected at each depth during the KN210-04 cruise. Lead PI: Ian Hewson, Cornell University
BCO-DMO Viral and Bacterial Counts Data Table: DeepDOM_viral_bact_counts.txt
BCO-DMO Viral and Bacterial Counts Data Table Link: http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/Deep_Atlantic_DOM/viral_bact_counts.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/Deep_Atlantic_DOM/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/Deep_Atlantic_DOM/viral_and_bacterial_counts%7D
BCO-DMO Viral and Bacterial Counts Dataset Landing Page: https://www.bco-dmo.org/dataset-deployment/528518
Data description and summary: This dataset includes 91 metatranscriptomes collected at 7 intermediate and 4 mega DeepDOM stations at discrete sampling depths. Seawater samples (8 L volume) were pre-filtered with 2.7 um GF/D filters and biomass was collected from 0.2 um PVDF sterivex filters (see Cavaco et al. 2022 and the cruise report for methods). File names include the DeepDOM station number, sampling depth (250) or water mass (DCM), filter replicate (either A or B), and the analysis type (metaT). Lead PI: Steven Hallam, Univeristy of British Columbia
Data description and summary: This dataset includes 20 metagenomes collected at 3 mega stations at discrete sampling depths. Seawater samples (20 L volume) were pre-filtered with 2.7 um GF/D filters and biomass was collected from 0.2 um PVDF sterivex filters (see Cavaco et al. 2022 and the cruise report for methods). File names include DeepDOM station number, water mass (e.g. NADW), sampling depth in meters (750m), and filter replicate (either A or B). Lead PI: Steven Hallam, Univeristy of British Columbia
Data description and summary: This dataset includes 184 16S rRNA gene amplicon sequencing samples that were processed using the Joint Genome Institute's (JGI) iTagger pipeline v2.0 (https://jgi.doe.gov/wp-content/uploads/2016/06/DOE-JGI-iTagger-methods.pdf). Seawater samples (2 L volume) were filtered with 0.2 um PVDF Sterivex filters (no pre-filtering, see Cavaco et al. 2022 and the cruise report for methods). File names include DeepDOM station number followed by either sampling depth (e.g. 250 meters) or water mass (e.g. AAIW).
Metatranscriptomes, metagenomes, and amplicon (16S rRNA gene sequencing) samples can be accessed under the NCBI Umbrella BioProject PRJNA805279: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA805279
For your convenience, BioProject accession numbers, datastream, file identifiers (inferred from the 'Title' field published on NCBI), and SRA links to individual samples are provided in this spreadsheet: DeepDOM_NCBI_MGX_MTX_Amplicon.xlsx
Data description and summary: This dataset includes 12 polyA selected eukaryotic metatranscriptomes (2 samples from the 5 um size fraction; 10 from the 0.2 um size fraction) sequenced from surface seawater at 10 of the DeepDOM intermediate and mega stations. This dataset also includes 3 trap samples from various stations. Lead PI: Sonya Dyhrman, Columbia University
Raw files and other associated files can be accessed and downloaded in the Joint Genome Institute (JGI) Genome Portal (https://genome.jgi.doe.gov/portal/) by searching using the key word deepdom. For your convenience, direct links to each sample (and associated files) are provided here DeepDOM_EukmetaT_surface.xlsx under the JGI_project_link column header.
Predation and Viral Lysis Experiment: Intracellular Metabolites in Marine Microorganisms during an Experiment Evaluating Microbial Mortality
Paper:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142611/ (Longnecker and Kujawinski, 2020).
Study description (from MetaboLights): This project considers the effects of predation and viral lysis on the metabolites found in the surface ocean. Using seawater from the surface ocean, we experimentally manipulated levels of predation and viral lysis. At the beginning and end of the experiment, we sampled the intracellular and extracellular metabolites. The extracts were analyzed using liquid chromatography-based targeted and untargeted metabolomics methods that we have modified for use with marine samples. Lead PI: Liz Kujawinski, Co-PI: Krista Longnecker
Sample Data Table on MetaboLights: https://www.ebi.ac.uk/metabolights/MTBLS461/samples
Metadata ('ISA Metadata') and Targeted and Untargeted metabolomics files (raw): https://www.ebi.ac.uk/metabolights/MTBLS461/files
Cavaco, M. A., M. P. Bhatia, A. K. Hawley, M. Torres-Beltrán, W. M. Johnson, K. Longnecker, K. Konwar, E. B. Kujawinski and S. J. Hallam (2022). Pathway-centric analysis of microbial metabolic potential and expression along nutrient and energy gradients in the western Atlantic Ocean Front Mar Sci 9. doi: https://www.frontiersin.org/articles/10.3389/fmars.2022.867310/full
Durkin, C. A., M. L. Estapa and K. O. Buesseler (2015). Observations of carbon export by small sinking particles in the upper mesopelagic. Mar Chem 175: 72-81. doi: https://doi.org/10.1016/j.marchem.2015.02.011
Durkin, C. A., B. A. S. Van Mooy, S. T. Dyhrman and K. O. Buesseler (2016). Sinking phytoplankton associated with carbon flux in the Atlantic Ocean. Limnol Oceanogr 61: 1172-1187. doi: https://doi.org/10.1002/lno.10253
Eggleston, E. M. and I. Hewson (2016). Abundance of Two Pelagibacter ubique Bacteriophage Genotypes along a Latitudinal Transect in the North and South Atlantic Oceans. Front Microbiol 7. doi: https://doi.org/10.3389/fmicb.2016.01534
Hoarfrost, A. and C. Arnosti (2017). Heterotrophic Extracellular Enzymatic Activities in the Atlantic Ocean Follow Patterns Across Spatial and Depth Regimes. Front Mar Sci 4(200). doi: https://doi.org/10.3389/fmars.2017.00200
Howard, E. M., C. A. Durkin, G. M. M. Hennon, F. Ribalet and R. H. R. Stanley (2017). Biological production, export efficiency, and phytoplankton communities across 8000 km of the South Atlantic. Glob Biogeochem Cycle 31(7): 1066-1088. doi: https://doi.org/10.1002/2016GB005488
Hurley, S. J., F. J. Elling, M. Könneke, C. Buchwald, S. D. Wankel, A. E. Santoro, J. S. Lipp, K.-U. Hinrichs and A. Pearson (2016). Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy. Proc Natl Acad Sci USA 113(28): 7762-7767. doi: https://doi.org/10.1073/pnas.151853411
Hurley, S. J., J. S. Lipp, H. G. Close, K.-U. Hinrichs and A. Pearson (2018). Distribution and export of isoprenoid tetraether lipids in suspended particulate matter from the water column of the Western Atlantic Ocean. Organic Geochemistry 116: 90-102. doi: https://doi.org/10.1016/j.orggeochem.2017.11.010
Johnson, W. M., K. Longnecker, M. C. Kido Soule, W. A. Arnold, M. P. Bhatia, S. J. Hallam, B. A. S. Van Mooy and E. B. Kujawinski (2020). Metabolite composition of sinking particles differs from surface suspended particles across a latitudinal transect in the South Atlantic. Limnol Oceanogr 65: 111-127. doi: https://doi.org/10.1002/lno.11255
Johnson, W. M., M. C. Kido Soule, K. Longnecker, M. P. Bhatia, S. J. Hallam, M. W. Lomas and E. B. Kujawinski (accepted). Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean. Limnology and Oceanography doi: https://doi.org/10.1002/lno.12275
Lohmann, R., E. Markham, J. Klanova, P. Kukucka, P. Pribylova, X. Gong, R. Pockalny, T. Yanishevsky, C. C. Wagner and E. M. Sunderland (2021). Trends of Diverse POPs in Air and Water Across the Western Atlantic Ocean: Strong Gradients in the Ocean but Not in the Air. Environ Sci Technol 55(14): 9498-9507. doi: https://doi.org/10.1021/acs.est.0c04611
Longnecker, K., L. Oswald, M. C. K. Soule, G. A. Cutter and E. B. Kujawinski (2020). Organic sulfur: a spatially variable and understudied component of marine organic matter. Limnol Oceanogr Lett 5: 305-312. doi: https://doi.org/10.1002/lol2.10149
Longnecker, K. and E. B. Kujawinski (2020). Intracellular metabolites in marine microorganisms during an experiment evaluating microbial mortality. Metabolites 10(3): 105. doi: 10.3390/metabo10030105
Motta, L. C., J. D. Blum, B. N. Popp, J. C. Drazen and H. G. Close (2020). Mercury stable isotopes in flying fish as a monitor of photochemical degradation of methylmercury in the Atlantic and Pacific Oceans. Mar Chem 223: 103790. doi: https://doi.org/10.1016/j.marchem.2020.103790
Rocke, E., M. G. Pachiadaki, A. Cobban, E. B. Kujawinski and V. P. Edgcomb (2015). Protist community grazing on prokaryotic prey in deep ocean water masses. PLoS One 10(4): e0124505. doi: https://doi.org/10.1371/journal.pone.0124505
- Holm, H. C., H. F. Fredricks, S. M. Bent, D. P. Lowenstein, J. E. Ossolinski, K. W. Becker, W. M. Johnson, K. Schrage and B. A. S. V. Mooy (2022). Global ocean lipidomes show a universal relationship between temperature and lipid unsaturation. Science 376(6600): 1487-1491. doi: DOI: https://doi.org/10.1126/science.abn7455
- Kido Soule, M. C., K. Longnecker, W. M. Johnson and E. B. Kujawinski (2015). Environmental metabolomics: analytical strategies. Mar Chem 177, Part 2: 374-387.doi: https://doi.org/10.1016/j.marchem.2015.06.029
- Kujawinski, E. B., K. Longnecker, H. Alexander, S. T. Dyhrman, C. L. Fiore, S. T. Haley and W. M. Johnson (2017). Phosphorus availability regulates intracellular nucleotide pools in marine eukaryotic phytoplankton. Limnol Oceanogr Lett 2: 119-129. doi: https://doi.org/10.1002/lol2.10043
- Longnecker, K., J. Futrelle, E. Coburn, M. C. Kido Soule and E. B. Kujawinski (2015). Environmental metabolomics: databases and tools for data analysis. Mar Chem 177, Part 2: 366-373. doi: https://doi.org/10.1016/j.marchem.2015.06.012
- Longnecker, K. and E. B. Kujawinski (2017). Mining mass spectrometry data: Using new computational tools to find novel organic compounds in complex environmental mixtures. Organic Geochemistry 110: 92-99. doi: https://doi.org/10.1016/j.orggeochem.2017.05.008
- Saw, J. H. W., T. Nunoura, M. Hirai, Y. Takaki, R. Parsons, M. Michelsen, K. Longnecker, E. B. Kujawinski, R. Stepanauskas, Z. Landry, C. A. Carlson and S. J. Giovannoni (2020). Pangenomics analysis reveals diversification of enzyme families and niche specification in globally abundant SAR202 bacteria. mBio 11(1): e02975-02919. doi: 10.1128/mBio.02975-19
Check out the website that the students and postdocs generated during the cruise: http://deep-dom.blogspot.com/