skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Deciphering ocean carbon in a changing world

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
 [1]; ORCiD logo [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [4];  [2];  [1]; ORCiD logo [11];  [12];  [2];  [13]
  1. Univ. of Georgia, Athens, GA (United States)
  2. Woods Hole Oceanographic Institution, Woods Hole, MA (United States)
  3. Univ. of Georgia, Savannah, GA (United States)
  4. Univ. of Washington, Seattle, WA (United States)
  5. Univ. of California, San Diego, La Jolla, CA (United States)
  6. Univ. of Tennessee, Knoxville, TN (United States)
  7. Oregon State Univ., Corvallis, OR (United States)
  8. Univ. of California, San Diego, La Jolla, CA (United States);
  9. Columbia Univ., Palisades, NY (United States)
  10. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  11. Univ. of Oldenburg, Oldenburg (Germany)
  12. Univ. Pierre et Marie Curie (France)
  13. Univ. of Chicago, Chicago, IL (United States)

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. The cycling of DOM over short and long time scales has profound impacts on the quantity of carbon sequestered in the oceans and the foundations of the food webs that support ocean life. At the heart of this cycle lie molecular-level relationships between the individual molecules in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have defied clear definition and study because both DOM and microbial communities consist of many thousands of individual components. Emerging tools in analytical chemistry, microbiology and informatics are breaking down the barriers to a fuller appreciation of these connections. Furthermore, we highlight questions that are being addressed using this new toolkit and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1254576
Report Number(s):
PNNL-SA-114532; KP1704020
Journal Information:
Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, Issue 12; ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 177 works
Citation information provided by
Web of Science

References (144)

Photo-lability of deep ocean dissolved black carbon journal January 2012
Diatom exudates influence metabolism and cell growth of co-cultured diatom species journal September 2009
Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton journal January 2012
Evidence for a persistent microbial seed bank throughout the global ocean journal March 2013
ABC transporters: one, two or four extracytoplasmic substrate-binding sites? journal October 2002
Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea: Drivers of DMSP degradation and DMS production journal February 2012
Microbial oceanography of the dark ocean's pelagic realm journal June 2009
Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria journal January 2013
Effect of nutrient amendments on bacterioplankton production, community structure, and DOC utilization in the northwestern Sargasso Sea journal January 2002
Impact of CO2 enrichment on organic matter dynamics during nutrient induced coastal phytoplankton blooms journal January 2014
Projected expansion of the subtropical biome and contraction of the temperate and equatorial upwelling biomes in the North Pacific under global warming journal February 2011
Recalcitrant Dissolved Organic Carbon Fractions journal January 2013
2,3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase journal February 2010
Marine sequestration of carbon in bacterial metabolites journal March 2015
High-field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter journal January 2013
Multiple B-vitamin depletion in large areas of the coastal ocean journal July 2012
Major role of planktonic phosphate reduction in the marine phosphorus redox cycle journal May 2015
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss journal March 2012
Interactions among dissolved organic carbon, microbial processes, and community structure in the mesopelagic zone of the northwestern Sargasso Sea journal July 2004
Major role of bacteria in biogeochemical fluxes in the ocean's interior journal March 1988
Bioinformatics: The Next Frontier of Metabolomics journal November 2014
Emergent Biogeography of Microbial Communities in a Model Ocean journal March 2007
Marine viruses — major players in the global ecosystem journal October 2007
Inefficient microbial production of refractory dissolved organic matter in the ocean journal June 2015
Concentrations, turnover rates and fluxes of polyamines in coastal waters of the South Atlantic Bight journal December 2014
The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana Reveal a Diverse Phosphorus Stress Response journal March 2012
Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon journal March 2010
Marine snow, organic solute plumes, and optimal chemosensory behavior of bacteria journal August 2001
The radiocarbon signature of microorganisms in the mesopelagic ocean journal April 2009
Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon journal April 2006
Molecular formulae of marine and terrigenous dissolved organic matter detected by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry journal July 2005
Families of transmembrane sugar transport proteins journal February 2000
Dissolved combined amino acids: Chemical form and utilization by marine bacteria journal September 1993
Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium journal October 2012
High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Humic and Fulvic Acids:  Improvements and Comparisons journal January 2002
Bacterial Taxa That Limit Sulfur Flux from the Ocean journal October 2006
Advanced characterization of marine dissolved organic matter by combining reversed-phase liquid chromatography and FT-ICR-MS journal September 2008
Global trends in the fluorescence characteristics and distribution of marine dissolved organic matter journal September 2011
Microbial structuring of marine ecosystems journal October 2007
High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures journal May 2015
Presence of dissolved nucleotides in the North Pacific Subtropical Gyre and their role in cycling of dissolved organic phosphorus journal January 2005
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea journal August 2010
Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark journal June 2015
Aerobic production of methane in the sea journal June 2008
Seasonality and vertical structure of microbial communities in an ocean gyre journal June 2009
Competition between photochemical and biological degradation of dissolved organic matter from the cyanobacteria Microcystis aeruginosa : Degradation of journal April 2015
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean journal December 2010
Mass spectral molecular networking of living microbial colonies journal May 2012
Carbon fluxes through estuarine bacteria reflect coupling with phytoplankton journal August 2013
Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species journal April 2015
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior journal January 2006
Graphical Method for Analysis of Ultrahigh-Resolution Broadband Mass Spectra of Natural Organic Matter, the Van Krevelen Diagram journal October 2003
Structure and function of the global ocean microbiome journal May 2015
A microbial source of phosphonates in oligotrophic marine systems journal September 2009
Radiocarbon in dissolved organic matter in the central North Pacific Ocean journal November 1987
Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers journal September 2014
Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria journal February 2014
Identification of the algal dimethyl sulfide-releasing enzyme: A missing link in the marine sulfur cycle journal June 2015
Characterizing dissolved organic matter fluorescence with parallel factor analysis: a tutorial: Fluorescence-PARAFAC analysis of DOM journal November 2008
Organic matter transformations in the upper mesopelagic zone of the North Pacific: Chemical composition and linkages to microbial community structure: ORGANIC MATTER IN THE UPPER MESOPELAGIC journal January 2012
An intercomparison of three methods for the large-scale isolation of oceanic dissolved organic matter journal April 2014
Characterization of a major refractory component of marine dissolved organic matter journal June 2006
Release of ecologically relevant metabolites by the cyanobacterium S ynechococcus elongatus  CCMP 1631 : Metabolomics of journal July 2015
Synthesis of Methylphosphonic Acid by Marine Microbes: A Source for Methane in the Aerobic Ocean journal August 2012
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea journal September 2008
Microbial degradation of dissolved proteins in seawater1: Protein degradation journal November 1983
A major biopolymeric component to dissolved organic carbon in surface sea water journal May 1997
Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters journal July 2014
Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean journal July 2010
Hidden cycle of dissolved organic carbon in the deep ocean journal November 2014
Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria journal May 2015
Determination of sugars in unconcentrated seawater and other natural waters by liquid chromatography and pulsed amperometric detection. journal January 1992
Potential for phosphite and phosphonate utilization by Prochlorococcus journal October 2011
Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean journal September 2011
Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction journal February 2010
Illuminating the dark matter in metabolomics journal October 2015
Searching molecular structure databases with tandem mass spectra using CSI:FingerID journal September 2015
Bacterivory and herbivory: Key roles of phagotrophic protists in pelagic food webs journal September 1994
Metabolic dependencies drive species co-occurrence in diverse microbial communities journal May 2015
Molecular dissection of bacterial acrylate catabolism - unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production journal February 2010
Aged black carbon identified in marine dissolved organic carbon: AGED BLACK CARBON IN MARINE DOC journal August 2010
Comparative genomics and mutagenesis analyses of choline metabolism in the marine R oseobacter clade : Choline metabolism in Roseobacters journal August 2015
Microbial Extracellular Enzymes and the Marine Carbon Cycle journal January 2011
Climate Change Impacts on Marine Ecosystems journal January 2012
Net community production of dissolved organic carbon journal September 1998
Determinants of community structure in the global plankton interactome journal May 2015
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes journal January 2015
Multiyear increases in dissolved organic matter inventories at Station ALOHA in the North Pacific Subtropical Gyre journal January 2002
Dissolved organic matter composition and photochemical transformations in the northern North Pacific Ocean: North Pacific Ocean DOM journal February 2015
Closely related phytoplankton species produce similar suites of dissolved organic matter journal March 2014
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment journal December 2004
Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray: Transcription of sulfur genes by Roseobacter communities journal September 2010
Radiocarbon analysis of neutral sugars in high-molecular-weight dissolved organic carbon: Implications for organic carbon cycling journal March 2006
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone journal September 2013
The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater: The response of prokaryotes to DOM in seawater journal May 2014
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource journal November 2010
Thermogenic organic matter dissolved in the abyssal ocean journal December 2006
Marine Photochemistry of Organic Matter book October 2014
Metagenomic Approaches for Exploiting Uncultivated Bacteria as a Resource for Novel Biosynthetic Enzymology journal May 2013
Utilization of amino acids by planktonic marine bacteria: Importance of clean technique and low substrate additions1,2: Amino acids and bacteria journal March 1984
Evidence for dissolved organic nitrogen and phosphorus uptake during a cyanobacterial bloom in Florida Bay journal January 2004
The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis journal February 2011
Molecular mechanisms underlying roseobacter–phytoplankton symbioses journal June 2010
The Crystal Structure of UehA in Complex with Ectoine—A Comparison with Other TRAP-T Binding Proteins journal May 2009
Single-taxon field measurements of bacterial gene regulation controlling DMSP fate journal February 2015
Genomic perspectives in microbial oceanography journal September 2005
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data journal October 2012
Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade journal August 2012
Constraining the 2-component model of marine dissolved organic radiocarbon journal August 2010
Ocean Warming–Acidification Synergism Undermines Dissolved Organic Matter Assembly journal February 2015
SAR11 marine bacteria require exogenous reduced sulphur for growth journal March 2008
Mass spectrometry of natural products: current, emerging and future technologies journal January 2014
Direct use of high molecular weight polysaccharide by heterotrophic flagellates journal September 1988
Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP journal February 2016
Marine Microbes See a Sea of Gradients journal November 2012
Bifurcated Degradative Pathway of 3-Sulfolactate in Roseovarius nubinhibens ISM via Sulfoacetaldehyde Acetyltransferase and (S)-Cysteate Sulfolyase journal July 2009
Get the most out of your metagenome: computational analysis of environmental sequence data journal October 2007
Annual flux of dissolved organic carbon from the euphotic zone in the northwestern Sargasso Sea journal September 1994
Viral lysis of Phaeocystis pouchetii: Implications for algal population dynamics and heterotrophic C, N and P cycling journal January 2009
Cryptic carbon and sulfur cycling between surface ocean plankton journal December 2014
Genomic and functional adaptation in surface ocean planktonic prokaryotes journal November 2010
Detection of glycolate oxidase gene glcD diversity among cultured and environmental marine bacteria journal October 2006
Genome Streamlining in a Cosmopolitan Oceanic Bacterium journal August 2005
Microbial uptake of dissolved organic matter in Mcmurdo Sound, Antarctica journal January 1981
A heat-induced molecular signature in marine dissolved organic matter journal February 2009
Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom journal May 2012
The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA journal February 2009
Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle journal January 2014
The organic complexation of iron in the marine environment: a review journal January 2012
Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean journal April 2014
Viral lysis of Micromonas pusilla: impacts on dissolved organic matter production and composition journal April 2013
Ocean's least productive waters are expanding journal January 2008
Dilution limits dissolved organic carbon utilization in the deep ocean journal March 2015
Stimulated Bacterial Growth under Elevated pCO2: Results from an Off-Shore Mesocosm Study journal June 2014
Effects of ocean acidification on marine dissolved organic matter are not detectable over the succession of phytoplankton blooms journal October 2015
Refining 31P nuclear magnetic resonance spectroscopy for marine particulate samples: Storage conditions and extraction recovery journal December 2005
Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition journal December 2013
Gene-centric approach to integrating environmental genomics and biogeochemical models journal January 2014
Natural Organic Matter and the Event Horizon of Mass Spectrometry journal December 2008
A new class of homoserine lactone quorum-sensing signals journal June 2008
Expression patterns reveal niche diversification in a marine microbial assemblage journal August 2012
Metabolism of dimethylsulfoniopropionate and glycine betaine by a marine bacterium journal September 1992
High abundance of virulence gene homologues in marine bacteria journal June 2009
Chitinases from Uncultured Marine Microorganisms journal June 1999

Cited By (52)

Impact of CO 2 on the elemental composition of the particulate and dissolved organic matter of marine diatoms emerged after nitrate depletion journal April 2018
Time‐series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems journal January 2020
Interactive effects on organic matter processing from soils to the ocean: are priming effects relevant in aquatic ecosystems? journal June 2018
Metabolome response to anthropogenic contamination on microalgae: a review journal December 2019
Dissolved Organic Matter Composition in a Marsh‐Dominated Estuary: Response to Seasonal Forcing and to the Passage of a Hurricane journal June 2019
Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre journal January 2018
Universal molecular structures in natural dissolved organic matter journal August 2018
Impact of Anthropogenic Organic Matter on the Distribution Patterns of Sediment Microbial Community from the Yangtze River, China journal July 2019
Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuary Synechococcus culture journal January 2019
Unveiling the enigma of refractory carbon in the ocean journal February 2018
Evolving paradigms in biological carbon cycling in the ocean journal July 2018
Alpha- and beta-mannan utilization by marine Bacteroidetes: Marine mannan utilization journal October 2018
Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters journal March 2019
Ammonia‐oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean journal August 2019
The microbial contribution to reactive oxygen species dynamics in marine ecosystems: Abiotic and biotic sources and sinks of ROS journal March 2018
On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South Pacific Gyre journal May 2019
Accurate Quantification of Laminarin in Marine Organic Matter with Enzymes from Marine Microbes journal February 2017
Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass Spectrometry journal December 2019
Ocean Acidification Experiments in Large-Scale Mesocosms Reveal Similar Dynamics of Dissolved Organic Matter Production and Biotransformation journal September 2017
Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics journal February 2018
Marine Bacterial Diversity in Coastal Sichang Island, the Upper Gulf of Thailand, in 2011 Wet Season journal June 2019
Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions journal January 2018
Seagrass‐associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration journal September 2019
Tree‐DOM: Dissolved organic matter in throughfall and stemflow journal February 2018
Resource heterogeneity structures aquatic bacterial communities journal May 2019
Significance estimation for large scale metabolomics annotations by spectral matching journal November 2017
Dissolved organic matter uptake by Trichodesmium in the Southwest Pacific journal January 2017
Ecological drivers of bacterial community assembly in synthetic phycospheres journal February 2020
Cross‐protection from hydrogen peroxide by helper microbes: the impacts on the cyanobacterium Prochlorococcus and other beneficiaries in marine communities journal February 2018
Dissolved organic sulfur in the ocean: Biogeochemistry of a petagram inventory journal October 2016
Where Carbon Goes When Water Flows: Carbon Cycling across the Aquatic Continuum journal January 2017
Formation of Chromophoric Dissolved Organic Matter by Bacterial Degradation of Phytoplankton-Derived Aggregates journal January 2018
Large Diversity and Original Structures of Acyl-Homoserine Lactones in Strain MOLA 401, a Marine Rhodobacteraceae Bacterium journal June 2017
Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment journal July 2017
Mixotrophic metabolism by natural communities of unicellular cyanobacteria in the western tropical South Pacific Ocean text January 2018
Crustacean zooplankton release copious amounts of dissolved organic matter as taurine in the ocean: Dissolved free taurine in oceanic waters journal June 2017
Fluorescent organic exudates of corals and algae in tropical reefs are compositionally distinct and increase with nutrient enrichment journal March 2018
Molecular characteristics of microbially mediated transformations of Synechococcus ‐derived dissolved organic matter as revealed by incubation experiments journal May 2019
Dissolved organic matter uptake by Trichodesmium in the Southwest Pacific text January 2017
The role of differential DMSP production and community composition in predicting variability of global surface DMSP concentrations journal October 2018
Isotopic composition of oceanic dissolved black carbon reveals non-riverine source journal November 2019
Mixotrophic metabolism by natural communities of unicellular cyanobacteria in the western tropical South Pacific Ocean: Mixotrophy in natural marine cyanobacteria journal April 2018
Toward a Regional Classification to Provide a More Inclusive Examination of the Ocean Biogeochemistry of Iron-Binding Ligands journal February 2017
High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter journal December 2017
Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation journal December 2018
A New Glider-Compatible Optical Sensor for Dissolved Organic Matter Measurements: Test Case from the NW Mediterranean Sea journal March 2017
Global Observing Needs in the Deep Ocean journal May 2019
Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments journal May 2018
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes journal March 2020
Ancestral Function and Diversification of a Horizontally Acquired Oomycete Carboxylic Acid Transporter journal April 2018
Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation text January 2019
Microbially-Mediated Transformations of Estuarine Dissolved Organic Matter journal March 2017