Biogeochemistry of Marine Dissolved Organic Matter

1. Why Dissolved Organics Matter: Take 3 – The Messiness of Nature (NEW)
Cindy Lee (State University of New York, USA)
I. Introduction: The DOC-POC continuum
II. Sorption processes
III. Biological lability
IV. Small scale physical-biological interactions
V. Quantification of inputs and removal at interfaces
VI. Air/sea interactions
VII. Change in DOC inventory with climate?
VIII. Closing thoughts
Acknowledgements
References


2. Chemical Characterization and Cycling of Dissolved Organic Matter
Daniel Repeta (Woods Hole Oceanographic Institution, USA)
I. Introduction
II. Isolation of DOM from seawater
III. Chemical characterization of DOM
A. Biopolymers

1. Polysaccharides

2. Proteins

3. Nucleic acids

4. Lipids
B. Humic substances
IV. Links between chemical composition and cycling
A. Introduction
B. Microbial cycling of biopolymers
C. Microbial cycling of humic substances
V. Future research
Acknowledgements
References


3. Metabolites and Small Molecules (NEW)
Elizabeth Kujawinski, Melissa Soule, Krista Longnecker (Woods Hole Oceanographic Institution, USA)
I. Introduction
A. Defining ‘metabolites’ and ‘small molecules’
B. Biologically relevant organic compounds
C. Rapid cycling in marine systems
II. Analytical methods to find metabolites and small molecules in seawater
A. Amines and alcohols
B. Small organic acids
C. Sulfur-containing organic compounds
D. Vitamins
E. Compatible solutes
F. Sugars and amino acids
III. Biogeochemical significance of metabolites and small molecules in seawater
A. Production of metabolites and small molecules by marine primary producers
B. Overflow metabolism and waste byproducts
C. Heterotrophic activity and transfer of compounds across trophic levels
D. Small molecules as signaling molecules
E. Role of grazing, predation, and viral lysis in cycling of metabolites and small molecules
F. Distribution of metabolites and small molecules in marine systems
G. Differences between dissolved and particulate organic matter in marine systems
IV. Summary
Acknowledgements
References


4. Carbon Isotopic Constraints on the Biogeochemistry of Marine DOM
Steven R. Beaupre (Stony Brook University, USA)
I. Introduction
A. A brief introduction to 13C and 14C analyses in marine DOM biogeochemistry.
II. Carbon Isotope Geochemistry Primer
A. Background on carbon isotopic abundances, nomenclature, processes (e.g., origins, radioactive decay, fractionation, mixing, etc…), and context (i.e., dynamic range of d13C scale vs. D14C scale vs. observed ranges in nature, etc…)
B. Processes influencing the incorporation of 13C and 14C into marine DOC.
C. Background information on DIC and its associated isotope ratios.
III. Methods of Analysis
A. Approaches (bulk, size fraction, compound class, etc…) to isotopic analyses with comparisons of their utilities and deficiencies.
B. Laboratory methods.
C. Blank corrections and the fundamental limits to measurement precision
IV. Marine DOC isotopic distributions.
A. The core of this chapter.
B. Presentation, comparison, and interpretation
C. Canonical measurements of isotopic measurements in bulk, size fraction, compound class, compound specific DOC.
D. Isotopic measurements of potential source materials to the marine DOC pool, including DIC, POC, riverine DOC, DOC from hydrothermal fluids, etc…
E. Spatiotemporal distribution and variability of these observations,
F. Vertical vs. horizontal, coastal vs. marine, station specific vs. global scales
G. Daily, seasonal, decadal scales (perhaps some brief discussion of longer, even paleo scales).
H. Non-traditional analyses (e.g., serial oxidations)
I. Range of observed values.
V. Marine DOC isotopic biogeochemistry
A. Synthesis of all the above information, in the context of interpreting DOC biogeochemistry by isotopic observations.
B. Isotopic constraints on the sources, sinks, and persistence of marine DOM.
C. Implications for other parameters (e.g., associated heteroatoms)
VI. Conclusions
A. Synthesis on the current state of knowledge, the associated deficiencies, and future challenges/opportunities.
Acknowledgements
References


5. Tracing DOM in the Ocean with UV-Visible Spectroscopy
Colin Stedmon (Technical University of Denmark, Denmark)
I. Introduction
A. Definitions
B. History
II. UV-Visible spectroscopy
A. Absorption
B. Fluorescence
C. Quantum yield
III. Sources, sinks and distributions
A. Terrestrial, planktonic, sediments, atmospheric deposition, hydrothermal.
IV. Linkages to DOC, biomarkers and compounds
A. DOC
B. Lignin,
C. Specific compounds
V. In situ sensor technologies
A. Calibration
B. Smoothing
C. Benefits/examples
VI. Conclusions and future research needs
Acknowledgements
References


6. DOM Remote Sensing (NEW)
Antonio Mannino (NASA GSFC, USA)
I. Ocean Color Remote Sensing from Airborne and Space Sensors
A. Overview of Ocean Color

1. Passive Remote Sensing

2. Active Remote Sensing
II. Passive Remote Sensing of DOM optical properties
A. CDOM Absorption Coefficients
B. CDOM Spectral Slopes
C. FDOM
III. Active Remote Sensing of DOM optical properties
A. CDOM Absorption Coefficients
B. FDOM
IV. Retrieval of DOC Concentrations and Fluxes
A. DOC from Passive Ocean Color
B. DOC from Lidar
V. Retrieval of DOM Processes
VI. Summary and Emerging Capabilities
A. Summary
B. UV and Hyperspectral Remote Sensing
C. Multi-Wavelength Lidar
Acknowledgements
References


7. DOM Production, Removal, and Transformation Processes in Marine Systems
Craig A. Carlson, Shuting Liu, Brandon Stephens, Chance English (UC Santa Barbara, USA)
I. Introduction
DOM Production processes
A. Photoautotrophic
i. Phyto
ii. Macroalgal
B. Grazer induced
C. Viral induced
D. Enzymatic solubilization
E. Prokaryotic production
i. Chemoautotrophy
ii. Release via heterotrophic processing
II. DOM removal
A. Biotic
i. Prokaryotic
ii. Eukaryotic

1. Protists Mixotrophy

2. Fungal

3. Filter feeders
B. Abiotic
i. Photooxidation
ii. Stripping
iii. ROS
iv. TBD
III. DOM Reactivity
A. DOM accumulation
i. Factors that lead to accumulation
B. Broad pools of lability
IV. DOM Transformation
A. Labile to Recalcitrant
i. Sources of DOM production
ii. Bacterial MCP
iii. Role of specific lineages SAR202 etc
iv. Photochemical transformations
v. Extracellular oxidation
B. Recalcitrant to Labile
i. Phototransformation of C=C bonds
ii. Unique enzymatic repertoire, metabolic economics
iii. Priming
V. Microbial community structure and DOM interactions
VI. Summary
Acknowledgements
References


8. Sediment Pore Waters
David Burdige (Old Dominion University, USA)
Tomoko Komada (San Francisco State University, USA)
Hussain Abdulla (Texas A&M University, USA)
I. Introduction and Scientific background (revise/up-date this section from the 2nd ed. chapter)
II. Composition and Dynamics of Bulk Pore Water DOM
A. Molecular weight distributions
B. Fluorescence and absorbance
C. Isotopes (13C and 14C)
D. High resolution mass spectrometry
E. NMR
F. DON and the C/N ratio of pore water DOM
G. DOS (Dissolved organic sulfur)
III. Composition and Dynamics of Pore Water DOM at the Compound and Compound-Class Levels
A. Short chain organic acids
B. Carbohydrates
C. Amino acids
IV. Modeling DOC Cycling in Marine Sediments
A. Production of recalcitrant DOC: General Observations
B. The multi-G + DOC model
C. Linking models of DOC cycling to terminal remineralization processes
V. Controls on DOC Concentrations in Sediments
A. Controls on DOC concentrations in surface sediments
B. Controls on DOC concentrations in deeply buried sediments
C. Redox controls on pore water DOC concentrations
D. Interactions between DOM and sediment particles and the possible role of DOM in sediment carbon preservation
VI. Benthic DOM Fluxes and Their Role in the Oceanic Carbon and Nitrogen Cycles
A. Benthic DOC fluxes
B. Benthic DON fluxes
C. The impact of benthic DOM fluxes on the composition and reactivity of oceanic DOM
VII. Conclusion and suggestions for further research


9. DOM in Hydrothermal Systems (NEW)
Susan Lang (WHOI, USA)
I. Introduction
A. Why hydrothermal systems are of interest to those who care about the biogeochemistry of marine DOM
B. Broad definition of hydrothermal circulation
II. Transformations that occur
A. Sources of DOM: autotrophy, abiotic synthesis reactions
B. Sinks of DOM: heterotrophy, thermal degradation
C. Additional types of alterations: condensation, cracking, hydrogenation
III. How type of hydrothermal system controls fate of DOM
A. High temperature axial

1. Net loss of DOM

2. possible synthesis of black carbon
B. Ultramafic influenced systems

1. Net gain of DOM

2. Abiotic synthesis of organics
C. Low temperature systems

1. Microbial processes
D. Ridge flank systems
E. Understudied systems
IV. Using DOM to infer subseafloor processes
V. Impact of hydrothermal systems on biogeochemistry of marine DOM
A. Sink of refractory DOM - current estimate 5% of annual RDOM loss
B. Production of DOM that stabilizes Fe for long distance transport
C. Source of 14C-free organics
VI. Major unknowns, future questions to address
Acknowledgements
References


10. Dissolved Organic Nitrogen in the Ocean
Deborah A. Bronk and Rachel E. Sipler (Bigelow Laboratory for Ocean Sciences, USA)
I. Introduction outlining objectives of the chapter
II. DON concentrations and composition
A. Chemical characteristics
B. Methods
C. Global distributions and fate
D. Relationship to other elements and variables
E. Concentration and composition: Research priorities
IV. Sources of DON
A. Autochthonous

1. Phytoplankton

2. N2 Fixers

3. Bacteria

4. Micro- and macrozooplankton

5. Viruses
B. Allochthonous

1. Rivers

2. Groundwater

3. Atmosphere
A. Methods
B. DON source rates
C. Sources of DON: Research priorities
V. Sinks for DON
A. Biological sinks
B. Chemical sinks
C. Methods
D. DON sink rates
E. Sinks for DON:
VI. Research priorities
Acknowledgements
References


11. Dynamics of Dissolved Organic Phosphorus
David M. Karl and Karin M. Björkman (University of Hawaii, USA)
I. Introduction
II. Terms, Definitions, and Concentration Units
III. The Early Years of Pelagic Marine P-Cycle Research (1884-1955)
IV. The Pelagic Marine P-Cycle: Key Pools and Processes
V. Sampling, Incubation, Storage, and Analytical Considerations
VI. DOP in the Sea: Variations in Space
VII. DOP in the Sea: Variations in Time
VIII. DOP Pool Characterization
IX. DOP Production, Utilization, and Remineralization
X. Conclusions and Prospectus
Acknowledgments
References


12. Understanding the Contribution of Organic Metal-Binding Ligands to DOM (NEW)
Kristen Buck (Oregon State University, USA)
Randie Bundy (University of Washington, USA)
I. Introduction
A. Role of organic ligands in trace metal cycling and ocean biogeochemistry
B. Operational definition of ligand pools (focus on iron)
II. Composition of organic ligands
A. Methods for characterizing the ligand pool composition- strengths and limitations

1. Electrochemistry (ASV, CLE-AdCSV)

2. Mass spectrometry (LC-ICP/ESI-MS)

3. Other methods (IMAC, DGT, NMR)
B. Major groups of Fe-binding ligands identified so far (sources and sinks)

1. Siderophores

2. Humics

3. EPS and thiols
C. What’s left- the composition of otherwise uncharacterized ligands
III. Distribution of Fe-binding ligands in the global ocean
A. Map of Fe-binding ligand datasets
B. Spatial distributions of stronger and weaker Fe-binding ligands

1. Surface

2. Inter-basin differences
C. Temporal cycling

1. Time series results

2. Residence times estimates
IV. Beyond Fe- organics that bind other metals
A. Organic complexation of other metals such as Cu, Co, Zn, Cd, Ni
V. Future Directions
Acknowledgements
References


13. Marine Photochemistry of Organic Matter: Processes and Impacts
David J. Kieber (State University of New York, USA)
Aron Stubbins (Northeastern University, USA)
Leanne C. Powers (State University of New York, USA)
William L. Miller (University of Georgia, USA)
I. Introduction update, fundamentals
II. Impact of Photochemistry on Elemental Cycles
A. Carbon

1. DOM Marine Food Web Dynamics

2. Photochemical Production of low molecular weight products
a. DIC
b. Carbon Monoxide
c. Organic products
B. Sulfur
C. Nitrogen and Phosphorus
III. DOM Photolability Spectrum and Fate of Terrestrial DOM in the Sea
IV. Impact of Photochemistry on Other Marine Processes
A. Radical Sources and Reactions
B. Organic Redox Transitions
C. Particles, Photoflocculation and Photodissolution
D. Natural Products
E. Microlayer
F. VOC Photoproduction
G. Sea Ice
H. Fate of Compounds of Concern
I. Marine Plastics
VI. Modeling Photochemistry
A. Fundamental Approaches
B. Relevant Examples
C. Climate Impact
VI Future Directions
A. Mechanistic Studies
B. Infochemicals/Circadian Rhythms
C. Molecular Techniques
Acknowledgments
References


15. Reasons Behind the Long-Term Stability of Dissolved Organic Matter
Thorsten Dittmar and Sinikka Lennartz (University of Oldenburg, Germany)
I. Introduction: The Paradox of DOM Persistence
II. The Environment Hypothesis
III. The Intrinsic Stability Hypothesis
IV. The Molecular Diversity (or Dilution) Hypothesis
V. The Unifying Ecology of Molecules Hypothesis
VI. Relevance in the Context of Climate Change
VII. Concluding Remarks
Acknowledgments
References


16. Riverine Dissolved Organic Matter
Robert G. M. Spencer (Florida State University)
Peter A. Raymond (Yale University)
I. Introduction
A. Sources: allochthonous vs autochthonous –

1. Overview of different sources of DOM in riverine environments.

2. Discussion of the dominance of allochthonous inputs.
B. Importance to estuarine and coastal processes –

1. What happens when riverine DOM reaches estuarine environments and the different processes / fates.

2. Tracer into the coastal ocean.
C. Relative importance of riverine inputs to different oceans – description of the terrestrial influence (e.g. lignin / black carbon data) in different ocean waters (Arctic / Atlantic / Pacific and surface vs deep) in context of riverine inputs.
II. Land to Ocean Transport
A. Mobilization to inland waters vs export to the ocean
B. Overview of fluxes from major rivers
C. Coastal vegetation inputs
D. Glacier inputs
III. Riverine DOM composition
A. 14C-Age
B. Linking composition to reactivity from headwaters to the deep ocean
C. Linking composition to microbial and photochemical degradation
IV. The Human Footprint
A. Ramifications for fluxes
B. Impacts on composition – climate, agriculture, and urbanization
Acknowledgements
References


17. DOM in the Arctic Ocean
Rainer Amon (Texas A&M University Galveston, USA)
Anja Engel, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
Karl Kaiser, Texas A&M University, USA
I. Introduction
A. Water Masses and Circulation
B. Sources of DOM to the Arctic Ocean

1. River Runoff Sources

2. Seawater Sources (Atlantic and Pacific inflow)

3. Biological Sources Within the Arctic Ocean
II. Composition of DOC Within the Arctic Ocean
A. Elemental and Isotopic Composition
B. Molecular Level Composition
C. Optical Properties – hydrography of CDOM in the Arctic Ocean
II. Distribution, exchanges with the subpolar Arctic and Mass Balance of DOM
Acknowledgments
References


18. DOC in the South China Sea (NEW)
Minhan Dai, Xiaolin Li, Yao Zhang and Feifei Meng (Xiamen University, China)
I. Introduction
A. South China Sea as a mini-ocean featuring boundary exchange processes with the land and open ocean
B. Water masses and thermohaline circulation: main patterns
C. Overall biogeochemical characteristics
II. DOC Distribution in the South China Sea
A. Spatial variability (horizontal, sectional and vertical distributions)
B. Temporal variability (Seasonal & inter-annual variations)
III. DOC Inventory, fluxes and mass balance
A. DOC stocks in the South China Sea basin (LDOC & RDOC)
B. Terrestrial inpu
C. Exchange with the northern Pacific Ocean
D. Atmospheric Input
E. Mass Balance
IV. DOC production, transformation and consumption
A. Shelf and slope (riverine plume, upwelling influence derived bio-production, seasonal coastal current)
B. Northern South China Sea (physical and biogeochemical processes along the Kuroshio intrusion)
C. DOC in the dark South China Sea (DOC consumption by heterotrophs, DOC production by dark DIC fixation)
D. DOC-prokaryotic interactions and the contributions to the deep DOC reservoir (extracellular enzymes, bacterial growth efficiency [=BP/(BP+BR)], transformation of LDOC to RDOC by prokaryotes)
E. Effects of mixing of water masses on DOC-prokaryotic interactions
V. Summary - Compare with North Pacific Ocean
VI. Open Questions and perspectives
Acknowledgements
References


19. The volatile organic carbon component of DOC (NEW)
Kim Halsey and Steve Giovannoni (Oregon State University, USA)

1) Introduction: The chemical nature of VOCs

2) The VOC cycle in the surface ocean: the magnitude of the VOC pool
i) What fraction of photosynthesis is lost as VOCs?
ii) How much carbon is cycled in the form of VOCs
iii) Spatial variability in the concentrations of selected VOCs
iv) Turnover time of the VOC pool

3) What are the sources of VOCs?
i) Phytoplankton energetics: VOCs and the photosynthetic quotient (PQ)
ii) Phytoplankton production pathways
iii) Photolysis and chemical degradation of DOC
iv) Atmospheric deposition

4) VOCs as bacterial growth substrates
i) Are some bacteria VOC specialists?
ii) VOC oxidation pathways
iii) Impacts on apparent bacterial growth efficiencies and bacterial production


20. Dynamics of Dissolved Organic Carbon in the Global Ocean (NEW)
Dennis A. Hansell (University of Miami, USA)
Cristina Romera Castillo (Institut de Ciències del Mar, Spain)
Chelsea N. Lopez (NASA GSFC, USA)
I. Introduction
II. DOC Concentrations and Global Distributions
III. Net DOC Production
IV. DOC Export with Overturning Circulation
V. Deep Ocean DOC Enrichment due to Sinking Biogenic Particles
VI. Budget of DOC in the Global Ocean
VII. Future Considerations
VIII. Summary
Acknowledgements
References


21. Modeling DOM from the Molecular to Global Scales (NEW)
Naomi Levine (Univ. of Southern California, USA)
Timothy DeVries (UC Santa Barbara, USA)
I. Process based models
A. DOM complexity & models
B. Dilution hypothesis, ecosystem dependence, recalcitrance
II. Ecosystem models/NPZD
A. Sources and sinks of DOM in these models

1. Operational definition of DOM (vs POM)

2. Agreement/Uncertainties in processes/parameters
B. Stoichiometry of DOM

1. BATS example
C. State-of-art ESM and DOM
III. Global carbon budgets
A. Export (globally and regionally)
B. Geographic differences
C. Carbon sequestration by DOC
D. Stoichiometry globally
E. Nutrient cycling through DOM
IV. Remaining uncertainties in DOM cycling/modeling
Acknowledgements
References