The Marine Biogeochemical Cycles: Carbon, Nitrogen, Phosphorus, Silicon, Sulfur, and Iron

Posted on May 12, 2024 in Geology

LECTURE 12: The Biological Carbon Pump and Microbial Carbon Cycling

Key Concepts

• Biological Carbon Pump: Mechanism by which the ocean absorbs atmospheric CO2 through phytoplankton photosynthesis. When phytoplankton die, some carbon sinks as detritus, transporting it from the surface to the deep ocean. Factors like microbial degradation and zooplankton activity affect the efficiency of carbon transfer.
• Particulate and Dissolved Organic Matter (POM and DOM):
  • POM (>0.7 µm): Consists of cell biomass and detritus; sinks based on size and density.
  • DOM (<0.7 µm): Includes degraded organic material and pollutants; does not sink but is advected and diffused.
• Microbial Carbon Pump (MCP): Microbes process organic matter, transforming labile compounds into refractory dissolved organic carbon (RDOC), affecting how long carbon is sequestered in the ocean.
• Carbon Export Efficiency: Describes the fraction of net primary production (NPP) that is exported out of the euphotic zone and varies across ocean basins and seasons.
• Alternatives to the Gravitational Biological Carbon Pump: Includes mechanisms like ocean mixing and the migrant pump (e.g., vertical migrations of copepods) that also contribute to the deep storage of carbon.

Modeling and Equations

• Tracer Conservation Equation: Describes changes in concentration due to advection, diffusion, and internal sources/sinks.
• 2-Box Ocean Model: Models surface and deep ocean concentrations and exchanges.
• Photosynthesis vs. Irradiance (P-I) Curves: Describe how phytoplankton photosynthesis varies with light intensity.

Important Details

• Seasonal Variability: Export and transport efficiency of carbon vary with season across different ocean basins.
• Microbial Interactions: Chemical cues between microbes influence the efficiency of the biological carbon pump.
• Enzyme Kinetics: The lecture covers Michaelis-Menten kinetics to describe reactions catalyzed by enzymes, including those involved in carbon processing.
• Global Patterns in DOC: Concentrations are highest in surface waters of ocean gyres and decrease along the ocean conveyor belt.

LECTURE 12: Microbial Respiration and the Ocean Carbon Cycle

Key Concepts and Definitions

• Microbial Respiration in Ocean: 65% of carbon fixed by phytoplankton at the San Pedro Ocean Time-series is respired back to CO2 in the surface ocean.
• Ocean Carbon Cycle: Box Model of Carbon Cycle: Involves residence time calculation and impacts of anthropogenic versus preindustrial contributions.
• Nutrient-Phytoplankton-Zooplankton (NPZ) Model: Models the interactions and dynamics of phytoplankton, zooplankton, and nutrients in ocean biogeochemical cycles.

Important Formulas

• Organic Matter Oxidation: Stoichiometry: 106 CO2 + 16 HNO3 + H3PO4 + 78 H2O → C106H263O110N16P + 150 O2. Calculate the amount of O2 needed for organic matter oxidation based on this ratio.
• Bacterial Growth Efficiency (BGE): Formula: BGE = BP / (BP + BR), Where BP is bacterial production and BR is bacterial respiration. A given BGE value of 0.15 is used to assess bacterial cell support from available carbon.
• Residence Time (𝜏): Formula: 𝜏 = Total Input / Total Output. Used to determine the time carbon or any element stays within a given reservoir.

Phytoplankton Population Dynamics

• Change in concentration over time: dP/dt = sources – sinks. Factors include advection, diffusion, specific growth rate, and mortality due to aggregation and sinking.

Models and Kinetics

• Michaelis-Menten Enzyme Kinetics: Describes the rate of enzymatic reactions turning substrates into products.
• Lineweaver-Burke Plot: Inverse of Michaelis-Menten equation to determine reaction rates and enzyme efficiency.
• Monod Curve: Used to describe the growth rate of phytoplankton under varying nutrient levels.
• Photosynthesis vs. Irradiance (P-I Curve): Similar to Michaelis-Menten but with irradiance on the x-axis and photosynthesis rate on the y-axis.

Systems and Feedback Loops

• Silicate Weathering: A negative feedback loop that influences atmospheric CO2 and temperature via silicate weathering.
• Snow Albedo Feedback: Describes how changes in snow cover can affect Earth’s albedo and influence climate.

LECTURE 13: The Marine Nitrogen Cycle

Overview

• Key Topic: Marine Nitrogen Cycle
• Importance: Nitrogen is the major limiting nutrient in ocean systems, crucial for marine life.

Key Concepts

• Redfield Ratio: 106 C : 16 N : 1 P
• Nitrogen Species:
  • Ammonium (NH4⁺): Most bioavailable, regenerated by bacterial degradation of organic matter.
  • Nitrate (NO3⁻): Taken up by phytoplankton and bacteria, requires reduction to NH3⁺ inside the cell.
  • Nitrogen (N2): Most abundant atmospheric gas, utilized by nitrogen fixers (diazotrophs).

Processes

• Nitrogen Fixation: Conversion of N2 into biologically usable forms by diazotrophs.
• Nitrification: Conversion of ammonia (NH3) to nitrate (NO3⁻).
• Denitrification and Anammox: Anaerobic processes converting nitrate or ammonium into gaseous forms of nitrogen, leading to N loss.

Calculations

• N* Calculation: Formula: 𝑁 ∗ = 𝑁 − 16 𝑃 + 2.9 mmol m⁻³. Indicates nitrogen fixation (N* > 0) or denitrification (N* < 0).

Microbial and Chemical Methods

• Genes and Proteins in Nitrogen Cycle:
  • Nitrogen Fixation: Genes (nifHDK), Protein (Nitrogenase).
  • Nitrification: Ammonia oxidation genes (amo), Protein (Ammonia monooxygenase).
  • Denitrification: Genes (nirS, nirK, norB, nosZ), Proteins include nitrate and nitrite reductases.
  • Anammox: Unique process using nitrite as electron acceptor to oxidize ammonium, with specific genes (hzoA/hzoB) and protein (Hydrazine oxidase).

Practical Application

• Identifying N Sources and Sinks: Use of chemical and microbial oceanographic methods to study regions that are sources or sinks of nitrogen.
• Public Datasets: Utilization of geochemical and –omic datasets to probe the nitrogen cycle.
• Impact of Climate Change: Expansion of Oxygen Deficient Zones may increase denitrification and anammox processes, impacting global nitrogen cycles and contributing to greenhouse gas emissions (N2O).

LECTURE 14: Carbon and Nitrogen Cycling in Marine Ecosystems

Learning Objectives

• Apply biogeochemical concepts in ecosystems inhabited by macrofauna.
• Understand carbon and nitrogen cycling in coral reefs, benthic sediment, and oyster aquaculture.
• Review roles of zooplankton and marine mammals in carbon cycling.
• Explore impacts of anthropogenic forces on these systems.

Key Concepts

• Charismatic Macro-fauna: Includes Cnidaria and Porifera which form reef ecosystems providing habitats and primary production bases.
• Porifera Anatomy and Feeding: No gut or nervous system, filters water through choanocytes for feeding. Unique in taking up dissolved organic carbon (DOC) from seaweed.
• Coral Reefs: Primary production via photosynthesis by zooxanthellae, which supports coral growth and food web dynamics.

Key Formulas

• Photosynthesis and organic matter synthesis: Translocation of synthesized matter to corals for metabolic processes.
• Coral Energy Balance: Involves translocated organic matter and waste exudation including nutrients for zooxanthellae photosynthesis.
• F-ratio (Formula 𝑓 = NO3− / (NO3− + NH4+): Estimates the proportion of nitrogen-based production derived from external (nitrate) versus recycled (ammonium) sources.

Carbon Cycling Dynamics

• Oyster Aquaculture: Improves water quality, CO2 and nitrogen removal, and habitat provisioning. Significant in nutrient cycling and biomass contributions.
• Zooplankton Carbon Biogeochemistry: Involved in primary production and carbon export through feeding and respiration in various marine zones.

Threats to Ecosystems

• Coral ecosystems face threats from bleaching, ocean acidification, and diseases, impacting their biogeochemical roles.

Diagrams and Models

• Included diagrams of coral reef communities, anatomy of hermatypic corals, and models depicting the roles of marine vertebrates in carbon cycling.

LECTURE 15: The Marine Phosphorus Cycle

Overview

• Key Concepts: Cycling and global budget of phosphorus, species, and concentration changes with depth.

Important Phosphorus Species

• Dissolved Organic Phosphorus (DOP)
• Methylphosphonate
• Polyphosphate (polyP)
• Lipid substitution
• Soluble Reactive Phosphorus (SRP)

Definition

• SRP is essentially inorganic phosphorus, Pi, also known as PO43−.

Behavior with Depth

• SRP increases with depth due to remineralization from dissolved and particulate organic phosphorus.
• DOP decreases with depth.

Dissolved Phosphate Dynamics

• Location: Increases in suboxic coastal sediments.
• Process: Liberated from mineral precipitates, especially via iron cycling. Iron-oxyhydroxides reduction leads to phosphate regeneration and release.
• Reference: Paytan and McLaughlin (2007)

Phosphorus in Biomolecules

• Includes: Lipids, DNA/RNA, and various metabolites.

Phosphorus Species and Burial

• Inorganic Phosphate: PO43− is the main inorganic form.
• Sediment Dynamics: P is remobilized during the degradation of organic matter and reduction of iron oxides. Most remobilized phosphate is precipitated as carbonate fluorapatite or adsorbed onto iron oxide particles.
• Reference: Compton et al. (2000)

Phosphorus Budget

• Redox State and Budget Simplification: Discussed by Claudia Benitez-Nelson (2016) and Van Mooy et al. (2015).

Uptake and Metabolism

• Methyl-phosphonate broken down by bacterioplankton into Pi and Methane/Ethylene (Sosa et al. 2016).
• Prochlorococcus uses methyl-phosphonate to form nucleotides for DNA & metabolism (Sosa et al. 2019).

Poly-Phosphate (polyP) Dynamics

• General Behavior: Associated with luxury uptake. Enriched in phosphorus-depleted subtropical Sargasso Sea compared to nutrient-rich temperate waters. Cycled quickly and preferentially remineralized from sinking particles to resupply P to the surface ocean.
• Reference: Patrick Martin et al. (2014)

Formulas and Definitions

• SRP: SRP = PO43−
• Phosphorus Remineralization: Occurs with depth, increasing availability of PO43− and decreasing DOP.

LECTURE 16: The Marine Silicon and Sulfur Cycles

Silicon (Si) Cycle

• Distribution: Higher Si concentrations around Antarctica and the North Pacific. Higher in the Pacific than the Atlantic due to the Ocean Conveyor Belt/Meridional Overturning Circulation.
• Siliceous Organisms: Diatoms, Radiolarians, and other Silicoflagellates use silica in their structures.
• Dissolved vs. Biogenic Si: Surface ocean is undersaturated with opal (biogenic Si, SiO2). Dissolution to silicate (SiO4-) controlled by temperature, sinking rate, food web structure, aggregation, and bacterial degradation of organic matrix.
• Marine Silicon Budget: Question of steady state with respect to silicon in the surface ocean. About 3% of Si is deposited as siliceous ooze on the seafloor.

Sulfur (S) Cycle

• Main Sources: Dissolution of evaporite minerals and oxidative weathering of pyrite.
• Main Sinks: Formation and burial of evaporites and pyrite.
• Sulfur Cycling Environments:
  • DMS production by phytoplankton-bacteria consortia in surface ocean.
  • Sulfate reduction fueled by organic matter degradation on continental shelf to H2S.
  • Sulfate precipitates out as CaSO4 at temperatures >150°C; H2S is leached from basalts at temperatures >400°C.
  • Atmospheric emission of SO2, outgassing of DMS and H2S.
• Biomolecules: Methionine, sulfur lipids, and other sulfur-containing metabolites.
• Sulfate Reduction Process:
  • Conversion of sulfate to Adenosine 5′-phosphosulfate (APS).
  • Reduction of APS to sulfite.
  • Transfer of sulfur atom of sulfite to the DsrC protein.
  • Reduction of the trisulfide to sulfide and reduced DsrC.

Important Formulas

• Stokes Equation (relevant to settling particles in fluid dynamics).
• Sulfate Reduction Steps (detailed biochemistry involved in reducing sulfate to sulfide).

Hypotheses and Models

• Silica Leakage Hypothesis: Explains drawdown of atmospheric CO2 during the last glacial period by release of Si-limitation.
• CLAW Hypothesis: Links phytoplankton production of DMSP, which is converted to DMS, to cloud nucleation and potential climate cooling.

LECTURE 17: The Marine Iron Cycle

Oxidation States

• Iron primarily exists in the +2 (Fe(II)) and +3 (Fe(III)) redox states on Earth.

Iron Cycle

• Involves the cycling of iron between Fe(II) and Fe(III), either abiotically or facilitated by microorganisms.

Abiotic Examples

• Rusting (Fe(II) to Fe(III) by oxygen)
• Reduction of Fe(III) to Fe(II) by iron-sulfide minerals

Biological Examples

• Fe(II)-oxidizing microbes

Iron Speciation

• Iron Forms:
  • Fe’ (dissolved Fe)
  • L’ (an organic ligand not bound to a metal)
  • FeL (iron bound to a ligand)
• Redox Reactions: Listed in thermodynamic order based on environment (pH neutral). Microbial reactions on the left; abiotic reactions on the right.
• Environmental Factors: O2, light, NO3−, Fe(II), Fe(III) typical of redox-stratified environments.

Global Iron Distributions

• Sources to the Ocean:
  • Riverine deposition
  • Atmospheric dust deposition
  • Glacial runoff
  • Iceberg sediments melting
  • Hydrothermal vent fluids
  • Release from anoxic sediments
• Sinks in the Ocean:
  • Burial of particulate iron.
• Internal Cycling: Between plankton, dissolved Fe pool, and particulate iron pool.

Iron Fertilization

• Iron Hypothesis:“Give me a tanker of iron, and I will give you an ice age” — John Martin
• Iron Fertilization Experiments: Involve adding iron to ocean regions to increase phytoplankton growth, potentially affecting climate change.

High-Nutrient, Low-Chlorophyll (HNLC) Regions

• Locations: North Pacific Ocean, Equatorial Pacific Ocean, Southern Ocean.
• Characteristics: High macronutrient levels but low phytoplankton abundance due to iron limitation.