10.4 Sediment Biogeochemistry and Diagenesis

Sediment Biogeochemistry Fundamentals

Sediment diagenesis covers the physical, chemical, and biological transformations that happen to sediments after they're deposited. These processes control how nutrients cycle between sediments and overlying water, how contaminants behave, and how faithfully sediments preserve records of past environments. Understanding diagenesis is central to aquatic biogeochemistry because sediments act as both reactors and archives.

Processes of sediment diagenesis

Diagenesis refers to all the changes sediments undergo after deposition, at relatively low temperatures and pressures (below ~200°C). Above that threshold, you're in the realm of metamorphism. Several interconnected processes drive diagenesis:

• Organic matter degradation: Microbes decompose organic material, releasing nutrients and dissolved organic compounds. This produces reduced substances like $\text{NH}_4^+$ and $\text{H}_2\text{S}$, which then participate in further reactions within the sediment.
• Mineral precipitation and dissolution: New minerals form in place (called authigenic minerals, like pyrite, $\text{FeS}_2$), while primary minerals like calcite dissolve. These reactions alter both sediment composition and porosity, which in turn affects how fluids move through the sediment.
• Redox reactions: Oxidized compounds get reduced, and reduced compounds get oxidized, driving the cycling of elements like Fe, Mn, and S. These reactions are tightly coupled to microbial metabolism.
• Pore water chemistry changes: As reactions proceed, concentration gradients develop in the water trapped between sediment grains. These gradients drive diffusion and advection of dissolved species (nutrients, metals, dissolved gases), connecting different sediment zones chemically.

All of these processes happen simultaneously and influence each other. For example, organic matter degradation consumes electron acceptors, which shifts redox conditions, which controls mineral stability, which changes pore water chemistry.

Redox zonation in marine sediments

One of the most important concepts in sediment biogeochemistry is that electron acceptors are used in a predictable vertical sequence. Microbes preferentially use whichever electron acceptor yields the most energy, so as you move deeper into the sediment and each acceptor is depleted, the next one takes over.

The sequence from top (highest energy yield) to bottom:

1. Oxygen (aerobic respiration)
2. Nitrate (denitrification)
3. Manganese oxides (Mn reduction)
4. Iron oxides (Fe reduction)
5. Sulfate (sulfate reduction)
6. Carbon dioxide (methanogenesis)

This redox cascade creates depth-dependent zones, each dominated by different microbial communities: aerobes near the surface, then denitrifiers, metal reducers, sulfate reducers, and finally methanogens at depth. The boundaries between zones aren't always sharp and can shift with seasonal changes in organic matter input or bottom-water oxygen levels.

Nutrient cycling implications across redox zones:

• Nitrogen: Nitrification ($\text{NH}_4^+ \rightarrow \text{NO}_3^-$) occurs in the oxic zone. Denitrification and anammox remove bioavailable nitrogen in the suboxic zone, making this a key location for permanent nitrogen loss.
• Phosphorus: In the oxic zone, phosphate adsorbs strongly to iron oxyhydroxides and stays locked in the sediment. When conditions turn anoxic, iron reduces and dissolves, releasing that phosphate back into the pore water and potentially into the overlying water. This is why oxygen depletion can trigger phosphorus release and worsen eutrophication.
• Iron and manganese: Both are reduced in anoxic zones and diffuse upward. When they hit oxic conditions, they re-oxidize and precipitate, creating a recycling loop at the redox boundary.

Benthic ecology effects: Burrowing organisms (worms, clams) physically mix sediments (bioturbation) and pump overlying water into burrows (bioirrigation). Both processes disrupt the neat redox zonation by introducing oxygen deeper into the sediment, which reshapes microbial community structure and accelerates organic matter decomposition.

Sediments as nutrient sources and sinks

Whether sediments act as a net source or sink of nutrients depends on the balance between release and retention processes.

As nutrient sources, sediments regenerate nutrients through organic matter decomposition. Dissolved phosphate and ammonium diffuse upward along concentration gradients into the water column. Physical resuspension events (storms, tidal currents) can also release pore water nutrients and particulate-bound nutrients in pulses.

As nutrient sinks, sediments remove nutrients from the water column through several mechanisms:

• Burial of organic matter below the zone of active decomposition
• Adsorption of phosphate onto iron oxyhydroxides in oxic surface sediments
• Denitrification in suboxic sediments, which converts bioavailable $\text{NO}_3^-$ to $\text{N}_2$ gas, permanently removing it from the system

Contaminant dynamics follow similar principles. Heavy metals like lead and copper adsorb to sediment particles and can be sequestered long-term. Persistent organic pollutants (PCBs, PAHs) accumulate in fine-grained, organic-rich sediments. Mercury methylation in anoxic sediments is particularly concerning because methylmercury is far more bioavailable and toxic than inorganic mercury, and it bioaccumulates through food webs.

Factors controlling source vs. sink behavior:

• Grain size: Fine-grained sediments (clays, silts) have more surface area for adsorption and tend to be more reactive than coarse sands
• Organic matter content: Higher organic loading fuels more microbial respiration, consuming oxygen faster and pushing redox boundaries closer to the surface
• Redox conditions: Oxic surface layers favor nutrient retention; anoxic conditions favor release
• Hydrodynamic regime: Calm environments allow stable redox zonation; turbulent conditions resuspend sediments and disrupt chemical gradients

Sediment records for environmental reconstruction

Because sediments accumulate over time, they preserve a layered chemical and biological record that can be used to reconstruct past environmental conditions. This makes them invaluable archives for understanding how ecosystems responded to past changes.

Types of sedimentary archives:

• Lake sediments: Annually laminated layers called varves can provide year-by-year resolution
• Marine sediments: Deep-sea cores can span millions of years, though with lower temporal resolution
• Coastal sediments: Salt marsh and estuarine deposits record local sea-level and land-use changes

Geochemical proxies are measurable chemical signatures that correlate with specific environmental variables:

• Stable isotopes like $\delta^{13}\text{C}$, $\delta^{15}\text{N}$, and $\delta^{18}\text{O}$ reflect changes in productivity, nutrient sources, and temperature/ice volume
• Trace element ratios (Mg/Ca, Sr/Ca) in biogenic carbonates serve as paleotemperature indicators
• Redox-sensitive elements (Mo, U) concentrate under anoxic bottom waters, marking past oxygen depletion events

Biomarkers are organic molecules preserved in sediments that trace specific sources or conditions:

• Lipid biomarkers distinguish terrestrial vs. marine organic matter inputs
• Pigments like chlorophyll derivatives indicate past primary productivity levels
• Molecular fossils (e.g., dinosterol from dinoflagellates) help reconstruct past community composition

Applications span a wide range of paleoenvironmental questions: reconstructing temperature and precipitation patterns, tracing shifts in ocean circulation (thermohaline circulation strength), identifying changes in upwelling intensity and productivity, and documenting oceanic anoxic events.

Limitations to keep in mind:

• Diagenetic alteration: Not all compounds preserve equally. Selective degradation can bias the record toward more resistant molecules.
• Bioturbation: Burrowing organisms mix sediment layers, smearing the temporal signal and reducing resolution.
• Spatial variability: A single core reflects local conditions, which may not represent regional or global trends. Multiple cores and independent proxies are needed for robust reconstructions.