Soft Sediment Ecosystems – Comprehensive Study Notes

Administrative Announcements

• Field-trip logistics

  • Hamilton students: meet at Gate 9 for the bus (both the Bowen and Mt Maunganui legs).

  • Tauranga students (Rocky-shore trip): new start time 12 PM Sunday (low tide occurs 14{:}40, giving better exposure).

• Quiz 1 deadline extended because of an IT outage

  • Original cut-off: Tuesday night.

  • New cut-off: Wednesday 11 : 30 AM.

Scope & Aims of Lecture 6

• Introduce soft-sediment (off-shore) ecosystems.

• Examine their biogeochemistry and the ecosystem services they provide.

• Lay physical foundations today; Lectures 7 & 8 will focus on organic–sediment interactions and the two dominant feeding modes.

Soft-Sediment Systems – Big Picture

• Cover ≈ 90 % of the seafloor.

• Habitable space is 3-D (surface + sub-surface) → high biodiversity & high organismal density.

• Sediment is mobile (waves, currents) → habitats are dynamic.

• Critical to: fisheries (cockles, mussels, nursery grounds), pollution monitoring (bio-indicator species), carbon sequestration, and benthic–pelagic coupling.

Biological Diversity Snapshot

• Support > 17 phyla + tens-of-thousands of foraminiferan species.

• Example density: nematodes up to 4.5 × 10⁶ ind m⁻².

• Many organisms tiny/cryptic → true richness likely underestimated (deep-sea sampling challenges).

Classifying Benthic Fauna

By Position

• Epifauna – live on sediment surface (e.g., scallops). Easy to census via divers or drop-cams.

• Infauna – live within sediment (e.g., Arenicola lugworms). Require coring + sieving.

  • Surface clues: feeding pockets, waste piles, ventilation holes.

• Interstitial fauna – microscopic animals inhabiting voids between grains (copepod nauplii, tardigrades etc.).

By Size Class

• Megabenthos > few cm (stingrays, rays).

• Macrofauna > 500\,\mu\text{m} (cockles, polychaetes, sponges).

  • Often act as bioturbators (sediment mixing, bio-irrigation → deeper O₂ penetration).

• Meiofauna 63–500 \mum (nematodes, harpacticoid copepods).

• Microfauna < 63 \mum (bacteria, archaea).

Feeding Modes & Functional Groups

Deposit Feeders

• Consume organic-coated sediment particles.

• Surface example: Hobsonia (polychaete) uses cilia to sweep across grains.

• Sub-surface example: Macoma/Macomona (bivalve)

  • Extends inhalant siphon to surface → draws down particles → sorts OM on gills → ejects inorganic waste as surface pseudofaeces.

• Arenicola marina (lugworm)

  • Creates a feeding pocket which it fluidises.

  • Can process several times its body weight daily, dragging O₂-rich water centimetres below the interface.

Suspension Feeders

• Capture particles from the water column.

• Passive: parchment worm sits in a U-shaped tube; ambient currents deliver food to its mucus nets.

• Active: mussels beat cilia → generate an inhalant current; organic particles captured on gills, non-nutritive material expelled as pseudofaeces.

Key Physical Drivers

Grain Size & Sorting

• First-order habitat control.

  • Coarse, sandy, well-sorted → higher energy → suspension feeders dominate.

  • Fine, muddy, poorly-sorted → low energy → deposit feeders dominate.

• Measuring methods

  • Stack of sieves (traditional, cheap).

  • Laser diffraction (high-resolution, costly).

• Sorting coefficient (after Folk & Ward 1957) \sigma\phi = \frac{\phi{84} - \phi{16}}{4} + \frac{\phi{95} - \phi_{5}}{6.6}

  • \sigma\phi \approx 1 ⇒ well sorted; \sigma\phi \ll 1 ⇒ poorly sorted.

Shear Stress vs Grain Size (Hjulström-type curve)

• Coarser grains behave intuitively: larger grain ⇒ larger critical shear stress.

• Clays & silts defy expectations: despite small size they demand higher stress because

  • Electrostatic attractions bind particles.

  • Smooth grain faces offer little bed friction.

Benthic Boundary Layer (BBL)

• Thin layer above seabed where flow slows logarithmically.

• Four sub-zones

  1. Outer (free-stream, fastest).

  2. Log layer (turbulent mixing; velocity drops \propto \log(z)).

  3. Viscous–sublayer (weak turbulence + molecular diffusion).

  4. Laminar diffusive film right at surface (almost no flow).

• BBL thickness shrinks under high current velocity ⇒ rapid mass transfer; grows (up to \sim10 m) in deep, quiescent basins ⇒ diffusion-limited exchange.

• Tank dye experiments show laminar streaking (low flow) vs turbulent dispersion (high flow).

Sediment Porosity & Oxygen Penetration

• Coarse sand → large pores → O₂ penetrates centimetres.

• Fine mud → tight packing → O₂ exhausted after millimetres.

• Transition zone is the RPD layer (Redox Potential Discontinuity).

Biogeochemistry & Microbial Zonation

• Sharp vertical redox gradient is among the world’s steepest.

• Aerobic surface ⇒ efficient OM oxidation:
  \text{CHO}2 + O2 \rightarrow CO2 + H2O + \text{energy}

• With depth, electron acceptors change → energy yield declines:

  • Nitrate reducers ⇒ sulfate reducers ⇒ methanogens.

• Aerobic metabolism produces far more ATP than anaerobic pathways (oxygen a superior terminal electron acceptor).

Primary Production & Energy Sources

• In-situ autotrophs

  • Microphytobenthos (diatom films – visible green sheen on tidal flats).

  • Chemotrophic bacteria (use reduced compounds, no light).

• Allochthonous supply dominates: phytoplankton fallout from the euphotic zone.

• Continental shelf (0–200 m)

  • Area: 7.6 % of ocean but produces ≈ 82.6 % of benthic biomass (nutrient-rich, short transit time).

• Abyssal plain (> 3 000 m)

  • Area: 77.1 % yet only 0.8 % of benthic biomass (nutrient poor + long particle transit allowing bacterial degradation en route).

Benthic–Pelagic Coupling (Cury & Biattez example)

• Winter mini-bloom → slight rise in benthic metabolism.

• Spring bloom → sharp benthic response.

• Summer mega-bloom → intense benthic demand; risk of temporary anoxia from OM overload.

• Demonstrates tight temporal linkage between surface productivity and seafloor processes.

Nitrogen Cycling in Soft Sediments

• Nitrogen is often limiting offshore, yet human loading (fertiliser, wastewater) delivers excess \text{N}.

• Healthy sediments detoxify via coupled nitrification–denitrification:

  1. Mineralisation: OM → \text{NH}_4^+ (ammonium).

  2. Nitrification (aerobic bacteria in oxic layer)
     \text{NH}4^+ \xrightarrow{O2} \text{NO}2^- \xrightarrow{O2} \text{NO}_3^-

  3. Denitrification (anaerobic bacteria in anoxic zone)
     \text{NO}3^- \rightarrow NO \rightarrow N2O \rightarrow N_2 \uparrow

• Requires BOTH oxic and anoxic microsites.

• If the oxic film collapses (high OM, low mixing) → ammonium accumulates → plankton/algal blooms → hypoxia/crashes: a vicious eutrophication cycle.

Ecosystem Services & Human Relevance

• Nutrient regeneration – maintains productivity without external fertilisation.

• Carbon sequestration – burial and anoxic preservation of OM.

• Fisheries support – nursery grounds for fin-fish; habitat for shellfish aquaculture.

• Pollution indicators – presence/absence of sensitive taxa tracks heavy metals, organic toxins, or nutrient enrichment.

• Climate links – sedimentary denitrification releases N_2, curbing reactive \text{N} in oceans.

Field Techniques & Upcoming Practical (Toapeka Point)

• Equipment/activities

  • Extract cores; record depth of oxic/anoxic transition.

  • Sieve (> 500 µm) to collect macrofauna; count & size individuals.

  • Note surface clues (mounds, burrow openings, pseudofaeces strings).

  • Measure grain size distribution; calculate sorting.

• Observational aims

  • Confirm predicted fauna from surface evidence.

  • Relate macrofaunal density to grain size & hydrodynamic exposure.

Ethical, Philosophical & Management Implications

• Balancing nutrient inputs: moderate enrichment can enhance productivity; excess triggers harmful algal blooms & dead zones.

• Conservation of bioturbators vital – large burrowers maintain O₂ penetration, supporting whole nutrient web.

• Recognising the invisible majority (micro/meiobenthos) in EIA and fishery management plans.

Key Literature Mentioned

• Edgar & Barrett (soft-sediment biodiversity).

• Tyler et al. (benthic boundary layer processes).

• Hjulström (sediment transport thresholds).

• Cury & Biatetz (benthic–pelagic coupling studies).

Summary Cheat-Sheet

• Position classes: Epifauna / Infauna / Interstitial.

• Size classes: Mega / Macro / Meio / Micro.

• Feeding modes: Deposit (surface/sub-surface) vs Suspension (passive/active).

• First-order physical driver: grain size.

• Key chemical feature: millimetre-scale O₂ gradient; need both aerobic & anaerobic bacteria.

• Nitrogen pathway: \text{OM} \rightarrow NH4^+ \xrightarrow{O2} NO3^- \xrightarrow{anoxic} N2.

• Service mantra: "bioturbation → oxygen → nitrification → denitrification → healthy coast".