All notes for Marine and Antarctic Ecosystems (copy)

Foundations of Marine Primary Production

• Definition of Primary Production: The formation of organic matter through the trapping of light energy and the assimilation of inorganic elements.

  • This is driven fundamentally by photosynthesis.

  • It is performed primarily by photoautotrophs (photosynthetic organisms).

  • Limiting factors include light (quantity, type, and wavelength) and nutrients (different forms of nitrogen and carbon).

• Definition of Productivity: The rate of the net incorporation of carbon into organic compounds.

  • This process involves the harvesting and transfer of inorganic carbon into organic carbon, fixed via energy derived from the light reactions of photosynthesis.

  • Standard Unit of Measurement: Gross productivity is ideally measured in kilograms of carbon fixed per meter squared per year ($kg\,C\,m^{-2}\,yr^{-1}$).

  • Estimation in the ocean is complex due to the open, three-dimensional nature of the environment compared to two-dimensional terrestrial systems.

• Production Balance: Production is the balance between growth (biomass accumulation via photosynthesis) and the loss of carbon/energy (conversion to carbohydrates or metabolic expenditure).

Marine vs. Terrestrial Primary Production

• Global Share: Marine primary productivity accounts for approximately $40\%$ of the Earth's total primary production. Some sources estimate this figure slightly higher, but $40\%$ is the established baseline for this unit.

• Comparison Metrics:

  • Net Primary Productivity (NPP): Marine and terrestrial systems are in the same "ballpark" or order of magnitude.

  • Total Biomass: Marine systems have significantly lower total biomass than terrestrial systems.

  • Turnover Rate: Marine systems exhibit much faster turnover compared to terrestrial systems.

• Explanations for Marine/Terrestrial Differences:

  • Generation Time: Phytoplankton cells may double their population daily. Seaweeds typically live for one to two years, whereas terrestrial trees can live for decades or centuries.

  • Carbon Storage: Terrestrial systems store carbon long-term in woody biomass. Marine systems are in a state of continual turnover.

  • Carbon Leakage: Marine carbon often "leaks" as particulate organic carbon or through the erosion of biomass into the water column.

Taxonomy of Marine Primary Producers

• Phytoplankton (Microalgae): Defined as being less than $2\,mm$ in size, though most are microscopic. All contain chlorophyll and perform photosynthesis.

  • Size Classes: Classified based on dimensions, with various names for different size groups.

  • Examples: Cyanobacteria (photosynthetic bacteria), dinoflagellates, coccolithophores, and diatoms.

• Macroalgae (Seaweed): Categorized into three main phyla based on pigmentation:

  • Rhodophyta (Red Algae): Contain chlorophyll a, sometimes c, and phycobilins (which provide the red color).

  • Chlorophyta (Green Algae): Contain chlorophyll a and chlorophyll b.

  • Ochrophyta / Phaeophyceae (Brown Algae): Contain chlorophyll a and c, and brown pigments such as fucoxanthin.

• Pigment Function: Colors are determined by the relative abundance of pigments. Pigments allow species to harvest light at different wavelengths, providing advantages in low-light or specialized environments.

The Mechanisms of Photosynthesis

• General Reaction Equation:     $6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2$

• The Flow of Biological Energy:

  1. Light energy is captured in the chloroplasts by pigments.

  2. Photosynthesis produces energy-rich carbohydrates and releases oxygen.

  3. Carbohydrates are split into $CO_2$ and water, making energy available for cellular functions (respiration).

• The Light Reaction:

  • Pigments harvest light.

  • Light energy is converted into chemical energy in the form of Adenosine Triphosphate ($ATP$) molecules.

• The Dark Reaction:

  • Uses the $ATP$ created in the light reaction.

  • Fixes carbon dioxide into sugar via the carbon cycle (Calvin Cycle).

  • Utilizes the enzyme Rubisco for carbon fixation.

• Chlorophyll a Structure: The primary photosynthetic pigment. It is embedded in the thylakoid membrane of the chloroplasts.

Light Dynamics in the Marine Environment

• Light Measurement: Measured as irradiance in units of micromoles of photons per meter squared per second ($\mu mol\,photons\,m^{-2}\,s^{-1}$). This is also referred to as Photon Flux Density.

• Depth Effects:

  • Attenuation: Irradiance decreases with depth as light is absorbed or scattered by water and particles.

  • Quality Change: Wavelengths change with depth. Red light is absorbed first (shallow). Blue light penetrates the furthest, creating a blue-dominated environment in the deeper photic zone.

• Water Clarity: Turbidity (dirtiness) caused by particles from estuaries or plankton blooms impacts light quality. Particles can either absorb or scatter light, altering the available wavelength spectrum regardless of depth.

Pigment Absorption and the "Green Window"

• Chlorophyll a Absorption: Exhibits two primary peaks at approximately $430\,nm$ (blue region) and $650\,nm$ (red region). There is very little absorbance between these peaks.

• The Green Window: The spectral gap where chlorophyll a does not absorb light. Accessory pigments (fucoxanthin, phycobilins) evolve to harvest light within this window.

• Advantages: Accessory pigments allow algae to maximize light harvesting across the spectrum, specifically in low-light environments.

Photoacclimation and Photosynthetic Curves

• Definition of Photoacclimation: A non-evolutionary response where an organism alters its photosynthetic apparatus (pigment number, pigment type, or reaction center density) within its lifetime to adapt to its light environment.

• The Photosynthetic Unit (PSU):

  • Pigments: Harvest/capture light energy.

  • Reaction Centers: Convert harvested light energy into chemical energy.

• P vs. I Curves: A plot of Photosynthesis ($P$) versus Irradiance ($I$). Features include:

  • X-axis: Irradiance ($\mu mol\,photons\,m^{-2}\,s^{-1}$).

  • Y-axis: Photosynthetic rate (measured via $O_2$ production).

  • Three Parts of the Curve:

    1. Light Limited Phase: Photosynthesis increases linearly with light.

    2. Light Saturated Phase ($P_{max}$): The rate reaches a plateau where more light does not increase photosynthesis.

    3. Photoinhibition: At very high light, the photosynthetic rate declines due to cellular damage.

• Key Photosynthetic Parameters:

  • $P_{max}$: Maximum photosynthetic rate.

  • $\alpha$ (Alpha): The initial slope of the relationship; indicates efficiency at low light.

  • $E_k$: The saturation irradiance ($\frac{P_{max}}{\alpha}$).

  • $R_d$: Dark respiration rate (measured in the absence of light).

  • $E_c$: Compensation irradiance; the light level where photosynthesis exactly balances respiration ($Net\,P = 0$).

Nutrient Dynamics and Productivity Status

• Nutrient Classifications for Seawater:

  • Oligotrophic: Low concentrations of essential nutrients and low carbon/primary production. Typical of the East Coast of Tasmania due to the East Australian Current (EAC), which brings nutrient-poor, warm tropical water.

  • Eutrophic: High rates of organic matter influx, usually when a limiting nutrient becomes non-limiting.

  • Hypertrophic: Extremely high nutrient/production levels.

• Nutrient Flux: Eutrophication can be natural (storms, sedimentation) or anthropogenic (pollution, aquaculture runoff). While sometimes viewed negatively, it represents an increase in production.

Principles of Nutrient Uptake and Limitation

• Liebig’s Law of the Minimum: Growth is not limited by total nutrient availability, but by the specific essential nutrient available in the smallest quantity relative to the organism's requirements.

• Essential Nutrients: Nutrients required for growth that cannot be replaced by another element. Examples include Nitrogen ($N$), Phosphorus ($P$), Iron ($Fe$), and Silica ($Si$).

• Uptake Mechanisms:

  • Seagrasses: Vascular plants with roots; take up nutrients from sediments.

  • Seaweeds/Phytoplankton: Non-vascular; take up nutrients via molecular diffusion across the cell surface.

• Uptake Kinetics:

  • Passive Diffusion: No energy required; uptake rate is a function of external concentration.

  • Active Transport: Requires energy (ATP); exhibits saturation kinetics.

  • $V_{max}$: Maximum nutrient uptake rate.

  • $K_s$: Half-saturation constant; the concentration where uptake is half of $V_{max}$.

• Competition: Phytoplankton generally have a higher surface-area-to-volume ratio than macroalgae, allowing for a much higher $V_{max}$ and the ability to outcompete seaweed for nutrients.

Nitrogen Acquisition in the Ocean

• Limiting Status: Nitrogen is typically the primary limiting nutrient in marine systems.

• Forms of Nitrogen: Nitrate ($NO_3^-$), Nitrite ($NO_2^-$), Nitrous Oxide ($N_2O$), Ammonium ($NH_4^+$), and molecular Nitrogen ($N_2$).

• New vs. Regenerated Production:

  • New Production: Driven by "new" nitrogen entering the system ($NO_3^-$ from upwelling).

  • Regenerated Production: Driven by recycled nitrogen ($NH_4^+$ from excretion/decomposition).

  • f-ratio: The ratio of new production to total production.

• Uptake Energetics:

  • Ammonium ($NH_4^+$): Taken up passively; energetically cheap. It is the form ultimately assimilated into amino acids.

  • Nitrate ($NO_3^-$): Requires active transport (energy) and must be reduced to ammonium within the cell before use.

Carbon and Ecological Stoichiometry

• Carbon Forms: Dissolved $CO_2$ and Bicarbonate ($HCO_3^-$).

  • $CO_2$ is low concentration but cheap (passive diffusion).

  • $HCO_3^-$ is high concentration but expensive (requires active transport and enzymatic conversion).

• Redfield Ratio: The theoretical stoichiometric balance for phytoplankton: $106C:16N:1P$.

• C:N Ratio as a Tool: A ratio of $C:N$ greater than $6$ in phytoplankton generally indicates nitrogen limitation. In macroalgae, the ratio is usually higher (e.g., $10$ to $13$), but still serves as a diagnostic for algal health.

• Other Nutrients:

  • Silica: Essential for diatom frustules (shells).

  • Sulfur: Used in osmoregulation and chemical defense (e.g., sulfuric acid in some seaweeds).

  • Iron: Limits growth in High Nutrient, Low Chlorophyll (HNLC) regions.

Questions & Discussion

Week 2

Introduction to Intertidal Ecology

• Environment Overview: The intertidal zone is characterized as a harsh environment for marine organisms because it effectively functions as a terrestrial environment for half of the tidal cycle.

• Driving Forces: The dynamic nature of this environment is driven primarily by tides and the subsequent impact tides have on various abiotic factors.

• Core Concepts:

  • Vertical Zonation: The occurrence of distinct vertical bands of species along the shore.

  • Horizontal Distribution: How wave energy and hydrodynamics modify community patterns from sheltered to exposed locations.

The Mechanics of Tides

• Gravitational Drivers: Tides are the result of the combined gravitational pull of the moon and the sun on the Earth's oceans.

• Tidal Alignment:

  • Spring Tides: Occur when the Earth, Moon, and Sun are aligned, resulting in the maximum range between high and low water (Mean High Water Spring and Mean Low Water Spring).

  • Neap Tides: Occur when the Sun and Moon are at right angles relative to Earth, resulting in the minimum tidal range.

• Global and Local Tidal Ranges: Tidal ranges vary significantly by geography:

  • Australia (Northwest): Ranges can reach $8\,m$, $10\,m$, or even $12\,m$.

  • Australia (Southeast/Hobart): The tidal range is relatively small, approximately $1\,m$ to $1.2\,m$.

  • Tasmania (North Coast): The range is approximately $3\,m$.

  • Bay of Fundy (Canada): Features the most extreme tides globally, reaching up to $16\,m$.

• Meteorological Influences: Tides are not solely gravitational; atmospheric pressure plays a role:

  • Low Pressure Systems: Can increase sea levels and elevate tides.

  • High Pressure Systems: Can decrease sea levels and lower tides.

Harshness of the Intertidal Environment

• Stress Factors: Marine organisms face rapid fluctuations in several abiotic parameters when exposed to air:

  • Temperature: Air temperature fluctuates more wildly than water temperature. Surfaces like rocks can reach extreme highs (over $35\,^\circ C$ in summer) or lows (near freezing in winter).

  • Salinity: Becomes a major stressor in tide pools due to evaporation (increasing salinity) or rainfall (decreasing salinity).

  • Moisture and Desiccation: The loss of water to the atmosphere is a constant threat when the tide is out.

  • Light Intensity and UV: Organisms are exposed to higher light intensity and more harmful wavelengths (UV) without the filtering effect of water.

  • Nutrient and Food Availability: Filter feeders (like barnacles and mussels) cannot feed without water. Photosynthetic organisms (seaweeds) are often restricted in their carbon uptake outside the water.

  • Gas Exchange: Necessary requirements include oxygen and carbon (Bicarbonate or $CO_2$) for respiration and photosynthesis.

Vertical Zonation: Patterns and Universal Schemes

• Global Commonality: Distinct bands of dominant species are a consistent feature in temperate intertidal regions.

• Case Study: Northern Hemisphere Pattern:

  • Low Zone: Dominated by mussels.

  • Mid-Low Zone: Red algae such as Palmeria.

  • Mid-High Zone: Green algae such as Ulva.

  • High Zone: Brown algae such as Ascophyllum.

• Case Study: South Arm, Tasmania:

  • Low Zone: Kelp species such as Lausonia.

  • Mid-Low Zone: Sessile invertebrates like the ascidian (sea squirt).

  • Mid Zone: Mussels.

  • High Zone: Barnacles.

• Historical Theory: Universal Zonation Scheme: Initially proposed to divide all shores into universal bands (Kelp bottom, Barnacles/Mussels middle, Lichens/Gastropods top).

• Modern Critiques: While banding is common, the specific species and patterns are not truly universal and are subject to local variation and exceptions.

Drivers of Zonation: Abiotic and Biotic Factors

• The Existing Paradigm:

  • Upper Limits: Restricted by abiotic tolerances (the physiological capacity to survive desiccation and temperature stress).

  • Lower Limits: Restricted by biotic interactions (competition and predation).

• Biotic Interactions:

  • Competition: Interaction for limited resources like space.

  • Predation/Herbivory: Animals consuming other animals or plants.

  • Facilitation: Positive interactions where one species creates habitat for another (e.g., seaweed growing on mussel beds).

• Recruitment: The settlement of larvae or spores. While recruitment can occur across many zones, post-recruitment mortality (due to stress or biology) determines the final adult distribution.

Experimental Case Studies in Zonation

• Joseph Connell (Scotland - Barnacles):

  • Species: Chthamalus (small, high zone) and Semibalanus (large, mid zone).

  • Findings: Chthamalus' upper limit was set by desiccation. However, when Connell removed the larger Semibalanus, the smaller Chthamalus survived well into the lower zone. This proved the lower limit of Chthamalus was set by competition for space.

• Robert Paine (Washington State - Predators):

  • Species: Mytilus (mussels) and Pisaster (sea star predator).

  • Findings: Removal of the predator Pisaster allowed the mussels to expand their distribution downward into the lower intertidal. This proved that predation sets the lower limit for the competitively dominant prey species.

Physiological Mechanisms of Seaweed Survival

• Seaweed Study (Fuchales):

  • Species Range: Different species occupy specific heights: Pelvetia (highest) down to Fucus species.

  • Abiotic Stress Testing: Transplants of lower-shore species to high-shore locations resulted in death, confirming abiotic stress limits.

• Desiccation and Recovery Mechanisms:

  • Water Loss Resistance: Studies showed that high-shore species do not necessarily lose water slower than low-shore species.

  • Photosynthetic Resistance: Photosynthesis stops at low water tissue levels for both high and low-shore species.

  • The Critical Difference: High-shore species (Pelvetia) exhibit a superior ability to recover photosynthesis rapidly and fully the moment they are re-wetted. They can begin photosynthesizing while still at a low state of tissue hydration, unlike low-shore species that require near-full rehydration.

Horizontal Distributions and Wave Exposure

• Water Motion Types:

  • Unidirectional Flow: Driven by tides and currents ($2\,m/s$ to $3\,m/s$).

  • Oscillatory Flow: Driven by breaking waves; can involve much higher energy and force.

• Flow Modification by Topography: Channels can increase flow speed through narrowing, while embayments decrease flow.

• The Splash Zone Effect: In high-exposure areas, the swash or splash can dampen desiccation stress, potentially shifting species higher up the shore than they would appear in sheltered areas.

Wave Energy as Stressor and Resource

• Wave Energy as a Stressor:

  • Pressure Drag: Direct force that can rip organisms from the substrate.

  • Abrasion: Sand and rocks suspended in the water column scrape and damage tissue (whiplash effect).

  • Hydrostatic Pressure: The weight of breaking waves can crush delicate structures.

• Wave Energy as a Resource:

  • Nutrient Delivery: Higher water motion brings more nutrients to seaweeds and plankton to filter feeders.

  • Reduced Stress: Constant splashing reduces desiccation and temperature spikes.

  • Oxygenation: Turbulent water prevents low-oxygen (hypoxia) zones.

  • Predator Refuge: Many predators (like sea stars or grazing mollusks) cannot attach firmly in high-flow areas, protecting prey.

Adaptations to High Wave Exposure

• Morphological Adaptations:

  • Toughness and Flexibility: Species like Bull Kelp (Durvillaea) are leathery yet flexible to bend with waves rather than snapping.

  • Streamlining: Shapes that offer low resistance to water flow.

  • Holdfast Strength: Highly developed attachment structures. In Durvillaea, the adhesive is often stronger than the rock itself.

  • Gas Floats (Pneumaticists): Species like Nereocystis use gas-filled floats to keep blades near the surface.

• Community Adaptations:

  • Clumping/Canopies: Growing together reduces the drag force on individual organisms. Internal temperatures in clumps are lower, and forces are dissipated through the group.

• Tissue Strength Strategies:

  • Red Algae: Typically have strong, thin tissue with high breaking strength.

  • Brown Algae: Rely on sheer thickness or mass to achieve strength.

• Regeneration: Some species can regrow from a holdfast if they are broken off, whereas others (like Bull Kelp) die if the stipe is severed.

Biogeographical and Local Variations in Zonation

• Scaling of Influences:

  • Local Scale: Driven by exposure to waves and slope of the shore.

  • Biogeographic Scale: Driven by ocean temperature (differences up to $10\,^\circ C$), nutrient availability (colder water is generally more productive), geology (porosity and chemical makeup of different rock types), and regional species pools (e.g., the arrival of the long-spine sea urchin in Tasmania changing dynamics).

Week 3

Characteristics of Temperate Rocky Reefs

• Definition: Marine ecosystems occurring on rock in cool to cold temperate waters globally. They are abundant throughout temperate regions.

• Subtidal Context: While previous discussions focused on intertidal reefs, these notes concentrate on subtidal reefs (below the low tide mark).

• Substrate Requirements: By definition, these reefs require a hard substrate. Seaweeds almost exclusively require rock for attachment.

• Depth Zonation:

  • Shallow Reefs: Dominated by habitat-forming seaweeds, particularly kelps. These form a highly productive biomass that supports diverse assemblages of fish, invertebrates, and smaller seaweed communities.

  • Deep Reefs: At depths where light penetration is too low for kelp (generally around 30\,\text{to}\,$40\,m), the community shifts. Assemblages are dominated by sessile invertebrates, including sponges, corals, bryozoans, and ascidians. These form diverse "sponge gardens."

The Great Southern Reef (GSR)

• Geographic Range: An interconnected rocky reef system spreading across all of Southern Australia. It extends thousands of kilometers from the West Australian coast, through Southern Australia and Tasmania, up to Northern New South Wales and Southern Queensland.

• Economic Value: Estimated at approximately $10,000,000,000$ to the Australian economy (based on data from roughly ten years ago). This includes contributions from commercial fisheries, recreational fishing, and tourism.

• Biodiversity:

  • Species Richness: High diversity across seaweeds, invertebrates, and fish.

  • Seaweeds: Approximately $1,500$ species across the GSR, with at least $750$ species in Tasmania alone. Many of these are endemic (found nowhere else).

• Dominant Species: Colonia radiata (Golden Kelp) is the primary habitat-forming species across the entire GSR in shallow waters (down to 20\,\text{to}\,$25\,m, depending on clarity). Other large brown seaweeds include Davila, Crayweed, Sargassum, and Systophera.

Physical (Abiotic) Drivers of Reef Assemblages

• Light:

  • Light intensity decreases with depth, and specific wavelengths are filtered out.

  • Coastal Water Variation: Contains more suspended particles (silt, phytoplankton). This causes light to be absorbed or scattered, shallowing the photic zone. In Bathurst Harbour and Port Davy (West Coast of Tasmania), tannin run-off from button grass creates dark, "tea-stained" water where light-dependent species may be limited to just 3\,\text{to}\,$4\,m depth.

• Wave Exposure: Influences species distribution. Different species occur on exposed versus sheltered coasts.

• Nutrients: Factors like nitrogen can be limiting, especially on the East Coast of Tasmania. Excess nutrients can stimulate the growth of epiphytic seaweed (filamentous algae growing on other plants) or phytoplankton blooms, which then limit light for reef species.

• Currents: Australia is influenced by unique currents running North to South on both the East and West coasts.

  • West Coast: Historically unusual as it is affected by a warmer current (the Leeuwin Current, though not named explicitly in the transcript, described as warm) rather than a cool current typical of other West Coast systems like South America.

  • East Coast: The East Australian Current (EAC) brings warm, nutrient-poor water further south towards Tasmania, impacting species like giant kelp forests.

Biological (Biotic) Drivers and Foundation Species

• Interactions: Main drivers include competition, predation (herbivory), disease, parasites, and facilitation.

• Foundation Species (Ecosystem Engineers): Species that create habitat and modify environmental conditions through their presence. Examples include seagrass meadows, kelp forests, mussel beds, and coral reefs.

  • Facilitation Mechanism: Acolonia (kelp) modifies the environment to benefit other species by:

    • Reducing wave energy (baffling waves).

    • Reducing light levels beneath the canopy ($10\%$ of ambient light).

    • Scouring sediment via frond movement (abrasion).

    • Providing habitat in the stipes, canopies, and "holdfasts" (the finger-like attachment structures) for mobile and sessile species.

• Ecological Scale: Larger and denser patches of kelp generally support higher species diversity.

Trophic Cascades and Urchin Barrens

• The Trophic Cascade Concept: A predator controls a herbivore, which in turn controls the primary producers (plants/seaweed). A cascade involves at least three trophic levels.

  • Direct Interaction: Predators have a negative effect on herbivores; herbivores have a negative effect on kelp.

  • Indirect Interaction: Predators have a net positive effect on kelp by limiting sea urchin populations.

• Case Study: Centriferoussephus rogzii: This sea urchin has moved south into Tasmanian waters over the last $30$ years. Studies by Scott Ling at IMAS demonstrated that removing these urchins leads to rapid recovery of the kelp canopy and understory algae.

• Case Study: Northern Hemisphere Otters: Where sea otters (predators) are abundant, sea urchins are few, and kelp forests thrive. When orcas shifted their diet to eat otters in the $1990s$, urchin populations increased, and kelp forests were decimated.

• Alternative Stable States: Ecosystems can switch between kelp-dominated and urchin-dominated (barrens) states. Transitioning back to kelp is difficult and often requires the reintroduction of large predators (like Rock Lobsters) or events like urchin disease outbreaks.

Seaweed: Classification and Function

• Three Main Groups:

  1. Chlorophyta (Green algae).

  2. Rhodophyta (Red algae): The most diverse group with over $7,500$ species.

  3. Ochrophyta, Class Vaefyce (Brown algae).

• Evolution: These groups arose independently. Chlorophytes and Red algae evolved $1.1\,\text{to}\,1.6 \times 10^9\,\text{years ago}$. Brown algae evolved around $450 \times 10^6\,\text{years ago}$, with larger kelps appearing $200 \times 10^6\,\text{years ago}$.

• Morphology (The Thallus): Seaweeds are not plants; the entire body is called a thallus.

  • Lamina/Fronds/Blades: Sites of photosynthesis and nutrient uptake.

  • Stipe: Provides stability and lifts the blades above the substrate.

  • Holdfast: Anchors the thallus to rock; does not take up nutrients.

  • Pneumatocysts: Gas-filled floats providing buoyancy to keep the blades upright.

• Functional Groups: Classification by function rather than taxonomy:

  • Filamentous: Fine, hair-like.

  • Foliose: Sheet-like (e.g., Ulva, Porphyra).

  • Corticated Foliose: Thickened sheet-like (e.g., Dicteota).

  • Coarsely Branched: (e.g., Codium).

  • Leathery Macrophytes: Large kelps.

  • Jointed Calcareous: Upright with calcium carbonate cell walls.

  • Crustose: Encrusting calcium carbonate layers.

  • Siphonous: Green algae (e.g., Caulerpa) where the whole individual functions like a single large cell/hose (can occur on soft sediment).

Seaweed Life Cycles and Reproduction

• Cell Division:

  • Mitosis: Asexual; results in two genetically identical diploid ($2n$) cells.

  • Meiosis: Sexual; results in haploid ($n$) gametes (eggs and sperm) or spores.

• Reproductive Strategies:

  1. Diplontic: Most of the life history is diploid. Only the gametes are haploid (e.g., Bull Kelp). Bull kelp have separate males (white conceptacles) and females (brown conceptacles).

  2. Haplontic: Most of the life is haploid; the diploid zygote stage is brief (common in freshwater Spiragyra).

  3. Alternation of Generations: Both haploid (gametophyte) and diploid (sporophyte) stages are free-living.

     • Isomorphic: The two stages look identical.

     • Heteromorphic: The two stages look different. In kelp, the sporophyte is large ($20\,m$) and the gametophyte is microscopic ($200\,\mu m$).

  4. Triphasic: Unique to red algae (e.g., Asparagopsis). Three phases: one haploid stage and two diploid stages (carposporophyte and tetrasporophyte).

  5. Asexual: Propagation via fragmentation (e.g., Caulerpa). Pieces break off and grow into new individuals.

Economic Importance of Seaweed

• Global Production: Approximately $38,000,000\,tonnes$ produced globally (as of $2022$), largely through aquaculture.

• Direct Consumption: Food (Nori for sushi), seaweed snacks, and chips.

• Bioproducts:

  • Phycocolloids: Agar and alginates used as thickeners in tinned foods, gravies, and shampoos.

  • Fertilizers: Plant biostimulants and soil conditioners.

  • Skincare: Face masks, moisturizers, and creams.

  • Infrastructure/Emerging: Bioplastics and animal feed additives. Asparagopsis is used in beef production to reduce methane emissions.

Seagrass: Classification and Evolution

• Definition: True flowering plants (Magnoliophyta) with vascular tissue (xylem/phloem).

• Evolution: Evolved from terrestrial marsh/swamp plants $65\,\text{to}\,100 \times 10^6\,\text{years ago}$ via three distinct evolutionary events.

• Diversity: Low global diversity (approx. $60$ species). Australia has $29$ species (approx. half the world's diversity), and $20$ are endemic.

• Tasmanian Species:

  • Zostromulleri: Intertidal mudflats; small leaves.

  • Heterozostra nigricolus: Subtidal; slightly larger.

  • Halophila australis: Petal-shaped leaves.

  • Amphibilis antarctica: Branching "Christmas tree" stems; found in the North.

  • Poseidonia Australis: "Strapweed"; large straps; found in the North.

Seagrass Morphology and Physiology

• Structural Components:

  • Leaves/Blades: Have a leaf sheath and a blade. They lack stomata (pores).

  • Lacunae: Internal gas spaces for buoyancy and gas transport throughout the plant.

  • Rhizomes: Horizontal stems growing in or on the sediment. They grow in modules called "internodes" separated by "nodes."

  • Roots: Grow from the nodes. Responsible for nutrient uptake and anchoring in soft sediment. Roots leak oxygen into the sediment to create an oxic layer, preventing toxic anoxia.

• Adaptations for Marine Life:

  • Tolerance to salinity.

  • Ability to photosynthesize wholly submerged in high-turbidity water.

  • Anchoring mechanisms against waves and tides.

  • Hydrophilus Pollination: Completing the reproductive cycle (pollination and fertilization) underwater.

Seagrass Reproduction

• Sexual Reproduction: Inconspicuous flowers release pollen/sperm into the water column. Fertilization results in fruit and seeds.

  • Seeds: Some species (Zostra) have hard coats forming "seed banks" in sediment. Others have membranous coats.

  • Fruits: Poseidonia produces buoyant fruits. When they waterlog and break, the non-buoyant seed sinks to the bottom.

  • Vivipary: Production of live offspring. Amphibilis seedlings germinate while still attached to the parent, eventually releasing as "grappling hook" structures that catch on the bottom.

• Asexual Reproduction: Horizontal expansion of rhizomes. A single Poseidonia clone in Western Australia has been measured covering $180\,km^2$.

Comparative Summary: Seaweed vs. Seagrass

Week 4

Introduction and Logistics

• Field Friendly Registration: Students must register on the "Field Friendly" platform immediately. Instructions are located in the PDF posted on Milo.

• Support: For any issues regarding registration, students should contact the lecturer or Camille.

• Deadline: Registration is mandatory before the field trip occurring next week.

• Lab Session: A laboratory session will follow the lecture where students will examine seaweed and aquatic samples.

Defining Secondary Production

• Basic Definition: Secondary production is the generation of biomass by heterotrophic organisms, as opposed to autotrophic primary production ($photosynthesis$ or $chemosynthesis$).

• Measurement Metrics:

  • It can be measured as the increase in biomass of individuals over a specific period (how much food consumed is converted into body weight).

  • At the community level, it is the sum of the production of all individual secondary producers in the system.

• Secondary Producers: Includes grazers, invertebrates (gastropods, bivalves, crustaceans, amphipods, shrimps, polychaetes), and higher-level consumers up to blue whales and orcas.

• Dual Roles: Some organisms, like certain Tasmanian sponges, exhibit both primary and secondary production. They contain endosymbiotic dinoflagellates (similar to corals) allowing them to utilize sunlight in shallow waters while also filter-feeding on primary producers.

Production vs. Productivity

• Semantic Distinctions: These terms are often used interchangeably, but technical differences exist:

  • Production: Refers to an absolute amount of biomass produced, generally per unit area ($\text{e.g., g/m}^2$).

  • Productivity: Refers to a rate of production per unit time ($\text{e.g., g/m}^2/\text{year}$).

• Standing Stock vs. Rate: Standing stock refers to the instantaneous biomass present in a system, whereas productivity describes the turnover and growth rate.

• Example: Kelp Forest vs. Urchin Barren:

  • A kelp forest has a biomass roughly $100$ times that of an urchin barren.

  • However, the productivity of an urchin barren can be high because microscopic diatoms on rock surfaces turn over every $1$ to $2$ days, regenerating rapidly despite low standing biomass.

Carrying Capacity and Subsidies

• Carrying Capacity: This is the theoretical ceiling for secondary production in any system, strictly limited by the total primary production available.

• Resource Ceilings: Secondary consumers cannot consume more than what is primary-produced. However, systems do not always reach this ceiling due to other mortality factors.

• Subsidies and Anomalies: High animal densities can exist in areas that seem to lack sufficient local primary production through several mechanisms:

  • Plankton Concentration: Strong currents may bring plankton generated elsewhere to a specific location (e.g., planktivorous species at Tinderbox).

  • Hotspot Tracking: Animals move tocapitalize on concentrated primary production from larger surrounding areas.

• Case Study: Fakarava Sharks, French Polynesia:

  • Massive densities of sharks congregate for one month per year.

  • The food resource consists of spawning aggregations of smaller groupers.

  • This creates an "inverted biomass pyramid" where the biomass of top predators outweighs lower trophic levels locally and temporarily.

Trophic Pyramids and Seasonal Dynamics

• Standard Distributions:

  • Abundance: Typically many small individuals at the base, fewer large individuals at the top.

  • Biomass: Generally high at the bottom, decreasing as one moves up the food web (except in subsidized/inverted cases).

• Seasonal Tracking: Secondary production usually tracks primary production with a slight lag (approximately one month).

  • In temperate areas, light and nutrient availability in summer spark primary production, followed by a secondary production peak.

  • Example (Seagrass in Western Australia): Small crustaceans and mollusks show strong summer peaks in population dynamics, with generations occurring every $1$ to $2$ months to respond rapidly to food availability. Populations collapse in winter when primary production ceases.

Energy Budgets and Production Calculation

• The central energy/mass budget equation:     $C = P + R + F + U$

  • $C$ = Consumption (total food intake measured in energy, carbon, nitrogen, etc.).

  • $P$ = Production (energy/mass added to body tissues or stored).

  • $R$ = Respiration (metabolic processes; often measured via oxygen to carbon dioxide conversion).

  • $F$ = Feces (egested material).

  • $U$ = Urine (excreted material).

• Components of Production ($P$):     $P = G + P_r$

  • $G$ = Growth (increase in individual body mass).

  • $P_r$ = Reproduction (energy lost to eggs, larvae, or juveniles).

Turnover and the $P/B$ Ratio

• $P/B$ Ratio: The ratio of annual production to mean biomass ($Turnover$).

• Body Size Correlation: The $P/B$ ratio is inversely related to body size.

  • Bacteria: $P/B$ ranges from $26$ to $300+$ (turning over nearly every day).

  • Meiofauna (nematodes/copepods): $P/B$ average is roughly $8$ (range of $3$ to $19$).

  • Macrofauna: Mid-range turnover.

  • Large Fishes: $P/B$ is often less than $1$ (adding only a fraction of their body weight per year).

Methods for Measuring Production

• Two-Dimensional Growth: For colonial organisms like bryozoans on kelp fronds, production is measured via area expansion over time.

• The Allen Method: A common fisheries technique involving tracking a specific cohort ($size class$) over its lifespan.

  • Calculates the mean number of individuals ($N$) and mean weight increase ($\triangle W$).

  • Production of cohort = $N \times \triangle W$.

• Generalizing via Body Mass (Microscopic Animals): Since measuring production in every individual snail or worm is impossible, researchers use regression equations based on metabolic theory:

  • Production can be estimated if individual biomass and environmental temperature are known.

Metabolic Theory of Ecology (MTE)

• Universal Laws: MTE describes universal relationships between temperature, body mass, production, and abundance.

• Abundance vs. Body Size: There is a strong negative relationship; you can have millions of small animals but very few large ones in the same area.

• The "Flat" Productivity Relationship: Research indicates that while abundance decreases and individual biomass increases with size, the total productivity per size class at the community level remains remarkably constant across several orders of magnitude in size.

• Emergence: This stability is considered an "emergent property" of the community, allowing ecologists to predict average productivity and identify disturbances (predation or pollution) when the curve deviates from the flat line.

Food Webs and Transfer Efficiency

• Food Chains: Simplified linear paths of energy (Primary Producer → Grazer → Carnivore).

• Transfer Efficiency (Ecotrophic Coefficient): The proportion of production transferred from one trophic level to the next.

  • Typically ranges between $0.1$ ($10$%) and $0.2$ ($20$%).

• Impact of Chain Length: Adding an extra link significantly reduces energy available at the top.

  • Example: $100\text{ g}$ phytoplankton → Krill → Whale ($35$% → $15$% efficiency) results in $5\text{ g}$ whale production.

  • Example with intermediate fish: $100\text{ g}$ phytoplankton → Krill → Herring → Whale (adding a $20$% link) results in only $1\text{ g}$ whale production.

• Complexity and Modeling: Modern ecology uses food webs because species feed at multiple levels. To manage complexity, species are grouped into "functional groups."

• Mass Balanced Models (Ecopath/Ecosim): These ensure that the mass starting at the base is accounted for through production, consumption, and detritus throughout the web.

Human Impacts on Production

• Eutrophication: Nutrient subsidies initially increase primary and secondary production. However, past a "tipping point," it leads to hypoxia ($oxygen depletion$).

• Dead Zones: High primary production leads to massive die-offs of invertebrates and fish. Global dead zones are increasing, notably in the Baltic Sea, Mediterranean, and East China Sea.

• Trolling/Trawling: Physical disturbance from bottom trawling drastically reduces benthic secondary production, mirroring maps of fishing intensity.

• Fishing Down the Food Web: Humans selectively remove high-trophic-level predators (sharks, large fish), forcing a shift toward catching smaller, shorter-lived, low-trophic-level species.

• Efficiency Shift (China vs. West):

  • Western fisheries target large "plate-sized" fish with low $P/B$ ratios (~$0.5$).

  • Chinese fisheries target smaller, faster-growing individuals with high $P/B$ ratios (~$5.0$).

  • This makes Chinese fisheries significantly more productive in terms of total food biomass for humans, at the cost of diversity and individual fish size.

Climate Change Implications

• Global Trends: Most scenarios predict a global decline in marine biomass and production.

• Uneven Distribution: Tropical regions are expected to suffer the greatest losses in production, while polar regions may see slight increases.

• Trophic Sensitivity: High-trophic-level species (large commercial fish) will decline more severely under climate change than primary producers at the base of the web.

Week 5

Field Trip Logistics and Introduction to ILO 3

• Field Trip Preparation and Safety:

  • Required App: All students must be signed up to the "Field Friendly" platform for field trip coordination.

  • Physical Requirements: Students are required to wear old shoes and clothes that can get wet. A raincoat is essential due to the prevalence of patchy rain.

  • Post-Field Procedures: A change of clothes can be left in the lab. Students must be punctual to maintain the tight timeline for sample collection and lab work.

• Learning Objectives:

  • ILO Three (Intended Learning Outcome 3): To describe the physical, chemical, and biological components of benthic marine ecosystems.

  • Scope: The focus is on benthic temperate ecosystems (specifically those around Tasmania), rather than pelagic, tropical, or polar systems.

  • Structure of Study: The material is divided into defining an estuary, identifying dominant habitats, and understanding environmental drivers through active workshop discussions.

Conceptualizing and Defining Estuaries

• Basic Definition: The most fundamental definition is a place where a river meets the sea, though this simplifies a highly dynamic process.

• 1960s Classic Definition: A semi-enclosed coastal body of water that has a free connection with the open sea and within which seawater is measurably diluted with freshwater derived from land drainage.

• Challenges to the Classic Definition:

  • Many estuaries do not have a "free connection" to the sea. They may be permanently, periodically, or intermittently open.

  • Seawater dilution is spatially and temporally dynamic, depending on whether tidal processes or river flooding are the dominant forces at a given time.

• Modern Scientific Debate: There are over $60$ definitions for estuaries in current literature because their characteristics are exceptionally varied.

Dynamics and Variation of Estuarine Systems

• Salinity Variations and the Salt Wedge:

  • In the Derwent Estuary, a salt wedge flows in. Depending on the tide, this wedge can reach as far as the Derwent Bridge, causing significant fluctuations in salinity.

  • During heavy rains, freshwater pulses from the River Derwent can push freshwater throughout the estuary, completely changing local conditions.

• Seasonal Closures and Inverse Estuaries:

  • Sediment Build-up: Some estuaries (e.g., Browns River in Kingston, Tasmania) experience sediment buildup at the mouth, closing them off for parts of the year.

  • Inverse (Negative) Estuaries: If an estuary is closed during summer, evaporation may exceed freshwater input from rivers and rain. This concentrates the salt, making the water more saline than the open ocean.

• Zonal Categorization (Upper, Mid, Lower):

  • Lower Estuary: Characterized by a free connection with the open ocean and dominated by marine forces (e.g., from the Iron Pot to the Tasman Bridge in the Derwent).

  • Mid Estuary: An area of strong saltwater and freshwater mixing, often featuring a salt wedge competing with a freshwater wedge.

  • Upper Estuary: Characterized by freshwater but still subject to daily tidal action (e.g., from Bowen Bridge to Bridgewater).

Classification and Global Context

• Classification Criteria: Estuaries are classified by geomorphology, ecological relevance, and tidal range.

• Tidal Range Scales:

  • Microtidal: Minimal tidal influence ($0-2$\,m). Tasmania is largely microtidal, with tides around $1.5$ meters.

  • Mesotidal, Macrotidal, and Hypertidal: Larger tidal influences (e.g., the Bay of Fundy or elements of the Northern Territory which can reach over $6$ meters).

• Tidal Influence on Ecology: Tides influence salinity, wave forcing, sediment grain size, and the distribution, function, and survival of organisms.

Societal and Ecological Importance

• Human Population Density: Estuaries are major hubs for human habitation. Approximately $95\%$ of Australia’s population lives in the coastal zone, with $61\%$ of the global population living on the shores of major bays and estuaries.

• Ecological Functions:

  • Critical transition zones (ecotones) linking terrestrial, freshwater, and marine environments.

  • High nutrient cycling and high primary productivity.

  • Regulation of water fluxes, sediments, and particles.

  • Nursery habitats for various species.

• Economic and Industrial Use: Used for transport, recreation (fishing, boating), and industry. Examples include paper and copper mills built on the Derwent for shipping access.

Estuarine Habitats: Focus on Soft Sediments

• Habitat Diversity: Habitats include subtidal zones, intertidal mudflats, seagrass meadows, mangroves (tropical/subtropical), and salt marshes (temperate).

• Soft Sediment Dominance:

  • Soft sediment (silt to coarse sand) is the most abundant habitat globally (approx. $80\%$ of the ocean) and locally. In the Derwent Estuary, seabed mapping by IMAS found that $96\%$ of the area is soft sediment.

  • Biodiversity in Sediment: This habitat supports high biomass. For example, there are roughly $130$ species of marine worms and $117$ species of crustacea found in the Hawkesbury River sediment.

• Threats to Soft Sediments: Often overlooked compared to more visible habitats. Major threats include dredging, trawling, sand mining, and nutrient/sediment inputs leading to light reduction and anoxia.

Functional Groups in Estuarine Benthos

• Infauna: Organisms living buried within the sediment (e.g., annelids, bivalves, crabs).

• Key Functional Roles:

  • Shredding: Breaking down organic matter for recycling.

  • Suspension Feeding: Transporting matter from the water column across the sediment-water interface.

  • Bioturbation: The physical movement and mixing of sediment and organic matter, which oxygenates the substrate.

The Biology and Ecology of Seagrass Meadows

• Botanical Classification: Seagrasses are true marine angiosperms (flowering plants), not seaweeds. They possess true roots, rhizomes, and flowers.

• Physiological Requirements:

  • They require high light levels to support non-photosynthetic tissues (roots/rhizomes) under the ground. This limits them to shallow, clear coastal waters.

  • Comparison to Seaweed: Seaweeds use a holdfast for attachment, whereas seagrasses anchor via an extensive root and rhizome system.

• Tasmanian Seagrass Species:

  1. Amphibolis antarctica (Tasmanica): Similar to seaweeds in appearance, found in rocky habitats.

  2. Halophila australis: An early colonizer, relatively rare in Tasmania.

  3. Posidonia australis: A long-lived keystone species (hundreds of years) found in northern Tasmania and the Furneaux/Kent Groups.

  4. Heterozostera nigricaulis: Subtidal species with a woody stem.

  5. Zostera muelleri: An intertidal species frequently found in estuarine mudflats.

  • Note: Two species of freshwater seagrass (Ruppia) also exist but are often categorized as freshwater plants.

Environmental Drivers of Estuarine Ecology

• Salinity: Viewed as the dominant influence on survival and community composition. Ranging from $0$ to $35$, it forces organisms to use strategies like osmotic stress management.

  • Crustacea are efficient osmoregulators.

  • Mollusks generally have lower osmoregulation ability.

• Dissolved Oxygen (DO): Enters the water via diffusion and photosynthesis. Oxygen solubility decreases as temperature and salinity increase. Low DO is common in summer, especially in closed estuaries.

• Grain Size: Impacts the space available for life and the amount of organic material trapped. Ranges from fine silt/clay to coarse sand.

• Water Flow and Bathymetry: Influences the position of the saltwater wedge and controls DO and temperature distribution.

Structural Complexity and Ecological Functioning

• Theory of Complexity: There is a positive correlation between structural complexity and biodiversity. This is due to increased surface area and a higher diversity of ecological niches.

• Seagrass vs. Soft Sediment Functioning:

  • Seagrass adds leaves, stems, and rhizomes to the sediment, providing more niches than bare soft sediment.

  • Epifauna: Organisms living on the surface of plants (e.g., copepods, snails, bryozoans).

  • Net Ecosystem Metabolism: During the day, seagrass produces oxygen ($O_2$) via photosynthesis and consumes carbon dioxide ($CO_2$). At night, both the plants and animals consume $O_2$ and release $CO_2$ via respiration. The total oxygen level depends on the balance of these processes and the biomass of organisms present.

Week 6

Soft Sediments 101: Definition and Distribution

• Global Scale and Coverage:

  • Oceans and coasts cover more than $70\%$ of the Earth's surface.

  • Most of the seabed consists of unconsolidated soft sediment, making it one of the largest habitat types on Earth.

  • Approximately $65.5\%$ of the planet is covered by ocean deeper than $150\,m$, nearly all of which is soft sediment.

• Habitat Structure:

  • Although soft sediments often appear to be featureless planes, they provide a complex three-dimensional environment for a diverse array of biota.

  • Photic Zone: In these areas, marine angiosperms (salt marshes, mangroves, seagrasses) are present and drive primary productivity.

  • Deep Sea (Below Photic Zone): Communities are dependent on subsidies from autotrophic communities. These subsidies include driftwood, plankton fall, and whale fall.

  • Processes in the Deep Sea: Specialized processes like sulfur dioxide breakdown and methanogenesis occur, though at much slower rates compared to shallow systems.

Factors Influencing Sediment Composition

• Key Variables: Soft sediments are complex and vary based on five interlinked factors:

  1. Size (Grain Size): The physical size of the particles.

  2. Depth: Closely correlated to size and physical energy.

  3. Origin: How the sediment arrived (terrestrial vs. biogenic).

  4. Organic Material: The amount of carbon/nutrients present.

  5. Productivity: Links back to organic material and energy flow.

• Classification System: Sediments are classified by size as gravel, sand, silt, or clay. Mud is typically a mixture of silt or clay.

• Physical Dynamics:

  • There is a strong relationship between tides, waves, and currents versus sediment size.

  • Depositional Environments: Low-energy environments where fine sediments (silt/clay) settle.

  • Erosional Environments: High-energy environments (like those with heavy wave action) where only larger grain sizes (gravel/sand) remain.

• Marine Zonation:

  • Intertidal Zone: The area between high and low tide; can be erosional or depositional.

  • Subtidal Zone: Broken into the Neuritic Zone (down to $200\,m$) and the Oceanic Zone.

  • Oceanic Strata: Sunlight penetrates the upper oceanic zone; the Aphotic Zone extends down to $400\,m$; the Abyssal Zone lies below that.

• Origin of Sediments:

  • Terrestrial: Originate from land. Riverine discharge is the largest source, bringing nutrients and sediments. Glacial ice and ice sheet melt are also significant sources.

  • Biogenic/Calcareous: Common in tropical regions where biological or chemical processes drive distribution.

Biodiversity and Taxonomic Groups

• Species Richness: Benthic species in soft sediments form one of the richest species pools on the planet due to the habitat's massive volume.

• Primary Producers and Base of Food Chain:

  • Bacteria: Essential for decomposing and remineralizing organic matter and nutrient cycling. They are ubiquitous and transfer carbon up the food chain.

  • Microphytobenthos (Benthic Microalgae): Often pinnate diatoms that form a biofilm on the sediment-water interface in the photic zone. They provide oxygen and uptake nutrients.

  • Marine Angiosperms: Seagrasses and seaweeds that stabilize the bed and create complex habitat structure.

• Dominant Infauna and Epifauna Taxa:

  • Polychaetes (Annelids): The most dominant taxa. Roles include burrowing, suspension feeding, filter feeding, and predation. They transform organic matter from the pelagic realm to the sediment interface.

  • Crustaceans: Include crabs, shrimps, ostracods, isopods, amphipods, and decapods. They are involved in shifting sediment and cover all feeding modes including parasitism.

  • Echinoderms: Sea stars, brittle stars, sand dollars, sea urchins, and sea cucumbers. They occupy all feeding modes from detritivores to active carnivores.

  • Mollusks: Snails, bivalves, and nudibranchs. They can be herbivores, detritivores, or active predators (e.g., whelks).

• Size-based Clades:

  • Macrofauna: Large enough to see with the naked eye.

  • Meiofauna: Smaller organisms like fine crustaceans and nematodes.

  • Microbiota: Protists and bacteria.

Functional Diversity and Traits

• Definitions:

  • Biodiversity: Includes all species, genotypic/phenotypic variation, and spatial/temporal variability.

  • Taxonomic Diversity: The average taxonomic pathway between randomly chosen individuals; a measure of heterogeneity and critical for food webs.

  • Functional Diversity: The range of things organisms do and the services they provide. It relates to ecosystem dynamics, stability, and productivity.

• Traits vs. Roles:

  • Traits: Physical or life-history characteristics of an individual (e.g., body size, morphology, movement, feeding habits, reproductive techniques such as $r$ vs. $k$ selection).

  • Roles: The ecosystem-level outcome of those traits (e.g., bioturbator, bioirrigator, gas exchange facilitator, organic matter recycler).

• Bioturbation and Bio-irrigation:

  • Animals create complex structures in the sediment.

  • Bioturbation (moving sediment) and bio-irrigation (moving water through sediment) accelerate organic matter breakdown and oxygenate deeper layers.

  • Large-bodied organisms can bioturbate deeper, significantly affecting oxygenation depth.

Ecosystem Processes: Carbon and Nitrogen Cycling

• Carbon Cycle (Benthic Perspective):

  • Soft sediments are depositional repositories for plankton fall, zooplankton fall, detritus, and driftwood.

  • Biota oxidize (break down), transport, convert, and recycle this carbon.

  • Net Ecosystem Metabolism (NEM): The balance between primary production and respiration.

  • Autotrophic System: Productivity dominates (NEM > 0); net oxygen production occurs.

  • Heterotrophic System: Respiration/consumption dominates (NEM < 0); net oxygen consumption occurs.

• Nitrogen Cycle:

  • Organic nitrogen is mineralized into ammonia ($NH_3$).

  • Nitrification: Ammonia is oxidized into nitrates ($NO_3^-$) in the oxic (oxygenated) sediment layer. This is driven by infaunal activity.

  • Denitrification: Nitrates are converted to nitrogen gas ($N_2$) in suboxic/anoxic sediment and released into the atmosphere. This requires both oxic and anoxic sediment zones.

Human Impacts on Soft Sediments

• Pollution Sources:

  • Plastics: Macro and microplastics. Coastal areas have high concentrations; studies in European fjords estimate up to $7,000\,plastic\,kilograms\,DS$.

  • Urban Residues: Pharmaceuticals, personal care products, and household chemicals.

  • Heavy Metals: Lead, Zinc, Mercury ($most\,toxic$), and Arsenic ($least\,toxic$). Metals like Zinc are a major legacy issue in the Derwent Estuary (once the 6th most polluted in the world).

  • Agricultural Residues: Pesticides and fertilizers (notably impacting the Great Barrier Reef).

• Oil Spills: Cause direct toxicity, smothering, and inhibition of gas exchange.

• Physical Disturbance: Industrial dredging, commercial trawling, and construction (pylons/wharves) turn over anoxic sediment, releasing buried toxins and killing sensitive species.

Nutrient Enrichment and the Pearson-Rosenberg Model

• The Pearson-Rosenberg Species Abundance Biomass Model:

  1. Pristine State: High species diversity, normal biomass, and abundance.

  2. Stimulation Phase: Moderate nutrients increase species richness and biomass as nitrogen is often a limiting factor.

  3. Transitory/Opportunistic Phase: Beyond a certain threshold, diversity drops. Biomass decreases, but abundance peaks due to a few $r$-selected opportunistic species (e.g., capitellid worms).

  4. Azoic/Grossly Polluted Phase: Oxygen is depleted; anoxic sediment reaches the surface. Only sulfur-reducing or methane-producing bacteria remain.

• Salmon Aquaculture Case Study:

  • In Tasmania, open marine cage systems release waste feed and fecal material ($solid\,organic\,matter$) and soluble nitrogen products (ammonia).

  • Approximately $76\%$ of nitrogen fed to fish is excreted as dissolved products across the gills.

  • Impacts are mitigated by depth, current flow, and tidal action.

  • Regulation in Tasmania is modeled on Pearson-Rosenberg theory to prevent sediments from reaching the azoic state.

Week 7

Coral Reef Introduction and Biogeography

• Global Distribution:

  • Corals typically occur in waters with temperatures between $18^{\circ}C$ and $36^{\circ}C$.

  • The most typical temperature range for coral reefs is $26^{\circ}C$ to $28^{\circ}C$.

  • They are generally found between $30^{\circ}$ North and $30^{\circ}$ South latitudes.

• Geographic Exceptions:

  • Distribution is heavily driven by oceanographic currents.

  • Sydney Harbor: Corals are growing and expanding, overtaking Algae-dominated reefs in the northern parts.

  • Lord Howe Island: Home to the most southern coral reef in the world.

• The Coral Triangle:

  • Location: Regions from Northern Australia extending out to the Philippines.

  • Biodiversity Statistic: Contains approximately $76\%$ of the world’s coral species.

  • Species Richness: Supports $6,006$ species of fish and more than half of the world's mangrove species.

  • Economic Value: Supports million-dollar tuna fisheries and tourism.

  • Epicenter: Western Indonesia (specifically Bird's Head Peninsula) has the highest coral and fish diversity globally.

Types of Coral Reefs

• Classification: Coral reefs are broadly classified into four main classes:

  • Patch Reefs: Isolated coral reefs occurring on the continental shelf. They are neither connected to mainland nor forming a barrier.

  • Barrier Reefs: Formed on the edge of a continental or island shelf. The Great Barrier Reef is the most famous example, spanning $2,000\,km$.

  • Fringing Reefs: Reefs that grow directly around the edges of islands or landmasses.

  • Atolls: Formed through a process where a fringing reef grows around a volcanic island. Over millions of years (e.g., Midway Atoll took $28 \times 10^6$ years), the land subsides into the ocean while the coral continues to grow upward toward the light, leaving a ring-shaped reef.

• Historical Examples:

  • Bikini Atoll (Marshall Islands): Famous for post-WWII nuclear testing. The US military placed a naval fleet (including an aircraft carrier) inside the atoll to test the impact of atomic bombs. It is currently a dive destination where an aircraft carrier sits at approximately $40\,m$ depth.

  • Elizabeth and Middleton Reefs: Located north of Lord Howe Island and part of New South Wales/Australian Marine Parks. These feature classic fringing reefs with unique lagoon systems in the center.

Coral Biology and Physiology

• Colonial Anatomy:

  • Corals are colonial animals sharing a common calcium carbonate skeleton.

  • The structure is made of individual animals called polyps.

  • Taxonomy: Closely related to anemones and jellyfish (described as an "upside-down jellyfish").

• The Coral Polyp:

  • Consists of a stomach tube and surrounding tentacles.

  • Tentacles use stinging cells to collect zooplankton from ocean currents.

• Symbiosis with Zooxanthellae:

  • Definition: Zooxanthellae are dinoflagellates (single-celled organisms with cilia) that live inside the coral polyp tissue (just beneath the epidermis).

  • Photosynthesis: They absorb carbon dioxide and sunlight to produce oxygen and energy for the coral.

  • Coloration: The characteristic colors of coral species are provided by their specific zooxanthellae.

  • Thermotolerance: Research suggests that after expelling zooxanthellae due to thermal stress, corals may absorb different, more thermally tolerant species of dinoflagellates during recovery.

Coral Reproduction and Restoration

• Asexual Reproduction:

  • Budding: A second polyp forms on the wall of the host. This results in low dispersal (settlement within $mm$ or $cm$) and identical DNA.

• Sexual Reproduction (Coral Spawning):

  • Corals release eggs and sperm on-mass into the water column.

  • Mass Spawning Strategy: Maximizes the probability of fertilization in the vast ocean.

  • Cues: Spawning is synchronized by tides, moon phases (often $1$ to $6$ nights after the first full moon in October), and temperature.

  • Hybridization Avoidance: Different species spawn at different times (e.g., night one vs. night six) to prevent cross-species fertilization.

  • Larval Development: Larvae settle on reefs and begin building calcium carbonate structures; most species acquire zooxanthellae after settlement.

• Restoration Technology:

  • Institutions are scaling up technology to produce millions of baby corals annually.

  • Focus: Making "coral babies" tougher and more adaptable to future marine heatwaves.

Physical Drivers and Environmental Factors

• Light: Critical for photosynthesis. Most corals are restricted to the top $30\,m$, though photosynthetic corals have been found in the mesophotic zone ($30\,m$ to $150\,m$) where light is extremely limited.

• Nutrients: Tropical waters are typically nutrient-poor (oligotrophic), leading to high light attenuation (water clarity).

• Sediment Loading: Agriculture (e.g., sugarcane farming in Queensland) increases sediment and fertilizers in rivers, which can smother reefs. Improved management is currently reducing these inputs.

• Cyclones: These are natural restructuring processes. However, the cumulative effect of frequent cyclones combined with other stressors (bleaching, pollution) reduces reef resilience.

Biological Interactions and Reef Ecology

• Bioeroders: Animals that consume or scrape the reef structure.

  • Parrotfish: Possess beak-like structures to scrape coral surfaces.

  • Crown-of-Thorns Starfish (COTS): Experience "boom and bust" population cycles. During booms, they consume coral at rates faster than the reef can recover, often leading to transitions from coral-dominated to algal-dominated reefs.

• Symbiotic Relationships: Many organisms live within the reef structure, such as "Christmas tree worms" (living in tubes inside the carbonate skeleton), oysters, and bivalves.

Threats to Coral Reefs: Bleaching and Overfishing

• Coral Bleaching:

  • Caused by thermal stress (warming water).

  • Mechanism: Corals expel their zooxanthellae, leaving the white skeleton visible. The coral is not immediately dead but is highly stressed.

  • Historical Frequency: Once every decade. Modern Frequency: Back-to-back events since $2000$.

  • 2016 Event: Driven by a strong El Niño; record-breaking sea surface temperatures caused massive die-offs of Giant Kelp in Tasmania and coral in the northern GBR.

  • 2024 Event: Represented the $5^{th}$ mass bleaching event since $2016$ and the $4^{th}$ global event. It had the largest spatial footprint recorded, affecting the entirety of the GBR.

  • Hard Coral Cover: The last annual report showed a $26\%$ to $30\%$ decline, the highest annual drop ever recorded on the GBR.

• Fishing Impacts:

  • Coral Trout: Highly territorial and prized; fishers can remove entire populations from a single reef quickly.

  • Dynamite Fishing: Used in some Pacific Islands for subsistence; stuns all fish but destroys reef structure.

  • Shark Finning: Removal of apex predators disrupts the entire trophic balance. Efforts are underway to educate communities on using the whole shark (e.g., meat and liver).

Tropical vs. Temperate Reef Comparison

• Tropical Reefs:

  • Warm, nutrient-poor.

  • Low primary productivity (except zooxanthellae).

  • High fish diversity; low macro-invertebrate diversity.

• Temperate Reefs:

  • Cool, nutrient-rich.

  • High primary productivity (Algae/Kelp dominated).

  • Lower fish diversity typically, though a "biodiversity hump" exists around Coffs Harbour due to the convergence of tropical and temperate species.

  • Higher mobile macro-invertebrate diversity.

Darwin’s Paradox: Scientific Debates

• The Paradox: Why do coral reefs have such high biodiversity and productivity when they exist in "oceanic deserts" (nutrient-poor waters)?

• The "Sponge Loop" Theory: Sponges filter massive amounts of water, digesting nutrients and excreting them in a form that other reef organisms can use, acting as nutrient pumps.

• Revisionist View: Recent research suggests "Darwin's Paradox" may be a case of "Chinese whispers," as no specific mention of the paradox was found in Darwin's original literature. Furthermore, many reefs are co-located near river systems that provide sufficient nutrients to support an "oceanic oasis."

Continental Shelf Habitats: General Characteristics

• Definition: Defined by the $200\,m$ depth contour. The shelf exhibits a low-relief, gentle gradient from $0\,m$ to $200\,m$.

• Economic Importance: Supports $80\%$ of global seafood catches.

• Mapping Gap: Only about $20\%$ of the continental shelf is mapped. Scientists often know more about the abyssal plains ($4,000\,m+$) than the shelf between $30\,m$ and $200\,m$.

• Geological Features:

  • Canyons: Carved by ancient river systems (e.g., the Derwent) when sea levels were lower. These canyons now funnel cold, nutrient-rich water from the deep sea onto the shelf.

  • Shelf Break: The sharp transition where the shelf drops off into the slope and abyssal plains.

Shelf Oceanography and Primary Productivity

• The East Australian Current (EAC): The primary driver of oceanography on the East Coast. It brings warm, nutrient-poor subtropical water southward toward Tasmania.

• Upwelling: When warm surface water moves offshore, it pulls up cold, nutrient-rich water. This stimulates phytoplankton growth, supporting the food chain for Krill, Jack Mackerel, and Bluefin Tuna.

• Phytoplankton: Microscopic photosynthetic organisms (Diatoms, Cyanobacteria). Responsible for $70\%$ of global oxygen and carbon dioxide uptake.

• Zooplankton: Drifting animals (Copepods, Krill, larval fish). Many perform "Diel Vertical Migration," staying deep during the day to avoid predators and rising to the surface at night to feed.

The Match-Mismatch Hypothesis

• Theory: The survival of a fish population with planktonic larvae depends on the timing of spawning matching the peak abundance of zooplankton (food).

• Tasmanian Case Study (Jack Mackerel):

  • Westerly winds cause upwelling of nutrient-rich subantarctic water.

  • Strong winds ($40$-day oscillation) lead to Krill swarms.

  • If the winds are calm, nutrients are low, leading to smaller Copepods instead of Krill. Without Krill, the Jack Mackerel fishery fails.

Benthic Habitats: Soft Sediments and Rocky Reefs

• Soft Sediments: Comprise $90^{th}$ percentile of the continental shelf area. Includes varied textures: coarse sand, shell grit, silt. Host to microphytobenthos, starfish, worms, and Flathead.

• Rocky Reefs: Biodiversity hotspots. Can be high-relief (cliffs) or low-relief (rock fragments).

• Canyons and Upwelling: Canyons like those in the Flinders Marine Park act as "nutrient pumps," supporting massive sponge gardens and diverse fish assemblages.

Temperate Mesophotic Ecosystems (TME)

• Definition: Sessile invertebrate-dominated reefs located between $30\,m$ and $150\,m$ depth.

• Light Constraints: Light is the primary driver of the transition from Algae/Kelp (Shallow) to Sponges/Corals (Mesophotic). As depth increases, red light is absorbed first, leaving only blue/purple wavelengths.

• Mesophotic Biology: Home to Black Corals (exoskeleton is black, but polyps look white), diverse sponges, and Butterfly Perch ($Caesioperca$).

• Research Methodology:

  • Multibeam Sonar: Maps the seafloor.

  • BRUVs (Baited Remote Underwater Video): Stationary cameras used to count fish.

  • ROVs/AUVs: Underwater robots used to photograph and fly grids over reefs.

  • Technical Diving: Highly specialized diving down to $150\,m$ requiring four hours of decompression for a five-minute working interval.

Case Studies and Marine Parks

• Tasman Peninsula: Features a relic coastline from $20,000$ years ago (under $80\,m$ to $120\,m$ of water) which has significant cultural connections to indigenous history.

• Port Stephens Study: Found zero overlap between fish communities in shallow (<30\,m) vs. mesophotic (>30\,m) zones. Shallow reefs had double the species richness, while mesophotic zones hosted specialists like Ocean Jacket, Nannygai, Dories, and Gummy Shark.

• Tasman Fracture Marine Park: Located in the Southwest Corner of Tasmania. Studies show rock lobsters grow significantly slower here than elsewhere, likely due to cold temperatures and reaching the ecosystem's carrying capacity.

Threats to Continental Shelf Habitats

• Pollution: Heavy rainfall and flood plumes (e.g., Coffs Harbour) can extend $6,400\,km$ offshore, smothering deep-sea corals and sponges with sediment.

• Marine Heatwaves:

  • Surface Heatwaves: Direct heating from sunlight of the upper water column.

  • Full Water Column Heatwaves: Warming of the entire body from top to bottom.

  • Subsurface Heatwaves: Most concerning; hot blobs of water move beneath the surface, undetectable by satellite sea surface temperature (SST) monitoring. These have been observed "glowing white" (bleaching) sponge gardens in $40\,m$ of water.

Week 8

Introduction and Scope of Oceanic Particles

• Instructor Identification: The lecture is delivered by Robert Strepek, a researcher at the Institute for Marine and Antarctic Studies (IMS). He is filling in for Philip Boyd. Strepek specializes in phytoplankton physiology, ecology, and biogeochemistry.

• Core Topic: The lecture focuses on the production, transformation, and decomposition of particles within the ocean. These particles are critical for understanding oceanic biogeochemistry and ecology.

• Visual Evidence: Particles are ubiquitous in the ocean, often appearing as tiny, drifting, or sinking flakes. Images from deep-sea submersibles like the Woods Hole Oceanographic Institute's Alvin show these particles even in the deepest parts of the water column.

• Importance of Particles:

  • Ecological Importance: They serve as a food source for various marine organisms.

  • Biogeochemical Importance: They act as a conduit for carbon sequestration, moving carbon from the atmosphere to the deep ocean.

Primary Particle Producers: Phytoplankton

• Definition: Phytoplankton are single-celled, free-drifting photosynthetic organisms. They function similarly to land plants by performing photosynthesis but are phylogenetically diverse, ranging from groups as different as humans are to mushrooms.

• Photosynthesis Process: They take inorganic carbon ($CO_2$) dissolved in seawater and convert it into complex carbohydrates and sugars using light energy.

• Size Diversity: Phytoplankton span three orders of magnitude in size, including:

  • Cyanobacteria: The smallest producers (the "shrews" of the phytoplankton world).

  • Colonial Nitrogen Fixers: Such as Trichodesmium, which can exceed $1000\,\mu m$ and be visible to the naked eye.

  • Phaeocystis: Found commonly in the Southern Ocean; they form large spheres held together by mucus or polysaccharides.

  • Diatoms: Characterized by long spines and a biogenic silica (opal) exoskeleton.

  • Coccolithophores: Known for their calcium carbonate plates (coccoliths).

Diatoms: The Nanotechnologists of the Ocean

• Frustule: The outer skeleton of a diatom, composed of biogenic silica ($SiO_2$), also known as opal.

• Ballast Effect: Biogenic silica is denser than seawater, acting as a ballast that causes diatoms to sink naturally.

• Protection: The hard exoskeleton serves as body armor to reduce mortality from grazing zooplankton.

• Morphology:

  • Pennate Diatoms: Feature bilateral symmetry (axis of symmetry along the long axis).

  • Centric Diatoms: Feature radial symmetry, appearing circular from the top, though some may be cylindrical.

• Observation via Epifluorescence: Under a microscope, living cells emit a red glow when excited by blue light. This is due to the photosynthetic pigment chlorophyll, allowing researchers to identify active, living cells.

Formation of Large Aggregates and Marine Snow

• Marine Snow: Large flocks of organic material formed by the aggregation of smaller particles.

• Aggregation Mechanisms:

  • Spines: Structural features like the long spines of Chaetoceros allow cells to interlock as their abundance increases.

  • Biological Glue (TEP): Cells release extra organic material, specifically Transparent Exopolymer Particles (TEP). These are sticky polysaccharides that act as a glue, increasing the contact rate and ensuring cells stay together upon contact.

• TEPP Detection: TEP is transparent but can be visualized using a stain called Alcian Blue, which specifically targets polysaccharides.

• Transition from Dissolved to Particulate:

  • Dissolved Organic Carbon (DOC): Includes polymers and gels measured in nanometers or kilodaltons.

  • Particulate Organic Carbon (POC): Formed when aggregates exceed a size threshold, typically around $1\,\mu m$.

• Bacterial Colonization: TEP is a rich energy source for bacteria. Using nucleic acid stains like DAPI (which emits blue light), researchers can see bacteria colonizing TEP strands to respire and transform the carbon.

Particle Sinking Dynamics and Thresholds

• Critical Thresholds: Aggregation and sinking often happen rapidly once a specific phytoplankton abundance is reached. In iron-fertilization experiments in the Northeast Pacific (Gulf of Alaska), sinking was negligible until a critical diatom density caused a massive spike in contact rates.

• Factors Driving Aggregation:

  1. Cell Geometry: Size and shape.

  2. Density: Presence of ballast like silica.

  3. Physical Factors: Shear forces and mixed layer depth.

  4. Stickiness: Concentration of TEP.

Tools for Measuring Particle Flux

• Satellites: Track blooms by measuring light emitted/reflected due to chlorophyll $a$. Rapid disappearances of blooms often indicate mass sinking events.

• Sediment Traps: These are cone-shaped devices deployed at various depths (e.g., $1\,km$, $2\,km$, and $4\,km$). A carousel at the bottom of the cone rotates every $10$ to $15$ days to collect settling material in separate cups.

  • Transit Time: Data from the North Atlantic Bloom Experiment (NABE) showed that a pulse of organic material takes about $20$ to $25\text{ days}$ to transit $1\,km$ vertically.

• BathySnap: A camera system on a tripod situated on the seafloor ($4000\,m$ depth). It takes periodic photos to observe the arrival of "marine snow."

  • Observations: Dr. Robert Lampitt's BathySnap footage shows the seafloor transforming from a barren landscape to being covered in a thick "mat" or "carpet" of green diatom material (saliceous ooze) within days of a surface bloom ending.

Ecological Transformations and Grazing

• Heterotrophic Grazers: Organisms that consume phytoplankton, thereby repackaging small particles into larger, denser ones. Groups include:

  • Nano-flagellates: (~$5\,\mu m$).

  • Ciliates and Copepods: Copepods have a specific affinity for diatoms.

  • Krill: Common in the Southern Ocean.

  • Salps: Gelatinous filter-feeders known as the "vacuum cleaners" of the sea due to their non-selective feeding.

  • Arrow Worms (Chaetognaths): Predatory zooplankton.

• Predator-Prey Oscillations: Phytoplankton biomass increases when growth rates ($\mu$) exceed grazing rates ($m$). Eventually, zooplankton populations respond, grazing the biomass down in a cyclical pattern.

• Fecal Pellets: The primary product of grazing. These are carbon-rich and dense.

  • Copepod Pellets: Small, log-shaped, often containing visible undigested chlorophyll fragments.

  • Salp Pellets: Large, extremely dense pellets that can sink at rates up to $400\,m/day$.

Microbial Decomposition and the Viral Shunt

• Bacterial Abundance: Seawater contains approximately $10^9$ bacterial cells per liter ($10^6$ per milliliter).

• The Viral Shunt: Viruses infect host cells (like cyanobacteria), causing them to burst (lysis). This releases organic material back into the dissolved pool, short-circuiting the transfer of carbon to higher trophic levels.

• Bacterial Activity: Bacteria colonize sinking particles because they are rich in organic material compared to the surrounding water. They use extracellular enzymes, such as Leucine Aminopeptidase (LEP), to decompose organic matter.

• Remineralization Length Scales: Different elements are recycled at different depths:

  • Nitrogen and Carbon: Broken down rapidly in the upper ocean (short length scale).

  • Biogenic Silica: Harder to break down and has lower demand; it typically sinks much deeper before dissolving.

Vertical Migration and the Biological Carbon Pump

• Diurnal Vertical Migration (DVM): Many zooplankton, like copepods, stay in the deep, dark ocean (down to $400$ or $600\,m$) during the day to avoid visual predators. They migrate to the surface at night to feed. This act accelerates carbon export because they consume organic matter at the surface and defecate at depth.

• The Biological Carbon Pump: The collective process of converting inorganic carbon to organic matter, which then sinks and is sequestered.

  • Global Flux: Approximately $10\,gigatons$ ($10^{10}\,tons$) of Particulate Organic Carbon (POC) sink out of the surface ocean annually. This is roughly equivalent to annual anthropogenic $CO_2$ emissions.

  • Efficiency: The pump is an inverted pyramid. While a large amount of carbon is fixed at the surface, only $5\%$–$50\%$ reaches $100\,m$, and only $1\%$–$10\%$ typically reaches the seafloor ($4000\,m$), where it may be sequestered for millennia.

The Nitrogen Cycle: Nitrification

• Process: The decomposition of organic material releases nutrients back into the water.

• Sequential Steps:

  1. Particulate Organic Nitrogen (PON) Decay: Bacteria feast on organic matter, causing PON to decline.

  2. Ammonium ($NH_4^+$) Release: The first inorganic form of nitrogen produced during decay.

  3. Nitrite ($NO_2^-$) Formation: Specialized bacteria oxidize ammonium into nitrite.

  4. Nitrate ($NO_3^-$) Formation: Further oxidation by distinct microbial specialists results in nitrate, the most oxidized form of nitrogen, which can then be mixed back to the surface to fuel new phytoplankton growth.

Week 9

Microbial Food Webs and Seasonality: An Introduction

• Small but Mighty Microbes: The lectures focus on the disproportionate impact that microscopic organisms have on global ocean systems. The microbial food web is a self-contained system where phytoplankton and heterotrophic bacteria interact through photosynthesis and the consumption of dissolved and particulate matter.

• Adriatic Sea Case Study: In the Adriatic Sea between Italy and Croatia, microbes produce extensive strands of mucilage. This phenomenon results from a combination of ocean physics and dissolved constituents produced by the microbial food web. These strands pose a significant problem for tourism (e.g., near Venice) as they create an unpleasant environment for swimmers and divers, reaching levels described as an epidemic.

• The Seasonal Cycle and Modeling: Microbes exhibit distinct seasonality. Research often utilizes mathematical models, such as a $1-D$ mathematical model ($27KB$ in size), to quantify microbial dynamics. Modeling allows for "thought experiments," such as performing sensitivity analyses to determine how changing specific components (e.g., surface ocean conditions versus subsurface conditions) affects the export of carbon.

The Roles and Life Cycles of Marine Viruses

• Viral Abundance: Viruses are the most abundant forms in the ocean. There are approximately $10^9$ viruses in every teaspoon of seawater and an estimated $10^{30}$ viruses in the global ocean. If placed end-to-end, these viruses would span across the nearest $60$ galaxies.

• Infection Rates: Every second, there are approximately $10^{23}$ viral infections occurring in the ocean. Viruses are agents of infection and disease, but they also serve as a vast reservoir of genetic diversity.

• Genetic Redistribution: Viruses facilitate Lateral Gene Transfer (horizontal gene transfer). When viruses lyse (burst) host cells, they redistribute genetic material, introducing novelty and variability into microbial communities.

• Viral Life Cycles:

  • Lytic Cycle: The virus sneaks nucleic acid into an oblivious host. The host makes copies of the viral nucleic acid, and the viruses self-assemble inside the host. Eventually, the virus causes the cell to burst (lysis), releasing new viruses to start the cycle again.

  • Chronic Cycle: This is a non-lethal cycle. Similar to the lytic cycle, the virus injects nucleic acid and the host creates copies. However, instead of bursting the host cell, the protein viruses "slip out" of the cell continuously, allowing the host to survive while the virus spreads.

Heterotrophic Bacteria and the Concept of Substrate-Controlled Succession

• Abundance and Size: There are approximately $10^6$ heterotrophic bacteria in every teaspoon of seawater. They are typically only a couple of microns ($\text{μm}$) in size. Because they are too small to be identified clearly via standard microscopy, researchers must use agar plating or molecular biological tools to determine community structure.

• Metabolic Versatility: Heterotrophic bacteria (also called organotrophs or phagotrophs) obtain energy from Particulate Organic Carbon (POC) or Dissolved Organic Carbon (DOC). They are highly versatile, capable of thriving in hot springs or breaking down pollutants like oil.

• Substrate-Controlled Succession: This concept, coined by Teeling, posits that microbial communities break down organic matter in a specialized, sequential order. Using the analogy of a burger:

  • One group of microbes specializes in eating the bun.

  • Another group specializes in the patty.

  • A third group targets the lettuce.

  • Together, as a community, they decompose the entire "phytoplankton bloom burger."

• Extracellular Enzymes and Solubilization: Most particulate matter is too large to enter a bacterial cell directly. Bacteria secrete axonal (external) enzymes that target specific substrates (e.g., proteins or sugars). These enzymes break the material down into smaller, dissolved forms that can be transported across the cell wall. This process is known as solubilization.

• Depth and Specialization: As particles sink through the water column (e.g., from $50m$ to $500m$ or even $4,000m$), they are continuously degraded. Bacteria at different depths are specialized to target the remaining molecules. Research from Hawaii using molecular biology shows unique genetic sequences at $4,000m$, indicating depth-specific microbial functionality.

Phytoplankton Seasonality and the Dynamics of the Spring Bloom

• The Bloom Trigger: The annual spring bloom is a pivotal event for carbon entry into the ocean. The cycle progresses as follows:

  • Winter: Reduced daylight, low solar angle, and storms reset the system, replenishing inorganic nutrients.

  • Spring: Day length (photoperiod) increases and the solar angle changes. Insulation heats the upper layer of the water, creating a density difference (stratification). This acts like oil on top of vinaigrette/salad dressing.

  • Growth: With light and nutrients available, phytoplankton biomass increases rapidly ("flipping the switch").

• Net Community Production: Seasonality is expressed not only in biomass but in rates. During the bloom, photosynthesis by autotrophs (the "engine room") dominates. As light fades, photosynthesis drops, bacterial respiration increases, and net community production can become negative.

• Nutrient Regimes:

  • F-ratio: The ratio of growth driven by "new" nutrients (like nitrate ($NO_3^-$)) versus recycled nutrients (like ammonium ($NH_4^+$)).

  • Early in the year, new nutrients drive the system; later, recycled nutrients (the "circular economy") play a larger role.

Trophic Transfers, Size Rules, and Ecological Efficiency

• The Importance of Size: Size dictates biomass, sinking rates, and cellular physiology.

  • Surface Area to Volume (S/V) Ratio: This ratio decreases as cell size increases. Smaller cells have a higher S/V ratio, allowing for more nutrient transporters on the cell membrane relative to their volume, making them more efficient in nutrient-poor environments.

• Trophic Transfer Efficiency: Energy is lost as it moves up the food web. Carbon and energy are partitioned into:

  • Respiration: Releasing $CO_2$.

  • Excretion: Releasing Dissolved Organic Carbon (DOC).

  • Growth/Biomass.

  • Egestion: Fecal pellets (POC).

• The Efficiency of Salps: While conventional food webs involving multiple transfers (e.g., bacteria → flagellate → ciliate → copepod) are inefficient, salps act as "underwater vacuum cleaners." They can consume a wide range of particle sizes directly, increasing efficiency by bypassing multiple trophic levels.

• Predator-Prey Oscillations: Grazing by microzooplankton (like flagellates with two whip-like flagella) creates feeding currents. If they graze faster than the prey grows, prey becomes scarce and energy-inefficient to hunt, causing the grazer population to drop and allowing prey to recover. This creates a natural oscillation.

• The "Iron Ferris Wheel": In some ocean regions, growth is limited by iron (anemia of the ocean). Elements like iron are tightly cycled between viruses, zooplankton, and bacteria in a system metaphorically called the "Ferris wheel."

Oceanographic Technology: Satellites and Robotic Floats

• Satellites: Used to detect pigments like chlorophyll (via HPLC) to monitor biomass from space. While effective for a global view, satellites only see the top couple of meters of the ocean ($2-D$ window).

• Argo/Robotic Floats: Autonomous robots that fill the gaps left by ships and satellites.

  • Mechanisms: They use an oil-filled bladder (sac) to change buoyancy. To sink, the oil is pulled into the float; to rise, it is pushed into an external bladder.

  • Mission: They are typically "parked" at $2,000m$ (park depth) to avoid biofouling (growth on sensors). Every $10$ days (the "ninja cycle"), they rise to the surface, measuring temperature, salinity (density), nitrate, and pH every meter. They transmit data via satellite before returning to depth.

  • Life Span: Highly flexible and pre-programmable, with a battery life of roughly $4$ years. They can operate under sea ice, though sea-ice inundation or punctures can cause float failure ("death rattle").

Global Biogeochemical Cycles: The Microbial Engine

• The Redfield-like Balance: A foundational equation for understanding the Earth system is:     $CO_2 + H_2O \rightleftharpoons CH_2O + O_2$     This balance between photosynthesis (carbon fixation) and respiration/decomposition maintains the atmospheric composition.

• Microbial Engines: A seminal paper by Paul Falkowski describes microbes as the engines driving the Earth's biogeochemical cycles (carbon, nitrogen, sulfur, hydrogen, and manganese). These cycles were beautifully balanced before the Industrial Revolution, keeping atmospheric $CO_2$ levels stable over geological time.

• Marine Snow and Sinking: Not all organic matter is recycled. In the North Atlantic or Gulf of Alaska, large blooms can aggregate and sink rapidly ($40$ to $50$ meters per day). Images of the seafloor at $4km$ depth show "green fuzz," indicating that phytoplankton reached the bottom without being fully grazed or decomposed.

Questions and Audience Interaction

• Question regarding the definition of non-living particles (Detritus):

  • Speaker's Response: Detritus typically consists of breakdown products, including fecal pellets from copepods, dead cells, and various heterogeneous particles that aggregate together. These are essentially the "breakdown fragments" of the system.

• Question regarding profiling under sea ice:

  • Speaker's Response: Floats have sensors that detect temperature. If the water is too cold ($-1.5^{\circ}C$), suggesting the presence of sea ice, the float will stop its ascent to avoid damaging itself on the ice. It will then store the profile data and attempt to transmit it later when it finds open water.

Practical Notes: Sensitivity Analysis and Modeling

• Objective: To understand the structure and sensitivity of ocean systems.

• Method: Using a control run of a model based on literature values, students perform a Sensitivity Analysis. This involves systematically changing one component (e.g., trophic transfer efficiency, usually around $30\%$, or nutrient values) and measuring the impact on carbon export.

• Process: Change a term → Observe change → Reset term → Change another term. This allows researchers to quantify which variables are most influential in the global carbon cycle.

Week 10

Environmental Characterization of Polar Regions

• Extreme Seasonality in Light:

  • Variations in light represent the most significant seasonal driver. At high latitudes, the cycle shifts from nearly $24$ hours of daylight in summer to nearly complete darkness in winter.

• Sea Ice Dynamics:

  • The defining characteristic of polar environments is the seasonal expansion and contraction of sea ice.

  • Antarctic Context: Antarctica is an isolated landmass at the South Pole, surrounded by the Southern Ocean. It is characterized by high seasonal flux in ice extent.

  • Arctic Context: The Arctic is an ocean surrounded by continents (landmasses), which restricts the mobility of the ice.

• Antarctic Circumpolar Current (ACC):

  • This is the world's strongest current, flowing in an easterly direction.

  • It is driven by powerful westerly winds ("Roaring Forties", "Furious Fifties", and "Screaming Sixties") and is uninterrupted by landmasses.

  • Fronts: The ACC contains distinct fronts, such as the Sub-Antarctic Front and the Polar Front.

    • These fronts manage the exchange of heat, salt, and carbon between the Southern Ocean and global oceans.

    • They provide nutrient-rich hotspots for foraging predators like seals and whales.

• Biogeography and Endemism:

  • Antarctica's long geological isolation and the sharp temperature gradients across fronts create strong biogeographic boundaries.

  • Faunal Endemism: There are an estimated $9,000$ species in the Southern Ocean. Approximately $70\% - 80\%$ of these species are endemic, meaning they are found nowhere else on Earth.

Oceanography and Water Masses

• Coastal and Slope Currents:

  • Slope Current: A west-flowing current closer to the coast, driven by coastal winds, which regulates exchange between coastal and open ocean systems.

  • Gyres:

    • Weddell Sea Gyre: A critical site for the formation of Antarctic Bottom Water.

    • Ross Sea Gyre: Maintains nutrients and particles on the shelf; aids in keeping the Ross Sea Polynya (open water surrounded by ice) open, creating a highly productive ecosystem.

• Specific Water Masses:

  • Antarctic Surface Water: The upper ocean layer shaped by seasonality, ice melt, and freshwater; controls stratification and phytoplankton bloom timing.

  • Circumpolar Deep Water (CDW): A warm, nutrient-rich water mass at mid-depth that supplies heat and nutrients to the surface and ice shelves.

  • Antarctic Bottom Water (AABW):

    • Extremely cold and dense water formed near the continental shelf.

    • Process: When sea ice forms, salt is expelled (brine rejection), leaving dense, salty water that sinks to the seafloor and spreads globally.

Bathymetry and Ice Impact

• Deep Continental Shelves:

  • Unlike typical continental shelves (roughly $200 - 300\,\text{m}$ deep), the Antarctic shelf is unusually deep due to the weight of the ice caps and historical ice movement.

  • Bathymetry values often reach $600 - 800\,\text{m}$, with some areas exceeding $1,200\,\text{m}$.

• Iceberg Scouring:

  • Icebergs act like "bulldozers" when they hit the seafloor (grounding).

  • They scrape the floor, leaving physical records and significantly impacting benthic ecosystems.

Global Importance of Polar Regions

• Thermohaline Circulation (The Global Conveyor Belt):

  • Brine rejection during sea ice formation creates dense water that sinks to the bottom.

  • This water contains high levels of dissolved oxygen, nutrients, and organic matter, effectively "ventilating" the deep ocean.

  • These water masses slowly travel north, rising in the Indian and Pacific Oceans.

  • Cycle Duration: It takes approximately $1,000$ years for a parcel of water to complete this global journey.

• The Albedo Effect:

  • Ice and snow act as major reflectors of solar radiation.

  • Snow can reflect up to $90\%$ of sunlight, whereas the open ocean reflects only $10\%$.

  • This process is crucial for regulating Earth's temperature.

• Sea Level Rise Mitigation:

  • Sea ice does not contribute to sea level rise directly through melting, as it is already in the water.

  • Land Ice (Global Guardian): Ice on land (glaciers/sheets) is the primary concern for sea level rise.

  • Projections:

    • If the entire Antarctic Ice Sheet melted, sea level would rise by approximately $60\,\text{m}$.

    • Melting of the Greenland Ice Sheet and other glaciers combined would result in a $7\,\text{m}$ rise.

• Ecosystem Services:

  • The Southern Ocean covers $30\%$ of the global ocean surface but absorbs $16\%$ of human $CO_2$ emissions.

  • It acts as a major carbon sink through phytoplankton pulses that sink to the deep ocean (sequestration).

  • Economic Valuation: Conservative estimates value the ecosystem services (fisheries, tourism, carbon storage) of the Southern Ocean at over $180$ billion dollars.

Types and Properties of Ice

• Land Ice:

  • Ice Sheets: Cumulative snow over hundreds of thousands of years on the continent.

  • Ice Shelves: Parts of the ice sheet that move off land and float on the water; can be hundreds of meters thick and extend hundreds of kilometers.

  • Icebergs: Freshwater ice carved from ice shelves/sheets. They are less dense than seawater and move via tides, wind, and currents. Massive "tabular" icebergs can be the size of Tasmania.

• Sea Ice Formation Cycle:

  • Seawater freezing point: $-1.8\,^\circ\text{C}$.

  • Grease Ice: First stage: waxy, oily-looking layer of crystals on the surface.

  • Pancake Ice: Ice crystals aggregate into circular discs.

  • Pack Ice: Thicker ice formed as "pancakes" raft together. It is dynamic and mobile, containing "leads" (cracks) used by ships for navigation.

  • Fast Ice: Sea ice that is "fastened" or attached to the coast, ice shelves, or grounded icebergs. It is stable and can persist for $1 - 3$ years, providing habitat for seals and penguins.

• Internal Structure of Sea Ice:

  • Sea ice is not a solid block. It contains a matrix of Brine Channels.

  • These channels house algae and organisms; they serve as the "seed" for the primary productivity blooms when the ice melts.

Arctic vs. Antarctic Sea Ice Comparison

• Geography:

  • Arctic: Ocean surrounded by land. Low precipitation; ice growth is aided by freshwater input from rivers.

  • Antarctic: Continent surrounded by ocean. High precipitation/snowfall; snow weight can sink sea ice, creating slushy pools.

• Ice Characteristics:

  • Thickness: Arctic ice is typically thicker ($2 - 3\,\text{m}$, up to $4 - 5\,\text{m}$); Antarctic ice is thinner ($1 - 2\,\text{m}$).

  • Age: Arctic ice is often multi-year (up to $7-8$ years old); Antarctic ice is dynamic, with most melting and regrowing annually (year or less in age).

  • Extent:

    • Arctic: $16$ million $km^2$ (winter) to $7$ million $km^2$ (summer).

    • Antarctic: $19$ million $km^2$ (winter) to $3-4$ million $km^2$ (summer).

  • Dynamics: Arctic ice is more symmetric and prone to collision; Antarctic ice is more asymmetric due to the open ocean edge.

Primary Productivity and Marine Snow

• Primary Productivity Blooms:

  • Occur around October (Spring) as sunlight returns.

  • Drivers: Light availability (+photosynthesis), ice melt (releasing trapped nutrients like Iron ($Fe$) and seeding organisms), and ocean stratification (keeping phytoplankton in the sunlit "mixed layer").

• The Marginal Ice Zone (MIZ):

  • The region ($100 - 200\,\text{km}$ wide) between dense pack ice and the open ocean. It is the most productive zone.

• Marine Snow:

  • Particulate organic matter (dead phytoplankton, zooplankton fecal pellets, diatom aggregates) that sinks from the surface into the deep.

  • This pulse of material supports rich benthic ecosystems and contributes to carbon sequestration.

• Under-Ice Algae: Significant productivity occurs on the underside of sea ice and ice shelves (often diatoms), forming a "mini-forest" that supports critters like krill before the main bloom.

Questions & Discussion

• Q: What determines the color of "Jade" icebergs?

  • A: It is related to the compaction of the ice and the crystal structure, which affects how it refracts light; it contains specific minerals/organic matter different from standard white/blue icebergs.

• Q: Does under-ice productivity contribute significantly compared to the main bloom?

  • A: While the Marginal Ice Zone (MIZ) blooms often swamp it in terms of sheer volume, under-ice algae are critical, especially for seeding and feeding benthic systems in coastal areas where ice persists longer.

• Q: Example Exam Question: Explain the physical process of brine rejection and its global implications.

  • A: 1. Process: Brine rejection occurs during sea ice formation as salt is excluded from the ice matrix. 2. AABW: This creates dense, cold, salty water that sinks. 3. Circulation: It drives the thermohaline circulation (global conveyor belt). 4. Ventilation: It redistributes oxygen, heat, and nutrients to the deep global ocean. 5. Climate: It helps regulate the global climate cycle over a $1,000$ year period.

• Q: Example Exam Question: Identify three differences between Arctic and Antarctic sea ice.

  • A: 1. Arctic ice is generally thicker ($2 - 3\,\text{m}$) than Antarctic ice ($1 - 2\,\text{m}$). 2. Arctic ice is multi-year (up to $8$ years), whereas Antarctic ice is mostly seasonal. 3. The Arctic is an ocean surrounded by land (constrained), while Antarctica is land surrounded by ocean (dynamic/unconstrained).

Week 11

Benthic Ecosystems of the Antarctic Seafloor

• Endemism and Richness:

  • $80 \text{ to } 90\%$ of the species found in Antarctic benthic ecosystems are unique to the region and found nowhere else on Earth.

  • Total species richness in Antarctica is estimated at approximately $9,000 \text{ species}$, which is considered as rich and diverse as the Great Barrier Reef.

• Geographic Isolation:

  • The high level of endemism is primarily attributed to long-term geographic isolation.

  • The separation between Antarctica and other continents (the Gondwana break apart) became complete approximately $53 \text{ million years}$ ago.

• Adaptations to Extreme Conditions:

  • Food Limitation: Organisms must adapt to highly seasonal food inputs. They build up lipid (fat) reserves during the summer.

  • Flexible Feeding Strategies:

    • The sea star Odenesta can switch from scavenging to deposit feeding and can use its tube feet to capture drifting particulate matter.

    • The sea urchin Sterochinus feeds opportunistically when food becomes available.

  • Reproductive Timing: Most organisms align reproduction with spring phytoplankton blooms and pulses.

  • Brooding: There is a high incidence of brooding (carrying offspring, similar to a male seahorse) rather than releasing pelagic larvae into ocean currents.

  • Microbial Pathways: Feeding on microbial and detrital pathways is critical for survival over winter when fresh material is scarce.

• Growth and Longevity:

  • Organisms are generally cold-adapted with narrow thermal tolerance ranges.

  • Many species are slow-growing and long-lived. For example, some Glass sponges ($Steralo$ sponge) are estimated to be up to $1,000 \text{ years}$ old.

  • Gigantism: Many species grow significantly larger than their relatives in temperate or tropical waters.

    • Sea Cucumbers: Filter-feeding sea cucumbers in the Ross Sea reach sizes of $30 \text{ centimeters}$ and are physically massive.

    • Sea Spiders: Antarctic species can grow to several centimeters in diameter, significantly larger than temperate species.

Drivers and Biodiversity of Benthic Habitats

• Physical Drivers:

  • Temperature: Some species, like certain ice fish, have extremely narrow temperature tolerance ranges.

  • Light and Ice: Macroalgal (microalgae/seaweed) communities are restricted to coastal areas or Subantarctic Islands where ice breaks out frequently, allowing light for photosynthesis. Invertebrate-dominated communities prevail where ice is persistent.

  • Iceberg Scouring:

    • Icebergs can be several hundred meters deep and act like a bulldozer, mowing down everything on the seafloor.

    • Intermediate Disturbance Hypothesis: In shallow areas ($0 \text{ to } 120 \text{ meters}$ deep), occasional scouring creates a patchwork mosaic of successional stages, which can lead to higher diversity than areas with no scouring or extreme recurring scouring.

• Distribution Patterns:

  • Depth Gradient: Abundance and diversity generally decrease with increasing depth.

  • Currents: Moderate to strong currents favor sessile invertebrates (filter feeders like corals and sponges). Low current areas with high primary productivity favor deposit feeders.

  • Substrate: Muddy basins host deposit feeders, while hard substrates host sessile communities.

    • Dropstones: Stones dropped by melting ice provide "hard substrate islands" in otherwise muddy environments.

• Mapping and Research:

  • Vanessa Lucia (IMAS): Developed "Seamap Antarctica" to quantify and map species distributions.

  • Biodiversity Hotspots: These are generally found in shallower areas with colder waters and moderate current flow.

  • $84\%$ of identified biodiversity hotspots occur in the coolest water regions of the shelf.

Physiology and Adaptations of Antarctic Benthic Fish

• Endemicity: Antarctic benthic and demersal fish show high endemicity but relatively low diversity, dominated by the family Notothenids (including ice fish and toothfish).

• Thermal Adaptations:

  • Antifreeze Proteins: Many fish have proteins in their blood to prevent ice crystal formation, as water temperatures can reach $-1.8\,^\circ C$.

  • Colder Metabolic Rates: Biological processes occur slowly in these temperatures.

• Buoyancy and Blood:

  • Lack of Swim Bladders: Evolutionarily, many species lost swim bladders and achieved neutral buoyancy through low-density bones and high lipid content.

  • Clear Blood: Some ice fish lack haemoglobin entirely. Because cold water is oxygen-rich, oxygen is transported directly in the plasma. These fish possess large hearts, large blood volumes, and large gill surface areas to compensate.

• Nesting: Some species, like ice fish in the Weddell Sea, produce demersal eggs and create massive nesting sites. One colony was found containing thousands of nests guarded by ice fish.

• Fisheries: Regulated by Camelar (Commission for the Conservation of Antarctic Marine Living Resources), focusing on Antarctic and Patagonian toothfish and mackerel icefish.

Pelagic Food Webs and Trophic Pathways

• Biomass Distribution:

  • Large biomass is concentrated at the base of the food chain (microbes and phytoplankton).

  • Biomass decreases as body size increases (top predators like whales and seals).

• Primary Producers:

  • Diatoms: Dominate coastal systems and ice edges.

  • Pennate Diatoms: Long, skinny structures adapted to live inside brine channels within sea ice.

  • Haptophytes (Phaeocystis): Form large jelly-like aggregations in open water and marginal ice blooms.

• Secondary Producers and Mid-Trophic Levels:

  • Zooplankton (amphipods, pteropods, copepods, jellies).

  • Mesopelagic Fish: Live between $200 \text{ to } 1,000 \text{ meters}$ deep; prey on secondary producers.

• Food Web Models:

  • Classical View: Phytoplankton > Krill > Whales.

  • Salp Food Chain: Often considered an "evolutionary dead end" because salps are mostly water with low protein/fat. They become important when krill are scarce but provide poor nutrition.

  • Regional Dominance:

    • Polar Front: Dominated by the copepod/mesopelagic fish pathway; Antarctic krill are less common.

    • Marginal Ice Zone: Highly krill-centric due to phytoplankton blooms.

    • Shelf Zone: Includes silverfish and squid as key components.

Biology and Life Cycle of Antarctic Krill

• Keystone Species: Euphausia superba (Antarctic krill) is the central keystone species.

• Biological Characteristics:

  • Diet: Consume primarily diatoms and some copepods.

  • Behaviour: Form massive, dense swarms (similar to bait fish) and undergo strong dial migration (moving up and down the water column to avoid predators).

  • Shrinking Adaption: Krill can moult and reabsorb tissue to shrink in body size when food is scarce.

• Life Cycle and Ice:

  • Juveniles are sea ice-associated over winter.

  • Sea ice provides shelter from predators and a food source (diatoms and detritus on the underside of the ice).

• Krill Fishery: Mainly focused on the West Antarctic Peninsula and islands like South Georgia and South Shetland; managed by Camelar.

Marine Megafauna: Whales, Seals, and Birds

• Whaling History:

  • Exploration was driven by whaling and sealing for oil and blubber (used for lighting).

  • $1904$: Norwegian whalers opened a station at South Georgia.

  • $7 \text{ species}$ of whales were successively exploited. "Right whales" were named for being the "right" (easiest) whales to harvest.

  • $1987$: A global moratorium on commercial whaling was established, managed by the International Whaling Commission (IWC).

• Antarctic Seals:

  • Leopard Seals: Top territorial predators, $2 \text{ to } 3 \text{ meters}$ long; hunt penguins and fish.

  • Crabeater Seals: Most abundant seal; $90\%$ of Antarctic seal stocks. They eat krill using specialized teeth that act like baleen filters.

  • Weddell Seals: Friendly seals that inhabit fast ice; use teeth to keep breathing holes open year-round.

• Penguins and Birds:

  • Approx. $5,000,000 \text{ penguins}$ in Antarctica.

  • Emperor Penguins: Largest penguin ($40 \text{ kilos}$). Breed over winter on fast ice. Chicks fledge in spring/summer to align with the food bloom.

  • Snow Petrols: Use ice for resting and predator avoidance.

Arctic Ecosystem Comparisons: Polar Cod and Polar Bears

• Arctic Food Web:

  • The central pathway is the Antarctic cod (Polar cod), which feeds on crustaceans.

  • Top predator: Polar Bear. Sea ice is a vital hunting platform for catching seals, walruses, and whales.

  • Decline: Decreasing Arctic sea ice thickness and early breakup force bears further north, leading to population declines.

• Whale Differences:

  • Baleen whales visit both poles but generally do not forage under ice.

  • Minke Whales: The only whales that occupy deep ice packs; they have a hard rostrum (nose) to poke through thin ice for breathing.

Environmental Change: Warming, Acidification, and Sea Ice Loss

• Drive by Carbon Dioxide:

  • Warming Pathways: Affects salinity, water masses, iceberg scouring, and causes sea ice/ice shelf loss.

  • Acidification: Affects the entire water column, particularly calcifying organisms.

• The Sea Ice "Heartbeat":

  • Antarctic sea ice crashed in $2013$. This trend of low extent continued through $2024$, $2025$, and into $2026$. This is seen as a potential tipping point.

• Regional Trends: The West Antarctic Peninsula is warming faster and losing ice more rapidly than East Antarctica.

Impact of Environmental Change on Ecosystem Components

• Benthic Communities:

  • Loss of cold-adapted species and invasion of king crabs (rare on the shelf currently).

  • Changes in dominance from corals/calcifiers to sponges due to acidification.

• Plankton and Krill:

  • Phenology Mismatch: A change in the timing of blooms can cause predators to miss their peak food period.

  • Krill vs. Salps: Loss of sea ice may lead to fewer krill and higher dominance of the less nutritious salp food chain.

  • Hatching Success: Increased $CO_2$ levels have been shown to reduce the hatching rate of Antarctic krill.

• Emperor Penguins:

  • Fast ice melt before chicks fledge causes colony failure (chicks cannot swim without adult waterproof feathers).

  • One study predicts emperor penguins could be quasi-extinct by $2100$. They are currently listed as Endangered on the IU CN Red List.

Questions & Discussion

• Question: Is the Arctic benthic system similar to the Antarctic one, and does the lack of large predators (like penguins) in the Arctic influence the benthic community?

• Response: Benthic systems in both hemispheres are influenced by cold-water minerals, sponges, currents, and food availability. Arctic systems still have demersal fish that behave as predators, eating brittle stars, amphipods, and worms on the seafloor, so the predatory dynamics at that level are similar even if the specific megafauna differ.

• Question: Regarding the shift to a salp-based food chain, is that considered a bad alternative?

• Response: Generally, yes. Salps have significantly lower nutritional value compared to Antarctic krill. While salps are part of the ecosystem, they represent a poor quality food source in terms of protein and fat for higher vertebrates.