Graduate Research Course
Ocean Biodiversity & Biochemistry
From sunlit plankton to hadal trenches — how life adapts to pressure, darkness, and chemistry across 11 kilometers of ocean depth, and how climate change is reshaping every layer.
Key Equations of Ocean Biochemistry
Light Attenuation (Beer–Lambert)
\( I(z) = I_0 \cdot e^{-k_d z} \)
Hydrostatic Pressure
\( P(z) = P_0 + \rho g z \quad \text{(+1 atm per 10 m)} \)
O₂ Solubility
\( C_{O_2}^{sat}(T) = A \cdot e^{-B/T} \)
Martin Curve (Particle Flux)
\( F(z) = F_0 \left(\frac{z}{z_0}\right)^{-b}, \quad b \approx 0.86 \)
Bioluminescence Quantum Yield
\( \Phi = \frac{\text{photons emitted}}{\text{molecules reacted}} \)
Coral Bleaching Threshold
\( P_{bleach} = \frac{1}{1 + e^{-k(DHW - DHW_c)}} \)
About This Course
The ocean covers 71% of Earth's surface and reaches depths exceeding 11 km in the Mariana Trench. From sunlit surface waters teeming with phytoplankton that produce half the planet's oxygen, through the twilight zone where the largest daily animal migration occurs, to hydrothermal vents where life thrives on chemical energy in total darkness — each depth zone presents unique biochemical challenges and extraordinary evolutionary solutions.
This course examines ocean life through the lens of physics and chemistry: how pressure reshapes protein folding at abyssal depths, why bioluminescence dominates communication below the photic zone, how chemosynthetic bacteria power entire ecosystems without sunlight, and how coral calcification depends on delicate carbonate chemistry now threatened by anthropogenic CO₂ emissions.
Every module includes MathJax derivations, SVG diagrams, and computational models. Cross-links to our Climate & Biodiversity, Oceanography, and Ecological Biochemistry courses provide broader context on Earth-system interactions.
Nine Modules
M0
Ocean Zones & Chemistry
Depth zones, temperature/salinity/O₂/pH profiles, thermohaline circulation structure, and light attenuation through the water column.
M1
Epipelagic (0–200 m)
Phytoplankton biochemistry, marine photosynthesis, zooplankton grazing, the microbial loop, and surface ocean food webs.
M2
Mesopelagic (200–1000 m)
The twilight zone, diel vertical migration (the largest biomass movement on Earth), bioluminescence chemistry, and oxygen minimum zones.
M3
Bathypelagic (1–4 km)
Deep-sea fish pressure adaptations, piezolyte TMAO biochemistry, giant squid physiology, and marine snow particle flux.
M4
Abyssal & Hadal (4–11 km)
Extreme pressure biochemistry with piezolytes, hadal trench endemism, barophilic bacteria, and life in the Mariana Trench.
M5
Hydrothermal Vents & Chemosynthesis
Black and white smokers, Riftia tubeworm symbiosis, sulfur-oxidizing bacteria, and anaerobic methane-oxidizing (ANME) archaea.
M6
Coral Reef Biochemistry
Zooxanthellae photosynthesis, CaCO₃ calcification, reef building mechanics, coral bleaching thresholds, and ocean acidification.
M7
Polar Ocean Life
Sea ice algae, Antarctic krill ecology, antifreeze glycoproteins, polar food webs, and Arctic amplification impacts on marine life.
M8
Climate Change Impacts
Ocean warming, acidification, deoxygenation, deep-sea mining threats, and depth-specific vulnerability assessment across all zones.
Recommended Textbooks
- [1] Thurman, H.V. & Trujillo, A.P. (2020). Essentials of Oceanography. 13th ed. Pearson.
- [2] Roberts, C.M. (2012). The Ocean of Life: The Fate of Man and the Sea. Viking.
- [3] Levinton, J.S. (2017). Marine Biology: Function, Biodiversity, Ecology. 5th ed. Oxford University Press.
- [4] Kaiser, M.J. et al. (2020). Marine Ecology: Processes, Systems, and Impacts. 3rd ed. Oxford University Press.