Cave Ecology

The complex network of caves were created at the beginning of the Third Age by the use of a powerful and unstable form of magic. As a result, the life contained within has mutated rapidly, which helped it adapt and survive in the new ecosystem created. Below lies the basic ecological and biological adaptation summaries for the life-sustaining caverns.

Sunspots
Light-emitting patches on the ceiling of the cave, as if the rock itself is covered with a glowing paint.

Sunspots are colonies of bioluminescent chemoautotrophic bacteria. High levels of the enzyme luciferase (Luc), existing in the cytosol, is responsible for the release of photons (at wavelengths within the visible spectrum); as the bacterium metabolizes ammonia into nitrogen gas, the combination of the byproducts and oxygen react with luciferase to create visible light. These bacteria possess a circadian clock (that of approximately 24 hours) that controls the phenotypic expression of Luc; for two thirds of it (roughly 16 hours), this enzyme is expressed and light is emitted, but for the other third (roughly 8 hours), the presence of thiocyanate, a Luc-inhibitor, prevents the reaction and release of photon.

The colonies range in size from only a few centimeters across to a diameter of several dozen feet. Cavern size seems to have a direct correlation to the size of these sunspots, but it appears that the colonies are capable of self-regulation as well, never growing past a certain size even in the largest of spaces. Mineral deposits on the ceiling, such as magnesium, iron, or sulphur, provide the necessary inorganic materials for bacterial metabolism, and sunspots tend to grow in dense populations along these veins. The bacterial colonies function much like a superorganism and engage in high levels of intracellular communication. The larger the colony grows, the more signaling molecules, called autoinducers, are produced and released; when the colony reaches a certain size, typically the diameter of six or so inches, the levels of autoinducers triggers the start of the circadian cycle via the production of thiocyanate and subsequent Luc-inhibition. In smaller colonies, the circadian clock appears to be inactive, and as a result these sunspots appear to never "turn off"; as such, they are sometimes dubbed "starspots" by the caves' inhabitants.

The wavelength of the visible light varies primarily on the chemical composition of the surrounding rock from which the bacteria colony grows upon. High magnesium will result in a white light, while larger copper concentrations will cause a blue light.

Sunspots' primary role is to provide the necessary light for photosynthesis. They also release carbon dioxide as a metabolic byproduct which is in turn utilized by the local fauna, although their CO2 production is minimal when compared to that produced by the various species of eukaryotes.

Flora
Thanks to the presence of bioluminescent sunspots, and aided by the remnants of the magic that created these caves, a surprising number of photosynthetic trees, shrubs, and flowers can be found within the cave systems. The years of continual cycles death and rebirth have created a thin layer of soil, but it is neither deep not particularly rich in nutritional value, so many of the species have had to adapt. Often times, roots and mycelium can be seen emerging from the topsoil when they cannot penetrate the rock.

Trees
Trees are most likely to be found in the upper caverns of the massive cave system. While the thin, rocky soil contains adequate amounts of essential elements like potassium, calcium, and phosphorus, it lacks the necessary levels of nitrates; as a result, many of the larger plants have adapted to draw in the nitrogen gas from the air (a byproduct of the sunspots). For example, in deciduous cave trees, the leaves are broader than their overworld counterparts, and the undersides often have large brown spots which are concentrated areas of symbiotic nitrifying bacteria which convert the nitrogen gas into nitrate. Conifers utilize a similar strategy, but their bacterial symbiotes gather along the trunk. This synergistic adaptation has allowed larger species like oaks and cedars to grow up into forests far away from the sun and dirt. Most are the size of their overworld counterparts, but there are parts where, probably due to the magical residue, the trees have grown to massive proportions.

Undergrowth
Most of the vegetation in the caves are ferns and mosses; their simple vascular system and low light requirements allows for a competitive edge over other shrubs and flowers with more complex structures. They tend to dominate in the smaller, darker corners of the caves but, particularly in the main bright caverns, the low-growing ferns can become crowded out by other plants.

Fungi
Particularly in the darker, deeper caves, fungi have cornered the ecological market. They thrive where it is too deep, and therefore too cold, for sunspots to grown on the open rocks. Large networks of fungal forests have sprung into existence in the deep, with some mushrooms towering up to twenty feet in the air particularly in areas near underground lakes and rivers which provide the necessary moisture content. Over the years, these fungi have adapted to lower their required water content both via the evolution of a waxy cuticle layer, and through an increase in the production of the protein chitin, which helps prevent desiccation and adds to the structural integrity of the mushroom's stalk. The mycelium is far-reaching, their hyphae snaking down through whatever pores the rock provides to serve as anchoring points for the massive fruiting bodies.

Fauna
Most creatures living within the caves have adapted by evolving additional rod receptors and retinal structures, similar tapetum lucidum, to better equip them for the dimmer cave light. Their coloration has also altered over time to better match their surroundings; most have taken on darker colors such as greys, blacks, and browns, and even greens, but others have become brighter, some even taking on bioluminescent properties.