Carbon Cycle

Carbon is the structural material of every living thing in miniBIOTA, and the carbon cycle is the path it travels from the air into plant tissue, through the food web, back into the substrate as detritus, and finally back into the water and air as CO2 through decomposition and respiration. Because the enclosure is sealed, the carbon budget is fixed: no new carbon enters from outside, and none leaves. Every molecule of organic carbon in the system was fixed by a plant or algal cell, and every one of those molecules will eventually be respired back to CO2 and fixed again.

The carbon cycle describes the movement of carbon through the atmosphere, living organisms, soil, water, and geological reservoirs. Carbon enters the biological cycle through photosynthesis, where plants and algae incorporate CO2 from the air or water into organic molecules. It moves through the food web as consumers eat producers and other consumers eat them. It returns to inorganic form through two pathways: respiration, where living organisms oxidize organic carbon for energy and release CO2 as a byproduct; and decomposition, where bacteria, fungi, and detritivores break down dead organic matter and release CO2 in the process.

In any ecosystem, carbon is constantly moving between living biomass, dead organic matter (detritus), dissolved organic carbon in water, and CO2 in air and water. The relative size of these pools and the speed of exchange between them define the carbon character of an ecosystem. Slow decomposition (as in cold, waterlogged, or acidic environments) causes organic matter to accumulate in the soil or sediment. Fast decomposition (as in warm, well-oxygenated, neutral-pH environments) keeps carbon cycling rapidly through the food web.

Florida's coastal and wetland ecosystems are globally significant carbon systems. Seagrass meadows store substantial carbon in their below-ground root and rhizome biomass and in the organic-rich sediments they build over time; this stored coastal carbon, often called blue carbon, is recognized as a significant and vulnerable carbon reservoir. Mangrove forests accumulate deep organic-rich sediments through slow decomposition under waterlogged, low-oxygen conditions, sequestering carbon at rates among the highest of any terrestrial or coastal ecosystem type.

Florida's freshwater systems vary between carbon sources and carbon sinks depending on nutrient state and vegetation cover. Clear, macrophyte-dominated lakes tend to be mild carbon sinks because plant production exceeds decomposition. Turbid, algae-dominated lakes can be carbon sources because algal production is rapid but decomposition of algal cells is also rapid, returning CO2 to the water and atmosphere quickly.

Florida's warm year-round temperatures accelerate decomposition compared to temperate regions, keeping carbon cycling fast and reducing the tendency for organic matter to accumulate. In enclosed, substrate-rich systems like miniBIOTA, however, decomposition rates are constrained by oxygen availability in the substrate, meaning carbon can accumulate in sediment anoxic zones even in a warm system.

The carbon cycle in a sealed enclosure is fundamentally different from any open system. In miniBIOTA, carbon does not enter or leave through gas exchange with the atmosphere, runoff to external water bodies, or burial in geological sediments. The total carbon in the system is fixed; all of it is continuously recycling through the same biological pathways.

This has several consequences that distinguish the miniBIOTA carbon cycle from any natural system.

CO2 is a shared, finite resource. Every molecule of CO2 in the enclosure air and dissolved in the water came from respiration or decomposition. When photosynthesis is active during daylight hours, producers consume CO2 from both the water column and the enclosure atmosphere. When production outpaces respiration across the enclosure, CO2 concentrations drop. Whether CO2 concentration ever reaches limiting levels for photosynthesis in miniBIOTA has not been measured.

The substrate is the dominant long-term carbon sink. In an open system, organic carbon can be exported downstream, buried in deep sediments, or released to the atmosphere. In miniBIOTA, organic carbon that is not fully decomposed accumulates in the substrate as detritus and humus. The Freshwater Lake substrate is described as having developing aerobic and anaerobic zones, with organic detritus accumulating above the sand base. This substrate carbon pool grows over time in the absence of dredging, harvest, or export.

Anaerobic zones slow decomposition and trap carbon. As organic matter accumulates in the substrate, deeper layers can become anoxic. Anaerobic decomposition is slower and less complete than aerobic decomposition, and it produces methane and hydrogen sulfide rather than CO2 as byproducts. The developing anaerobic zone in the Freshwater Lake substrate represents carbon that is cycling on a much slower timescale than the rest of the system.

In the marine and salt-influenced sediments (Mangrove Forest, Marine Shore, Seagrass Meadow), the relevant anaerobic pathway is sulfate reduction rather than the methanogenesis more typical of freshwater sediment. Sulfate-reducing bacteria break down organic matter using sulfate instead of oxygen, producing hydrogen sulfide and bicarbonate alkalinity as byproducts. This distinguishes marine anaerobic decomposition from the freshwater case in one important respect: the sulfide produced is not itself an acid, and carbonate-dissolving acidity in these sediments would require a separate step, either sulfide oxidation at an oxygenated boundary or respiratory CO2 accumulating in porewater. A Seagrass Meadow water test on August 1, 2026 found elevated alkalinity alongside low dissolved calcium, a pattern consistent with active sulfate reduction and carbonate dissolution occurring somewhere in this cross-biome sediment system, though the mechanism has not been isolated or measured directly.

Rain drainage provides a possible route for dissolved organic carbon and fine particles from Prairie through Lakeshore toward Freshwater Lake. The amount and net direction of carbon transfer are unmeasured; the passive subsurface connections equalize water levels bidirectionally. Mangrove litter at the Marine Shore margin supplies a separate marine-side context, not a freshwater-to-marine water connection.

Freshwater Lake is the carbon hub of the aquatic freshwater system. Submerged macrophytes (tapegrass, sagittaria, Amazon sword) fix carbon through photosynthesis and transfer it to the food web through grazing by Slough Crayfish, snails, and amphipods, and through senescence into the detritus pool. The organic detritus substrate is the main long-term carbon storage site in the lake. Developing anaerobic zones below the aerobic surface layer represent carbon that is cycling slowly or not at all on human timescales. Dissolved organic carbon in the water column is processed by the microbial community and consumed by filter feeders.

Prairie supports investigation of terrestrial carbon fixation and transfer through plant–consumer relationships, roots, litter and soil life. Historical grasshopper feeding is not current population evidence, and crickets can be omnivores. Litter enters decomposition directly. Comparative production rates and carbon export to Freshwater Lake remain unmeasured.

Mangrove Forest produces carbon through its canopy and understory. Mangrove leaf litter is the most distinctive carbon input in this biome: thick, waxy leaves decompose slowly and accumulate as organic matter in the mangrove floor substrate. Cockroaches, isopods, and other forest-floor invertebrates are the primary processors of this litter, converting it from large leaf fragments to finer organic particles and eventually to soil organic matter. The Mangrove Forest is likely the terrestrial biome with the slowest carbon turnover due to the combination of dense litter production and slow decomposition rates of mangrove material.

Seagrass Meadow fixes carbon through seagrass production and macroalgal growth. Grazing transferred seagrass and macroalgal carbon to consumer biomass, but the larger-bodied grazers have been lost over 2026: the Eelgrass Isopod and hard-surface snails are extirpated or near-zero, the Mud Crab is being deliberately removed, and the Variegated Sea Urchin was extirpated September 1, 2026. More producer carbon now enters the detritus pathway ungrazed. The partial Caulerpa die-off of August 29, 2026 is a direct instance: a pulse of algal carbon moved straight into decomposition rather than through a consumer. Common Atlantic Marginella, previously listed here as a grazer, was a predator and sediment bioturbator; corrected July 29, 2026. Ungrazed seagrass material enters the detritus pathway in the substrate. The Seagrass Meadow substrate, like the Freshwater Lake substrate, likely accumulates organic carbon over time. A water test on August 1, 2026 found elevated alkalinity alongside low dissolved calcium, evidence consistent with active anaerobic sediment processes and carbonate cycling in this substrate, though not yet isolated from the biome's calcifying organisms or from possible cross-biome transport.

Lakeshore and Marine Shore are transition biomes where biofilm and algae on glass and substrate surfaces fix small amounts of carbon that are grazed directly by snails, amphipods, periwinkles, and Eastern Melampus. These biomes also receive organic inputs from adjacent biomes through water movement and animal activity.

Primary producers (tapegrass, sagittaria, Amazon sword, duckweed, seagrasses, macroalgae, terrestrial grasses, biofilm) are the carbon entry point: they fix CO2 into organic matter and make it available to the food web.

Herbivores and grazers (Slough Crayfish, bladder snails, Malaysian Trumpet Snails, amphipods, grasshoppers, crickets, Mud Crab, and introduced marine hard-surface snails) transfer plant carbon into animal biomass, which is either consumed by the next trophic level or enters the detritus pool when the animal dies. The Variegated Sea Urchin filled this role in the Seagrass Meadow until its extirpation September 1, 2026.

Filter feeders and microcrustaceans (Daphnia, Moina, copepods, Ghost Shrimp) capture dissolved organic carbon, phytoplankton, and suspended particles from the water column, transferring fine particulate carbon into animal biomass.

Detritivores and substrate processors (cockroaches, millipedes, isopods, Malaysian Trumpet Snails, amphipods) break down organic litter and detritus into finer particles, increasing the surface area available to microbial decomposition and accelerating carbon mineralization back to CO2.

Microbial community (bacteria and fungi in substrate and water column) is the final decomposition layer: it mineralizes organic matter to CO2, completing the carbon loop. The microbial community is the most important carbon processor by mass throughput, though it is the least directly observed.

Lighting System drives primary production, which is the only pathway by which CO2 is converted to organic carbon in miniBIOTA. Without the Lighting System, the carbon cycle stops at its entry point. PAR intensity and photoperiod control how fast carbon is fixed.

Rain System provides a potential route for dissolved and particulate material from Prairie through Lakeshore toward Freshwater Lake. Transport amounts, frequency and effects remain unmeasured. The freshwater and marine water networks are separate; within each network passive subsurface connections are bidirectional and equalize water levels.

Climate System influences decomposition rates through its effect on enclosure temperature. Warmer temperatures accelerate microbial activity and decomposition; if the chiller's repair affects enclosure thermal dynamics, it may indirectly affect how quickly organic matter is mineralized in the substrate.

Substrate carbon accumulation (ongoing): The Freshwater Lake substrate is accumulating organic detritus with developing anaerobic zones. As the organic layer deepens, the ratio of anaerobic to aerobic decomposition increases, slowing carbon mineralization and building up a persistent organic layer. This buildup is common in small enclosed freshwater systems and can eventually affect water chemistry, benthic oxygen availability, and substrate conditions for invertebrates. The rate of accumulation, its current depth, and whether it is approaching a threshold that would affect benthic organism health are all unknown.

Anaerobic zone oxygen demand (undocumented risk): Anaerobic decomposition in the Freshwater Lake substrate produces hydrogen sulfide and consumes whatever dissolved oxygen diffuses into the near-substrate layer. The Freshwater Lake dossier identifies dissolved oxygen in the substrate zone as a documented measurement gap with potential consequences for benthic invertebrates. Malaysian Trumpet Snails, amphipods, and juvenile shrimp are all substrate-associated organisms that could be affected by low DO in the benthic layer.

Terrestrial-to-aquatic carbon transport (unmeasured): Rain-driven drainage could carry dissolved organic carbon and fine particles from Prairie through Lakeshore toward Freshwater Lake. Whether this contributes a meaningful carbon or nutrient input relative to in-lake production remains unknown; no quantitative export or beneficial fertilization is established. Rain-cycle disruption changes this potential pathway but does not establish that all terrestrial carbon input stops.

CO2 balance and photosynthesis limitation (unmeasured): Whether the sealed enclosure's CO2 pool can sustain continuous photosynthesis at current production rates, or whether daytime production in heavily planted biomes periodically depletes CO2 to limiting concentrations, has not been measured. This is the most fundamental unresolved question in the miniBIOTA carbon cycle.

Marine sulfate reduction, alkalinity production, and carbonate dissolution (new, August 1, 2026): A Seagrass Meadow water test found elevated alkalinity alongside dissolved calcium notably low relative to expected seawater, with magnesium not depleted, ruling out simple dilution. The working model is that anaerobic sulfate reduction in Mangrove Forest and Seagrass Meadow sediment supplies alkalinity as a byproduct distinct from any direct acidifying effect of the hydrogen sulfide it also produces, while calcification and mineral precipitation elsewhere in the same biomes remove calcium and alkalinity together. Carbonate dissolution, if occurring, would depend on a separate acid source such as sulfide oxidation at an oxygenated boundary or respiratory CO2 in porewater. Whether this mechanism is active, and at what rate, is unmeasured; see [Seagrass Meadow](../biomes/seagrass-meadow.md) for the measurement and [Mangrove Forest](../biomes/mangrove-forest.md) for the documented but only partially traced subsurface transport route.