Among the problems and miscalculations encountered in the first mission were overstocked fish dying and clogging filtration systems, unanticipated condensation making the "desert" too wet, population explosions of greenhouse ants and cockroaches, and morning glories overgrowing the "rainforest", blocking out other plants. In addition, construction itself was a challenge, such as manipulating the bodies of water to have waves and tidal changes was a difficulty.[20][21]
There was controversy when the public learned that the project had allowed an injured member to leave and return, carrying new material inside. The team claimed the only new supplies brought in were plastic bags, but others accused them of bringing food and other items. More criticism was raised when it was learned that, likewise, the project had been pumping oxygen inside, to make up for a failure in the balance of the system that resulted in the amount of oxygen steadily declining.[22]
The oxygen inside the facility, which began at 20.9%, fell at a steady pace and after 16 months was down to 14.5%. This is equivalent to the oxygen availability at an elevation of 4,080 meters (13,400 ft).[23] Since some biospherians were starting to have symptoms like sleep apnea and fatigue, Walford and the medical team decided to boost oxygen with injections in January and August 1993.
Daily fluctuation of carbon dioxide dynamics was typically 600 ppm because of the strong drawdown during sunlight hours by plant photosynthesis, followed by a similar rise during the nighttime when system respiration dominated. As expected, there was also a strong seasonal signature to CO2 levels, with wintertime levels as high as 4,000-4,500 ppm and summertime levels near 1,000 ppm. The crew worked to manage the CO2 by occasionally turning on a CO2 scrubber, activating and de-activating the desert and savannah through control of irrigation water, cutting and storing biomass to sequester carbon, and utilizing all potential planting areas with fast-growing species to increase system photosynthesis.[24]
Many suspected the drop in oxygen was due to microbes in the soil.[citation needed] The soils were selected to have enough carbon to provide for the plants of the ecosystems to grow from infancy to maturity, a plant mass increase of perhaps 20 tons (18,000 kg).[25] The release rate of that soil carbon as carbon dioxide by respiration of soil microbes was an unknown that the Biosphere 2 experiment was designed to reveal.[citation needed]
The respiration rate was faster than the photosynthesis (possibly in part due to relatively low light penetration through the glazed structure) resulting in a slow decrease of oxygen. A mystery accompanied the oxygen decline: the corresponding increase in carbon dioxide did not appear. This concealed the underlying process until an investigation by Jeff Severinghaus and Wallace Broecker of Columbia University's Lamont Doherty Earth Observatory using isotopic analysis showed that carbon dioxide was reacting with exposed concrete inside Biosphere 2 to form calcium carbonate, thereby sequestering both carbon and oxygen.[26]
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