The lower oxygen limit (LOL) in plants marks the oxygen (O2) level where the metabolism shifts from being predominantly aerobic to anaerobic; recent work has shown that respiratory-based indicators of this metabolic shift are well-correlated with changes in chlorophyll a fluorescence signals. The physiological and biochemical changes at the root of this relationship have not been well-described in the literature. The processes involved are spatially separated: chlorophyll fluorescence is associated with the lightdependent reactions and emanates from the chloroplasts whereas aerobic respiration and fermentation occurs in the mitochondria and cytosol, respectively. Evidences outlined in this thesis are used to suggest the mechanistic link between these three regions of the cell is a fluid exchange of cellular reductant. When mitochondrial respiration is inhibited as a result of inadequate O2, used as a terminal electron acceptor, glycolytic reductant in the form of NADH accumulates in the cytosol. Reductant imbalances between the cytosol and organelles can be adjusted indirectly using translocators. Excess chloroplastic reductant is used to reduce the plastoquinone (PQ) pool via NADPH-dehydrogenase, a component of the chlororespiratory pathway, effectively decreasing the photochemical quenching (qP) capacity thereby inducing a switch from minimum fluorescence (Fo) to a higher relative fluorescence (F) value where qP < 1. Subjecting dark-adapted photosystems to low-intensity light increased Fo to a slightly higher F value due to a lightinduced reduction of the oxidized PQ pool when the O2 was above the LOL, but decreased F as a result of a PSI-driven oxidation of the already over-reduced PQ pool when the O2 was below the LOL. Low O2 was also shown to increase violaxanthin deepoxidation and non-photochemical quenching (qN), likely a reflection of the overreduced state of the photosystems and associated pH decrease. Dynamic controlled atmosphere (DCA) is a fluorescence-based controlled atmosphere (CA) system that sets the optimum atmosphere for fruits and vegetables based on a product’s fluorescence response. Experiments in this thesis on the relationship between O2, temperature, light, metabolism, pigmentation and chlorophyll fluorescence were used to interpret the physiology behind fluorescence changes, suggest improved DCA techniques and outline potentially profitable avenues for future research.