Comparative transcriptome combined with metabolomic and physiological analyses revealed ROS-mediated redox signaling affecting rice growth and cellular iron homeostasis under varying pH conditions

Abstract

Mechanisms by which soil pH affects rice growth await further elucidation. We have used a Systems Biology approach to elucidate the nature of the damage caused by extreme pH to plant growth and iron homeostasis, and the adaptive plant responses elicited. Optimum pH for rice growth was pH 6. Comparative transcriptome analysis revealed that 83% of 1318 DEGs were down-regulated at pH 4, while 73% among of 1168 DEGs were up-regulated at pH 8. GO enrichment analysis showed significant enhancement of oxidation-reduction and oxidative stress responses. Environmental pH regulated cellular oxidation-reduction processes and metabolic pathways controlling rice growth. Additionally, pH affected cellular iron-homeostasis by regulating root apoplastic iron deposition. Low pH enhanced iron mobilization from root apoplast and accumulation in plant tissues, and down-regulated iron transport related genes to prevent iron toxicity. Conversely,high pH induced blockage of iron mobilization from root apoplast. Rhizosphere pH affected aerenchyma formation and exodermis-apoplastic barriers under control of ROS, already weakened and enhanced by low pH and high pH, respectively. ROS-mediated redox signaling plays an important role in regulating rice growth under varying pH conditions. Cellular iron homeostasis was disturbed through regulation of iron plaque formation and apoplastic iron mobilization in rice roots under acidic and alkaline conditions.