Disturbed electron transport beyond PSI changes metabolome and transcriptome in Zn-deficient soybean

Low Zn availability in soils is a problem in many parts of the world, with tremendous consequences for food and feed production because Zn deficiency affects the yield and quality of plants. In this study we investigated the consequences of Zn-limitation in hydroponically cultivated soybean (Glycine max L.) plants. Parameters of photosynthesis biophysics were determined by spatially and spectrally resolved Kautsky and OJIP fluorescence kinetics and oxygen production at two time points (V4 stage, after five weeks, and pod development stage, R5–R6, after 8–10 weeks). Lower NPQ at 730 nm and lower quantum yield of electron transport flux until PSI acceptors were observed, indicating an inhibition of the PSI acceptor side. Metalloproteomics showed that down-regulation of Cu/Zn-superoxide dismutase (CuZnSOD) and Zn‑carbonic anhydrase (CA) were primary consequences of Zn-limitation. This explained the effects on photosynthesis in terms of decreased use of excitons, which consequently led to oxidative stress. Indeed, untargeted metabolomics revealed an accumulation of lipid oxidation products in the Zn-deficient leaves. Further response to Zn deficiency included up-regulation of gene expression of cell wall metabolism, response to (a)biotic stressors and antioxidant activity, which correlated with accumulation of antioxidants, Vit B6, (iso)flavonoids and phytoalexins. •Zn deficiency (Zn0) leads to electron transport disturbance in soybean leaves.•OJIP kinetics show specific photosynthesis inhibition on the PSI acceptor side.•Metalloproteomic analyses confirm decreased Cu/Zn-SOD and CA abundance in Zn0.•Zn0 upregulates the EXORDIUM gene, which promotes growth in low CO2.•Zn0 caused lipid oxidation and induction of secondary metabolites counteracting ROS.