Transcriptome and proteome analyses reveal high nitrate or ammonium applications alleviate photosynthetic decline of Phoebe bournei seedlings under elevated carbon dioxide by regulating glnA and rbcS

Abstract Background Phoebe bournei (Hemsl.) Y.C. Yang is a precious timber species and is listed as a national secondary protection plant in China. P. bournei seedlings show obvious photosynthetic decline when grown long-term under an elevated CO2 concentration (eCO2). This decline can be alleviated by high nitrate or ammonium applications. However, the underlying mechanisms of photosynthetic decline and the regulation of photosynthesis by nitrogen under eCO2 have not yet been elucidated. Results We performed transcriptomic and proteomic analyses of P. bournei of seedlings grown under an ambient CO2 (AC) concentration (350 ± 70µmol·mol− 1) and applied with either a moderate level of nitrate(0.8 g per seedling, N), a high level of nitrate (1.2 g per seedling, hN), or a moderate level of ammonium (0.8 g per seedling, A) and compared them with those of seedlings grown under an elevated CO2 (EC) concentration (700 ± 10µmol·mol− 1,i.e., AC_N vs EC_N, AC_hN vs EC_hN, AC_A vs EC_A) to identify differentially expressed genes (DEGs) and differentially expressed genes (DEGs). We identified 4528 (AC_N vs EC_N), 1378 (AC_hN vs EC_hN), and 252 (AC_A vs EC_A) DEGs and 230, 514, and 234 DEPs, respectively, of which 59 specific genes and 21 specific proteins were related to the regulation of photosynthesis by nitrogen under eCO2. A combined transcriptomic and proteomic analysis identified 7 correlation-DEGs-DEPs (cor-DEGs-DEPs) genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of these cor-DEGs-DEPs genes revealed crucial pathways involved in glyoxylate and dicarboxylate metabolism and nitrogen metabolism. The rbcS and glnA cor-DEGs-DEPs genes were enriched in these two metabolisms. We propose that the rbcS and glnA cor-DEGs-DEPs genes play an important role in photosynthetic decline and nitrogen regulation. Conclusions Transcriptomic and proteomic profiles of P. bournei were used to evaluate elevated CO2 effects on photosynthesis and nitrogen regulation. The elevated CO2 triggered the downregulation of glnA and RbcS, thus causing photosynthetic decline. High nitrate or ammonium applications alleviated the downregulation of glnA and rbcS and, hence, alleviated photosynthetic decline.