C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant’s response to microorganisms.

The application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. In the present study, we measured the effects of supplying 5 mM nitrate on the growth of nodules, primary root, and lateral roots under light at 28 °C or dark at 18 °C conditions. Photographs of the nodulated roots were periodically taken by a digital camera at 1-h intervals, and the size of the nodules was measured with newly developed computer software. Nodule growth was depressed approximately 7 h after the addition of nitrate under light conditions. The nodule growth rate under dark conditions was almost half that under light conditions, and nodule growth was further suppressed by the addition of 5 mM nitrate. Similar results were observed for the extending growth rate of the primary root as those for nodule growth supplied with 5 mM nitrate under light/dark conditions. In contrast, the growth of lateral roots was promoted by the addition of 5 mM nitrate. The 2D-PAGE profiles of nodule protein showed similar patterns between the 0 and 5 mM nitrate treatments, which suggested that metabolic integrity may be maintained with the 5 mM nitrate treatment. Further studies are required to confirm whether light or temperature condition may give the primary effect on the growth of nodules and roots.

Soybean is an important crop for human food and feed for livestock. World soybean production is increasing especially in North and South America. Soybean seeds contain a high percentage of protein about 35–40%, and they require a large amount of nitrogen compared with other crops. Soybean plants make root nodules with rhizobia, and rhizobia can fix atmospheric N2 and give the fixed N to the host soybean plants. Also, soybean can absorb nitrogen usually nitrate from soil or fertilizers. The amount of total assimilated nitrogen in shoot is proportional to the soybean seed yield either from nitrogen fixation or from nitrogen absorption, and the nitrogen availability is very important for soybean cultivation. Maintenance of a high and long-term nitrogen fixation activity is very important for a high production of soybean. However, application of chemical nitrogen fertilizers usually depresses nodule formation and nitrogen fixation. Nitrate in direct contact with a nodulated part of roots causes severe inhibition of nodule growth and nitrogen fixation, although a distant part of nodules from nitrate application gives no or little effect. Deep placement of slow-release nitrogen fertilizers, coated urea, or lime nitrogen promoted the growth and seed yield and quality of soybean without depressing nitrogen fixation.

The ammonium produced by nitrogen fixation in the bacteroid is rapidly excreted to cytosol of infected cell of soybean nodules and then assimilated into glutamine and glutamic acid, by glutamine synthetase/glutamate synthase pathway. Most of the nitrogen is further assimilated into ureides, allantoin, and allantoic acid, via purine synthesis, and they are transported through xylem to the shoots. Nitrate absorbed in the roots is reduced by nitrate reductase and nitrite reductase to ammonia either in the roots or leaves. The ammonia is also assimilated by glutamine synthetase/glutamate synthase pathway, and mainly transported by asparagine, and not ureides. The nitrogen transported into leaves is readily utilized for protein synthesis, and then, some of them are decomposed and retransported to roots, apical shoots, and pods via phloem mainly in the form of asparagine.

Leguminous plants form root nodules with rhizobia that fix atmospheric dinitrogen (N₂) for the nitrogen (N) nutrient. Combined nitrogen sources, particular nitrate, severely repress nodule growth and nitrogen fixation activity in soybeans (Glycine max [L.] Merr.). A microarray-based transcriptome analysis and the metabolome analysis were carried out for the roots and nodules of hydroponically grown soybean plants treated with 5 mM of nitrate for 24 h and compared with control without nitrate. Gene expression ratios of nitrate vs. the control were highly enhanced for those probesets related to nitrate transport and assimilation and carbon metabolism in the roots, but much less so in the nodules, except for the nitrate transport and asparagine synthetase. From the metabolome analysis, the concentration ratios of metabolites for the nitrate treatment vs. the control indicated that most of the amino acids, phosphorous-compounds and organic acids in roots were increased about twofold in the roots, whereas in the nodules most of the concentrations of the amino acids, P-compounds and organic acids were decreased while asparagine increased exceptionally. These results may support the hypothesis that nitrate primarily promotes nitrogen and carbon metabolism in the roots, but mainly represses this metabolism in the nodules.