Transcriptome and Metabolome Analyses Reveal That Nitrate Strongly Promotes Nitrogen and Carbon Metabolism in Soybean Roots, but Tends to Repress It in Nodules.

Shinji Ishikawa,Yuki Ono,Sayuri Tanabata,Takuji Ohyama,Kuni Sueyoshi,Norikuni Ohtake

doi:10.3390/plants7020032

Shinji Ishikawa, Yuki Ono + Show 4 more

Open Access

https://doi.org/10.3390/plants7020032

Copy DOI

Abstract

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.

Highlights

Soybean is a globally important legume crop that provides proteins and lipids to humans and livestock
We investigated the direct effects of nitrate on the nodule growth of soybean plants cultivated with hydroponics, in which the diameters of the horizontal axes of individual nodules were measured by a slide caliper [21] or the nodule area, fitted to an ellipse oval, was determined through photographs periodically taken by a digital camera [10]
Transcriptome and metabolome analyses of soybean roots and nodules treated with 5 mM of nitrate (NO3 − ) for 24 h revealed that supplying nitrate to the culture solution remarkably affected the expression of genes for enzymes involved in nitrate absorption and nitrogen assimilation in the roots

Summary

Introduction

Soybean is a globally important legume crop that provides proteins and lipids to humans and livestock. Because soybean seeds contain a high concentration of protein, approximately 35–40%, they require relatively larger amounts of nitrogen than do cereal grains to obtain the same seed yield [1]. Harper [2] previously reported on the importance of both N2 -fixation by root nodules and inorganic nitrogen absorption by roots to obtain the optimum yield of soybeans. It is well known that nodulation and the nitrogen fixation activity of root nodules are suppressed when the nodulated roots are exposed to a high concentration of combined nitrogen—especially nitrate, a major form of inorganic nitrogen in the upland soil, which strongly inhibits nodulation and N2 fixation in Plants 2018, 7, 32; doi:10.3390/plants7020032 www.mdpi.com/journal/plants

Methods

Results

Conclusion