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Responses of metabolic pathways in soybean nodules and roots to long-term indirect nitrogen supply by dual-root system

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Abstract

Background and aims

While the effects of fertilizer nitrogen (N) on N fixation in soybean nodules lead to both local inhibition and systemic regulation, the specific mechanism is not clear. This study aimed to elucidate the mechanism by which systemic N regulation affects soybean root growth and N fixation.

Methods

Dual-root soybean plants containing unilateral nodulation were cultivated using grafting and sand culture with the addition of N-containing nutrient solution to the non-nodulated root portion and N-free nutrient solution to the nodulated portion during the VC-R1 period (28 d). The effects of N supplementation on changes in the expression of genes and proteins, as well as metabolite levels, in nodules and roots were examined, together with an evaluation of alterations in metabolic pathways in response to the indirect N supply.

Results

The results demonstrated that a 28-day supply of N to non-nodulated part of the root reduced nodulation while promoting the growth of the root system on the nodulation side. A comparative evaluation of the soybean plants cultivated with and without N supplementation revealed that N promoted the synthesis of signaling compounds, such as asparagine and trehalose, in nodules and inhibited flavonoid-associated metabolic pathways. Starch syntheis in nodules under long-term high-N was inhibited while the metabolism of organic acids was enhanced. Long-term indirect N supply also influenced pathways associated with amino acid metabolism and phenylpropanoid biosynthesis pathway in the roots.

Conclusion

The different response metabolic pathways of roots and nodules supported the different characteristics of soybean roots and nodules after indirect nitrogen supply. Additionally, the duration of nitrogen supply affects the regulatory pathway of nitrogen fixation of nodules.

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Data availability

All data that support the findings of this study can be found in the article and/or Supplementary Information.

Abbreviations

N:

Nitrogen

ARA:

Acetylene reduction activity

SNA:

Specific nitrogenase activity

DAMs:

Differentially accumulated metabolites

DEGs:

Differentially expressed genes

DEPs:

Differentially expressed proteins

GO:

Gene Ontology

KEGG:

Kyoto encyclopedia of genes and genomes

TMT:

Tandem mass tag

UPLC-ESI-MS/MS:

Ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry

UPLC-MS/MS:

Ultra-performance liquid chromatography/tandem mass spectrometry

VC:

Cotyledon stage

R1:

Initial flowering stage

Asp:

Asparagine

CYP73A:

Trans-cinnamate

C3′H:

5-O-(4-coumaroyl)-D-quinate 3′-monooxygenase

ENO:

Enolase

glgA:

Glycogen synthase

glgB:

Glycogen branching enzyme

glgc:

Glucose-1-phosphate adenylyltransferase

Gln:

Glutamine

Glu:

Glutamate

GOGAT:

Glutamine 2-oxoglutarate aminotransferase

GS:

Glutamine synthetase

HCT:

Shikimate O-hydroxycinnamoyltransferase

HK:

Hexokinase

I2H:

isofl

avone 2′-hydroxylase

IFS:

Isoflavone synthase

MDH:

Malic dehydrogenase

MRM:

Multiple reaction monitoring

otsB:

Treh

a

lose-6-phosphate phosphatase

PEPC:

Phosphoenolpyruvate carboxylase

PFK:

6-phosphofructokinase

PK:

Pyruvate kinase

scrK:

Fructokinase

PAL:

Phenylalanine ammonia-lyase

4CL:

4-coumarate-CoA ligase

CAD:

Cinnamyl-alcohol dehydrogenase

ALT:

Alanine transaminase

gdhA:

Glutamate dehydrogenase (NAD(P)+)

SS:

Sucrose synthase

TPS:

Trehalose-6-phosphate synthase

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Acknowledgements

We gratefully acknowledge financial support from the China Postdoctoral Science Foundation (Project NO. 2022M710651), Heilongjiang Provincial Postdoctoral Science Foundation (Project NO. LBH-Z22076).

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Authors and Affiliations

  1. College of Agriculture, Northeast Agricultural University, Harbin, China

    Xiaochen Lyu, Xuelai Wang, Chao Yan, Chunmei Ma & Zhenping Gong

  2. College of Resources and Environment, Northeast Agricultural University, Harbin, China

    Sha Li

  3. College of Engineering, Northeast Agricultural University, Harbin, China

    Shuhong Zhao

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  1. Xiaochen Lyu
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were mainly performed by Xiaochen Lyu, Xuelai Wang, Sha Li, Chao Yan, Chunmei Ma, Shuhong Zhao and Zhenping Gong. The first draft of the manuscript was written by Xiaochen Lyu with help from Zhenping Gong, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Zhenping Gong.

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Supplementary information

Below is the link to the electronic supplementary material.

Pot plot of dual-root soybeans (Fig. S1), preparation of dual-root soybean plants material (Fig. S2), the qRT-PCR data (Fig. S3). The primer sequences used for qRT-PCR (Table S1), soybean nodules metabolomics data (Table S2), soybean roots metabolomics data (Table S3), soybean nodules proteomics data (Table S4), soybean roots proteomics data (Table S5), soybean nodules transcriptome data (Table S4), soybean roots transcriptome data (Table S6).

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Lyu, X., Wang, X., Li, S. et al. Responses of metabolic pathways in soybean nodules and roots to long-term indirect nitrogen supply by dual-root system. Plant Soil (2024). https://doi.org/10.1007/s11104-024-06518-9

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