Scion varieties and nitrogen levels affect carbon and nitrogen assimilation in apple via modulating rhizosphere microbial structure and function

Abstract

The efficiency of carbon and nitrogen uptake in apple trees is co-regulated by plant genotype and rhizosphere microbial communities. However, the mechanisms by which different scion varieties modulate microbial structure and function under varying nitrogen levels remain poorly understood. In this study, Malus sieversii was used as the rootstock, onto which three scion cultivars (M. sieversii, Malus domestica cv. Hanfu, and Malus domestica cv. Red Fuji) were grafted under two nitrogen regimes. A combination of ¹³C/¹⁵N isotope labeling, Illumina MiSeq amplicon sequencing, and metagenomic analysis was employed to elucidate how scion-rootstock interactions and nitrogen availability affect carbon and nitrogen acquisition. Under nitrogen-deficient conditions, Red Fuji exhibited stronger root activity and larger root surface area, indicating enhanced nutrient foraging capacity. Conversely, under nitrogen application, Hanfu showed significantly greater ¹³C and ¹⁵N uptake, with 5.7-fold and 1.6-fold higher ¹³C accumulation in roots and stems, respectively, and markedly higher ¹⁵N utilization efficiency in roots and leaves compared with M. sieversii. In parallel, Hanfu under nitrogen input showed enrichment of beneficial microbial taxa and more complex microbial co-occurrence networks. Metagenomic analysis and random forest analyses revealed that the relative abundance of specific functional genes related to carbon and nitrogen transformation (rbcL, abfA, napB/C, nasA) was significantly higher under specific scion-nitrogen combinations, contributing to enhanced microbial carbon fixation and nitrogen reduction. Collectively, these results demonstrate that scion genotype modulates rhizosphere microbial structure, physiological root traits, and carbon-nitrogen distribution patterns, thereby improving nutrient uptake efficiency under different nitrogen inputs.

Acknowledgements

This research was financially supported by the Xinjiang Production and Construction Corps Key Research Projects (2024AB038), the National Natural Science Foundation of China (32360718), and the Xinjiang Apple Industry Technology System (XJLGCYJSTX04-2024-).

Author contributions

F.Z. and K.Y. conceived and supervised the project. H.Z., W.Z., and D.Y. designed the experiments. H.Z., D.Y., X.L., H.S.M.A., and J.X. performed the greenhouse and laboratory work. Y.L. and S.Y. contributed to data collection and sample processing. H.Z., W.Z., and D.Y. conducted data analysis. H.Z. drafted the manuscript. F.Z. and K.Y. revised the manuscript critically for important intellectual content. All authors reviewed and approved the final version of the manuscript.

Data availability

All relevant information and data are provided in the article and its supplementary materials.

Conflicts of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Supplementary material

Supplementary material is available at Horticulture Research online.

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