Nitrogen deficiency drives fungal compositional shifts without functional changes in wheat rhizosphere

Nitrogen (N) deficiency reduces crop yield, but this effect may be mitigated by symbiotic interactions between crops and fungi. However, the response of wheat-fungal interactions to N deficiency remains unclear. We hypothesised that wheat cultivars with a higher reported nitrogen use efficiency (NUE), would induce shifts in the fungal community composition and functional profiles within the wheat rhizosphere to tolerate N deficiency. A glasshouse experiment was conducted to examine the effects of N deficiency on the rhizosphere fungal communities of wheat (Triticum aestivum L.) cultivars Gladius (low N-use efficiency) and Mace (high N-use efficiency). Plants were grown until the mid-anthesis stage in a Dermosol soil treated with either 0 (Low-N) or 90 kg N ha⁻¹ (High-N). The rhizosphere fungal communities were characterised using quantitative PCR, ITS rRNA metabarcoding, and metagenomics. The abundance and diversity of the rhizosphere fungal community were not significantly influenced by N deficiency in either Mace or Gladius cultivars (P > 0.05). However, the fungal community composition showed significant variation across N treatments in Mace (P < 0.05), whereas no such effect was observed in Gladius (P > 0.05). Differential abundance analysis and fungal trait predictions indicated a reduction in fungal symbionts in both cultivars under N deficiency (P < 0.05). Metagenomic analysis demonstrated that fungal functional profiles remained unaffected by N deficiency (P > 0.05) but significantly differed between Mace and Gladius (P < 0.05). This study reveals intraspecific variation in rhizosphere fungal responses to N deficiency between Mace and Gladius. The metabarcoding and metagenomic data suggest functional redundancy within the fungal community, which may enhance wheat resilience under N-deficient conditions. These findings highlight the potential of using fungal community stability in developing biofertiliser products for sustainable agriculture.