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Purpose <p>Crop domestication reshapes rhizosphere microbial communities, yet its effects on nitrogen use efficiency (NUE) in C4 cereals such as millet remain unclear.</p> Methods <p>We assessed how domestication influences rhizosphere microbiome assembly and its association with NUE in millet. Six genotypes representing wild (<i>Setaria viridis</i>), landrace, and cultivated (<i>Setaria italica</i>) stages were grown under two nitrogen levels (N0, N25) in a greenhouse. Rhizosphere bacterial and fungal communities were profiled using 16S rRNA and ITS sequencing. Diversity indices, PERMANOVA, LEfSe, correlation analysis, structural equation modeling, and network analysis were applied.</p> Results <p>Fungal communities were more strongly affected by domestication than bacterial communities, showing marked reductions in alpha diversity and shifts in community composition across genotype groups. In contrast, bacterial diversity remained relatively stable. Under nitrogen addition (N25), wild genotypes with higher NUE were positively associated with specific fungal taxa, including <i>Phlyctis</i> (Lecanorales, Ramalinaceae), <i>Trichoderma</i>, and <i>Gibellulopsis</i>, whereas these associations were absent in highly domesticated cultivated genotypes. In wild millet, plant traits mediated the enrichment of <i>Phlyctis</i> (Lecanorales, Ramalinaceae), while nitrogen addition enhanced its network centrality but reduced the connectivity of other NUE-associated fungal taxa.</p> Conclusion <p>These findings suggest that domestication weakens beneficial plant-fungal interactions critical for nitrogen acquisition, providing insights into ecological trade-offs of crop improvement and highlighting the potential of microbiome-informed breeding strategies to enhance NUE in millet.</p>

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Domestication reshapes rhizosphere microbiome structure and weakens fungal diversity and microbial associations with nitrogen use efficiency in millet

  • 期刊论文

  • 发表日期：

    2025年8月11日

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  • Yufeng Deng,
  • Chunxu Song,
  • Meicheng Zhao,
  • Feng Zhu

摘要

Purpose

Crop domestication reshapes rhizosphere microbial communities, yet its effects on nitrogen use efficiency (NUE) in C4 cereals such as millet remain unclear.

Methods

We assessed how domestication influences rhizosphere microbiome assembly and its association with NUE in millet. Six genotypes representing wild (Setaria viridis), landrace, and cultivated (Setaria italica) stages were grown under two nitrogen levels (N0, N25) in a greenhouse. Rhizosphere bacterial and fungal communities were profiled using 16S rRNA and ITS sequencing. Diversity indices, PERMANOVA, LEfSe, correlation analysis, structural equation modeling, and network analysis were applied.

Results

Fungal communities were more strongly affected by domestication than bacterial communities, showing marked reductions in alpha diversity and shifts in community composition across genotype groups. In contrast, bacterial diversity remained relatively stable. Under nitrogen addition (N25), wild genotypes with higher NUE were positively associated with specific fungal taxa, including Phlyctis (Lecanorales, Ramalinaceae), Trichoderma, and Gibellulopsis, whereas these associations were absent in highly domesticated cultivated genotypes. In wild millet, plant traits mediated the enrichment of Phlyctis (Lecanorales, Ramalinaceae), while nitrogen addition enhanced its network centrality but reduced the connectivity of other NUE-associated fungal taxa.

Conclusion

These findings suggest that domestication weakens beneficial plant-fungal interactions critical for nitrogen acquisition, providing insights into ecological trade-offs of crop improvement and highlighting the potential of microbiome-informed breeding strategies to enhance NUE in millet.