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Background and Aims <p>Soil conditions and plant compartment identity both shape plant-associated microbial communities, but how they jointly influence microbial assembly and functional differentiation in fine-scale, highly connected habitats remains unclear. We addressed this using the grass <i>Lepturus repens</i> on a coral island, where contrasting soil types occur in close proximity.</p> Methods <p>By coupling 16S rRNA and ITS amplicon sequencing with shotgun metagenomic sequencing of soil samples, we compared community composition, assembly processes, and co-occurrence networks across bulk soil, rhizosphere, and phyllosphere compartments, and explored the metabolic potential encoded in the soil communities.</p> Results <p>Despite the short distances separating soil types, physicochemical contrasts were associated with differentiation of soil microbial communities; however, this differentiation weakened progressively along the soil–rhizosphere–phyllosphere continuum. Assembly mechanisms varied among compartments and between bacteria and fungi: deterministic processes predominated in bacterial communities, whereas stochastic processes were more important for fungi. Soil metagenomic profiles indicated that differences in annotated functional potential were concentrated in upstream resource-use processes, including substrate depolymerization, transport, carbon acquisition, and regulation, rather than in broad changes to central metabolism. Genome-resolved analysis indicated that key annotated functions were unevenly represented among the recovered bacterial metagenome-assembled genomes.</p> Conclusion <p>These findings indicate that fine-scale soil heterogeneity was associated with microbiome differentiation across plant compartments and differences in soil microbial functional potential, even where microbial dispersal potential was expected to be high.</p>

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Fine-scale soil heterogeneity shapes compartment-specific microbial assembly and soil microbial functional differentiation in Lepturus repens on a coral island

  • 期刊论文

  • 发表日期：

    2026年7月30日

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  • Shengen Zhong,
  • Shunfen Wang,
  • Yimin He,
  • Kaiwen Yang,
  • Yuhang Wen,
  • Ziyang Zhang,
  • Mo Shi,
  • Liaoyuan Zhang,
  • Wenxiong Lin,
  • Xin Qian

摘要

Background and Aims

Soil conditions and plant compartment identity both shape plant-associated microbial communities, but how they jointly influence microbial assembly and functional differentiation in fine-scale, highly connected habitats remains unclear. We addressed this using the grass Lepturus repens on a coral island, where contrasting soil types occur in close proximity.

Methods

By coupling 16S rRNA and ITS amplicon sequencing with shotgun metagenomic sequencing of soil samples, we compared community composition, assembly processes, and co-occurrence networks across bulk soil, rhizosphere, and phyllosphere compartments, and explored the metabolic potential encoded in the soil communities.

Results

Despite the short distances separating soil types, physicochemical contrasts were associated with differentiation of soil microbial communities; however, this differentiation weakened progressively along the soil–rhizosphere–phyllosphere continuum. Assembly mechanisms varied among compartments and between bacteria and fungi: deterministic processes predominated in bacterial communities, whereas stochastic processes were more important for fungi. Soil metagenomic profiles indicated that differences in annotated functional potential were concentrated in upstream resource-use processes, including substrate depolymerization, transport, carbon acquisition, and regulation, rather than in broad changes to central metabolism. Genome-resolved analysis indicated that key annotated functions were unevenly represented among the recovered bacterial metagenome-assembled genomes.

Conclusion

These findings indicate that fine-scale soil heterogeneity was associated with microbiome differentiation across plant compartments and differences in soil microbial functional potential, even where microbial dispersal potential was expected to be high.