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Background and Aims <p>The endophytic root microbiota of native pioneer plants plays a crucial role in toxicity mitigation, oligotrophic adaptation, and plant growth promotion (PGP), making them essential for ecological restoration in heavily antimony (Sb) tailings. However, current research has focused mainly on abundant taxa (AT), leaving rare taxa (RT) largely unexplored.</p> Methods <p>Root and rhizosphere samples of <i>Miscanthus sinensis</i> (Chinese Silvergrass) and <i>Boehmeria nivea</i> (Ramie) from Sb tailings were analyzed. RT were identified from 16S rRNA amplicon data at &lt; 0.01% relative abundance. Metagenome-assembled genome (MAG) binning and KEGG annotation were used to elucidate RT metabolic potential.</p> Results <p>Approximately 96% of endophytic communities consisted of RT, mainly Proteobacteria and Actinobacteria, with distinct host-specific across different plants. These RT play a more important role in interconnected ecological networks than AT and are more strongly influenced by soil physicochemical factors, especially Sb concentration. Such strong environmental filtering imposes deterministic community assembly (NST &lt; 0.5). Procrustes analyses demonstrate that RT disproportionately contribute to the functional potential of root endophytic and play a dominant role in key processes including heavy metal (HM) resistance, nutrient cycling, and PGP. Metagenomic binning further identifies RT such as <i>Pseudodokdonella</i>, <i>Homoserinimonas</i>, <i>Polaromonas</i>, <i>Rhodanobacter</i>, and <i>Variovorax</i>, whose MAGs encode diverse metabolic genes coexisting within taxa.</p> Conclusion <p>This study revealed that rare endophytes, despite their low abundance, play a critical yet overlooked role in mining ecosystems. Their high diversity supports key ecosystem functions such as metal detoxification and nutrient cycling, making them promising bioinoculants to enhance phytoremediation in metalloid-contaminated environments.</p> Graphical Abstract <p></p>

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Hidden potential of rare root endophytes in native plants for phytoremediation in antimony mine tailings

  • 期刊论文

  • 发表日期：

    2025年11月28日

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  • Hanbing Gao,
  • Zhaohui Guo,
  • Shikai Li,
  • Chi Zhang,
  • Min Shen,
  • Xiao He,
  • Rui Xu

摘要

Background and Aims

The endophytic root microbiota of native pioneer plants plays a crucial role in toxicity mitigation, oligotrophic adaptation, and plant growth promotion (PGP), making them essential for ecological restoration in heavily antimony (Sb) tailings. However, current research has focused mainly on abundant taxa (AT), leaving rare taxa (RT) largely unexplored.

Methods

Root and rhizosphere samples of Miscanthus sinensis (Chinese Silvergrass) and Boehmeria nivea (Ramie) from Sb tailings were analyzed. RT were identified from 16S rRNA amplicon data at < 0.01% relative abundance. Metagenome-assembled genome (MAG) binning and KEGG annotation were used to elucidate RT metabolic potential.

Results

Approximately 96% of endophytic communities consisted of RT, mainly Proteobacteria and Actinobacteria, with distinct host-specific across different plants. These RT play a more important role in interconnected ecological networks than AT and are more strongly influenced by soil physicochemical factors, especially Sb concentration. Such strong environmental filtering imposes deterministic community assembly (NST < 0.5). Procrustes analyses demonstrate that RT disproportionately contribute to the functional potential of root endophytic and play a dominant role in key processes including heavy metal (HM) resistance, nutrient cycling, and PGP. Metagenomic binning further identifies RT such as Pseudodokdonella, Homoserinimonas, Polaromonas, Rhodanobacter, and Variovorax, whose MAGs encode diverse metabolic genes coexisting within taxa.

Conclusion

This study revealed that rare endophytes, despite their low abundance, play a critical yet overlooked role in mining ecosystems. Their high diversity supports key ecosystem functions such as metal detoxification and nutrient cycling, making them promising bioinoculants to enhance phytoremediation in metalloid-contaminated environments.

Graphical Abstract