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Aims <p>Intensive agricultural practices, particularly greenhouse cultivation, are known to alter soil properties, but their impact on the soil health status and underlying microbial mechanisms remain poorly understood.</p> Methods <p>Here, we conducted a comprehensive survey of 51 citrus orchards (39 greenhouse and 12 outdoor) to assess soil health index, microbial communities, ecological cluster dynamics, and their associations.</p> Results <p>Greenhouse cultivation significantly improved the overall soil health score by 20.94%, alongside higher pH, nutrient availability, and organic carbon fractions. While bacterial diversity and structure remained stable, fungal diversity decreased and community structure significantly altered in greenhouses. Network analysis showed greenhouse management selectively increased the relative abundance of bacterial modules #1, #3, #4, and #7 and fungal module #5, while suppressing bacterial modules #2 and #8 and fungal modules #2 and #6. Critically, the suppressed bacterial module #2 (dominated by oligotrophic Acidobacteriales and Ktedonobacterales) was negatively correlated with soil health, whereas the enriched fungal module #5 (dominated by eutrophic Hypocreales) was positively correlated. Structural equation modeling further revealed fungal module #5 had the greatest positive direct effect on soil health, affected by available zinc (AZn) and magnesium (AMg), while bacterial module #2 exerted the strongest negative effect, influenced by available phosphorus (AP).</p> Conclusions <p>Greenhouse cultivation fosters a healthier soil state by inducing a functional reorganization of the microbial community, characterized by the suppression of ecological clusters dominated by oligotrophic-associated taxa and the enrichment of eutrophic and functionally versatile fungal clusters, thereby contributing to a more productive and sustainable agricultural ecosystem.</p>

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Functional reorganization of microbial ecological clusters is associated with citrus soil health enhancement under greenhouse cultivation

  • 期刊论文

  • 发表日期：

    2026年2月28日

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  • Chenhong Liu,
  • Qi Zhao,
  • Lin Zhang,
  • Fuzhi Ke,
  • Xuebin Xu,
  • Senxiang Yu,
  • Jiaping Lang,
  • Tida Ge,
  • Cong Wang,
  • Haoqing Zhang

摘要

Aims

Intensive agricultural practices, particularly greenhouse cultivation, are known to alter soil properties, but their impact on the soil health status and underlying microbial mechanisms remain poorly understood.

Methods

Here, we conducted a comprehensive survey of 51 citrus orchards (39 greenhouse and 12 outdoor) to assess soil health index, microbial communities, ecological cluster dynamics, and their associations.

Results

Greenhouse cultivation significantly improved the overall soil health score by 20.94%, alongside higher pH, nutrient availability, and organic carbon fractions. While bacterial diversity and structure remained stable, fungal diversity decreased and community structure significantly altered in greenhouses. Network analysis showed greenhouse management selectively increased the relative abundance of bacterial modules #1, #3, #4, and #7 and fungal module #5, while suppressing bacterial modules #2 and #8 and fungal modules #2 and #6. Critically, the suppressed bacterial module #2 (dominated by oligotrophic Acidobacteriales and Ktedonobacterales) was negatively correlated with soil health, whereas the enriched fungal module #5 (dominated by eutrophic Hypocreales) was positively correlated. Structural equation modeling further revealed fungal module #5 had the greatest positive direct effect on soil health, affected by available zinc (AZn) and magnesium (AMg), while bacterial module #2 exerted the strongest negative effect, influenced by available phosphorus (AP).

Conclusions

Greenhouse cultivation fosters a healthier soil state by inducing a functional reorganization of the microbial community, characterized by the suppression of ecological clusters dominated by oligotrophic-associated taxa and the enrichment of eutrophic and functionally versatile fungal clusters, thereby contributing to a more productive and sustainable agricultural ecosystem.