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Purpose <p>Soil acidification has become a major constraint on agricultural productivity, and conventional lime application offers limited recovery of overall soil health. Here, we systematically compared the effects of three soil amendments-humic-based (LYPH1), lime-based (LYPH2), and alkaline organic-inorganic fertilizer (LYPH3)-against a conventional fertilization control (CK) to elucidate the multidimensional mechanisms by which they improve acidified soils.</p> Methods <p>A field experiment was conducted to evaluate soil physicochemical and biological parameters and to calculate the Soil Health Index (SHI). The study assessed the impact of the three amendments (LYPH1, LYPH2, and LYPH3) as well as the control (CK) on the soil’s health and its microbiome. Metagenomic analyses were performed to identify the enriched microbial taxa and key functional genes involved in nutrient cycling.</p> Results <p>Results showed a clear gradient of improvement following the trend LYPH3 &gt; LYPH1 &gt; LYPH2 &gt; CK, with LYPH3 exhibiting the strongest enhancement of soil health. Metagenomic analyses revealed the functional potential of LYPH3 to significantly enrich core functional taxa, including <i>Gammaproteobacteria</i>, <i>Gemmatimonadetes</i>, <i>Nitrospira_D</i>, and <i>Reyranella</i>, which were associated with the enrichment of key functional genes involved in carbon stabilization(<i>SDHC</i>, <i>tfrB</i>), nitrification(<i>amoC_B</i>), and phosphorus activation (<i>phoC</i>, <i>htxA</i>). This coordinated enrichment of microbial taxa and functional genes coincided with enhanced microbially mediated carbon stabilization, nitrogen transformation, and phosphorus mineralization.</p> Conclusion <p>Through the synergistic optimization of soil physicochemical properties and microbial attributes, LYPH3 achieved a substantial improvement in soil health in acidified croplands. The evidence for these mechanisms is primarily association-based, linking specific microbial taxa and their associated genes to key biogeochemical processes. Overall, our findings demonstrate that the alkaline organic–inorganic amendment (LYPH3) enhances soil health by selectively enriching a consortium of core microbial taxa and functional genes involved in C, N, and P cycling, thereby promoting these key nutrient cycling processes. This strategy represents an effective and sustainable approach for restoring acidified agricultural soils.</p>

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Microbial responses of soil health enhancement through alkaline organic-inorganic fertilization

  • 期刊论文

  • 发表日期：

    2026年4月22日

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  • Chengsen Zhao,
  • Xiaoyue Zhang,
  • Siyuan Zheng,
  • Yuzhuo Zhao,
  • Hua Xie,
  • Yunyou Zheng,
  • Luotian Lu,
  • Yonghong Liu,
  • Fenghua Ding,
  • Qinwen Zeng,
  • Bin Ma,
  • Xinwei Song

摘要

Purpose

Soil acidification has become a major constraint on agricultural productivity, and conventional lime application offers limited recovery of overall soil health. Here, we systematically compared the effects of three soil amendments-humic-based (LYPH1), lime-based (LYPH2), and alkaline organic-inorganic fertilizer (LYPH3)-against a conventional fertilization control (CK) to elucidate the multidimensional mechanisms by which they improve acidified soils.

Methods

A field experiment was conducted to evaluate soil physicochemical and biological parameters and to calculate the Soil Health Index (SHI). The study assessed the impact of the three amendments (LYPH1, LYPH2, and LYPH3) as well as the control (CK) on the soil’s health and its microbiome. Metagenomic analyses were performed to identify the enriched microbial taxa and key functional genes involved in nutrient cycling.

Results

Results showed a clear gradient of improvement following the trend LYPH3 > LYPH1 > LYPH2 > CK, with LYPH3 exhibiting the strongest enhancement of soil health. Metagenomic analyses revealed the functional potential of LYPH3 to significantly enrich core functional taxa, including Gammaproteobacteria, Gemmatimonadetes, Nitrospira_D, and Reyranella, which were associated with the enrichment of key functional genes involved in carbon stabilization(SDHC, tfrB), nitrification(amoC_B), and phosphorus activation (phoC, htxA). This coordinated enrichment of microbial taxa and functional genes coincided with enhanced microbially mediated carbon stabilization, nitrogen transformation, and phosphorus mineralization.

Conclusion

Through the synergistic optimization of soil physicochemical properties and microbial attributes, LYPH3 achieved a substantial improvement in soil health in acidified croplands. The evidence for these mechanisms is primarily association-based, linking specific microbial taxa and their associated genes to key biogeochemical processes. Overall, our findings demonstrate that the alkaline organic–inorganic amendment (LYPH3) enhances soil health by selectively enriching a consortium of core microbial taxa and functional genes involved in C, N, and P cycling, thereby promoting these key nutrient cycling processes. This strategy represents an effective and sustainable approach for restoring acidified agricultural soils.