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Long-Term Organic Fertilization Enhances Soil Fertility and Reshapes Microbial Community Structure with Decreasing

Suyao Li1, Yulin Li1, Xu Yan1

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|January 28, 2026
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Summary

Long-term fertilization improves soil fertility and rice yield, especially with combined organic and inorganic fertilizers. However, these benefits decrease with soil depth, impacting microbial communities and functions.

Keywords:
functional gene abundancelong-term fertilizationmicrobial co-occurrence networknutrient cyclingsoil profile

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Area of Science:

  • Agricultural Science
  • Soil Science
  • Microbiology

Background:

  • Intensive agriculture demands understanding fertilization's impact on soil health and productivity.
  • Deeper soil layers' responses to fertilization are understudied compared to surface soils.

Purpose of the Study:

  • To investigate long-term fertilization effects on soil physicochemical properties, microbial diversity, community structure, and functional genes at varying soil depths.
  • To assess the influence of inorganic, organic, and combined fertilization regimes on paddy soil ecosystems.

Main Methods:

  • Analysis of soil samples from a 40-year fertilization experiment across three depths (0-20, 20-40, 40-60 cm).
  • Evaluation of soil organic matter, total nitrogen, phosphorus, and potassium.
  • Assessment of microbial diversity, community structure (using co-occurrence networks), and functional gene abundances.
  • Measurement of rice yield under different fertilization treatments.

Main Results:

  • Organic and combined fertilization significantly enhanced topsoil fertility indicators and rice yield.
  • Fertilization effects on soil properties diminished with increasing soil depth.
  • Microbial diversity decreased with depth; community structure was primarily influenced by depth, with surface layers showing nutrient-driven variations.
  • Functional gene distribution was depth-dependent, with surface soils rich in decomposition genes and deeper soils favoring anaerobic processes.

Conclusions:

  • Long-term fertilization significantly impacts soil fertility, microbial communities, and functions in a depth-dependent manner.
  • Combined organic-inorganic fertilization offers the greatest benefits for soil fertility and yield.
  • Soil depth is a critical factor shaping microbial community structure and function in fertilized paddy soils.