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Duration of Spent Mushroom Substrate Return Affects Microbial Assembly and Nitrogen Metabolism to Promote Functional

Yihong Yue1, Yu Jiang2, Yuchen Zhang1

  • 1National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.

Microorganisms
|June 26, 2026
PubMed
Summary

Long-term spent mushroom substrate (SMS) return improves soil fertility and microbial stability in rice paddies. Continuous application (3 years) enhances nutrient accumulation and nitrogen cycling, mitigating risks associated with short-term use.

Keywords:
community assemblynitrogen cyclingpaddy soilreturn durationspent mushroom substrate (SMS)

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Area of Science:

  • Agricultural Science
  • Soil Microbiology
  • Environmental Science

Background:

  • Spent mushroom substrate (SMS) is crucial for agricultural waste recycling and soil improvement.
  • The long-term ecological effects of SMS application duration are not well understood.
  • Understanding microbial and nutrient dynamics is key to sustainable paddy management.

Purpose of the Study:

  • To investigate the impact of different spent mushroom substrate (SMS) return durations on soil fertility, microbial communities, and nitrogen cycling.
  • To compare the ecological effects of 0, 1, and 3 years of SMS return in rice-mushroom systems.
  • To assess the risks and benefits of varying SMS return durations for sustainable agriculture.

Main Methods:

  • Metagenomic sequencing was used to analyze soil microbial communities and nitrogen cycling genes.
  • Soil nutrient levels (organic matter, total nitrogen, total phosphorus) were measured across different SMS return durations.
  • Co-occurrence network analysis was employed to study microbial community structure and interactions.

Main Results:

  • Soil nutrients initially decreased then increased; 3-year SMS return (y3) significantly enhanced late-stage nutrient accumulation compared to 1-year (y1) and control (y0).
  • Bacterial and archaeal assembly shifted towards deterministic processes with increasing SMS duration, while fungal diversity decreased.
  • Nitrogen cycling in y1 posed risks (e.g., N2O emissions), whereas y3 mitigated nitrogen loss and showed resilience in nitrogen-cycling gene structure.

Conclusions:

  • Initial SMS return can cause ecological fluctuations and environmental risks.
  • Continuous SMS return (3 years) promotes functional stability and enhances soil fertility in paddy ecosystems.
  • SMS return duration is critical for balancing soil improvement and environmental risk mitigation in sustainable agriculture.