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The Microbial Community Succession Drives Stage-Specific Carbon Metabolic Shifts During Agaricus bisporus Fermentation: Multi-Omics Reveals CAZymes Dynamics and Lignocellulose Degradation Mechanisms

Summary

This research examines how different bacteria in mushroom compost work together to break down agricultural waste during the growing process. Scientists tracked microbial communities over 15 days of fermentation, finding that early stages use bacteria specialized in breaking down plant fibers, while later stages shift to bacteria that handle more complex compounds. Understanding these microbial changes helps optimize mushroom cultivation and reduce agricultural waste.

Background

Agaricus bisporus cultivation relies on efficient composting and fermentation processes to convert agricultural waste into usable carbon sources. The third fermentation or spawn-running phase is critical for mushroom yield and quality, yet the microbial-driven mechanisms remain insufficiently explored despite advances in industrial composting technology.

Objective

This study integrates metagenomic and metabolomic data to systematically analyze microbial community succession and carbon source metabolism transitions during the third fermentation cycle of Agaricus bisporus, aiming to optimize fermentation efficiency and lignocellulose degradation strategies.

Results

Principal Coordinate Analysis revealed significant microbial community separation across fermentation stages. Planctomycetota (21.67-40.58%), Pseudomonadota (14.35-31.07%), and other phyla showed stage-specific dominance patterns. Stage B exhibited enriched cellulase-producing bacteria (Pseudomonadota, Actinomycetota), while stages C-D were dominated by Planctomycetota, particularly Maioricimonas rarisocia. CAZyme analysis showed cellulose-degrading enzymes (GH1, GT2) peaked in stage B, while lignin degradation increased in later stages.

Conclusion

Microbial community succession drives stage-specific metabolic shifts: early stages (B) rely on cellulose-degrading microbes with GH enzyme systems, while later stages (C-D) are driven by Planctomycetota through CAZyme-mediated complex polysaccharide and lignin degradation. This findings provide mechanistic insights for optimizing fermentation processes and agricultural waste utilization through targeted microbial engineering strategies.
  • Published in:Microorganisms,
  • Study Type:Observational Study,
  • Source: PMC12735553, PMID: 41471959
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