Harnessing the greenhouse microbiome: Novel strategies to improve greenhouse crop productivity and resilience: A review

Document Type : Review Article

Authors

1 Department of Soil Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran

2 Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran

Abstract
Greenhouse agriculture has become a cornerstone of modern horticulture, enabling year-round production, efficient resource use, and resilience to climate variability. Globally, protected cultivation exceeds 500,000 hectares, achieving 15–30% higher yields than open-field systems. However, its sustainability is constrained by dependence on mineral fertilizers and pesticides, which degrade soil health and suppress beneficial microbial diversity. Harnessing the greenhouse microbiome offers a transformative pathway to improve nutrient cycling, enhance plant growth, suppress pathogens, and strengthen tolerance to abiotic stresses. Microbiome-based interventions such as biofertilizers, microbial stimulants, and biochar- or compost-enriched substrates can reduce fertilizer use by 20–40% while maintaining or increasing yield by 10–25%. This review synthesizes advances in microbial biotechnology and omics-based insights into plant–microbe interactions. It further discusses synthetic biology and host-mediated gene editing as tools to design resilient holobionts for controlled-environment systems. Integration with precision agriculture, through AI, sensor networks, and digital twins, enables real-time monitoring and traceability of microbial products. Overall, microbiome-driven greenhouse management can enhance productivity, reduce greenhouse gas emissions, and align profitability with sustainability goals, representing a key strategy for climate-smart and circular horticulture.

Keywords


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Volume 3, Issue 1
Winter 2026
Pages 1-15

  • Receive Date 10 September 2025
  • Revise Date 20 October 2025
  • Accept Date 29 November 2025
  • First Publish Date 29 November 2025
  • Publish Date 01 March 2026