Beyond the Single Isolate: Leveraging Plant-Associated Microbial Communities for Crop Resilience

Abstract

The future of sustainable agriculture will require practical microbial solutions that reduce chemical inputs while maintaining productivity. While existing literature reviews focus on laboratory science, they rarely address the practicalities of farm implementation. Low rates of adoption suggest a translational gap. This review translates current scientific insights for the relevant end user (farmers). Pesticides and fertilisers disrupt naturally occurring microbial communities that maintain plant health and resilience. Applications of beneficial microbes to restore plant health or improve productivity currently employ single-strain inoculants. The targeted application of a consortium of multiple microorganisms, a "synthetic community" (SynCom), including biocontrol agents, biostimulants and biofertilisers, is superior. The "SynCom" approach could be considered the Swiss army knife of sustainable agriculture, with each member of the community performing overlapping functions. While SymComs have shown success in laboratory and greenhouse trials, field reliability has been inconsistent, either due to variability in production or stability issues in the field. The future of sustainable agriculture will require greater collaboration between scientists and farmers at a local level, specifically, the application of microbes from local soils that are adapted to local environmental conditions, investment in monitoring successes and failures, and application via seed coating using currently available infrastructure.

Keywords: biocontrol agents; biofertilisers; pesticides; seed coating; synthetic microbial communities.

Figure 1

Factors contributing to global soil degradation. Land clearance and extreme weather events lead to land degradation directly contributing to reduced soil health. In turn this can lead to drought because land degradation reduces soil water retention. Intensive agriculture requires large inputs of fertilizers and industrial machinery which further lead to land degradation and loss of soil biodiversity. Human dietary choices lead to crop monocultures and intensive animal production that cause reduced soil quality. Overall, industrial farming and pollution are key agents of soil decay that also disrupt soil microbial populations (based on information from the UN Environment Programme https://www.unep.org/news-and-stories/story/five-reasons-why-soil-health-declining-worldwide, accessed on 17 December 2025).

Figure 2

Biological control strategies. Potential biocontrol agents can be identified through culture-based methods to isolate hyperparasites or antagonists. These can be screened for use as live biocontrol agents or for metabolites which are bioactive against the pathogen. Microbial community analysis can be used to identify biocontrol agents that can be used in combination as a synthetic community.