Harnessing microbes to support food security

Pankaj Trivedi; Professor, Institute for Texas Tech Genomics for Crop Abiotic Stress Tolerance; Texas Tech University. Manuel Delgado-Baquerizo, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC). Brajesh K. Singh, Hawkesbury Institute for the Environment, Western Sydney University.

Soil and plant-associated microbiomes constitute the most diverse and abundant communities on the planet. These microbiomes are foundational to planetary health and sustainable agriculture. Synthetic microbial communities (SynComs) are simplified, and intentionally designed consortia of microorganisms used to study microbial interactions, understand complex ecosystems, and develop applications like bioremediation and improved plant health. Microbes have long been applied as inoculants for biocontrol or biostimulation in agricultural systems and to degrade contaminants for site remediation. However, their efficacy varies with climate, soil type, and other environmental factors. SynComs are often either single isolates or undefined extracts from compost or other organic substrates, which likely cannot compete with indigenous microbiomes. Their benefits are often small or do not persist, requiring repeat applications even within a growing season. This is a major issue, and we need to find solutions if we want to harness the full potential of the crop microbiome to support food security under global change.

Friends and long-term collaborators Drs. Pankaj Trivedi (USA); Manuel-Delgado Baquerizo (Spain); and Brajesh K. Singh (Australia) at Mountain Campus of Colorado State University.

The good news is that there is a large amount of literature about ecological and eco-evolutionary theory to tackle this major issue. Back in 2023, three friends and long-term collaborators visited Colorado State University Mountain Campus to discuss multiple on-going collaborations. Among these discussions, we decided to put together some of these ecological theories in a Viewpoint to increase visibility and spark further discussion in the research community. For example, applying "Biodiversity–ecosystem function" theory can help design SynComs by considering functional redundancy, phylogenetic diversity, and multitrophic interactions within the constituting members. Applying "meta-community theory" in combination with the 'priority effect' (order and timing of arrival effect on colonization success) can unravel and predict the mechanisms, success, and effectiveness of SynCom colonization. "Invasion theory" can further help understand SynCom application's impact on the native communities from competition, coalescence, and interaction processes between a few inoculated taxa in SynComs and the whole soil microbiome. This information can be pivotal towards passing regulatory hurdles for field trials. Furthermore, applying "ecological networks, multitrophic interactions, and food web theory" can help simplify nature's complexity to select keystones within ecological networks, which are especially important for conducting a particular ecosystem function. Integrating "ecological theories" with modelling tools (including machine learning, genome-scale modelling) can be instrumental in predicting the dynamics and systems properties of the microbiome and microbiome-host or environment interactions, leading to the successful use of SynCom technology.

Few examples of ecological theories to better predict the success of SynComs in terrestrial environments. This figure was created in BioRender (https://biorender.com/)

Effectively harnessing the microbiome requires new approaches, recognizing that microbes living in natural and managed systems typically do so as communities, not as populations of single organisms functioning alone. Applying ecological theories to provide new insights on the principles that govern the establishment, dynamics, stability, and vulnerability of the SynComs holds a translational promise for the rational design of powerful microbiome-targeted interventions. However, realizing the full potential will require industrial innovations related to formulation development to construct robust and stable SynComs with predictable behaviors. Also, biosafety and regulatory requirements for implementing microbiome engineering in the real world need to be systematically addressed.