The Problem
Global food systems are facing difficult challenges: One in seven people still suffers from inadequate nutrition, while the growing global population is expected to increase food demand by at least 50% by 2050 1,2. This results in the intensifying competition for critical resources such as land, water, and energy – a challenge already evident today.
Climate change threatens global food security by exacerbating these challenges. Rising stresses, such as extreme heat, high soil salinity, and desertification, are putting food availability at high risk3,4. Many countries, particularly developing ones, face worrying uncertainties regarding reduced agricultural yields due to the effects of climate change 1. These factors highlight the urgency for comprehensive mitigation and adaptation strategies to secure a sustainable food supply for the future.
Our project idea was inspired by the heat and aridity of last summer (2023). Even Switzerland - a country known for its abundance of water - suffered from droughts. We urgently have to address climate change with sustainable solutions that preserve and protect our planet and our future on it. Our team was fascinated by the complex symbioses between plants and microorganisms. We wondered if we could use this interaction to address these challenges in agriculture
Symbiotic Solutions
Plant growth-promoting rhizobacteria (PGPR) are beneficial microbes that significantly enhance plant growth and resilience to environmental extremes and pathogens. They colonize the rhizosphere (the soil region close to plant roots) and support plant health by boosting nutrient absorption, improving soil structure, increasing water retention, protecting plants against phytopathogens and interacting with the plant’s systemic stress responses5,6.
PGPR can form biofilm structures on plant roots. These biofilms are composed of a matrix of extracellular polymeric substances (EPS) that can retain or attract water and form a protective barrier against environmental stresses. For instance, Pseudomonas putida forms a biofilm that combats drought stresses, while the biofilm of Bacillus amyloliquefaciens enhances salt stress tolerance in barley7.
Our Approach
Our goal is to develop a bacterium that produces an enhanced biofilm around plant roots, increasing the plant's ability to withstand stress from drought and heavy soil use. Improving targeted biofilm production around plant roots optimizes the existing symbiotic relationship between rhizobacteria and plants, especially in situations with external stress factors such as water scarcity.
Molecular Mechanism
To achieve a strong biofilm, we will genetically modify Pseudomonas sp.IsoF to overexpress cyclic di-GMP (c-di-GMP) when in proximity to plant roots. C-di-GMP is a secondary messenger molecule, which regulates biofilm production. We explore two distinct pathways that complement each other to increase c-di-GMP levels: our first strategy increases the expression of diguanylate cyclase (DGC), an enzyme essential for c-di-GMP synthesis. Our second strategy targets phosphodiesterase (PDE), an enzyme responsible for degrading c-di-GMP. We will inhibit PDE transcription using dCas9 and sgRNA to prevent c-di-GMP breakdown.
To limit the metabolic stress on our engineered bacteria we will only induce its increased biofilm production when it is near plant roots. This requires a sensing system that enables the bacteria to detect xylose, a sugar that is exuded by plant roots. When xylose is sensed, the bacteria activates a positive feedback loop. This not only triggers the mechanisms to increase c-di-GMP, but also starts the production of a toxin which is an integral part of our killswitch design.
Image Description:
- The plant roots exude xylose, a type of sugar, into the surrounding soil. The engineered Pseudomonas sp. IsoF bacteria detect this xylose, which triggers the subsequent steps in biofilm formation.
- When close enough to the root and upon the detection of xylose, our pathway in the modified Pseudomonas sp. IsoF bacteria is activated. This activation results in the overexpression of c-di-GMP, a key secondary messenger molecule in bacteria.
- The production of c-di-GMP is critical for initiating and regulating the formation of biofilm. It also coordinates the recruitment of more bacteria.
- The bacteria form a robust biofilm around the plant roots. This biofilm serves to protect the roots and enhance their resilience against environmental stresses such as drought or overexploited soil.
To ensure environmental safety and prevent the spread of our engineered bacteria beyond the target plant, we will incorporate a kill switch through a toxin/antitoxin system. This mechanism will trigger cell death when the bacteria move away from the root zone by stopping the production of the antitoxin, while the toxin is still produced.
Biological Background
When we started our research we came across a paper in which Da-Cheng Wang et al.7 studied the application of the Plant Growth Promoting Rhizobacterium (PGPR) Bacillus amyloliquefaciens on plant roots to increase their drought tolerance. We consulted various labs at the University of Zurich (UZH) and came across the Pseudomonas species IsoF in the Eberl lab. This strain is known for its capacity to reduce pathogens in plants, as well as for its ability to outcompete other bacterial species. Recognizing this, we saw an opportunity to harness this strain’s inherent beneficial traits and further enhance it by addition of the plant growth-promoting property of increasing drought resistance. The goal of our project was therefore to combine the inherent strengths P. sp. IsoF has, with new features, creating a bacterium with a selective advantage which offers enhanced resilience to plants against changing climate conditions.
Upon further research we discovered that various Pseudomonas species are suited to enhance biofilm formation through the upregulation of c-di-GMP production. Since c-di-GMP is a second messenger it influences the regulation of multiple genes. Enhancing the biofilm this way results in more ways to increase the biofilm production than if we were to only target a single gene.
With our project we want to create a sustainable approach by leveraging synthetic biology to enhance the resilience of agricultural systems.