Inspiration
Climate change poses various challenges in ecosystems, leading to fluctuations in temperature; this makes trees bloom earlier in the season, a so called ‘false spring’. This also happens to fruit trees in orchards. After a false spring, a sudden frost can set in and damage the blooming flowers, resulting in the loss of fruits.
This phenomenon is observed across numerous fruit trees during blooming season, such as almonds, peaches, apples, and plums, with cherries being particularly susceptible. Frost damage causes serious economic losses annually due to frost damage of fruit blossoms which amount to billions of euros affecting consumers worldwide. Moreover, reduced food production adversely affects food security, and the loss of environmental biodiversity will exacerbate existing challenges. As a team from near the Betuwe, the Netherlands’ center of fruit production, we want to tackle this problem.
The Project
To address the problem, we proudly present our solution - PseuPomona, a bacterium engineered to restore the flowering time of plants. Our bacterium will be applied to the soil, and secrete an antiflorigen, a hormone that temporarily inhibits flowering from occurring. The antiflorigen will be taken up by the roots and travel to the buds. The flowering will stay inhibited until the false spring has passed. As long as the flowers remain in their buds, they are well protected from frost.
Developing a completely new synbio solutions requires a comprehensive evaluation of its societal implications from the project's beginning, and through each phase of product development. To do this, inclusion of stakeholders is needed from the earliest development stages. With this stakeholder integration as one of our main goals, we collaborated closely with farmers, researchers and policymakers during the development of PseuPomona. Stakeholder input continuously shaped our project with eleven Dutch cherry farmers. We discovered that restoring the flowering to combat the consequences of climate change would have a great positive impact on the farmers’ harvest. As a farmer noted: this year, in the Netherlands, just 3-4 days of a flowering delay would have saved 30% of the harvest. Extrapolating to the worldwide production of fruit, such losses would be a catastrophe!
To make sure our product would be functional, we tested protein secretion systems, the expression of several antiflorigens, and promoters active in soil temperatures relevant in spring ensuring our bacteria can respond to the environmental signals.
Since our project includes contained release of an engineered bacterium in the environment, biosafety must be ensured. Therefore, we designed several control switches to ensure that the bacterium stays confined to its application site and can be removed on demand. Additionally, a barcode detection method was developed for easy in-situ monitoring of our bacteria in the soil. Besides these, we also built biosensors to make sure our bacteria will only produce the desired proteins within proximity of tree roots and specific molecules that induce expression of the protein.
We built three models to demonstrate the complex behaviours of our bacteria in the diverse environment of the soil. Novel agent-based models were built to interact with each other at multiple levels, investigating the cell growth and protein secretion at both population and cell scales. They provided suggestions for the application of our product based on the results. Moreover, in our agent-based models, we can actually see how bacteria would move in the soil and how proteins would be synthesized in the cells! The machine learning model contains two parts: one for estimating the expression level of a key flowering gene in different temperatures, and the other for predicting the local temperature changes to allow for precise application of PseuPomona. Biocontainment is one of the most important challenges in safe usage of synthetic microbes. Therefore, in parallel with testing these strategies in the wet lab we also developed an Ordinary Differential Equation (ODE) model capable of simulating our biosafety systems in a resource- and temperature-dependent manner.
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Future Prospects
The inspiration from PseuPomona came from the increasing concern about climate change, leading to frost damage to many plants; impacting both production and quality of many fruits and crops, which causes losses of billions of euros each year. Through strain design, model building and product development, we proposed a straightforward and more sustainable method for the world to combat frost damage in plants. Using PseuPomona, we foresee a product that ensures farmers no longer have to worry about the frost damage to their orchard, and a bacterial platform with protein secretion systems for future plant-relative research.
