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Light-up plants and tunable roots signal new solutions for climate crisis

There has been no rain for a month. The soil around a farmer’s wheat plants is bone-dry. In the past this could have led to the loss of the whole crop – but one flick of a genetic switch means the root systems can begin to adapt to the drier conditions.

01 March 2024

The same plants notice the sodium in the soil is too high, and recruit microbes to regulate the concentration in the soil surrounding their roots - something they can also do when there isn’t enough phosphorus.

These are just some of the possible futures opened up by research at the Earlham Institute into interactions between plants and their microbiomes.

Dr Sarah Guiziou has joined the Institute as a Career Development Fellow. She is working on plant root development and plant-microbiota interaction. 

Just like the human microbiome, plants have their own system of microbes living on and around them. A plant’s microbiome can affect growth, resilience, and pathogen resistance. 

Plant-beneficial bacteria can improve salt tolerance and reduce sodium accumulation in the soil, or make vital nutrients like iron and phosphorus more available. 

Roots, with the support of beneficial bacteria, will take up increased nutrients and water from the soil. And a healthy microbiome could even increase crop yield - without the use of fertilisers and pesticides.

“When I was younger I wanted to do something practical to help people,” says Dr Guiziou. “Initially, I wanted to be a physician - but eventually I chose to take a degree in engineering. 

“I specialised in biochemical engineering and that is where my interest in integrases and engineering in plants began.”

Dr Sarah Guiziou photographed through a gap in a lab bench

Dr Sarah Guiziou, Career Development Fellow at the Earlham Institute

Initially, I wanted to be a physician - but eventually I chose to take a degree in engineering. I specialised in biochemical engineering and that is where my interest in integrases and engineering in plants began.

Tuning in

In a plant’s root system, primary roots grow downwards. Spreading out of the primary roots are a web of finer, lateral roots. Plants are able to adapt the architecture of this system depending on environmental conditions.

For example, in desert plants, a widespread shallow net of lateral roots is found. This allows plants to collect more of the limited rainfall. A deeper main root finds underground sources of water.

The warming climate is increasing the frequency and length of droughts. Plant pathogens are proliferating. At the same time, there is an acknowledgement within the agricultural sector of the need to reduce the use of both fertiliser and pesticides. 

The crisis is unfolding so rapidly that traditional breeding programmes will not be able to move quickly enough to safeguard food systems.

Synthetic biology could mean we can improve tolerance to the climate crisis within one or two generations. Improving the root structure of plants and the symbiosis between the root and its microbiome could support sustainable crop production.

Dr Guiziou is planning to construct a computer-like biological circuit in cells which would prompt plants to change their root system in response to the external environment.

Integrases - enzymes which remove or add elements to DNA sequences – can be used to engineer a section of DNA to respond to external conditions. 

A particular situation - an overabundance of one chemical, or a dearth of another - would trigger the cell to behave in a predetermined way, such as switching to different root architectures over the course of root growth. 

Dr Guiziou is engineering root architectures in Arabidopsis thaliana using integrase-based technology to facilitate the adaptation of plants to the fast change of climate
Arabidopsis in a growth plate

Signal for help

A plant’s microbiome could also be recruited to help signal what a plant needs to the farmers.

Dr Guiziou will be working on two model species of bacteria, Bacillus subtilis and Pseudomonas fluorescens. These bacteria families already colonise the plant root, with some strains improving nutrient availability, modifying production of plant hormones, or defending against plant pathogens by producing antimicrobials.

Introducing a circuit within these bacteria would allow them to switch to more plant-beneficial phenotypes in response to changes in the external conditions. Dr Guiziou says she first began exploring this concept during her PhD, which involved engineering logic circuits in bacteria. 

“The cell can be engineered to respond to particular chemicals in the environment, or to a lack of them,” she says. “For example, we’ve shown that cells can be engineered to fluoresce to signal what chemicals are present or absent.”

Dr Guiziou will be working on two model species of bacteria, Bacillus subtilis (pictured) and Pseudomonas fluorescens
Bacillus subtilis growth culture

Dr Guiziou also engineered fluorescence changes in Arabidopsis root cells, creating a circuit which switched from blue fluorescent protein (BFP) to red fluorescent protein (RFP) and was controlled by an early development lateral root promoter. 

She says potential long-term outcomes of her work could be new solutions to overcome environmental hardships, including drought and nutrient-poor soils. As well as increasing yield, this could also lead to reduced fertiliser and pesticide application.

This research is part of the Earlham Institute’s strategic focus on systems and synthetic biology, helping to shape the field of systems genomics while placing genes in the context of pathways and networks.

Dr Guiziou earned her PhD in synthetic biology at the University of Montpellier. She followed this with work on plant synthetic biology as an EMBO Postdoctoral Fellow at the University of Washington, developing integrase tools to record gene expression during plant development. She joined the Earlham Institute in April 2023.

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Amy Lyall

Scientific Communications and Outreach Officer