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Can plant traits be modified without modifying their DNA? Netherlands study says yes

The study led by ecologist Dr Alexandre Jousset says plants can be improved without modifying their DNA. This approach involves making changes to the plant microbiome.

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New Delhi: Plant breeding has always focused on improving the genetic material or the DNA of the plants. Both selective breeding and genetic modification (GM) have the same objective — adding new traits to the plant by modifying its DNA. 

But, a recent research has the potential to turn the practice on its head.

Ecologist Dr Alexandre Jousset’s team at the Institute of Environmental Biology, Utrecht University, in the Netherlands, has shown in a study, released in August, that plants can be improved without modifying their DNA, and this approach involves making changes to the plant microbiome.

The microbiome is the genome of all the bacteria, viruses and fungi that inhabit and interact with the plant. These interactions are independent of the plant’s interaction with its environment. Earlier research has shown certain organisms are ‘beneficial’ to plants, while others are ‘harmful’ and need to be removed from the plants’ environment.

This approach has led to many interventions aimed at improving plant traits. But, when applied in field experiments, they gave inconsistent results.

The reason for the inconsistency was the incomplete understanding of the plant-microbe interaction, according to Dr Jousset’s paper.

In an email interaction with the author, Dr Jousset, who was the lead author of the study, explained: “Plant and (their) microbes are intertwined. You don’t have ‘beneficial’ microbes. Rather an organism is always co-regulated with its microbiome.” This is called the holobiont model.

Also read: Scientists are in a race to save the humble banana from extinction

Testing hypothesis

Jousset’s laboratory focuses on developing strategies to increase stress tolerance in plants. His team investigated the role of holobiont in maintaining hormonal balance. They used ethylene regulation as a model since it was well-characterised. Ethylene plays an important role in plant growth, immunity and stress tolerance. It promotes micronutrient uptake and directs them to the aerial parts of the plant.

In a previous study, Jousset’s team had found that both the plant and its microbiome can regulate hormones equally. They hypothesised that effects of editing the plant genome and changing the microbiome must be the same.

To test their hypothesis, they created a minimal holobiont model consisting of the plant and one bacterium. They used Arabidopsis thaliana, a model plant for all genetic modification experiments. The bacterium used was Pseudomonas putida, a common root colonising bacterium, according to Dr Jousset’s paper.

To make ethylene, a plant first makes its precursor, 1-aminocyclopropane 1-carboxylic acid (ACC). Ethylene production can happen either through the plant or the microbiome in a holobiont.

So in the minimal holobiont, Dr Jousset’s team created two setups and sought the difference in their ethylene levels. One where they edited the plant genome to make excess ACC without changing the microbial DNA, and in the other, they edited the microbe to stop conversion of plant ACC to ethylene. The plant genome was not edited and it produced normal levels of ACC.

Both setups produced higher levels of ethylene. The higher ethylene levels resulted in higher shoot concentrations of microelements — iron, zinc and copper, and macroelement — phosphorus. Thus, the results of editing the plant genome or its microbiome were the same.

These findings can help design better crops. 

As the human population increases, insecurities of food quality and quantity also increase. Globally, over two billion people are malnourished. Even in populations with enough calorie intake, micronutrient and vitamin deficiencies exist. 

Genetically modified crops here offer a possible solution. But their environmental impact adds another layer of complexity to an existing problem. Jousset’s solution can help us address this issue.

Asked about Dr Jousset’s paper, Dr Karen Polizzi, a synthetic biologist at Imperial College London, said his method was quite useful.

“This could be a way to improve plant traits more rapidly than genetic engineering of plants or traditional crop breeding,” she told the author in an email interaction.

However, Polizzi, who uses genetic modification strategies to correct problematic cell behaviour, said: “To do so, the trait of interest has to be something that can be affected by bacteria.”

On this, Jousset clarified that “(all) information whether drought, nutrients, pathogens, is processed by both, plant and microbial genes. We are now expanding the concept to encompass the whole network of plant hormones.”

Also read: What’s the fuss over the new variety of GM cotton that farmers are batting for

No editing of microbial DNA

Dr Jousset’s approach does not involve editing microbial DNA.

“The strategy described in the paper involves genetically modified microorganisms (GMOs). This approach is not feasible in field conditions. Instead, we are developing non-GMO strategies to manipulate the abundance of the genes of interest in the microbiome,” he said.

Dr Jousset’s team has a spin-off company that helps farmers and breeders. Their aim is to make horticulture and agri-foods more sustainable using microbiome remedies. Under greenhouse conditions, they have achieved a 25 per cent growth in tomatoes in normal soil but a high number of pathogens. In onions, they managed a 50 per cent growth in production in field experiments. 

“All in all, we build on community ecology to improve microbiome. Instead of searching for ‘magic’ microbes and hammering them into a given system, we play a set of judo moves based on the ecological forces assembling microbiome composition,” Jousset said.

Ameya Paleja is a science writer based in Hyderabad. He writes about genetics, microbes, clean energy and future tech at Coffee Table Science.

Also read: Indian farmers can’t wait anymore, they are sowing seeds of GM crops one Bt brinjal at a time


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