What happens when differences meet

By Inge Ruigrok

Roux’s fascination with plants started long before he became a researcher. His parents were farmers, and as a child he collected seeds from wild plants, planted them in pots, and watched them grow. His parents eventually gave him a square metre of their garden to cultivate. He started with wheat, then moved on to vegetables. At 16, he already knew he wanted to understand how plants adapt to their environment. 

At university, a population genetics course opened another door. He became interested not only in how phenotypic traits vary in plants, but also in the genes responsible for those differences. That curiosity led him to ecology, evolutionary biology, quantitative genetics and molecular , disciplines that would eventually come together in PATHOCOM, funded by an ERC Synergy Grant. Receiving it at 43 felt like ‘reaching a scientific Holy Grail. You cannot imagine what it meant to me.’

For the project, Roux has teamed up with Detlef Weigel, director at the Max Planck Institute for Biology in Tübingen, whose expertise lies in molecular biology and genomics-driven genetics, and Joy Bergelson, a professor at New York University who works in evolutionary ecology and co-evolutionary genomics. Almost 30 postdocs, Ph.D. students, engineers and technicians are involved. The teams travel between laboratories and spend time to ensure ideas can cross scientific boundaries.

‘The key is communication,’ Roux says. 

A plant is rarely alone

A small flowering plant, Arabidopsis thaliana, is at the centre of PATHOCOM. ‘We often think of disease as a single pathogen attacking a host’, says Roux. ‘In nature, infections are rarely so simple. Plants can harbour several pathogen species, or several strains of the same species, simultaneously. In natural populations, we have found communities containing multiple pathogens, sometimes as many as eight. Coinfection is more common than single infection.’

The researchers want to understand how these pathogen communities live alongside their host and affect one another. What happens when pathogens meet? Do they compete? Can one make a plant more vulnerable to another? Can particular combinations increase infection? And how do the plant’s genes, its microbiota and the environment affect the outcome?

Some of the answers are already surprising. 

Neighbouring plants, for example, may prevent disease from spreading. ‘A greater diversity of neighbouring plant species can create a barrier that slows transmission, while also increasing the diversity of the Arabidopsis microbiota’, says Roux. ‘That microbial diversity may, in turn, make plants more resilient by stimulating their immune systems or by producing substances that suppress pathogens.’

Then there are the pathogens themselves. In a large experiment involving almost 100 strains of two bacterial species, the team tested pairwise combinations and found that some combinations increased infection. Roux is cautious about calling this ‘cooperation’. The term suggests that the pathogens recognise one another and both benefit. The experiments do not yet show that. For now, he describes it as a ‘positive interaction’.

The distinction matters. His work shows that relationships between organisms are not always easy to describe. It also raises a broader question: could similar interactions occur in other hosts? ‘We can imagine that something similar can happen in humans: some pathogenic strains could interact to infect people more effectively.  And these positive interactions would depend on host genetics. I might become sick, while you might not.’

The team is now adding another variable: temperature. As average temperatures rise, plant immunity can weaken, and pathogen populations can grow, potentially allowing them to spread into new areas.  ‘New pathogens are appearing in southern France that were not present there 10 or 20 years ago. Because of climate change, they are moving northwards’, Roux says.

In one planned experiment, they will work on a Manhattan rooftop to see how different weather conditions affect interactions between plants and pathogens. 

Roux and his colleagues ultimately want to predict what these interactions could mean for natural populations as the environment changes. He knows that this will not be easy because ‘there are many variables at play.’ Still, he says, understanding even part of that complexity would be a significant step forward.

Coming out in academia

The idea of community also runs through another part of Roux’s story.

Earlier in his career, Roux was reluctant to be open about his LGBTQIA+ identity. He would answer honestly when asked but rarely brought it up himself. He worried that being open might affect his career or how colleagues viewed him.

That began to change around seven or eight years ago, particularly after he married his husband. Today, he is open about being LGBTQAI+ and believes that researchers of his generation have a responsibility to be visible for those coming after them. 

His concern is not simply about representation for its own sake. He has seen how the absence of visible role models can shape the way young researchers imagine their futures.  ‘Young scientists need to see that there is more than one way to belong in science. Seeing an openly LGBTQIA+ researcher win an ERC grant and build a career might make them think: ‘I can do that too.’

Roux’s decision to be visible has also made him more aware of what happens when academic environments fail to make space for people.

After he spoke at a seminar about his own experiences as a young researcher who had been afraid to reveal his membership in the LGBTQIA+ community, two doctoral students approached him privately to say that they, too, did not know how to conduct themselves, particularly when faced with homophobic comments. Roux and a few colleagues subsequently established a charter within the French academic community to tackle discrimination against LGBTQIA+ people.

He has also argued for better data on the representation and career progression of LGBTQIA+ researchers. ‘Without knowing how many LGBTQIA+ researchers apply for major grants, how many feel able to disclose their identity, or where researchers might be lost along the way, it is difficult to understand whether there are barriers - and what form they might take.’ 

Making space for difference

People around him strongly influenced Roux’s career.  Joy Bergelson, now his Synergy collaborator, was his postdoctoral supervisor. He describes her as one of the most influential people in his scientific career. One piece of advice has stayed with him: ‘She once told me, Fabrice, when you have ideas, there is no competition. I found that very powerful.’

He also credits former colleague Dominique Roby with showing him the value of crossing disciplinary boundaries. More recently, he says, Detlef Weigel has impressed him with ‘his work capacity and how quickly he can think about new ideas. It is highly stimulating.’

From these researchers, Roux says, he has learned lessons that go beyond the science itself: how to build international networks, how to lead them and how to navigate the politics of academia.

Now, he is passing on some of that perspective. 

When asked what he would tell his younger self, he returns to what first drew him to science: passion. ‘Keep doing the research you care about,’ he says. ‘And do not let other people's views of your sexual orientation determine your path.’ He is careful, though, not to rewrite the past. ‘I do not know whether I would tell my younger self not to worry, because the past was not always easy.’ What he can say now is simpler: ‘It is possible to be yourself and to succeed if you work in an open-minded and stimulating environment like the one I recently joined at Paris-Saclay.’

Biography

Fabrice Roux is a CNRS research director at the laboratory 'Ecology, Society and Evolution' at the University of Paris-Saclay. He obtained his Ph.D. in 2004 and subsequently spent one year as a junior lecturer in the Laboratory of Genetics and Evolution of Plant Populations (GEPP) at the University of Lille. Then, after spending one year in the laboratory of Joy Bergelson in the department of Ecology and Evolution at the University of Chicago, he obtained a permanent CNRS position in 2006. His research focuses on uncovering the genetic basis of complex adaptive traits in plants in the context of global environmental change.