The hidden helpers: how microbes quietly shape the lives of plants

Around the turn of the century, Julia Vorholt was walking through the countryside outside Toulouse, in southern France, collecting leaves from perfectly healthy plants. 

No diseases. No strange symptoms. 

Just green, thriving leaves. But she was not studying the plants themselves. She was after something else – something tiny, invisible and largely ignored. 

“Every plant leaf we sampled was populated by bacteria,” she recalls. “And when we came back a year later, the same bacterial strains had recolonised a new generation of plants. There was so much similarity in the microbial populations, not only among plants growing at the same time in the same plot but also from year to year.” 

Julia Vorholt had not expected such stability. The prevailing view at the time was that microbes on leaves are just passers-by – whatever is present by chance in the air or soil will end up in and on leaves. But what she saw hinted at something else: order, recurrence and maybe even that the plants were selecting microbes.

“It made me wonder – why are they there? And why is the composition always similar? Why are the same types of microbes coming back?” she says. 

The question led her down a path no one else seemed interested in. It was not about disease causing microbes or the classic nitrogen-fixers. It was about the quiet ones – the background bacteria that do not scream for attention but might be doing something important. 

Back then, the term plant microbiome did not even exist. But the mystery had her hooked. She began isolating and experimenting. What if these invisible passengers were part of the reason healthy plants stayed healthy? 

Outsider science 

In 2001, Julia Vorholt joined a renowned institute of the French National Centre for Scientific Research specialising in plant microbe research in Toulouse. But it did not take her long to realise that her work and her ideas did not quite fit the mainstream. 

Most laboratories in the institute focused on the obvious actors: deadly pathogens or microbes clearly benefitting the plants, such as those that help plants grow by fixing and supplying essential nitrogen. Her quiet leafdwellers, however, defied categorisation. 

“For them, I was scientifically an outsider,” she says. “And I was told that many times. ‘What you are doing is unlikely to lead anywhere. Why would anyone care about these microbes in the background’?” 

Born in western Germany, between Cologne and Aachen, Vorholt had studied microbial biochemist. She was not trained in plant biology. 

“My entry point was microbiology,” she says. “I had studied methylotrophs – bacteria that consume methanol and are common on leaves. That was the first clue that my background might not be irrelevant for understanding microbes in the context of plants.” 

Her move to Toulouse had come through a stroke of luck. But the culture clash was real. 

“It was a difficult time,” she says. “Some students working with me even got bad grades because their topic supposedly did not fit into the general theme of the institute, plant–microbe interactions.” 

Vorholt, however, was not that easily deterred. 

“I did not take it personally, which was important. They were warning me – not because they were not well meaning but out of concern that I was risking my future. And I had this feeling: Maybe it is not me, but the environment that does not fit?” 

The methanol clue 

One of the earliest findings hinting at interaction between plants and their leaves microbes came from examining a single bacterial species: Methylorubrum extorquens. 

“We showed that it consumes methanol produced by the plant that the plant cannot use itself,” Vorholt says, “This gives the bacteria exclusive access to a food source, thereby creating their own niche on the plant surface.” “We had expected this outcome; it was a logical hypothesis to test.” 

But her group’s discovery came about through further exploratory research. They wondered what proteins other than those needed to use methanol the bacterium produced when colonising plants and what their role was. One protein out of several hundred caught their attention, leading to the discovery of the essential protein for leaf colonisation. This regulatory hub was later shown to be widespread among the large group of Alphaproteobacteria. 

“If you knock the gene out,” she explains, “the bacteria simply cannot establish themselves on the plant.” 

This mechanistic work laid the foundation for a broader, community-level perspective. After five years in Toulouse, her contract was ending. But her ideas were just beginning to take shape.

“I was in between disciplines where it was not obvious to find a natural fit,” she says. “The plant section said: ‘You are a microbiologist.’ The microbiologists and biochemists said: ‘You are doing ecology.’ And the ecologists said: ‘That is not ecology’.”

She applied for positions in France, Munich – and Zurich. She was offered but declined Munich and moved with her family to Switzerland in 2006. The next chapter of the puzzle could begin. At the Hönggerberg Campus of ETH Zurich, high above Lake Zurich in a sleek new laboratory, Julia Vorholt found something she values deeply: scientific freedom.

“The opportunity to come here was extraordinary,” she says. “Because I had all the freedom of curiosity-driven research. It enables remarkable flexibility in research directions.”

Fluorescent imaging reveals how bacteria colonize the leaf surface – not randomly, but in complex patterns.

Patterns in the chaos

She used that freedom to do something bold at the time: She started looking not only at one group of bacteria, the methylotrophs, but asked what all the other bacteria were doing on the leaf. She pioneered the application of proteomics to entire microbial communities from leaves – metaproteomics – and then combined this approach with metagenome sequencing to develop metaproteogenomics.

“We prepared and trained extensively for the sampling campaigns,” she explains. “We chose different plant species, including soybean and clover from fields outside Zurich, as well as wild Arabidopsis plants. Our goal was to harvest the bacterial communities efficiently and without disrupting their natural state, enabling us to capture snapshots of bacterial physiology in situ.”

The approach worked remarkably well.

“It helped us to understand not just which bacteria were present but what they were doing when colonising plants under environmental conditions with all the stresses that come with it.”

“We learned something fascinating,” she adds. “Not only were the organisms similar and appeared consistently across plant species and geographical locations, but the proteins we found in these communities were remarkably similar. And this suggests that, in a way, the organisms are adapting similarly to different plant hosts.”

“The finding strongly suggested that we could focus on a single representative model system – learn as much as we can – and potentially apply what we learn to other plants, including crop plants,” she explains.

This was not just a chance observation. It hinted at rules – shared principles in shaping the assembly, survival and function of bacteria on plant surfaces.

The synthetic garden

Vorholt then embarked on an ambitious new phase of her research: rebuilding microbial communities from scratch – one strain at a time. Her team developed simplified ecosystems – first a few, then hundreds of bacteria – and tested how they interacted with one another and with the plant.

“We wanted to understand the basic interaction networks that exist,” she explains. “Are there dominant players? Are there suppressors? What happens when you remove one? What happens if you add one late?”

It was like planting a garden – her co-workers acting as the gardeners. They selected the microbes, composed them together, gave them a chance to grow and then observed the living systems. These simplified communities enabled her team to ask clear questions – and get real answers.

“I have always been interested in these very small living objects,” she recalls. It brought her back to her childhood curiosity about the invisible world – this time with tools to truly see it.

“Back then, I just did not know what I was really looking at.”

Now she did. Her laboratory also developed new tools to observe what each microbe was doing – and even gently control individual cells under the microscope.

“We needed ways to see what is really going on,” she says. “That is how we learned who is supporting whom and who is being pushed out.”

Fluorescent imaging reveals how bacteria colonize the leaf surface – not randomly, but in complex patterns.

Microbial interactions

The synthetic communities revealed intricate microbial relationships. When bacteria were added or left out, the composition of the community shifted in response. Some kept others out. Some created balance. Others caused collapse.

“If we inoculate our plants first with certain strains, let them colonise the leaves and then try to add other bacteria later – can they still also get a foothold on the plant?” says Vorholt. “The answer often was: no. We saw that the sequence of arrival mattered.”

This order of arrival shaped not just the short-term structure of microbial communities but also long-term behaviour. It was ecology, community dynamics and timing all at once.

Some strains even depended on others to survive. Remove one, and another failed.

“There are organisms that can help others grow – for example, by producing something they need,” she explains. “But we also see the opposite: one helps another get established but then gets pushed back.”

They were watching community assembly in miniature. Relationships formed, shifted and broke. Hidden hierarchies emerged – all on the surface of a single leaf.

The microbes were not just coexisting. They competed and cooperated in familiar ways.

In Julia Vorholt’s communities, bacteria formed alliances – or pushed others out – in a manner very similar to what was known from the behaviour of animals and plants, macroorganisms, in ecosystems.

Vorholt’s team began mapping the interactions between bacterial strains – pair by pair, network by network – watching how dynamics depended on time, strain combinations and nutrient availability.

“Some strains had no effect alone, but in combination with others, they changed the outcome,” Vorholt says. “We began to see community behaviour – not just species behaviour.”

“We saw interactions that indicated shared ancestry,” she adds. Close relatives tended to behave similarly – but also antagonised each other, sometimes damaging each other’s cell wall.

To help disentangle this, her group developed computational tools to analyse the interactions at scale. “We could not track it by hand anymore,” she says. “We needed systems that could handle thousands of possible relationships and help us to see the patterns.”

These were not just invisible communities. They had invisible yet highly dynamic histories – layered, inherited and alive.

Predicting the microbial future

After years of careful experiments, Julia Vorholt and her team began to wonder: could microbial communities be predicted?

It seemed unlikely – so many factors shape them, from timing to chemistry to chance. But patterns slowly began to emerge. And with the right tools, these patterns could potentially be modelled.

“We wanted to go beyond just observing what happens,” Vorholt says. “We wanted to predict it. To say, if we combine these two strains, this is what we expect. And then test whether it is true.”

Her team built models to simulate microbial interactions, informed by the bacterial genome sequences and by studying the bacteria on well-defined resources, examining one substrate at a time.

“Now we can predict microbial interactions in our systems with up to 90% accuracy. This is not perfect, but it shows us where something unexpected is happening – and where our knowledge is still missing.”

The models opened up questions that once seemed unanswerable. Which microbes are helping others? Which strains are interchangeable? Which ones simply compete for limited resources when establishing themselves on a leaf?

“If we see that a prediction fails,” she says, “that is when we look closer. Something is going on that we do not understand yet.”

It was a big change – from observing microbial communities to designing them. If you could predict a microbial community’s behaviour, maybe one day you could engineer it to have specific, useful functions.

“The better we are at modelling and predicting outcomes,” Vorholt explains, “the more opportunity we have to bring in an organism on purpose – and make sure that it can establish itself.”

Now that they could predict how communities behave, they wanted to go a step further: design them to protect plants.

Could they build a microbiome that makes a plant more resilient to disease, drought or stress?

“It would be a dream if we could design communities that would strengthen the health of the plants,” Vorholt says. “Engineering useful, environmentally friendly microbiomes – that is the vision.”

Into the wild?

In a series of experiments, they added different mixes of bacteria to plants and then infected them with a pathogen. Some did not help – but others protected the plants surprisingly well.

“We predicted that resistance to a pathogen should increase if we combine certain strains,” she says. “And our experiments confirmed that this is the case. The pathogen did not establish as easily.”

It was the first glimpse of something powerful: microbial communities could be tuned – like instruments in an orchestra – to enhance plant resilience.

But the potential of engineered microbial communities extends beyond just defence. Some microbial blends could possibly help plants to grow faster or tolerate nutrient-poor environments.

“It is not only about resistance,” Vorholt explains. “Sometimes it is about support. About how a plant manages energy, stress or competition.”

These discoveries could lead to more sustainable farming – using biology, not chemicals, to support crops.

“This is exciting,” she says, “because we are not just studying life. We are learning to collaborate with it.”

Designing microbial communities in the laboratory was one thing. But real-world plants do not grow in controlled chambers. They live under shifting weather, surrounded by unpredictable microbes.

Could combinations of bacteria isolated from the environment survive when brought back as consortia – or were they just showing impact in the laboratory?

“Based on what we have learned, we can now begin to ask: can we transfer these communities to other environments?” she says. “Can they establish themselves, persist and, over time, perform their intended function in the field?”

“I am a laboratory person,” she admits with a smile, “but translating rational design principles into practical field applications is important. The challenge is immense given all the complex environmental interactions.”

Precise microbial inoculation: Bringing designed communities to life on growing plants.

The plant pushes back

For years, Vorholt’s team had focused on what microbes are receiving from the plant and how they interact with each other. But what about the other way around?

“We started asking: how does the plant actually respond to all these non-pathogenic bacteria?” she says. “Is it just passively letting them land – or is it reacting?”

The answer was both simple and profound.

Her laboratory discovered that plants mount a consistent, low-level immune-like response to a wide variety of microbes. They called it the general non-self response.

“This is like a universal handshake,” Vorholt explains. “Regardless of which microbe appears – if someone has not learned the handshake, they trigger this core response.”

In a landmark study, the team tested dozens of bacteria from plant leaves and found the same pattern again and again: a core set of 24 genes switched on, preparing the plant to defend itself. Even friendly strains triggered this subtle but important alarm. And there was more.

“The general non-self response does not just react – it protects,” says Vorholt. “The plant is pre-emptively strengthening itself, even when no threat is apparent, even when things look quiet. It is boosting its defences against real pathogens like Pseudomonas syringae,” says Vorholt.

In subsequent experiments, they pushed the idea further: could the plant’s response actually steer the assembly of the microbial community, and in what quantities?

They found that it could. “It functions like a brake on the fastest-growing bacteria.”

“This response varies depending on how many bacteria there are, how long they have been there, and even whether they are alive,” Vorholt says. “It is dose-sensitive. The more the plant perceives, the stronger the reaction.”

And that reaction, in turn, shaped the microbiome.

“This is a feedback loop,” she explains. “The microbes impact the plant, and the plant pushes back – shaping the community.”

What began as a simple question – why do the same microbes keep returning? – had become something more profound: a living conversation.

“This is no longer merely about microbial colonisation,” Vorholt says. “It is about interaction, influence and balance.”

The cell inside the cell

After years of studying bacteria on plants, Julia Vorholt began exploring a very different type of mutually beneficial coexistence: one microbe living inside another – a process called endosymbiosis. This is how ancient bacteria became parts of our cells, such as mitochondria or chloroplasts. Could something like that happen again? Could they watch it as it unfolded?

“We were implanting bacteria into host cells to understand the first steps in endosymbiosis,” Vorholt says. “We wanted to see: can they survive? Can they adapt? And can the host tolerate them?”

They used a model fungus and inserted selected bacteria directly into its inside, the cytoplasm – creating an entirely new, artificial symbiosis.

“At first, it is a cost to the host,” she explains. “The fungus slows down. It is stressed. But over time, we saw adaptation. The system becomes more stable.”

What they were witnessing was not just coexistence – it was evolution in motion. The bacteria, once foreign, began to integrate. The fungus learned to tolerate them. How could they become cellular roommates?

“We saw that, over time, the cost of this endosymbiosis became less,” Vorholt says. “There were adaptations going on in the genome of the host system. It was becoming a new unit.”

Under the microscope, they could see it: cells within cells, reshaping each other – replaying, in miniature, a transformation that may have happened similarly billions of years ago.

“It is fascinating to observe that in real time,” she says. “To see something that is usually locked in history – happening in front of you.”

In a way, it mirrored her own journey: assembling fragments and pushing boundaries.

Experimental endosymbiosis: A bacterium is injected into a fungal cell, recreating ancient cellular mergers.

Recognition

For years, Julia Vorholt had worked on the edge of her field – pursuing questions that did not fit into neat categories. Now, things were starting to change. The microbiome, once obscure, had become a global research frontier. And people were paying attention, especially as it became clear that the gut microbiome was crucial to human health.

“I was invited to be a candidate for the Board of Directors of the International Society for Molecular Plant–Microbe Interactions,” she says. “Which really told me – yes, I have also arrived in that field.”

Her ideas, once seen as peripheral, were now central. Microbial communities were no longer just the domain of gut health. The phyllosphere – the surface of plants – had become a frontier in its own right. And Vorholt had helped to map it.

Recognition came surprisingly. Perhaps most unexpectedly, in 2017, when she received an invitation from Bill Gates’ office.

“He was interested in a private tutorial. We spent two hours discussing science. It was special – a moment where I thought: this really has come a long way from when I was told ‘nobody will ever care’.”

Part of her impact came from how she worked.

“We deposited our strains early on so anyone could request them,” she says. “Sometimes we even shipped entire communities to other laboratories.”

“I think this is part of our responsibility,” she says. “To make what we develop available. If we want to understand how microbial communities shape plant life, it has to be a shared effort.”

Even so, the recognition felt personal. Years earlier, she had been warned: what you do will lead you nowhere. Now, she was helping to lead the field forward.

And yet, she remains cautious.

“It is not about being right,” she says. “It is about asking questions that open new doors. That is the part I enjoy together with a team of engaged and curious researchers."

Julia Vorholt and her team enjoying dinner under the vines – a community studying communities

The future in the leaf

For Julia Vorholt, the mystery that started on a leaf never really ended. It only got deeper.

Her work revealed that healthy plants rely on hidden communities of microbes – organised, interactive and essential. Nature, she showed, is less about isolated individuals and more about the relationships between them.

“Our research is fundamental in essence,” she says. “But it is very important also to think about whether we can translate the knowledge to benefit an ecosystem.”

She still runs experiments. Still refines models. Still builds synthetic communities. But more and more, she finds herself thinking in systems – in balances, histories and resilience.

“It is not just about one organism anymore,” she says. “It is about the network. About who is there, who came first and what the organisms do together.”

The impact goes far beyond science. As climate change stresses crops, designing helpful plant microbes is becoming urgent. Just like gut microbes affect human health, plant microbes could be key to healthier, more resilient crops.

“This is the same principle,” she says. “A hidden community that helps maintain balance. If we understand that community, we can embrace it – rather than fight against it.”

But for Julia Vorholt, the goal was never to control nature – it was to understand it and work with it. She helped to bring real scientific precision to a field once overlooked. Today, thanks to her and her team, we are finally learning how the invisible microbes on plants shape their health and resilience.

And for her, it all goes back to the beginning.
“Even before I could see them, I knew something was there.”

That instinct had become a career. A field. A quiet revolution.
And it all started with a leaf.