Plants select microbial functions over microbial identity

A hidden world beneath our feet

Plant roots are surrounded by vast communities of microorganisms that help plants acquire nutrients, resist disease, and cope with environmental stress. Yet despite their importance, scientists have long struggled to understand why certain bacteria become successful members of a plant's root microbiome while others do not.

An international team led by researchers at Aarhus University and Utrecht University has uncovered new principles that help explain this puzzle. By analysing nearly 1,000 bacterial genomes and reconstructing root microbiomes in the laboratory at an unprecedented scale, the researchers discovered that plants consistently create an environment that selects for bacteria carrying particular functional capabilities, regardless of their species identity. 

The collaborative project brought together complementary expertise in plant biology, microbiome research, genomics and computational analysis, allowing the researchers to tackle questions that would have been difficult for either group alone. “This research was truly a collaborative effort,” says Simona Radutoiu, professor at Aarhus University who co-led the research alongside Ronnie de Jonge at Utrecht University. “Since the start of the project in 2019, we've been working shoulder to shoulder with Ronnie’s group.”

Looking beyond bacterial identity

The team studied the root microbiome of three very different plants: barley, Lotus, and Arabidopsis. They were chosen because of the different beneficial partnerships they are known to form. Barley associates with arbuscular mycorrhizal fungi, which help plants acquire nutrients from the soil, primarily phosphorus. Lotus, a model legume, can partner with these fungi and nitrogen-fixing bacteria. By contrast, Arabidopsis lacks both types of intracellular symbiosis, making it an ideal comparison species. 

The researchers applied series of microbial communities differing in functions and complexity to each plant to understand which bacteria would be selected into their root microbiomes. They found that the bacterial communities associated with each plant were taxonomically distinct yet shared a surprisingly similar set of biological functions. 

"We found that different plants created environments that select for different bacterial species, but they end up with microbiomes that perform many of the same jobs," explains Simona. "This demonstrates that the plant root is a selective environment for functions rather than specific bacterial identities." 

Among the most important functions were those involved in utilizing plant-derived nutrients, acquiring essential compounds, and interacting with both plants and other microbes. 

A core toolkit for life in plant roots

One of the study's most striking findings was that different plant species appear to create environments that select for different types of bacteria. Arabidopsis and barley were relatively permissive, allowing a broader range of bacterial partners to colonize their roots. Lotus roots, by contrast, were far more selective. Fewer bacterial strains were enriched, but those that succeeded carried a broader range of useful functions, effectively acting as microbial "Swiss army knives."

Despite the unprecedented diversity of plants and microbes studied, the researchers identified only 266 bacterial functions that were consistently enriched across all root microbiomes examined. These functions represented about 3% of the total functional diversity detected but appeared to form a core toolkit for successful root colonization. 

Importantly, no single bacterium possessed all these functions. Instead, the essential capabilities were distributed across members of the bacterial community, highlighting the cooperative nature of root microbiomes. 

Microbiome-based solutions

The researchers believe their findings will support future efforts to develop microbiome-based solutions for agriculture and identify plant genes that contribute to enrichment of microbes with beneficial functions at the root-soil interface. “Our discoveries provide a new framework to design communities that benefit plants and identify plant genes promoting their enrichment,” says Simona.

As agriculture faces increasing pressure from climate change and the need to reduce chemical inputs, understanding how plants naturally create environments that select for beneficial microbes may become an important tool for building more resilient cropping systems.