Plants have microbiomes like humans do, now scientists have learned how they work

A single teaspoon of healthy soil can hold as many as a billion bacteria, yards of fungal threads, and a menagerie of microscopic grazers. These organisms form the root microbiome, which helps keep plants fed, watered and defended against drought and disease.

New research now argues that plants are not just passive tenants in this world but active managers that build hand‑picked below‑ground crews, a process the authors call functional team selection (FTS).

The study is led by Regents’ Professor Nancy Collins Johnson of Northern Arizona University, working with César Marín of Universidad Santo Tomás in Chile.

How plants create microbiomes

A microbiome is the collective genomes and activities of bacteria, fungi, viruses, and other tiny life forms that live in and around a host.

In plants the action centers on the rhizosphere, the thin shell of soil that sticks to roots and hums with chemical chatter.

Microbes in this region swap nutrients, growth hormones, and signals with their hosts, often trading nitrogen or phosphorus for sugars.

Under drought conditions, some bacteria exude sticky biofilms that help roots hang on to water, improving crop yields in experimental fields.

Yet the community is no free‑for‑all; opportunistic pathogens lurk, and beneficial species can be crowded out by chance or by a sudden fertilizer surge.

Understanding how plants steer the mix in the root microbiome is therefore critical for sustainable farming.

Scientists sequence the 16S rRNA gene from rhizosphere samples and routinely detect more than 5,000 operational taxonomic units on a single maize plant.

That microbial diversity rivals the entire bacterial roster of many animal gut microbiomes, underscoring how much genetic potential lies just outside a root tip.

Plant microbiomes shaped by stress

Johnson’s earlier field work showed that adding chemical fertilizer for eight years shifted arbuscular mycorrhizal fungi toward strains that taxed big bluestem grass more than they helped it.

The finding hinted that low‑nutrient stress is not just tolerated but needed to keep the symbiosis honest.

Other studies echo the pattern: under conditions of water scarcity, maize roots release flavonoids that attract drought‑tolerant microbes, whereas well‑watered plants skip the recruitment drive.

Selective pressure, in other words, acts like an admissions test for the root community.

This ecological sorting sets the stage for evolution, because microbes that pass the test multiply and share genes for the traits the plant needs. Over time the soil becomes a living memory of past hardships.

Plants secrete up to 40 percent of the carbon they fix as root exudates, a spill that serves as both payment and message to microbes.

Compounds such as malic acid call in growth‑promoting Bacillus, while terpenes can ward off unwanted invaders.

Functional team selection (FTS) idea

Johnson and Marín propose that four ingredients – selection force, host constitution, microbial diversity, and time – determine whether a functional team selection (FTS) pathway opens.

When the mix is right, a plant and its hand‑picked allies act as one adaptive system rather than as separate parts.

“Functional teams are unlikely to evolve in benign environments with no stress and ample resources because they lack the selection pressure that is required to curate the composition of the microbiome,” Johnson said.

Her remark underlines why crop inoculants bought off the shelf often disappoint farmers who apply them to fertile, irrigated soils.

Plants, microbiomes, and FTS

The framework leans on the recently articulated Law of Increasing Functional Information, which holds that complex systems tend to explore ever more effective configurations when variation meets selection.

Roots and microbes, stars and minerals all follow comparable rules, differing only in the building blocks they shuffle.

Hazen and colleagues illustrated the law with examples that range from heavy‑element synthesis in stars to enzyme evolution on Earth, arguing that a drive toward functional novelty bridges physics and biology.

By situating FTS within that broader law, Johnson’s team claims no special exemption for life; they simply place roots and their microbiomes on the same playing field as galaxies.

Lessons for agriculture

Worldwide sales of microbial biofertilizers are booming, yet meta‑analyses show that many products fail to colonize roots or boost yields once they leave the greenhouse.

FTS suggests that success will improve when products are matched to the stresses and nutrient limits of specific root microbiomes rather than offered as universal cures.

Breeders could also select crop varieties that reward resident mutualists instead of favoring short‑term fertilizer responses.

That shift would align genetic improvement with the slow buildup of local microbial teams instead of tearing them down each season.

Adopting FTS thinking could also cut greenhouse‑gas emissions because successful microbial teams often help plants capture nitrogen from air and recycle soil carbon, trimming demand for energy‑intensive fertilizer. Lower fertilizer demand translates to fewer nitrous oxide emissions, a potent greenhouse gas.

FTS from soil to other systems

The authors argue that FTS can illuminate animal guts, coral reefs, and even human‑made bioreactors because each hosts a crowd whose joint output beats any single member.

Testing the idea across systems may reveal design rules for building resilient microbiomes in medicine and industry.

A similar logic already guides fecal microbiota transplants that restore healthy gut ecosystems after recurrent infections, proving that designed consortia can outperform single‑strain probiotics.

Cross‑talk between fields may speed the jump from proof of concept to routine practice.

Where research goes next

Johnson and Marín want field trials that run for multiple plant generations, use minimal fertilizer, and track microbial genomes alongside plant performance.

Such studies would put FTS to the test by asking whether curated teams stay stable and beneficial when weather and management shift.

Meanwhile ecologists are building network models that predict which microbes form keystone partnerships under drought, salinity, or heat waves.

If those models hold, future crops may come with recommended microbial seed mixes tailored to local stress profiles instead of chemical input schedules.

The study is published in The ISME Journal.

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