Root microbes shape how a legume responds to higher CO₂

Root microbes can substantially change how plants respond to additional carbon dioxide, according to experiments with the model legume Lotus japonicus. Nitrogen-fixing bacteria enabled much stronger growth responses, while a community of other root bacteria shifted the balance between roots and shoots without increasing overall plant weight.

The study, led by Marina Cotta and colleagues, was posted on bioRxiv on November 9, 2026. It is a preprint and has not been certified by peer review.

A controlled underground community

Plants use CO₂ to build organic compounds through photosynthesis, but growth also requires nutrients, particularly nitrogen and phosphorus. Microbial partners can help supply them. Rhizobia are bacteria that fix atmospheric nitrogen inside root nodules; arbuscular mycorrhizal fungi can improve phosphorus acquisition. The researchers also investigated commensal bacteria: other members of the root community, distinct from these established nutrient-providing partnerships.

The team developed an enclosed growth platform called EcoChamber. Germ-free seedlings grew in sterilized peat, allowing researchers to introduce known microbes rather than work with an uncontrolled soil community. Temperature, humidity and light were controlled.

Plants grew for five weeks at CO₂ concentrations of 200, 400 or 800 parts per million. Six treatments compared germ-free plants with plants receiving a mycorrhizal fungus, the nitrogen-fixing bacterium Mesorhizobium loti, a community of 15 commensal bacterial isolates, or selected combinations of these partners. The main measurements drew on two to four independent experiments per treatment and CO₂ level.

Researchers measured shoot and root fresh weight, shoot length, chlorophyll and nodules. Automated sensors tracked chamber CO₂ exchange, while DNA-based methods assessed bacterial abundance and community composition.

Nitrogen partners unlocked stronger growth

Germ-free plants did respond to higher CO₂. Raising the concentration from 400 to 800 ppm increased shoot fresh weight by 37% and root fresh weight by 29%. But plants associated with nitrogen-fixing bacteria showed substantially stronger responses.

With M. loti alone, shoot fresh weight increased by 137% across that same CO₂ comparison. With all three microbial groups present, the increase was 82%. These percentages describe changes from each treatment’s own starting level, not which treatment produced the largest plants.

The three-partner treatment had the highest average shoot and root fresh weights and chlorophyll content, although not every difference between treatments was statistically significant. Thus, the results support benefits from combined partnerships without establishing that every partner improved every trait.

Mycorrhizal fungi alone did not improve growth. The authors attribute this to sufficient available phosphorus in the peat, making that partnership less useful under these particular conditions.

Commensal bacteria alone produced the highest root-to-shoot weight ratios without increasing total plant fresh weight. This indicates a different distribution of plant growth, not necessarily a growth benefit. Whether it reflected microbial signals, nutrient stress or another mechanism remains unresolved.

Carbon uptake is not carbon storage

Chambers containing plants with rhizobia generally showed stronger net daytime CO₂ uptake, especially at elevated CO₂. However, the equipment measured the combined balance of photosynthesis and respiration by plants and microbes. It could not separate those processes or distinguish aboveground from belowground respiration.

Bacterial DNA relative to plant DNA also increased under elevated CO₂. That finding suggests greater bacterial colonization relative to plant tissue, rather than simply more bacteria because plants were bigger. It is a DNA-based indicator, not a direct measurement of microbial carbon storage.

A separate test collected organic carbon released by roots into water over 24 hours. At 800 ppm compared with 400 ppm, measured release rose 1.6-fold in germ-free plants and 1.2-fold with rhizobia plus commensals. With commensals alone, release fell to 0.55 times the lower-CO₂ value; that treatment was tested in only one experiment.

These measurements cannot establish exactly where the additional carbon went. Bacteria remaining attached to roots could have consumed some carbon during collection, an unmeasured contribution acknowledged by the authors.

What remains uncertain

The experiment involved one legume, a defined microbial community and sterilized peat over a short growth period. Its findings need testing across other plants, soils and field conditions. Increased nodulation was consistent with greater nitrogen-fixing capacity, but did not itself directly measure fixation rates.

Most importantly, greater plant growth or root-associated bacterial abundance does not demonstrate lasting soil carbon storage. Microbes can also release carbon through respiration and decomposition. The study identifies microbial partnerships as an important influence on plant responses to CO₂, not a proven route to greater climate protection.