Plant Root Comity

Plant roots create an ambiance in the soil – the rhizosphere – that helps them manage nutrient provision and thwart pests. Roots are a magnet to soil bacteria and fungi, whose concentration in the rhizosphere is 100 times that of surrounding soil. “Plant roots are exposed to an enormous amount of soil biodiversity; a handful of soil can contain more than 5000 species that operate together in plant-soil feedback.” said Dutch terrestrial ecologist Wim van der Putten.

Roots recognize microbes that are helpful and those that are trouble. Beneficial bacteria are essential for robust roots. Bacteria nest in roots and then protect their homestead. “In the rhizosphere, the plant-associated microbiome is intricately involved in plant health and serves as a reservoir of additional genes that plants can access when needed,” explained American botanists Marnie Rout & Darlene Southwort.

Roots invite beneficial microbes by sugars and organic compounds that are energy rich. The rhizosphere is awash with metabolites exuded by plant roots. The choice of metabolite at a root meristem depends on whether friend or foe is at the receiving end.

Those unwelcome are treated to hostile chemical concoctions, in attempts by roots to fortify themselves against intrusion. Those same pest toxins recruit specific species which have evolved tolerance.

Benzoxazinoids (BXs) are a class of secondary metabolites used against pests aboveground and below. Roots put out BXs early in life, when they are most vulnerable. The beneficial rhizobacterium Pseudomonas putida is not put off by BXs. It treats BXs as a beacon to find suitable employment.

Plants put out a welcome mat to helpful microbes, providing the molecular building blocks to promote beneficial colonization of roots. Plants dispense specific sugars from their cell walls that activate bacterial genes which induce biofilms. The rhizosphere becomes a rich nesting site for a microbial community beneficial to a plant.

“Plants modulate symbiosis with microbes through flavonoid molecules,” said American biogeochemist Ilenne Del Valle. “Plants change a couple of (oxygen/hydrogen) groups here and there in the flavonoid, and this allows them to use soil conditions to control which microbes they talk to. It’s a gorgeous example of evolution,” marveled American biogeochemist Caroline Masiello.

“Early in its growth cycle, a plant is putting out a lot of sugars which many microbes like. As the plant matures, it releases a more diverse mixture of metabolites. The microbes that become more abundant in the rhizosphere are those that can use these metabolites,” reported American microbiologist Trent Northern.

Most plant species nip their nitrogen from the soil themselves. But many plant groups get their supply via cooperative and symbiotic relationships with nitrogen-fixing bacteria and fungi.

Soil bacteria and fungi reduce atmospheric nitrogen (N2) to ammonia (NH3), but they can only fix nitrogen when intimate with a plant by being welcomed. Plants capable of such symbiotic relationships grow better in nitrogen-poor soil than do competitors without an ally for nitrogen fixation.

In soils with deficient nitrogen or other nutrients, plants recruit help. In doing so they pay a cost. “These relationships with symbionts are metabolically costly,” said Masiello. “Plants have to pay the microbes in photosynthesized sugar, and in exchange the microbes mine the soil for nutrients. Microbial symbionts can be really expensive subcontractors, sometimes taking a significant fraction of a plant’s photosynthate. Plants don’t waste photosynthate supporting microbial help they don’t need.”


Ishi Nobu, The Web of Life, BookBaby (2019).

Ilenne Del Valle et al, “Soil organic matter attenuates the efficacy of flavonoid-based plant-microbe communication,” Science Advances (29 January 2020).

Plants manipulate their soil environment to assure a steady supply of nutrients,” ScienceDaily (29 January 2020).