Life in the Rhizosphere

News 12 08 01 1The Rhizosphere

Roots are leaky. That is, some of the sugars transported from the leaves down to the roots may diffuse into the narrow area of soil near the roots.

Plant roots also secrete polysaccharides and glycoproteins (sometimes called mucilage) and other organic compounds.

Thus, to soil-dwelling microorganisms, plant roots are like donut shops, good sources of carbs.

Plant roots may also exude amino acids and proteins as well as slough off dead root cells. So, roots may also be a source of nitrogen for soil microbes.

Thus, the soil adjacent to the roots is like an oasis in the nutrient “desert” that is the bulk soil.

This area of the soil directly affected by plant roots is called the rhizosphere.

Bacteria and fungi not only live adjacent to the roots, but some can actually live inside the roots. Such microbes are known as root endophytes.

All of the microorganisms dwelling in the rhizosphere and within the root (endophytes) are collectively referred to as the root microbiome.

Who Are These Root Dwellers?

What bacteria phyla constitute the root microbiome? And what factors influence which phyla are present in these microbial communities?

These questions have recently been addressed in two papers published in the August 2, 2012, issue of Nature. (See references below)

Briefly, both studies, using the model plant Arabidopsis thaliana, have characterized the root microbiota based on genetic sequencing data. In natural soils, Arabidopsis plants are preferentially colonized by Actinobacteria, Proteobacteria, Bacteroidetes and Chloroflexi species.

Also, both studies concluded that the bacterial communities in the rhizosphere and the endophytic compartment within the root are most strongly influenced by soil type and are apparently affected to a much lower degree by host genotype.

The results of these studies are important because a deeper understanding of the root microbiome, and the soil factors affecting it, may offer opportunities to increase plant growth and to reduce susceptibility to plant pathogens, particularly in sustainable agricultural systems.


1. Lundberg, D.S., et al. (2012) “Defining the core Arabidopsis thaliana root microbiome.”
Nature, Vol. 488, pp. 86–90. (Abstract)

2. Bulgarelli, D., et al. (2012) “Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.” Nature, Vol. 488, pp. 91–95. (Abstract)

For a more detailed description of these studies, please see: Getting to the Root—Unearthing the Plant-Microbe Quid Pro Quo.

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