To human eyes, the soil may look like a brown layer of plant mush that fits into the rocks, but it is actually a highly complex living environment. Not only must the bacteria that live within it share their space with small animals, protozoa and fungi, but they also must work around giant complexes of tree roots. These roots are not just static objects but take an active part in shaping the microbial communities around them.

As an ex-biochemist, I am used to the idea of studying plant-microbe interactions by exploring only one plant and one microbe, so I was fascinated by recent research at the University of North Carolina at Chapel Hill and other institutions that looked at entire microbial ecosystems. Researchers collected two types of soil from different locations and grew samples of the plant Arabidopsis thaliana in each one. They then collected soil that had grown around the roots and looked at the bacterial species within that soil, as well as the bacterial species growing within the roots themselves. Collaboration with a next-generation sequencing team allowed them to identify the various bacterial species present. They found that a subset of all the bacteria in each soil was found clustered around the roots, and an even smaller subset was allowed inside. Examining the bacteria inside each plant revealed a core microbiome common to all the plants as well as a separate set of bacteria that plants recruited depending on soil type.

Because bacteria help to provide nourishment for plants, such information might help investigators find ways to tweak plant-bacteria interactions in ways that enable vegetation to grow and possibly even thrive in nutrient-poor soils.

Adapted from the Lab Rat blog at blogs.ScientificAmerican.com/lab-rat

COMMENT AT ScientificAmerican.com/oct2012

This article was originally published with the title Underground Network.

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