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Underground Communities: The plant roots that collect bacteria

The views expressed are those of the author and are not necessarily those of Scientific American.


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

A fluorescent micrograph capturing the presence of bacteria (shown as green) on the surface of an emerging Arabidopsis lateral root (plant nuclei shown in blue). Image created by Sarah Lebeis and reposted here with permission. Credit below.

As an (ex)-biochemist I’m used to the idea of studying plant-microbe interactions by taking one plant and one microbe and seeing what chemicals they produce, so I was fascinated by recent research from the University of North Carolina that looked at entire microbial ecosystems. The researchers went outside, collected two types of soil from different locations and grew samples of the plant Arabidopsis 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 root itself.

Collaboration with a NextGen sequencing team (the Department of Energy’s Joint Genome Institute) allowed them to identify the different bacterial species present. They found that a subset of all the bacteria in the soil were found clustered around the roots, while an even smaller subset were allowed inside. Looking for similarities between the bacteria from each plant revealed a core microbiome, a set of specific bacterial species that the plant was attracting from the soil towards itself.

Arabidopsis thaliana - the plant most commonly used by plant-scientists. Credit below.

It was also found, however, that as well as this core microbiome, the pattern of bacteria that the plant recruited varied depending on the type of soil. Dr Dangl, the lead researcher, suggested that this might be for nutritional reasons – plants often use bacteria to help provide their nutritional requirements and in different soil types different bacteria may be more useful. This points to a fascinating interaction between the plants and the bacteria, a secret underground community of mutual benefit.

This interaction isn’t just a highly interesting story, it also has huge potential for further research. Arabidopsis is relatively easy to genetically manipulate, removing certain genes from the plant and seeing how long these interactions last could start to show how these interactions form. Dr Dangl comes from a background of working with plant immune systems so another potentially interesting area is how the plant distinguishes between the bacteria that it wants to keep in and around its roots, and those it wants to get rid of.

As plants collect bacteria for nutritional reasons it might also be possible to tweak those interactions to support plant growth in nutrient-poor soils. By manipulating the plant microbiome rather than the plant itself there is the potential to promote growth and development in areas where plants may find it difficult to thrive.

Credit for image 1: Published in Lundberg, D.S., Lebeis, S.L., Paredes, Yourstone, S., Gehring, J., Malfatti, S., Tremblay J., Engelbrektson A., Kunin V., Glavina del Rio, T., Edgar., R.C., Eickhorst, T., Ley, R. E., Hugenholtz, P., Tringe, S.G., and Dangl, J.L. 2012. Nature 488: 86-90.

Credit link for image 2

Thanks to Dr Dangl for agreeing to an interview.

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.





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