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Studies Characterize Arabidopsis Root Microbial Communities

NEW YORK (GenomeWeb News) – A pair of studies in Nature today are revealing the repertoire of microbial organisms residing in and around the roots of Arabidopsis plants.

An international team led by investigators at the University of North Carolina at Chapel Hill used 16S ribosomal RNA sequencing to characterize the root microbial communities in hundreds of plants from eight Arabidopsis thaliana accessions that were grown in two different soils.

"Science has long been fascinated with the spectrum of relationships between plant and microbe that span from pathogenic to mutually beneficial," UNC researcher Jeff Dangl, that study's senior author, said in a statement. "With our results we are adding new details to this complex landscape."

Dangl and his colleagues grew each of the A. thaliana plants tested from seeds that had been surface sterilized using soil from two pesticide-free sites: Mason Farm, which is maintained by the North Carolina Botanical Garden, and a crop research station in Clayton, NC.

Collaborators at the Department of Energy's Joint Genome Institute then used 16S rRNA Roche 454 GS FLX/Titanium sequencing to identify the microbes present within the root, in the so-called endophytic compartment, in the rhizosphere region right around the root, and in the soil overall.

Consistent with the notion that specific microbes are more likely to associate with the plant hosts than others, the team's analyses of 524 endophytic compartment samples, 613 rhizosphere samples, and 111 soil samples indicated that the microbial communities found in and around Arabidopsis roots differed from those in the soil at large.

By comparing the microbes present across the plant samples, the researchers defined what they call a core root microbiome for Arabidopsis — a set of microbes associated with Arabidopsis roots across the conditions and plant developmental stages tested.

Within the roots, for example, microbial communities often included bacteria from a few main phyla such as Actinobacteria and Firmicutes, along with bugs from certain families from the Proteobacteria phylum.

But the microbial communities found inside and right around the roots also varied depending on the soil that plants were grown in, researchers reported, while the plants' stage of development and genetic background seemed to have more modest influences over the root microbiomes.

"The core in the center tells you Arabidopsis wants some set of microbes, and they want Arabidopsis," Dangl said in a statement. "But the soil-specific interactions suggest that in different soil and nutrient compositions, the plant might need to recruit certain bugs to provide particular ecosystem services."

Going forward, researchers reportedly plan to look in more detail at how a plant's genetic profile impacts its interactions with microbes and alter the collection of organisms found in and on the root.

The team is also interested looking at how the presence or absence of certain microbes affects plant function — research that is expected to help distinguish between bugs that are beneficial to plant health or traits of interest and those that are more detrimental.

"In the same way that microbes play critical roles in and around our own bodies, we are adopting this concept of host-associated metagenomics in plant genomics as well, as it will ultimately lead to predictive interventions that will increase plant health and productivity, disease resistance, and carbon capture," co-author Susannah Tringe, who heads the metagenome program at JGI, said in a statement.

A second Nature study, this one by German researchers, verified some of the findings by Dangl and his colleagues, uncovering additional clues to some of the soil-specific differences in root microbial collections.

Investigators at the Max Planck Institute for Plant Breeding Research used 16S rRNA sequencing on the Roche 454 Titanium platform to compare microbial communities in and on Arabidopsis roots with those found in the soil in which plants were grown. In this case, the soil came from a sandy site in Golm, Germany and a clay and silt-rich region in Cologne, Germany.

Their analyses identified some of the same key phyla comprising the within-root microbial communities as those highlighted by the American-led team, including Proteobacteria and Actinobacteria. German researchers also saw enrichment for microbes from another phylum, Bacteroidetes, in the A. thaliana root microbiomes.

Again, the soil type affected the composition of root microbe communities to a certain extent, with plant genetic background adding another subtle layer of influence over the relative abundance of specific bacterial operational taxonomic units in the community.

For instance, the researchers reported, in soil samples from Cologne, a species of Actinocorallia bacteria was around 10 times as common in the roots of A. thaliana plants from one ecotype as it was in the roots of A. thaliana with a different genotype.

That team's follow-up studies indicated that a fraction of the Arabidopsis root microbiome can assemble in other kinds of plant material as well, hinting that some of the microbial associations are contingent on specific plant features and metabolism while others occur more generally.

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