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Tree roots and their microbial partners may provide answers to productivity

Topics: Clean Energy Supercomputing Biological Systems Computational Biology

Researchers investigate cottonwood poplars in Tennessee to understand plant root microbiomes.Researchers investigate cottonwood poplars in Tennessee to understand plant root microbiomes.OAK RIDGE, Tenn., Nov. 13, 2013 – The ability to make plants grow stronger and more quickly is a key goal in the effort to develop better biofuels and better understand plant efficiency. Researchers at the U.S. Department of Energy’s Oak Ridge National Laboratory have gone straight to the roots to understand microbes that may play a role in reaching that goal.

In a paper published in PLOS ONE, a team led by Christopher Schadt of the lab’s Biosciences Division investigated two naturally occurring riverbank populations of cottonwood poplars in Tennessee and North Carolina. The study collected data on two watershed-level populations of the tree to understand the genotypic and environmental origins of variation in the root-associated microbiome.

“This study was one of the most comprehensive done on any tree in that it examined plant association patterns of both bacteria and fungi, in two states, over two seasons,” Schadt said.

They found that bacterial and fungal microbiomes varied across habitat niche, space, and, often, season. Depending on given space, weather and location, the microbiomes inside the trees’ roots could work in different ways—and could, with further study, be manipulated to do much more.

“We found that the microbes in the plant roots are dramatically different from those outside the roots just millimeters away,” Schadt said. “This implies the host is selecting its microbial associates.”

Many of these microbes have been implicated in promoting plant growth, but based on Schadt’s team’s discovery, it’s possible these microbiomes could be manipulated to promote plant growth, which could result in increased productivity, stress resistance and greater efficiency.

“Knowing this information could have a number of implications for forestry practices, carbon cycling and biomass production for biofuels,” Schadt said. In response to changes in the global environment due to fossil fuel use, each of these areas face unique challenges and opportunities that could potentially benefit from a better understanding of beneficial plant-microbe interactions.

Other authors of the paper, titled “A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees,” are Migun Shakya (now a postdoctoral associate at Dartmouth College), Neil Gottel (now a postdoctoral associate at the University of Texas), Hector Castro, Zamin Yang, Lee Gunter, Jessy Labbé, Wellington Muchero, Gregory Bonito, Rytas Vilgalys, Gerald Tuskan and Mircea Podar.

Other institutions contributing to the study were the University of Tennessee, Duke University, Dartmouth College and the University of Texas.

PLOS ONE is an online scientific journal published by the Public Library of Science that covers original, primary research done in any discipline within science and medicine.

This work was performed as part of the Plant Microbe Interfaces project at ORNL, supported by the DOE Office of Science. More information on the project can be found at

UT-Battelle manages ORNL for DOE’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, please visit