Gene sequencing of samples from 57 Panamanian tree species gives scientists a look at host diversity in the plant microbiome

EUGENE, Ore. — Sept. 15, 2014 — Each tree species has its own bacterial identity. That's the conclusion of University of Oregon researchers and colleagues from other institutions who studied the genetic fingerprints of bacteria on 57 species of trees growing on a Panamanian island.

"This study demonstrates for the first time that host plants from different plant families and with different ecological strategies possess very different microbial communities on their leaves," said lead author Steven W. Kembel, a former postdoctoral researcher in the UO's Institute of Ecology and Evolution who is now a professor of biological sciences at the University of Quebec at Montreal.

For the research — published in the online Early Edition of the Proceedings of the National Academy of Sciences — researchers gathered bacterial samples from 57 of the more than 450 tree species growing in a lowland tropical forest on Barro Colorado Island, Panama.

Using DNA sequencing technology housed at the UO's Genomics Core Facility, scientists sequenced the bacterial 16S ribosomal RNA gene isolated from the samples. That gene, which biologists call a barcode gene, allowed researchers to identify and measure the diversity of bacteria based on millions of DNA fragments produced from bacterial communities collected from the surfaces of leaves, said Jessica Green, a professor at both the UO and Santa Fe Institute.

"Some bacteria were very abundant and present on every leaf in the forest, while others were rare and only found on the leaves of a single host species," Kembel said. "Each tree species of tree possessed a distinctive community of bacteria on its leaves."

In the world of microbiology, plant leaves are considered to be a habitat known as the phyllosphere. They are host to millions of bacteria, Kembel said. "These bacteria can have important effects — both positive and negative — on the health and functioning of their host plants," he said. "For example, while some bacteria on leaves cause disease, others may protect the plant against pathogens or produce hormones that increase plant growth rates."

In the animal microbiome, the researchers noted, studies comparing large numbers of species have shown that host diet — for example, herbivory versus carnivory — has a large effect on the structure of microbial communities in their guts. The new study, Kembel and Green said, provides a comparable understanding of the host attributes that explain patterns of microbial diversity in the plant microbiome.

"We found that the abundance of some bacterial taxa was correlated with the growth, mortality, and function of the host," Kembel said. These included bacteria involved in nitrogen fixing and the consumption of methane, as well as bacteria linked to soil and water.

Dominating the bacterial communities were a core microbiome of taxa including Actinobacteria, Alpha-, Beta- and Gamma-Proteobacteria and Sphingobacteria. Some types of bacteria, the researcher found, were more abundant when growing on the leaves of fast-growing or slow-growing tree species, or on leaves with different concentrations of elements such as nitrogen or phosphorous.

"Because of the importance of the microbiome for the growth and function of the host, understanding the factors that influence bacteria on the leaves of different trees could have important implications for our ability to model and conserve biological diversity and ecosystem function," Kembel said. "Ultimately, we hope that understanding the factors that explain variation in bacterial abundances across host species will help us better manage biological diversity in forests and the health and function of forest ecosystems."

Co-authors on the study with Green and Kembel are: Timothy K. O'Connor, a former technician in the UO Institute of Ecology of Evolution now at the University of Arizona; Holly K. Arnold, a former doctoral student in the UO Institute of Ecology and Evolution now at Oregon State University; Stephen P. Hubbell of the Smithsonian Tropical Research Institute in Panama and the University of California, Los Angeles; and S. Joseph Wright, of the Smithsonian Tropical Research Institute.

The Center for Tropical Forest Science of the Smithsonian Research Institute, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs Program, National Science Foundation, John D. and Catherine T. MacArthur Foundation, the Mellon Foundation and Small World Institute Fund were the leading supporters of the research.

Media Contact: Jim Barlow, director of science and research communications, 541-346-3481, jebarlow@uoregon.edu

Sources: Steven Kembel, Canada Research Chair and assistant professor, Department of Biological Sciences, University of Quebec at Montreal, 514-987-3000 ext. 5855, kembel.steven_w@uqam.ca, and Jessica Green, associate professor of biology, University of Oregon, 541-285-3562, jlgreen@uoregon.edu

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