Plant Microbiomes Are Mostly Determined by the Environment, Not Genetics

The bacteria living on and inside plants can contribute to overall plant health and nutrition. Scientists have long hoped that artificially manipulating the microbiota of crop plants could result in healthier, disease-resistant plants with greater quantities of vitamins and minerals. A new study published in Nature Communications, however, suggests that influencing the microbiome of a plant might not be easy.

Researchers from Duke University studied a flowering plant in the mustard family called Boechera stricta. The wildflower normally grows throughout the Rocky Mountains. They analyzed the genome of the plant and grew hundreds of genetically identical clones. The seedlings were moved to outdoor experimental sites in Idaho and left to grow for a few years. When the researchers returned, they analyzed 440 individual plants to determine which bacteria were present. They found 4,000 types of bacteria, mostly from the groups Proteobacteria and Actinobacteria. The researchers found that genetics made very little difference in determining the microbiome of a plant. Instead, most differences were due to environmental conditions and the age of the plant. Temperature, soil moisture, and pH all made a larger difference than the plants’ genomes. Genetics were attributed to only 5% of overall microbial diversity.

Crop breeders and agricultural scientists hope to manipulate plant microbiomes in order to grow crops that are healthier and more nutritious. The microbes found on plants can determine how resistant that particular crop is to pests, disease, and drought. Certain bacteria can also help individual plants absorb minerals from soil, allowing agriculturists to grow healthier foods. Previous research had investigated whether or not genetic modifications could change the microbiome of a plant but these studies were based in the laboratory. This new study provides a more realistic scenario by using genetically identical plants grown outdoors in gardens. The authors found that genetics played a very small role in determining microbiomes. They note that while controlled breeding could be used to influence the bacteria growing on the plants, genetic manipulation on its own may not be especially useful.


Maggie R. Wagner et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications (2016).

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