UC Berkeley study analyzes tomato microbiomes

Norma Morella/Courtesy

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In a study published Thursday by Proceedings of the National Academy of Sciences of the United States of America, UC Berkeley researchers suggest it may be possible to select for plant microbiomes that are better adapted to their environment.

Researchers conducted the study in UC Berkeley’s Oxford Tract greenhouses using an “experimental evolution” approach to collect tomato microbiomes over four generations. Researchers found that by the fourth generation, only 25% of the microbes from the first generation of tomatoes remained.

“So, at the moment, there’s a lot of interest in … selecting for the microbiome that confers the best plant health or human health,” said Britt Koskella, study co-author and campus integrative biology assistant professor. “(The goal) is to figure out how to help get microbiomes to that point, especially in agricultural settings where that’s often not the case.”

To analyze the surface microbiomes of tomatoes, lead author Norma Morella first removed the microbiomes from the surface of tomato plants grown at the UC Davis Student Farm. She then placed the microbes into a sterile buffer, which was sprayed onto tomato seeds to be grown in the greenhouse. This process was then repeated over four generations.

In the field, plants are covered with microbes from the air, surrounding plants, rainwater and other environmental sources, according to Morella. She added that the “strength” of the greenhouse is that researchers were then able to measure how many of these environmental microbes stayed throughout the generations.

“(Microbes) from the field that stuck around largely dominated the microbial communities on the plants,” Morella said in an email. “This leads us to believe that many of the microbes that find themselves on plants might not actually be well-adapted to that environment.”

Morella added that this well-adapted microbiome also seems to have a “robust” response to invasion by other microbiota, which could impact the creation of pre- or probiotics or microbiome manipulation.

While the study worked to “eliminate” environmental factors that could change results, this could have limited the scope of the study’s results, according to Devin Coleman-Derr, campus plant and microbial biology adjunct assistant professor.

Morella acknowledged that plants in the field may be impacted by microbes in the surrounding environment, but added that their research points to what might occur in the wild.

Since the greenhouse environment is not sterile, the plants did experience some environmental dispersal, according to Morella. She added that the final experiment of the study also suggests that the adapted microbial communities fared better than the nonadapted communities.

“Taken together, I believe that using similar methodology- it may be possible to select for a well-adapted phyllosphere community even in an agricultural field setting,” Morella said in an email.

Contact Emma Rooholfada at [email protected] and follow her on Twitter at @erooholfada_dc.