UNH Today

As climate change brings higher and more volatile temperatures and increases the risk of diseases spreading to areas where they have not traditionally impacted, many organisms must quickly adapt to survive. Fortunately, they have help from their tiny ecosystem partners—their microbiomes, the communities of microorganisms they host, may help them respond to environmental pressures. UNH scientists are leading research into how synthetic, engineered microbiomes could help plants adapt faster and better to changing environmental conditions.

Plant microbiomes, including bacteria, fungi, and viruses that live in and around plants, can reduce infections, improve stress tolerance, and boost growth and reproduction. Anna O’Brien, an assistant professor of cellular, molecular, and biomedical sciences with UNH’s College of Life Sciences and Agriculture (COLSA), is part of an emerging field focusing on synthetic microbiomes—engineered microbial communities designed to replicate or enhance natural microbiome functions. These synthetic microbiomes could significantly improve the climate resilience of plants.

“Traditional agricultural breeding in crops and livestock has demonstrated the utility of purposefully harnessing evolution for organism change,” said O’Brien. “Yet some species may not have enough genetic variation for traits we want to improve.”

Since plant microbiomes harbor significant diversity, altering the microbiome can significantly influence plant traits, she added.

“We want to explore which selection methods help us leverage the evolutionary and metabolic power of microbiomes to create products containing more beneficial microbes (also known as microbial inoculants) for crops and other plants,” said O’Brien.

O’Brien, along with COLSA graduate student Ciana Lazu, is testing synthetic microbiome breeding methods on duckweeds, an aquatic plant species that is particularly useful in research. The team is particularly interested in whether the benefits of synthetic microbiomes will continue at elevated temperatures, a condition that will likely become more common as climate change progresses.

O’Brien and Lazu theorize that building synthetic microbiomes out of microbes sourced from plants in the same evolutionary family as duckweed could increase the chance of a beneficial response. Incorporating new microbes is not without risks, as introducing unfamiliar microbes can sometimes harm the host or disrupt its native microbiome. To address this, the researchers are testing microbes collected from duckweed—along with closely related plants, like watermeal, and distantly related plants, like floating crystalwort—all found at Mill Pond in Durham, NH. They aim to evolve, or “breed”, microbial inoculants that will reliably enhance growth and adaptation in duckweed.

The researchers also theorize that adding some microbes from closely related hosts could increase the variation within the microbiome, producing a stronger response to breeder selection—and leading to better inoculant products. This approach, O’Brien said, could create more effective synthetic microbiomes that help plants like duckweed better tolerate the stresses associated with climate change.

Ultimately, this research aims to determine the best methods for breeding microbial inoculants that alter plant and even animal microbiomes, helping crops and other species adapt to rapidly changing environments. Duckweed, with its fast reproductive cycle, is ideal for studying these effects, but the implications could extend to other species as well.

“There’s a gap in the research about using evolutionary history as a predictor for microbiome breeding and to better understand how we can benefit from plants’ microbiomes,” said Lazu.

Beyond its utility as a “stand-in” for other plants, duckweed itself has broader environmental benefits. It efficiently absorbs nutrients and chemicals from its surroundings, making it an ideal candidate for bioremediation—the process by which plants clean soil and water. Another focus of O’Brien’s lab and part of her New Hampshire Agricultural Experiment Station research is understanding how duckweed could serve as a sustainable alternative to chemical fertilizers, acting as “green manure” by absorbing runoff nutrients and fertilizer, which can then be harvested and reapplied to farms.

“Duckweed is a local, untapped resource that holds potential to benefit New Hampshire’s environmental and agricultural health,” Lazu added. “Through further study of duckweed and its microbiome, we can uncover ways to help everyday New Englanders.”

This project is supported by the National Science Foundation, BIO-MCB, Award #2300059.