Each vineyard has a unique microbiome

While a few known strains of bacteria can destroy plants, it’s likely that hundreds to thousands of other species actually help them—living in a complex, interwoven community that, when working at its best, can help the plant survive tough times.

A new study documents the microbes that live among grapevines and considers their influence on the plants’ health. The study is part of a larger push to understand the roles microbes play in agriculture.

A team led by Associate Professor Jack Gilbert, a microbial ecologist at Argonne National Laboratory and the University of Chicago, wanted to explore these communities.

5 vineyards over 2 years

Gilbert’s team led research that may help farmers encourage healthier plants without pesticides. They sampled microbes in the soil, roots, leaves, flowers, and grapes from the plants in five New York vineyards over every season in the span of two years.

“One of our key findings was that the vast majority of the bacteria come from the soil,” says Argonne researcher Sarah Owens. “The leaves, roots, flowers, and grapes all had the same bacteria but in different abundances, which may suggest that different parts of the vine are recruiting different species.”

For example, plants can encourage certain microbes to grow by producing chemicals or nutrients that those microbes like, she says.

However, each vineyard had its own unique microbial signature, Owens says, “even when the vineyards were just half a mile down the road from one another.”

They also tracked differences associated with the soil’s pH and its proportions of carbon and nitrogen. “The type and content of soil, the climate, the plant varieties and how the vineyard is managed—these are all expressed in the microbiome, and we have to understand them if we want to translate this knowledge into practical applications,” Owens says.

Selecting bacteria

“The next step,” Gilbert says, “would be to see if we can find microbes that would help farmers specifically manipulate the properties of a crop—more fruit or more drought-tolerant, for example.”

To do so, they need to first predict which bacteria might be helping the crop, based on just the genomic data.

Argonne postdoctoral researcher Pamela Weisenhorn, also a study author, is working with Argonne computational biologist Christopher Henry to develop methods to tease out community metabolic models from metagenomic data.

By feeding the data through software that flags genes with known functions, Weisenhorn can pick out organisms that appear beneficial and build simulations of how they might interact with the plant and what they’re producing. This narrows the list of potential bacterial partners for field trials.

“Ultimately,” Gilbert says, “we hope to give farmers more information on the invisible—how plants use microbes to respond to climate and conditions.”


And perhaps in the process they could also give winemakers more clues to pin down exactly what makes up the elusive terroir—the taste of a wine from grapes grown in a particular region—a mystery that has tantalized oenophiles since winemaking began.

Additional study authors are from Sparkling Pointe Winery, the FMC Center for Agricultural and Environmental Biotechnology, and the University of California, Davis.

The study appears in the journal mBio. The Earth Microbiome Project, the FMC Center for Agricultural and Environmental Biotechnology, and a postdoctoral research grant from the Basque Government supported the work. The University of Chicago Research Computing Center provided computational resources.

Source: University of Chicago