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Researchers Find Diverse Soil Microbiome Influences Various Parts of Grapevine

NEW YORK (GenomeWeb) – The microbes living in the soil of a vineyard serve as a reservoir for the bacteria growing on the various parts of grapevines, according to a microbiome study from researchers at Argonne National Laboratory and elsewhere.

As they reported in mBio today, Argonne's Jack Gilbert and his colleagues examined the soil microbiome as well as that of the plant's roots, leaves, and grapes or flowers to try to gauge whether the microbiome influences wine's terroir, or its unique characteristics. They found that most of the bacteria living on the aboveground portions of the grapevine were also found belowground, though with differences in abundance and diversity.

"Growers have been sub-selecting the best regions to grow grapes over thousands of years, but the science of that is poorly understood," Gilbert said in a statement. "Just the same as the human biome plays a role in health, bacteria have intricate associations with plants that affect disease resistance, stress tolerance, and productivity."

Gilbert and his colleagues collected and analyzed Merlot grapevine samples from five vineyards located within a two-mile stretch on Long Island, New York. At each spot, they gathered soil, root, leaves, flowers, and grape samples during the course of a growing season. They then characterized the bacteria in these samples using 16S rRNA amplicon sequencing and shotgun metagenomics.

While none of the operational taxonomic units (OTUs) the researchers uncovered were found in all samples, three OTUs linked with Bradyrhizobium, Steroidobacter, and Acidobacteria species were present in three quarters of the samples.

Overall, the researchers noted, the belowground samples — bulk soil, root zone soil, and roots — shared between a third and nearly a half of their OTUs, while sharing among the aboveground samples occurred at much lower rates.

Additionally, the majority of the bacterial taxa found in the plant organ samples were also in the soil samples, though at different abundance levels. This suggested to Gilbert and his colleagues that the soil might serve as the source of bacteria that inhabit other parts of the plant.

They also note that aboveground samples, which were dominated by Proteobacteria, were less diverse than belowground samples, which also harbored Proteobacteria in addition to Acidobacteria, Bacteroidetes, and Verrucomicrobi. The researchers theorized that aboveground samples could be less diverse due to their exposure to greater variations in temperature, ultraviolet radiation, and humidity.

The type of sample, whether it be bulk soil, root, flower, leaf, or grape, the researchers added, could explain nearly half of the microbial community structure. For instance, they said that belowground and aboveground samples could be differentiated by their relative abundance of Chthoniobacteraceae, Betaproteobacteria, and Pseudomonas viridiflava.

The predicted functions of the bacteria living on the aboveground and belowground parts of the grapevine also varied. Aboveground bacteria were enriched for signal transduction, cellular processes and signaling, membrane transport, and xenobiotic biodegradation, and metabolism, among other functions. Grape and leaves, the researchers noted, had the highest relative abundance of genes involved in xenobiotic biodegradation and metabolism.

Bacteria from leaves and roots samples, meanwhile, were enriched for genes associated with nitrogen metabolic pathways. Root samples also were enriched for iron, potassium, and sulfur metabolism, suggesting that the potential for siderophore production was highly enriched in Merlot root samples. This, the researchers added, might be beneficial to the plant as it could reduce pathogen growth.

For comparison, Gilbert and his colleagues also examined the microbiomes of Merlot grapes grown in Bordeaux and of freshly crushed Merlot grapes from California. Despite differences in geography, they reported that the bacterial communities among these plants were highly similar.

Still, the researchers noted that the bacterial community structure of the root and soil samples was also influenced by soil pH and its carbon to nitrogen ratio, while the leaf- and grape-associated microbiomes were also affected by soil carbon levels and showed variations from year to year. Further, certain vineyards also exhibited differences in the abundance of certain microbes, like Rhizobiaceae and Bradyrhizobium, in their soils.

The researchers noted that these variations could indirectly influence the characteristics of the resulting wine as the soil microbes appear to be the source of the bacteria living elsewhere on the plant.

"From the wine industry's perspective, terroir comes from the plant's physiology, the chemical nature of the grapes, and the yeast that do the fermenting work," Gilbert said. "We don't have evidence that bacteria are specifically contributing to terroir, but our next step is to figure out how those bacteria are affecting the chemistry of the plant." 

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