As if you needed any more evidence that microbiomes matter, wife-and-husband team Caroline Roper and Philippe Rolshausen have given us a microbiome study around the phenomenon of grapevines that escape Pierce’s disease.
Winegrapes as a crop are uniquely susceptible to diseases due to their propagation method. Existing grape varietals such as Cabernet Sauvignon, Chardonnay, and Zinfandel are relics from the eighteenth century or earlier, kept alive through cuttings that are grafted onto more robust rootstocks. They cannot be bred for disease resistance due to consumer rejection of hybrid varietals. In France it is even illegal to breed with traditional grape varietals. Grapevine pathologists are thus always assured of a job.
Pierce’s disease is caused by the bacterium Xylella fastidiosa, the “hard-to-grow xylem vessel-dweller”, Xf for short. The bacterium gets injected into the water-conducting vessels of grapevine and other hosts, where it forms a film on the inside of these microscopic channels. It was thought that the bacteria build up to such high numbers there that they block the flow of water to the leaves and cause scorching. However Hossein Gouran showed in his Ph.D. research that the bacteria in the film are not the life stage associated with the scorching. Rather, it is the free-floating stage of the bacteria that induces the actual disease. These cells that have broken free produce an enzyme that flows up the xylem vessels and attacks the cells in the leaves, causing the scorch symptoms. This revelation is so new that Roper and Rolshausen do not acknowledge it in the introduction to their study.
Pierce’s disease has long been a minor nuisance in California’s grape-growing regions, showing up on field margins that are near streams. The native sucking insect known as the blue-green sharpshooter picks up the bacterium in the wild streamside vegetation and then disperses into the nearby grapevines, where it feeds on green stems. It inserts its mouthparts into the xylem vessels, where it injects the bacterium as part of its feeding behavior. The leaves on that segment of stem are the ones that show symptoms, but after the leaves drop in the fall and the vine has undergone a chilling period, it can emerge pathogen-free in the spring.
If that were the end of the story, it would be a mere footnote in the litany of diseases of grapevine. Now, though, the introduction of the much larger glassy-winged sharpshooter from the southeastern US into southern California has given the Xf bacterium the upper hand in that region’s grape industry. The new insect can inject Xf into the woody tissue of the grapevine, causing a much more devastating infection, and it avoids wild vegetation, instead moving extensively through the region’s orchards and vineyards. Entire vineyards fail because of Pierce’s disease, and in northern California grape-growing facilities one can find wanted posters showing hideous blowup photos of the glassy-winged sharpshooter.
The real footnote of this disease story is that in vineyards that are ravaged by Pierce’s disease, occasionally there will be a lone grapevine that has escaped the disease. This surprise cannot be the result of genetic resistance because all the grapevines in the vineyard are clones of centuries-old varietals. With microbiome research all the rage, Roper and Rolshausen and their research groups asked if there was something about the microbiome of the escaped vines that protects them from Xf.
Serious microbiome research has only become possible with the development of so-called “next-generation” DNA sequencing technologies, new methods of reading off millions of DNA sequences in parallel. The sequence is the order of the four possible building blocks of DNA, strung together in long strands to form a code that a cell can read for its instructions. Roper and Rolshausen used one such technology, the Illumina system, where the millions of DNA segments get anchored to a tiny surface for a microscopic light show. Since a DNA strand is made up of two halves that fit together perfectly, when one half is removed it can be recreated based on the sequence of the other half. By monitoring the construction of the missing portion, one can determine the sequence of both halves. Every new DNA building block that the Illumina machine adds generates a tiny flash of light from each anchored segment, with a different color representing each of the four building block types. The sequence of colors in the series of recorded images corresponds to the sequence of a DNA strand at a particular spot on the surface, and given the millions of sequences recorded, with some computation the entire sample’s DNA sequences can be characterized.
The Illumina technology is useful in microbiome work thanks to DNA barcoding. There are a few genes that are universal, contributing to a microbe’s basic cell structure and functioning. In particular, the genes for the ribosome are indispensable, comprising the main part of the machinery for reading the DNA code. They vary hardly at all from microbe to microbe because the vast majority of possible changes would be lethal. This consistency makes these genes easy to find in the jumble of DNA. However, there are segments in the DNA of these genes that do not get used in the ribosome, and therefore are free to mutate without consequence. Different mutations are carried by different lineages, and the resulting DNA sequences can allow a researcher to distinguish different groups of microbes.
Roper and Rolshausen extracted the sap from symptom-free vines in southern California vineyards ravaged by Pierce’s disease and in northern California hotspots of Pierce’s disease and used ribosome DNA barcodes to compare the sap microbial community to that of the sap from nearby vines that had succumbed. They looked at both bacteria and fungi, and while some of the fungi they found were interesting, there were too few to pick out a consistent trend between symptomatic and asymptomatic vines. The bacterial communities were indeed different, although not nearly as rich as the bacterial community of a soil or a human gut, and the researchers mentioned a lot of the bacterial groups found, using the Latin, for anyone who is interested. The key finding was that asymptomatic vines were low in Xf but had a high level a certain bacterial strain called Pseudomonas, which is known to have biocontrol properties. Is this the key factor allowing the vines to stay healthy? More research is needed.
With a strain of bacteria able to protect grapevines from Pierce’s disease, conventional ag research’s aim would be to commercialize the strain, with the hope of allowing private laboratories to make a profit by providing vineyard owners with another specialized input. The high-margin winegrape-growing corporations would in turn be able to increase profits by extracting higher yields from their centuries-old relics, while any artisanal grower without the means to inject all her vines with a specially formulated bacterial preparation would be economically disadvantaged. By contrast, the aim of agroecological research would be to seek management techniques that any grower could use that would increase the resistance of the vines to Xf. This would be in the context of promoting overall agroecosystem health and community benefit. I would even surmise that if varietals bred for disease resistance were ever to find acceptance, it would be by wine club members dedicated to small agroecologically managed vineyards. More agroecological research is needed.