By: Judit Monis, Ph.D. – Vineyard and Plant Health Consultant
The summer and fall are the seasons for vineyard managers and winemakers to start to plan for new vineyard development. Since late summer to fall is the busiest with harvest, why not get a head start? Furthermore, the best time to scout the vineyard and observe symptoms associated with diseases is in the summer and fall seasons.
My philosophy is if you wish to develop a healthy vineyard you need to plan ahead. When planting a new vineyard, unless you are willing to take whatever is left at the nursery (not recommended), you will need to place your order with a nursery at least one year ahead of the planting season. With so many different diseases that are not regulated by certification programs, I recommend you hire a knowledgeable plant pathologist (consult with me!) to help you determine the best time to perform vineyard block and vine inspections as well and how and when to collect plant and soil samples for pathogen detection.
Diseases Originate in the Vineyard
Growers must be aware that many grapevine diseases can generate in the vineyard. If a grower is replacing a vineyard, leaving the land fallow (with no vines) for a long period (2-3 years) may have advantages. If the vines removed were infected with leafroll (GLRaVs) or red blotch (GRBV), it will be important to take some precautions. Some species of leafroll associated viruses (GLRaVs) are transmitted by mealybugs and GRBV is transmitted by the three-cornered alfalfa hopper. It is important to be careful when removing vines, as portions of infected roots can remain in the ground and be a source of reinfection. When mealybugs are present in the vineyard block, these will be able to transmit the viruses to the new vineyard. In this situation, it would be impossible to determine if the symptoms in the vineyard are due to a newly vineyard planted with infected material or if it became infected by mealybugs that remained in the vineyard unless there is a priori testing data. I am always asked to “play detective” but without prior knowledge (i.e., testing prior block or the incoming plantings), it is a difficult proposal.
Agrobacterium vitis (the crown gall causal agent) and some fungi are soil borne pathogens and can be propagated in nursery material as well as field selections or be present in the soil prior to planting. Agrobacterium vitis and a diverse group of fungal pathogens are present and sometimes latent (no symptoms are visible) in vineyards. For example, the crown gall disease agent can be present in certified planting material without showing symptoms until a stress factor (physical or freeze damage) occurs. The stress caused by the grafting process is enough to induce typical galling if pathogenic strains of Agrobacterium vitis are harboring withing the sourced vines. Grafted vines commonly display excess callus formation, enlarged graft unions, and galls. Some symptoms are typical of crown gall disease while others could be difficult to diagnose visually. To be safe this type of planting material should be analyzed at a laboratory as it may not be easy to distinguish between bacterial galling and callusing during the grafting process (the nursery will probably claim that what you are seeing is callus but this is not always the case).
Traditional Diagnostic Methods May Fail to Detect Certain Pathogens
Testing the vines and soil before planting will give an indication of the type of fungal and bacterial organisms present. Depending on the method used for testing, information of beneficial microorganisms and nematodes present in the vineyard soil can be obtained.
Traditional methods such as microbiological culture for the detection of Agrobacterium and fungal pathogens may fail to detect these pathogens in the laboratory. While microbiological culture in plates with identification using microscope and/or further biochemical and molecular characterization are still being used, there are some important drawbacks to these methods. The plating of microbes is prone to competition between different fungal and bacterial species. Generally, the microorganism that grows faster will be identified but may not necessarily be the cause of symptoms of disease. Even when a more specific method is used for identification (i.e., polymerase chain reaction), the method may not be specific enough to characterize the fungi and bacteria. For example, there are many Agrobacterium vitis stains that are non-pathogenic and do not cause crown gall disease.
Next Generation Sequencing as a Virus Discovery Tool
The next generation sequencing (NGS) technique also known as high throughput sequencing (HTS) or deep sequencing is able to determine the complete sequence of the genetic material present in a vine. The data obtained is analyzed with software that is able to compare sequences available in a database and provides a list of the bacteria, fungi, or viruses present in a given sample. The method can provide relative quantitative data (copy number) of the presence of each organism found.
Initially, the NGS method was used as a tool to discover new plant viruses. In 2011, NGS lead to the discovery of the first DNA virus to infect grapevines, Grapevine vein clearing virus a Badnavirus associated with severe vein-clearing and vine decline syndrome in Missouri. Subsequently, NGS has allowed the discovery of other DNA viruses: such as GRBV, Grapevine Geminivirus A, Wild Vitis virus 1, and many grapevine RNA inhabiting viruses (e.g., Grapevine virus E, F,G, H, I, J, K, L, M, N, etc.). The application of NGS will continue to allow for the discovery of new viruses. Clearly, the biological capabilities of the newly discovered viruses must be studied to determine if they pose a threat to vineyard health.
Next Generation Sequencing as a Diagnostic Tool
Recently at the 20th ICVG (International Council for the Study of Grapevine Viruses and Virus-Like Diseases) held last year in Thessaloniki, experts discussed the application of NGS (aka HTS) technology for diagnostic purposes. Comparative studies have allowed replacing the woody index technique with NGS in quarantine programs. For example, the NGS technology is already being applied for the verification of clean planting stock as well as exclusion of infected material in new variety introductions quarantine and certification programs in Italy and USA.
Commercial laboratories offer the testing of soil and plant tissue using NGS technology to detect bacterial and fungal pathogens in soil, planting stock material and established vineyards.
The NGS technology has become a powerful diagnostic tool but requires technical knowledge and expertise to interpret the results. Because of the complexity of the results, expertise is needed to determine which of the microorganisms present in the tested material might be damaging to the vineyard health. I have experienced receiving loads of data (enormous lists of fungi and bacteria) to sort out and determine the relevance of the findings. The information has allowed me to help clients make informed propagation, planting, and managing decisions.
Future research will allow us to answer what is a pathogen copy number required to initiate infection and cause disease. In my opinion, grapevine growers and winemakers will benefit when the NGS technology is widely applied to grapevine testing. The application of new technologies will increase the health of planting material and subsequently decrease of presence of harmful pathogens in planted vineyards and ultimately increase wine quality. I envision that in the near future the NGS technology will allow certification programs world-wide to exclude pathogenic bacterial, fungal, and viral species from their foundation blocks.
Judit Monis, Ph.D. provides specialized services to help growers, vineyard managers, and nursery personnel avoid the propagation and transmission of diseases caused by bacteria, fungi, and viruses in their vineyard blocks. Judit (based in California) is also fluent in Spanish and understands some Italian is available to consult in all wine grape growing regions of the world. For more information or to request a consulting session at your vineyard please contact juditmonis@yahoo.com or visit www.juditmonis.com
