Down to the Nitty-Gritty

Tools to determine soil health and detect soil-borne diseases

Published online: Feb 06, 2018 Articles James Woodhall, University of Idaho
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This article appears in the February 2018 issue of Potato Grower

Soil represents one of the most diverse and complex substances on the planet. Healthy soils are essential for growing potatoes. But what makes a healthy soil? Firstly, there are the abiotic components of soil structure and fertility that need to be considered. However, recently, more attention is being given to the biotic component of soils, particularly the microbiota.

It has been said there are more organisms in a gram of soil than there are humans on the planet. Due to the sheer amount of species present in soil, sophisticated techniques based on next-generation sequencing have helped us understand soil microbiology in ways we could never imagine before. These approaches will help us identify what makes a particular soil conducive to plant health based on various measures such as the microbes contributing to fertility in some way or producing some kind of disease suppression. Understanding the mechanisms could help formulate new, sustainable soil-borne disease control strategies.

Soil-borne diseases are a considerable constraint to potato production. Diseases such as black dot and powdery scab continue to cause significant quality losses; Rhizoctonia can cause qualitative and quantitative losses approaching 30 percent of marketable yields; and Pythium leak and pink rot can rot the tubers in the field. The Verticillium early die complex continues to be a problem for many growers. In addition, many nematode species can affect potato production, sometimes interacting with many of the pathogens listed above, thereby worsening the problem. Fortunately, robust soil tests are now available to detect these pathogens and nematodes prior to planting. Advances in molecular detection techniques mean that, where conventional tests did not exist before, robust, real-time PCR assays can be used to detect these pathogens prior to planting and inform disease management decisions.

Although real-time PCR is now a reality for growers to test the soil, we still need to understand how exactly the results can be interpreted into direct management actions. We need a greater understanding of the inoculum thresholds for disease to occur. We also need a greater understanding of the various strains of some of the pathogens. Rhizoctonia exists as a species complex of different anastomosis groups. A test for all Rhizoctonia species (like many conventional tests) will therefore not be a suitable indicator of disease risk since some Rhizoctonia groups do not infect potato. In addition, for pathogens such as Rhizoctonia that have highly clustered distributions in the field, an adequate sampling strategy is required, as well as the ability to extract DNA from a biologically relevant sample size. For this reason, University of Idaho plant pathology labs typically extract DNA from soil samples weighing 250 grams.

As we understand more about the soil microbiota, many of these questions will be answered. It is likely that soon we will not just be testing for pathogens using real-time PCR, but also for indicators of plant health such as disease-suppressive microbial species. Should sequencing methods become cost-effective and more sensitive, they may even replace real-time PCR completely. However, with whatever technology we use, it is essential we have growers who are willing to be early adopters of such technologies and that they are willing to work closely with researchers to ensure the technology is effective at getting the answers they need.