Detecting Plant Root Diseases & Pests

Scott Trimble

October 14, 2020 at 3:30 am | Updated October 14, 2020 at 3:30 am | 6 min read

Early detection means early root disease control

Soil-borne pests and diseases are harder to detect than those on the aerial parts of a plant. Visible symptoms in leaves and stem appear only in the final stages of the attacks. If plants are treated at this point, it may be difficult to avoid plant injury, as plants could already have been severely impacted. Early detection and identification are key to prevent crop loss. There are, however, only a few instruments available which can help in monitoring crops on the field to prevent or arrest soil pests and pathogen growth.

Crop Loss Due to Pests and Diseases

It is common to have pests and pathogens attacking plants. However, monocultures, which are the prevailing means of growing crops, increase the intensity of attacks by enabling easy spread of the causal organisms. A recent study covering sixty seven countries investigated loss of crops. They found that, on a global scale, five main food crops suffered losses ranging from ten to forty percent due to pests and diseases. The loss in different crops was as follows:

  • Rice – 25 to 41 percent
  • Maize – 20 to 41 percent
  • Wheat – 10 to 28 percent
  • Potato – 8 to 21 percent
  • Soya bean – 11 to 32 percent

Experts identified 137 pathogens and pests affecting these five crops, including bacteria, fungi, viruses, oomcyetes, nematodes, arthropods, vertebrates, molluscs, and parasitic plants.

Subscribe to the CID Bio-Science Weekly article series.

By submitting this form, you are consenting to receive marketing emails from: . You can revoke your consent to receive emails at any time by using the SafeUnsubscribe® link, found at the bottom of every email. Emails are serviced by Constant Contact

Soil-borne Plant Diseases and Pests

The soil is a special ecosystem dictated by soil conditions—like pH, moisture content, and organic matter availability—where the different soil organisms interact with the plants through its roots. Normally, all the organisms, even those that cause diseases or behave as pests, live in a balance with other species.

When any of the soil conditions are changed unfavourably, it can encourage the growth of one particular set of microflora or microfauna at the expense of others. If these are pests or pathogens, the attack on plants’ roots can be severe enough to affect its performance and yield. Good soil management is, therefore, one of the best ways to deal with soil diseases and pests.

Figure 1: “Potato plant infected with potato mop-top virus.” FAO ( Image credits:

In the soil, disease-causing pathogens include bacteria, fungi, viruses, actinomycetes, phytoplasma, and protozoa.

  • Damping-off or tissue destruction is produced by fungal species of Rhizoctonia, Fusarium, and Pythium.
  • Downy mildew is caused by fungal species parasitizing the plants.
  • Root rot is caused by Phytophthora.
  • Vascular wilts are produced by fungi, such as Verticillium.
  • Infections of wounds or openings are caused by bacteria, for example, Agrobacterium radiobacter var. Tumefaciens in beetroot.

Some of the common soil pests are nematodes, ants, aphids, snails, slugs, and rodents. For example, nematodes can cause gall-like lesions, while snails, slugs, and rodents feed on parts or whole roots.

The effects of the pests and pathogens are not restricted to the roots and can be seen as symptoms on leaves, a reduction in the rate of development and growth of plants, and in extreme cases can also affect plant survival (Figure 1).

Ways to Detect Soil Diseases and Pests

The losses that soil pathogens and pests cause are partly because the causal organisms are working underground, out of sight, and are difficult to detect. By the time the symptoms appear in the above-ground aerial parts, the damage to the plant is substantial. There is also the danger that if the pathogens and pests are not contained they can spread and establish themselves in/on neighbouring plants and increase crop loss.

It is, therefore, crucial to detect incidence of pest and disease attacks as soon as possible. Many methods are currently available. Some of the more important ones are mentioned below.

Destructive Methods

Many of the methods involve destructive sampling and are not suitable for repeat testing, as they involve loss of crops. Most of them are expensive, time-consuming, and require laboratory and skilled personnel.

  1. Culturing: The pathogens are grown in artificial media to isolate and identify them. This is expensive and requires a well-equipped laboratory and trained personnel. Most growers will not have such a developed facility close by.
  2. Baits: There are many kinds of baits that can be used to trap pests to identify and count them. These are easy and cheap, and they are are traditionally used on farms.
  3. Traditional microscopic examination of plant tissue: This involves taking samples of roots and examining them with the aid of microscopes to detect pathogens or the effects of pests and diseases. The procedure requires a laboratory. Microscopic tests are more suitable for pathological research studies than regular checks for farms or forestry projects where plant health has to be monitored. It also requires expertise in identification and familiarity of a wide range of pathogens, mirco-pests, and the types of damage caused.
  4. Immunological methods: The method used is called the enzyme-linked immunosorbent assay (ELISA), where the antigens unique to each pathogen bind to specific antibodies. This method can be used to identify a mixture of pathogens that are difficult to differentiate morphologically and to quantify their numbers.
  5. Nucleic Acids: Polymerase chain reaction (PCR) method identifies the pathogens by amplifying the nucleic acid sequences of their DNA. PCR can identify specific species easily, but requires one to two days. This method requires a laboratory.

Non-Destructive Methods

There are also some non-destructive modern methods to detect and identify pest and disease incidences, which are now available.

  1. Imaging Techniques: Even before visual symptoms of pest and disease attacks develop, there are physiological changes within the plant, due to the stress from the attack. These changes are picked by a shift in spectroscopy, i.e. the light the plant absorbs and reflects back. This technique has been applied to small devices. It is also used on a large scale to produce hyperspectral satellite images to detect crops and trees that have been infected with pests and diseases. Infra-red, Near Infra-red (NIR) or Fluorescence spectroscopy can be used for imaging.

    The CI-710 Miniature Leaf Spectrometer, produced by CID BIo-Science, is a small hand-held device based on NIR-based spectroscopy, which can be easily used in farms and forests to measure plant stress due to pest and disease attacks.

  2. Biosensors: Plants emit volatile organic compounds (VOCs) to promote growth, defense, and communication. So the VOCs they release in response to attacks by pests and pathogens will be different from that of a healthy plant. VOC profiling is done by using gas chromatography mass spectrometry (GC-MS). Use of VOC as biosensors is useful for early detection of infection before symptoms appear. It has been successfully used to identify late blight caused by Phytophthora infestans and dry rot by Fusarium coeruleum in potato tubers, post-harvest.
  3. Root Imagers: These are devices which take high-resolution digital images of the entire root system. The images are analysed by software to calculate root dimensions. The images show damage to roots and change in their architecture due to pest and pathogen attack. A transparent root-tube is inserted into a drilled hole in the field near plants. The roots of the plants grow around the tube, and the scanner unit can be inserted in the root-tubes to take images of the surrounding root system as frequently as is necessary, non-destructively, throughout the crop period. Many tubes can be installed on a farm or orchard and multiple plants’ roots can be scanned on a single day.

    The CI-600 Root Imager and the CI-602 Narrow Gauge Root Imager are two minirhizotrons produced by CID Bio-Science. They both have the same functions and can be used to image roots to a depth of around one meter. The CI-600 has a wider diameter than the newer CI-602, which can be used with narrower tubes. They both come with the “Root-Snap” software, which helps to distinguish root from the background soil. The devices take colour digital pictures in six seconds. This method is by far the fastest and cheapest of the modern methods in detecting root problems.

Preventing and Treating Pest and Diseases

Since pests and disease development is an indication of the soil ecosystem that is off balance, one of the best ways to prevent infections would be to ensure ideal growing conditions. The soil should neither be water-logged or dry. Provide the right amounts of fertilizers, as too much can kill beneficial microbes that maintain soil health. Crop rotation and intercropping will reduce build-up of populations of any single species in the soil. With the help of simple tools, like the root imagers, a grower can also easily keep track of the health of the crops and detect any problems caused by pests and disease attacks in the soil.


See More:

CI-600 In-Situ Root Imager

CI-602 Narrow Gauge Root Imager

CI-710s SpectraVue Leaf Spectrometer

Chlorophyll Analysis Using Vegetation Indices

Spectral Data and Thermotolerance in Plants

How Leaf Reflectance Measures Plant Stress

Versatile Uses of Leaf Spectral Information

Cadmium Toxicity in Plants

Leaf Spectroscopy

Intro to Precision Forestry

Tree, Crop & Plant Stress – A Primer on Abiotic and Biotic Stressors

Nitrogen Dynamics in Forest Trees

Growth Regulators and Bio-stimulants Boost Plant Growth and Yield

Adapting Production to Drought

NIR & Spectroscopy in Agriculture & Crop Science

Vijayalaxmi Kinhal
Science Writer, CID Bio-Science
Ph.D. Ecology and Environmental Science, B.Sc Agriculture


Cahill, D.M. (1999). Detection, identification and disease diagnosis of soilborne pathogens. Australasian Plant Pathology 28: 34.

FAO. AGP-Soil borne pests and diseases. Retrieved from

Mattupalli, C., Seethepalli, A., York, L.M., & Young, C.A. (2019). Digital Imaging to Evaluate Root System Architectural Changes Associated with Soil Biotic Factors. Phytobiomes Journal, 3:102-111.

Martinelli, F., Scalenghe, R., Davino, S., Panno, S., Scuderi, G., et al. ( 2015). Advanced methods of plant disease detection. A review. Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 35, 1-25. ff10.1007/s13593-014-0246-1ff.ffhal-01284270f

Pam Kan-Rice, P. (2019, February 11). Pests and Pathogens Place Global Burden on Major Food Crops. Retrieved from

Randive, P.U., Deshmukh, R. R., Janse, P.V., & Kayte, J.N. (2018).Study of detecting Plant diseases using Non-Destructive Methods: A Review. International Journal of Emerging Trends & Technology in Computer Science (IJETTCS), 7. Retrieved from

Soil-borne diseases. (2014, December 14). Retrieved from

Xhemali, B., Bresilla, B., & Cacaj, I. (2015). Comparison of methods used for detection and identification of soil-borne plant pathogens affecting vegetable crops. Journal of Agriculture and Forestry. 61. 1070-1074. 10.7251/AGSY15051070X.

Request a quote for a CID Bio-Science Product

Pricing and all related materials will be sent directly to your inbox.