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10 Vital Minirhizotron Applications for Agricultural Research

Image of a person inserting a CID Bio-Science minirhizotron into a root tube.

Dr. Vijayalaxmi Kinhal

July 26, 2022 at 6:45 pm | Updated July 26, 2022 at 8:07 pm | 8 min read

  • Minirhizotrons are a recent addition to a scientist’s toolbox, providing information on underground dynamics.
  • Scientists can explore the relationship between roots and shoots along with the cumulative effect on crop yield.
  • Using minirhizotron systems improves our knowledge of root responses to the environment, fertilizers, irrigation, and tillage, enhancing crop water and nutrient use efficiency.
  • Ten typical applications of minirhizotrons are discussed, including root morphology, irrigation assessment, disease detection, and fertilizer application.

What is a minirhizotron?

A minirhizotron, or minirhizotron system is a non-destructive root monitoring installation, designed to miniaturize large-scale rhizotron laboratory systems. These installations are made up of durable, transparent tubes installed in the ground and a light-weight cylindrical imaging device which is lowered into the tubes to collect high-resolution images and track season-to-season root growth and soil changes.

Minirhizotron Applications

The development of minirhizotrons fills a crucial gap that existed until recently. Root systems and dynamics have been long understudied due to a lack of simple and non-destructive observation tools. Minirhizotron root imagers that provide high-resolution scans at varying depths and allow repeated data collection are changing our understanding of below-ground processes and furthering agricultural research. Some primary minirhizotron applications are for the research topics discussed below.

1. Root Morphology

Due to the lack of basic information on root morphology, most studies still focus on getting data on root type, length, diameter, depth, branching angle, and surface area. Scientists need to know the root morphology as it impacts water and nutrient absorption, resource storage, hormone production, and anchorage. A single species can have several root types like the tap, adventitious, lateral, basal, and fine roots for different functions, see Figure 1.

Agricultural scientists explore these basic root features in interactions with the below-ground environment at different phases of crop growth or biotic and abiotic stresses. The root system’s morphology, architecture, and size influence shoot growth, size, development, and ultimately the yield. Root morphology is essential to understanding the relationships between the root and shoot systems.

Image of Figure 1: Root morphological components

Figure 1: “Root morphological components of mungbean, corn, and onion seedlings depicting adventitious (adv), basal, lateral, and taproots (tap),” Leskovar and Stoffella, 1995. (Image credits: https://doi.org/10.21273/hortsci.30.6.1153)

2. Root Lifespan

Root lifespan is important as it reflects the plant’s ability to acquire and conserve resources from the soil. Significant differences exist in root longevity, even in perennial trees. For example, 40 percent of Prunus avium roots survive for more than 14 days, but only 6 percent of Picea sitchensis roots live longer than 14 days.

Root lifespan, mortality, and turnover are crucial for many reasons, but mainly because of their role in nutrient cycling and flux in the soil.

Despite numerous studies, we still need to learn much about root longevity and how various external and internal factors influence it. Interior characteristics, plant age, season, resource uptake, carbon allocation, and root structure influence lifespan. Soil nutrient and water availability, soil temperature, and season can also have an effect.

3. Root Biomass

Graph for Figure 2: Proportions of maize root biomass

Figure 2: “Proportions of maize root biomass C in coarse (>2 mm) and fine (>0.5 and ≤2 mm) root samples from different soil depths of the DOK trial averaged over management treatment,” Hirte et al. 2017. (Image credits: https://doi.org/10.3389/fpls.2017.00284)

Root biomass is an essential feature for studies tracking plant responses to the environment and soil carbon sequestration. Root biomass shapes soil communities and is, therefore, necessary to study if we are to maintain soil fertility and long-term sustainable yields from agricultural lands.

Proportions of root biomass can be influenced by agricultural management, amount and type of manure and fertilizers, soil depth, soil type, and field placement (between or within rows); see Figure 2. The recent establishment of soil carbon as a major carbon sink has increased interest in root biomass formation and accumulation for soil carbon modeling and identifying options for climate change mitigation.

4. Detecting Diseases and Nematodes

Photo of roots for for Figure 3: Root rot and stunting symptoms of BRR

Figure 3: “Root rot and stunting symptoms of BRR: (A) The lesions are microscopic at first but later become visible as the lesions expand. In more advanced cases, the entire root system is blackened and eventually rotted away. (B) The root tips are starting to blacken,” Lookabaugh & Shew, 2011. (Image credits: (A) Mike Munster  and (B) Plant Path Departmental Slide Collection, http://ncsupdicblog.blogspot.com/2011/10/black-root-rot-in-landscape.html )

Fungi, bacteria, and nematodes cause root diseases. Root diseases can be a serious problem, especially for orchard trees. The damage to roots follows a complex and characteristic pattern of colonization by the microbes, leaving a trail of dead brown root tissues; other symptoms include wilts, rot, galls, and cankers.

These symptoms can be identified in root scans giving scientists a picture of the changing effects of diseases and pests to understand pathology.

5. Mycorrhiza

Image of Figure 4: Micorrhizal vs control observations. Images of roots six weeks after fissure interverence.

Figure 4: Roots observations with the minirhizotron tubes and CID Bio-Science’s CI-600 In-Situ Root Imager of tree treatment with mycorrhiza and control under fissure stress. The treated trees have more root length, volume, and surface, Zhang et al., 2021. (Image credits: https://doi.org/10.1016/j.ecolind.2021.107800).

Most tree roots form symbioses with mycorrhiza or fungi to increase nutrient uptake efficiency. However, the pattern of foraging will depend on the interaction between root morphology, soil fertility, and type of fungi. There are two main types of mycorrhiza. Arbuscular mycorrhiza (AM) live within the root tissue, and ectomycorrhiza (EM) live outside the roots themselves.

Predicting the foraging patterns in soils of different fertility and how trees exploit the symbioses to gain nutrients can be essential to understanding plant nutrition, response to stress, as well as ecosystem nutrients, and carbon cycling.

6. Drought Studies

With incidences and severity of droughts and dry spells increasing due to climate change, most studies have focused on responses in the shoots, not roots. However, crop roots are susceptible to soil water deficit, especially in the seedling and vegetative stages, which can affect the yield of crops in the latter stages. Roots are also the first plant organs that respond to drought. It is soil water deficit conditions that reduce transpiration to improve plant water use efficiency.

Knowing how roots respond to drought in terms of length, volume, or density is essential. Many species grow deeper roots in drought, but sometimes the reverse is also true. Similarly, the branching and architecture of roots could also change in response to soil water availability. These responses are difficult to generalize and need to be studied for each species and cultivar to maintain yield in a changing climate. Crop breeding for drought tolerance also relies on root scans to monitor root responses.

7. Irrigation Methods

Improving irrigation methods is integral to helping crop plants avoid the effects of drought. New irrigation methods and water sources are emerging as water resources get scarce and the demand for food rises to feed a growing population. For example, the sub-surface direct root-zone or the partial root-zone drying systems cut evaporation and percolation losses of surface irrigation.

In all cases, root responses that depend on species and cultivar must be tested before recommending new varieties to farmers.

8. Water Schedule

It is crucial to monitor and manage irrigation rates to supply only the necessary water. Too much water supply can reduce crop water use efficiency and cost the farmer more. Hence, more and more research is aimed at optimizing water schedules. Instead of recommending watering at 100% field capacity, scientists these days are reducing the water amounts and scheduling to improve water use efficiency and yield.

Once again, new irrigation schedules must be tested before making the recommendations. Accurate, non-destructive, repeated root scanning to monitor growth, root distribution, length, volume, and longevity speed up research and allows scientists to improve crop water use efficiency and give better advice.

9. Fertilizer Application

Excessive use of fertilizers has been driving loss of soil fertility and has led to widespread soil and water pollution. Moreover, as adoption of precision agriculture principles increases, finding ways to optimize fertilizer use and yield is becoming a greater research focus. Root scans are a standard in studying root responses to fertilizers when choosing suitable cultivars or recommending the correct nutrient amounts and schedules.

Scientists are considering not only current seasons but also residual nutrients and cropping patterns to give advice more fine-tuned to regional cropping patterns and needs. Most often, less nitrogen fertilizers produce better yield, backed by knowledge of root responses to the nutrient application and shoot attributes.

Graphs for Figure 5: 2011-2012 season vs 2012-2013 season. Graphs of tillering, flowering, and ripening. Y axis is labeled "soil depth (cm), X axis is labeled "Root surface area density (cm^2 cm^-3)

Figure 5: “Effect of different tillage practices on root surface area density at tillering stage (157 DAS in 2011–2012 and 144 DAS in 2012–2013), flowering stage (212 DAS and 213 DAS) and ripening stage (249 DAS and 245 DAS) in two winter wheat growing seasons,” Guan et al., 2015. (Image credits: https://doi.org/10.1016/j.still.2014.09.016)

10. Tillage

The use of tillage changes the soil structure, affecting rainfall-runoff, water percolation, soil erosion, and soil respiration. Therefore, the effect of tillage on root dynamics is being studied to ensure a sound root system, especially in rainfed conditions. Often tillage is combined with practices like growing cover crops and mulching to improve soil structure, water retention, and fertility.

Scientists are using minirhizotrons to study root growth and dynamics throughout the crop cycle to understand the interactions of soil moisture and nutrients with crop needs in different growth phases, see Figure 5.

Current Tools

The minirhizotrons and root imagers used to make root scans are sophisticated and offer high-resolution images of roots. For example, the CI-600 In-Situ Root Imager and CI-602 Narrow Gauge Root Imager manufactured by CID Bio-Science Inc make studying roots easy. One imager can be used with many root tubes, and observations can be taken as often as needed without disturbing the roots or interfering with their subsequent growth. Therefore, the tools provide more accurate information on root dynamics, which was not possible with earlier root observation techniques.


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


Photo from Dr. Shinsuke Agehara of Florida State University.


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