Development of a Novel Soil-Borne Disease Management Strategy, Health Checkup Based Soil-Borne Disease Management (HeSoDiM)

Development of a Novel Soil-Borne Disease Management Strategy, Health Checkup Based Soil-Borne Disease Management (HeSoDiM)

Published: 2020.07.10
Accepted: 2020.07.10
Division of Plant Disease Management, Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Japan
Department of Molecular Microbiology, Tokyo University of Agriculture


Soil-borne diseases can cause significant negative impacts on crop production. To combat these diseases, most farmers have been using chemicals such as soil fumigants to disinfest the field soils before scheduled planting. These conventional applications, however, often result in an excess use of the chemicals, thereby increasing disease control costs and inhibiting agricultural sustainability and environmental conservation. To avoid the unnecessary use of chemicals for disease management, it is necessary to diagnose and assess the disease-occurrence potential before planting in each field then implement the appropriate control measures based on the potential degree. Because such decision-making systems are based on health check-up systems, we named the system as the Health checkup-based Soil-borne Disease Management (HeSoDiM). HeSoDiM is a promising strategy to realize sustainable agriculture by decreasing input of costs and environmental stresses to arable lands, and necessary to be more propagated through further research and development on this novel soil-borne disease management system.

Keywords: Disease management, HeSoDiM, Soil-borne disease, Soil fumigation


Soil-borne diseases have generally been recognized to cause significant yield losses and be difficult to control once it has occurred during cultivation.  To prevent the occurrences, farmers are necessary to determine action of countermeasures, such as use of soil fumigation and crop rotation, etc., before cultivation.  Although decision making system for disease control has been developed against various air-borne diseases by weather-based pest forecasting, such short-term predictive approach is not applicable to soil-borne diseases in fields, because control measures against the diseases that occurred during cultivation are quite limited, so that it generally takes a longer period between timing of forecasting (i.e. before cultivation) and disease occurrence, leading to insufficient accuracy of the forecast on the disease occurrence.  It is therefore necessary to develop alternative strategies to make decision for the control of soil-borne diseases, as a substitute of the conventional weather-based pest forecasting system.  In addition, the most interests for farmers are to know actual effective control measures after the decision.  Based on these backgrounds, we made a novel strategy, based on the concept of periodic health checkup system as a basic tool for preventive medicine, to diagnose and assess disease-occurrence potential (D-potential), then make decision appropriate control measures based on degree of the D-potential before planting in each field, and named the disease management strategy as Health Checkup-Based Soilborne Diseases Management, i.e. HeSoDiM.  In this paper, we introduce the outline of HeSoDiM and current situation on the efforts to propagate this disease management system in Japan.  


Soil-borne diseases have been recognized to cause serious economical damages for crop production and are difficult to control once the symptom appeared in fields (Komada 1998). In some cases, owing to rapid decrease and aging of Japanese farmers in Japan, the disease occurrence in fields often triggers farmers to quit and abandon farming.  To ensure and realize sustainable agriculture, therefore, it is significant to perform appropriate management against soil-borne diseases.  Farmers usually take chemical approaches for the management in Japan; soil fumigants are most used to prevent the occurrence.  Particularly, at local regions where the diseases constitutively occur, the chemicals are extensively used before planting as scheduled.  However, such application style often causes overdose of the fumigants into fields not necessary to disinfestation, and the excess use of chemicals leads to loss of farmers’ income due to superfluous labor and cost of chemicals for the application.  In addition, correspondence against recent global trend to enhance regulation for the use of soil fumigants based on farmers’ health and environmental conservation is important to increase value of Japanese agricultural products internationally.

To decrease the excess use of soil fumigants and prevent the disease occurrence effectively, it is desirable to forecast disease occurrence of each field, then make decision of management with selecting effective control methods suitable to the degree of occurrence.  However, as former described, pest forecasting system, which has been carried out against aboveground diseases based on weather forecast, is not directly applicable to soil-borne diseases in fields owing to the forecast timing (i.e. before cultivation), leading to insufficient accuracy of the forecast.  In addition to such temporal disadvantage, complexity of soil environmental factors functioning as a cause of disease occurrence also results in difficulty of the disease forcasting.


To develop a strategy alternative to the above weather-based pest forecast, we referred the concept of preventive medicine; similar strategy to periodic health checkup system, which is one of the major efforts of medicine, were applied for management of soil-borne diseases.  In the periodic health checkup system, the degree of human health is evaluated and maintained based on values in each diagnostic item, such as blood pressure and blood glucose level, by comparing to each established reference value, then when values of diagnostic items deviate from each reference value, we keep our health by improving the values through various measures, such as exercise and medication, etc.  Our novel strategy is to adapt the concept and strategy of preventive medicine for soil-borne disease management, and we named this management strategy as “HeSoDiM”, which represents abbreviation of the phrase, “Health Checkup-Based Soilborne Diseases Management” (Tsushima and Yoshida 2012, Tsushima 2014).

HeSoDiM consists of three components, “diagnosis”, “assessment of disease occurrence potential (D-potential)” and “decision of management” (Fig. 1), and contents of each component must be built up by each target disease and crop cultivating condition, since each microbial pathogen has diverse ecological characteristics and also factors of disease occurrence depend on each disease and crop.  When HeSoDiM against an soil-borne disease is newly constructed, component “diagnosis” is first determined; core diagnostic parameters associated to the occurrence of the target disease are selected among parameter candidates, such as soil physical and chemical properties (soil pH and degree of field drainage, etc.), disease severities in the field at previous cropping season and biological properties of soil (qualitative and quantitative information of causal pathogens and microbial diversity, etc.).  Then, D-potential (three levels from level 1 [low D-potential] to level 3 [high D-potential] in principle) is assessed based on integrated results of these diagnostic parameters in addition to the cultivation information interviewed from farmers.  Lastly, decision of management is made by extension workers together with farmers from management menu corresponding to each D-potential level.  For example, in the case that D-potential is evaluated as level 1, cultural control approaches, such as appropriate fertilization and cropping resistant cultivars, are mainly carried out.  As for level 2 and 3 of D-potential, biological and/or minimum chemical controls, and soil fumigants and/or crop rotation are mainly applied, respectively.  It is important that actual measure based on the D-potential level is finally determined through discussion and getting consensus between farmers and extension workers, as is the case of determining actual solution strategy for health care by discussion between patients and doctors based on the results of health check.  By practicing HeSoDiM every crop season by modifying each component into more suitable criteria through PDCA cycle, farmers can get benefit by avoiding “unreasonable” and “excess” countermeasure practices (Fig. 2).  Actually, several proof experiments of HeSoDiM against club root of Chinese cabbage supported by an agri-consultant revealed that practicing this disease management system can successfully avoid unnecessary use of chemicals and increase farmers income by over 10% (Fig. 3).

So far HeSoDiM has been developed against several major soilborne diseases in Japan, such as club root of cruciferous vegetables, bacterial wilt of tomato, etc., through two National research projects supported by funded by Ministry of Agriculture, Forestry and Fisheries, Japan (MAFF) (Table 1).  The developed HeSoDiM against each soil-borne disease was compiled into manual books for extension workers in 2013 and 2016, respectively, and then published them on the web site ( ( (Fig.4).   The first manual book published in 2013 explains concept and strategy of HeSoDiM and actual protocols for the practice against bacterial wilt of tomato, rhizome rot of ginger, root rot of lettuce, Phytophthora rot of soybean and club root of cruciferous vegetables (including cabbage and broccoli).  In the case of HeSoDiM of Phytophthora rot of soybean caused by Phytophytora sojae developed by Toyama agriculture, forestry and fisheries research center, its core diagnostic parameters are determined as 1) disease occurrence in the field at previous cropping season (optionally, soybean stem-trapping of the pathogen from target soil if necessary), 2) degree of field drainage, 3) seeding condition, 4) soil pH, 5) soil type and 6) microbial diversity in soil, based on results of hitherto ecological and epidemiological studies.  Each measured value of the above parameters is translated to score (from 0 to 3), then D-potential is calculated based on integrated value of the scores and number of diagnostic parameters actually used (Table 2). As for management menu to prevent the occurrence, various cultural and chemical control methods are sorted by each D-potential level (Table 3).  Although these contents are summarized as the manual book, it also strengthens the importance of PDCA practicing: evaluation of D-potential and making decision of disease management (Plan), performing disease management according to the plan (Do), evaluation of the validity of the disease management after cultivation (Check), then modification and turning of diagnostic parameters and/or criteria of scoring to be more suitable for the results of disease occurrence in the previous cropping season (Act).  It is the significant characteristics of HeSoDiM to change criteria of its each component flexibly by adopting PDCA cycle.

The second manual book published in 2016 mentions each actual protocol for the practice of HeSoDiM against rhizome rot of ginger (revised version), Verticillium wilt of cabbage, Fusarium yellows of celery, white rot of Welsh onion, Chinese cabbage yellows, lettuce big-vein disease, lettuce drop, strawberry anthracnose, Fusarium wilt of strawberry and potato scab.  In the case of HeSoDiM of Fusarium yellows of celery caused by Fusarium oxysporum f.sp. apii, developed by Nagano Prefectural Vegetable and Flower  Experiment Station, its core diagnostic parameters are verified as 1) disease occurrence in the field at the previous cropping season, 2) degree of recovery on soil fungal diversity after soil fumigation based on PCR-DGGE analysis and 3) DNA amount extracted from soil, and the manual also mentions evaluating method for D-potential level and recommended control methods by each level.  Likewise, in the manual book of lettuce big-vein disease, developed by Kagawa Prefectural Agricultural Experiment Station and Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, the causal viral amount extracted from soil based on realtime PCR analysis and disease occurrence in the field at the previous cropping season are mentioned as significant diagnostic parameters, as well as introducing method for D-potential calculation and effective control methods by each D-potential level.


It is primarily important for the success of HeSoDiM to choose appropriate diagnostic parameters based on the causal pathogens, disease characteristics and condition of target fields, etc.  Therefore, ensuring and choosing from a wide variety of parameters are promising for the success, and it has become possible to perform such selection by recent technological progresses.  Our development of a basic method for soil microbial community analysis, particularly, contributes to establish strategy and practice of HeSoDiM.  It has generally been recognized that occurrence of soil-borne diseases is associated to physiochemical and biological factors of soils in addition to qualitative and quantitative factors of causal pathogens in soils.  Although involvement of soil microbial community structure in the disease occurrence has less been verified as a biological factor so far, our developed basic analytical protocols for the community structures using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) (Hoshino and Matsumoto 2004, Morimoto and Hoshino 2008, Oba and Okada 2008) reveal novel association of the structures to occurrence of diseases, such as Fusarium yellows of celery (Fujinaga et al. 2012), Chinese cabbage yellows (Nagase et al. 2014), tomato corky root (Sekiguchi 2011), bacterial rice seed diseases (Takahashi et al. 2018) and white root rot of Japanese apricot (Yoneda et al. 2012).  Thus, microbial community structures have impacts on the occurrence or suppression of several soil-borne diseases, and applying our basic technique for verifying the structure leads to more suitable evaluation of D-potential and selection of control methods in HeSoDiM.


As described above, more propagation of HeSoDiM practices contributes promotion of sustainable use of arable land, as well as increase of farmers’ income, through appropriate soil-borne disease management.  Because each HeSoDiM summarized in the manual books was developed based on experimental data of fields at a region under a particular cultivation condition, its applicable area is limited.  To realize the broad propagation of HeSoDiM, it is necessary to develop the management system flexibly changeable corresponding to cultivation conditions, such as cropping season, soil type and degree of disease resistance of cultivated plants.  In addition, because population aging and depopulation is rapidly continuing in Japan, number of extension workers are also rapidly decreasing, which leads to insufficient propagation of HeSoDiM using the developed manual books.  To solve these problems for the propagation, we are developing artificial intelligence (AI) assisting HeSoDiM practice adaptative to conditions of target fields, which automatically suggests appropriate diagnostic parameters, D-potential level and control methods recommendation, by a research project funded by MAFF (FY 2018-2022).  In the research project, we are carrying out proof experiments in the management against five groups of soil-borne diseases (club root of cruciferous vegetables, white rot of Welsh onion, Verticillum diseases of Chinese cabbage and chrysanthemum, Oomycetes diseases of onion and ginger and bacterial wilt of tomato and ginger), at fields of various locations and cultivation conditions, then obtained data relating to the experiments and results are used for construction and machine learning of AI.  We are also developing an interface (mobile application) to utilize the AI system by farmers and extension workers.  Using such supporting system, it is expected that expansion of HeSoDiM is effectively promoted, resulting in contribution to farmer’s income and sustainable use of arable land.


Promotion of sustainable agriculture is a significant fundamental target to solve worldwide food supply issue.  Because HeSoDiM emphasizes the prevention of disease occurrence, more propagation of this soil-borne disease management system is a promising strategy to realize sustainable agriculture by decreasing input of costs and environmental stresses.  We will continue efforts on research and development to propagate HeSoDiM to achieve promotion of sustainable agriculture in Japan and also worldwide including Asian countries.


This work was supported by a grant from commissioned the following three project studies, Ministry of Agriculture, Forestry and Fisheries, Japan.

・Development of a new soil-borne disease management: health checkup based soil borne disease management (FY2011-2013)

・Development of next generation technologies on soil-borne disease management (FY2013-2015)

・Development of field checkup system for soil-borne disease management using artificial intelligence (FY2018-2022)


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