Soil Disinfestation: From Soil Treatment to Soil and Plant Health.

This feature article tracks 100 years of soil disinfestation, from the goal of eradicating soilborne pathogens and pests to much milder approaches, aimed at establishing a healthier soil, by favoring or enhancing the beneficial soil microflora and introducing biological control agents. Restrictions on the use of many chemical fumigants is favoring the adoption of nonchemical strategies, from soilless cultivation to the use of physical or biological control measures, with more focus on maintaining soil microbial diversity, thus enhancing soil and plant health. Such approaches are described and discussed, with special focus on their integrated use.

Soil suppressiveness to fusarium disease: shifts in root microbiome associated with reduction of pathogen root colonization.

Soil suppressiveness to Fusarium disease was induced by incubating sandy soil with debris of wild rocket (WR; Diplotaxis tenuifolia) under field conditions. We studied microbial dynamics in the roots of cucumber seedlings following transplantation into WR-amended or nonamended soil, as influenced by inoculation with Fusarium oxysporum f. sp. radicis-cucumerinum. Disease symptoms initiated in nonamended soil 6 days after inoculation, compared with 14 days in WR-amended soil. Root infection by F. oxysporum f. sp. radicis-cucumerinum was quantified using real-time polymerase chain reaction (PCR). Target numbers were similar 3 days after inoculation for both WR-amended and nonamended soils, and were significantly lower (66%) 6 days after inoculation and transplanting into the suppressive (WR-amended) soil. This decrease in root colonization was correlated with a reduction in disease (60%) 21 days after inoculation and transplanting into the suppressive soil. Fungal community composition on cucumber roots was assessed using mass sequencing of fungal internal transcribed spacer gene fragments. Sequences related to F. oxysporum, Fusarium sp. 14005, Chaetomium sp. 15003, and an unclassified Ascomycota composed 96% of the total fungal sequences in all samples. The relative abundances of these major groups were highly affected by root inoculation with F. oxysporum f. sp. radicis-cucumerinum, with a 10-fold increase in F. oxysporum sequences, but were not affected by the WR amendment. Quantitative analysis and mass-sequencing methods indicated a qualitative shift in the root's bacterial community composition in suppressive soil, rather than a change in bacterial numbers. A sharp reduction in the size and root dominance of the Massilia population in suppressive soil was accompanied by a significant increase in the relative abundance of specific populations; namely, Rhizobium, Bacillus, Paenibacillus, and Streptomyces spp. Composition of the Streptomyces community shifted significantly, as determined by PCR denaturing gradient gel electrophoresis, resulting in an increase in the dominance of a specific population in suppressive soils after only 3 days. This shift was related mainly to the increase in Streptomyces humidus, a group previously described as antagonistic to phytopathogenic fungi. Thus, suitable soil amendment resulted in a shift in the root's bacterial communities, and infection by a virulent pathogen was contained by the root microbiome, leading to a reduced disease rate.

Soil Suppressiveness to Fusarium Disease Following Organic Amendments and Solarization.

Soil suppressiveness to soilborne pathogens can evolve following the incorporation of plant residues in the soil and solarization. We studied its occurrence by assessing disease incidence and severity in sandy soil which was infested after the disinfestation treatment. Disease incidence and severity of crown and root rot in cucumber plants inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum macroconidia were reduced by 20 to 80% when seedlings were planted in the tested soils 2 to 34 months after soil amendment. Residues of Diplotaxis tenuifolia (wild rocket [WR]), Artemisia dracunculus (tarragon), Salvia officinalis (sage), and Brassica oleracea var. italica (broccoli) were most effective for inducing soil suppressiveness. Effective soil suppressiveness continued to be evident after repeated inoculations and plantings in the same soil without additional treatment between inoculations. Moreover, residues of WR induced soil suppressiveness in two additional tested soils differing in their physical and chemical properties. Residues of Rosmarinus officinalis (rosemary), Coriandrum sativum (coriander), Mentha piperita (peppermint), and B. oleraceae var. botrytis (cauliflower) induced disease suppression at the first inoculated planting but not upon repeated inoculation and planting. The contribution of soil solarization to the evolution of soil suppressiveness, albeit evident, was inconsistent. Soil suppressiveness to Fusarium crown and root rot was also observed when cucumber seed were sown in soils which were initially amended with WR residues and later infested with F. oxysporum f. sp. radicis-cucumerinum chlamydospores. There is a potential for the use of plant residues for inducing soil suppressiveness and further contributing to the control of diseases caused by soilborne pathogens.

Microbial aspects of accelerated degradation of metam sodium in soil.

Preplant soil fumigation with metam sodium is used worldwide to control soilborne diseases. The development of accelerated degradation of pesticides in soil, including metam sodium, results in reduced pesticide efficacy. Therefore, we studied microbial involvement in accelerated degradation of methyl isothiocyanate (MITC) following repeated soil applications of the parent compound, metam sodium. MITC degradation was reduced in soil with a history of metam sodium applications following sterilization, indicating the key role of microorganisms in accelerated degradation. Accelerated degradation of MITC was induced by inoculation of soil with no previous application of metam sodium with soil with a history of metam sodium applications. We developed a method to extract the active microbial fraction responsible for MITC degradation from soil with a history of metam sodium applications. This concentrated soil extract induced accelerated degradation of MITC when added to two different soils with no previous application of metam sodium. An extensive shift in total bacterial community composition in concentrated soil extracts occurred after a single metam sodium application. Two Oxalobacteraceae strains, MDB3 and MDB10, isolated from Rehovot soil following triple application of metam sodium rapidly degraded MITC in soil with no previous application of metam sodium. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of bacterial community composition showed relative enrichment of MDB3 following metam sodium application, suggesting its potential in situ involvement in accelerated degradation development in Rehovot soil. Responses of resident Oxalobacteraceae community members to metam sodium applications differed between Rehovot and En Tamar soils. Isolate MDB10 did not induce accelerated degradation of MITC in En Tamar soil and, with the slow dissipation of MITC, soil suppressiveness of accelerated degradation is suggested. The isolation and identification of MITC-degrading bacteria might be helpful in developing tools for managing accelerated degradation.

Accelerated degradation of metam-sodium in soil and consequences for root-disease management.

We studied the development of accelerated degradation (AD) of methyl isothiocyanate (MITC) following repeated applications of its parent compound, metam-sodium (MS). Laboratory studies and four sets of field experiments were conducted during 2002-04 in three commercial fields in Israel. Repeated applications of MS to the three soils in the laboratory under controlled conditions demonstrated AD of MITC in some soils. In a peanut field, MS significantly reduced the incidence of Pythium pod rot and improved pod quality after a single application but its effectiveness was greatly reduced after two applications. In a second experiment, MS was significantly effective after a single application in controlling Verticillium wilt in potato but its efficacy diminished after three consecutive applications. In an additional experiment, fumigation with MS following single or double applications was more effective in reducing Verticillium wilt severity of potato compared with triple applications. Soils which did not develop AD of MITC were also recorded. Preplant MS fumigation of melon fields was effective at reducing sudden wilt following a single and two consecutive applications. Our study shows that development of AD of MITC might occur following repeated applications of MS in commercial fields. The data on MITC dissipation in soil following repeated MS applications under controlled conditions indicate the chemical's potential loss of activity under regular agricultural practices and the need for a management strategy to prevent such a development.

Rain-based soil solarization for reducing the persistent seed banks of invasive plants in natural ecosystems - Acacia saligna as a model.

BACKGROUND: A large persistent seed bank of invasive plants is a significant obstacle to restoration programs. Soil solarization was demonstrated to be an effective method for reducing the seed bank of Australian acacias. However, use of this method in natural habitats might be limited due to the requirement to moisten the soil by irrigation. This study examined the possibility of replacing irrigation by trapping the soil moisture caused by the most recent rainfall, i.e. rain-based soil solarization (RBS). RESULTS: Exposure of Acacia saligna seeds to 57 °C at 20% soil moisture for 68 h resulted in almost complete loss of seed viability. Similarly, RBS treatment significantly reduced the viability of A. saligna seeds buried at a soil depth of 1-19 cm as well as seed density in the natural seed bank, and almost completely eliminated seedling emergence from natural seed banks of A. saligna and other environmental weeds. CONCLUSION: Our results indicate that RBS is an effective method for reducing the seed bank of invasive plants in natural habitats located in various climate regions characterized by different soil types. This is the first demonstration of a successful application of RBS for soil disinfestation. © 2018 Society of Chemical Industry.

Controlled laboratory system to study soil solarization and organic amendment effects on plant pathogens.

ABSTRACT A controlled laboratory system for simulating soil solarization, with and without organic amendment, was developed and validated using physical, chemical, and biological parameters. The system consists of soil containers that are exposed to controlled and constant aeration, and to temperature fluctuations that resemble those occurring during solarization at various depths. This system enables a separate analysis of volatiles and other components. We recorded a sharp decrease in oxygen concentration in the soil atmosphere followed by a gradual increase to the original concentration during solarization in the field and heating in the simulation system of soil amended with wild rocket (Diplotaxis tenuifolia) or thyme (Thymus vulgaris). The combined treatment of organic amendment and solarization (or heating in the controlled system) was highly effective at controlling populations of Fusarium oxysporum f. sp. radicis-lycopersici. Changes in soil pH, enzymatic activities, and microbial populations followed, in most cases, trends which were similar under both solarization and the heating system, when exposed to controlled aerobic conditions. The reliability and validity of the system in simulating physical, chemical, and biological processes taking place during solarization is demonstrated.

Generation and Dissipation of Methyl Isothiocyanate in Soils Following Metam Sodium Fumigation: Impact on Verticillium Control and Potato Yield.

The fate of methyl isothiocyanate (MITC) was studied in agricultural soils following metam sodium (MS) application in a controlled system and under field conditions as it was related to disease control. Soil samples were collected from 34 field sites in Israel with no history of MS application. The generation and dissipation curves of MITC in these soils, under controlled conditions, varied significantly among the soils, as reflected by the concentration by time (C × T) product. This value was significantly related with the mortality level of Fusarium oxysporum f. sp. radicis-lycopersici as a test organism and sand content of the soils. Seven field experiments were conducted in potato fields from 2001 to 2004. The MS treatments significantly reduced Verticillium wilt incidence and severity in five and four experiments, respectively, out of seven. Combining MS with formalin was more effective for controlling disease than MS alone in most cases. A significant relationship was found between mortality of F. oxysporum f. sp. radicis-lycopersici in soil samples to which MS was applied under controlled conditions and the incidence of Verticillium wilt disease in the field, and between CMITC × T products and the incidence of Verticillium wilt disease in the field. These tests can be used for preplant assessment of potential MS efficacy.

Temperature Response of Chickpea Cultivars to Races of Fusarium oxysporum f. sp. ciceris, Causal Agent of Fusarium Wilt.

Use of resistant cultivars and adjustment of sowing dates are important measures for management of Fusarium wilt in chickpeas (Cicer arietinum). In this study, we examined the effect of temperature on resistance of chickpea cultivars to Fusarium wilt caused by various races of Fusarium oxysporum f. sp. ciceris. Greenhouse experiments indicated that the chickpea cultivar Ayala was moderately resistant to F. oxysporum f. sp. ciceris when inoculated plants were maintained at a day/night temperature regime of 24/21°C but was highly susceptible to the pathogen at 27/25°C. Field experiments in Israel over three consecutive years indicated that the high level of resistance of Ayala to Fusarium wilt when sown in mid- to late January differed from a moderately susceptible reaction under warmer temperatures when sowing was delayed to late February or early March. Experiments in growth chambers showed that a temperature increase of 3°C from 24 to 27°C was sufficient for the resistance reaction of cultivars Ayala and PV-1 to race 1A of the pathogen to shift from moderately or highly resistant at constant 24°C to highly susceptible at 27°C. A similar but less pronounced effect was found when Ayala plants were inoculated with F. oxysporum f. sp. ciceris race 6. Conversely, the reaction of cultivar JG-62 to races 1A and 6 was not influenced by temperature, but less disease developed on JG-62 plants inoculated with a variant of race 5 of F. oxysporum f. sp. ciceris at 27°C compared with plants inoculated at 24°C. These results indicate the importance of appropriate adjustment of temperature in tests for characterizing the resistance reactions of chickpea cultivars to the pathogen, as well as when determining the races of isolates of F. oxysporum f. sp. ciceris. Results from this study may influence choice of sowing date and use of chickpea cultivars for management of Fusarium wilt of chickpea.

Development of crown and root rot disease of tomato under irrigation with saline water.

ABSTRACT We studied the effect of water salinity on the incidence and severity of crown and root rot disease of tomato, as well as on the pathogen and on the plant's response to the pathogen. Irrigation with saline water significantly increased disease severity in tomato transplants inoculated with Fusarium oxysporum f. sp. radicis-lycopersici, and mineral fertilization further increased it. In one field experiment, disease incidence in plots irrigated with saline water (electrical conductivity [EC] = 3.2 +/- 0.1 dS m(-1)) and in those irrigated with fresh water (EC = 0.4 +/- 0.1 dS m(-1)) was 75 and 38%, respectively. Disease onset was earlier and yield was lower in plots irrigated with saline water. In a second field experiment, final disease incidence 250 days after planting, was 12% in plants which had been irrigated with saline water (EC = 4.6 +/- 0.1 dS m(-1)) and 4% in those irrigated with fresh water (EC = 1.2 +/- 0.1 dS m(-1)). Irrigation of tomato transplants with 20 mM NaCl did not inhibit plant development, but partial inhibition was observed at higher NaCl concentrations. Growth of the pathogen in culture or survival of conidia added to soil were not affected by saline water. Plants which were preirrigated with saline water were more severely diseased than those preirrigated with tap water. It was concluded that disease increases effected by saline water are associated with the latter's effect on plant response.

High-nitrogen compost as a medium for organic container-grown crops.

Compost was tested as a medium for organic container-grown crops. Nitrogen (N) loss during composting of separated cow manure (SCM) was minimized using high C/N (wheat straw, WS; grape marc, GM) or a slightly acidic (orange peels, OP) additives. N conservation values in the resultant composts were 82%, 95% and 98% for GM-SCM, OP-SCM and WS-SCM, respectively. Physical characteristics of the composts were compatible with use as growing media. The nutritional contribution of the composts was assessed using cherry tomato (Lycopersicon esculantum Mill.) and by means of incubation experiments. Media were either unfertilized or fertilized with guano (sea-bird manure). Plant responses suggest that N availability is the main variable affecting growth. Unfertilized OP-SCM and WS-SCM supplied the N needed for at least 4 months of plant growth. Root-galling index (GI) of tomato roots and number of eggs of the nematode Meloidogyne javanica were reduced by the composts, with the highest reduction obtained by OP-SCM and WS-SCM, at 50% concentrations. These composts, but not peat, reduced the incidence of crown and root-rot disease in tomato as well as the population size of the causal pathogen, Fusarium oxysporum f. sp. radicis-lycopersici.

Effect of moisture on thermal inactivation of soilborne pathogens under structural solarization.

ABSTRACT Structural solarization of greenhouses for sanitation by closing them involves dry heating to 60 degrees C and higher with a consequent low relative humidity (RH) ( approximately 15%), thus requiring an extended period for thermal inactivation of pathogens. In an attempt to enhance pathogen control by increasing moisture during the hot hours of the day, various regimes of inoculum moistening were studied. However, wetting inoculum of Fusarium oxysporum f. sp. melonis and F. oxysporum f. sp. radicis-lycopersici resulted in less effective pathogen control compared with that of dry heating. Fifty percent effective dose (ED(50)) values of thermal inactivation of wetted and dry inoculum for the former pathogen were 18 and 7 days, respectively, and for the latter, a respective 9 and 4 days. This was because wetting resulted in inoculum cooling due to evaporation, which eventually led to its drying. A model describing the drying of wet inoculum in a wetted greenhouse, based on the fact that there was an approximately 10 degrees C difference between greenhouse and ambient temperatures, was proposed. A double-tent system reduced this difference to 1 to 2 degrees C, reduced moisture loss, and led to improved inoculum inactivation of F. oxysporum f. sp. radicis-lycopersici. Thus, the ED(50) value of thermal inactivation was reduced from 15 days to 1 day, because this system provided both high temperature ( approximately 60 degrees C) and high RH ( approximately 100%), resulting in effective wet heating.

Weakening and Delayed Mortality of Fusarium oxysporum by Heat Treatment: Flow Cytometry and Growth Studies.

ABSTRACT Survival of Fusarium oxysporum f. sp. niveum following heat treatments was studied using flow cytometric, physiological, and microscopic assays. We exposed germinating conidia to sublethal temperatures from 36 to 42 degrees C for 60 min, followed by rhodamine 123 staining and flow cytometry, and found increasing levels of fluorescence that reflect a change in mitochondrial membrane potential, indicating a weakening induced by stress. Viability of conidia or germinating conidia of the fungus exposed to heat decreased with increasing temperature, as assessed by fluorescent staining. However, viability was higher than that assessed with the 5-day-long plate count method and was further reduced 13 and 24 h after treatment, suggesting delayed mortality of the heat-treated germinating conidia. Delayed mortality was substantiated by observing these conidia with light and fluorescent scanning electron microscopy and by subculturing single germinating conidia that had been previously heated. Programmed cell death was not observed in heat-treated conidia or germinating conidia of F. oxysporum based on the detection of plasma membrane phosphatidylserine translocation, cell-cycle measurements, detection of DNA fragmentation, or microscopic observation of apoptotic bodies. We hypothesize that propagules, which survived the heating and apparently are alive, may undergo further irreversible detrimental processes, eventually leading to their death by yet unidentified mechanisms. These findings suggest that pathogen propagules also might be affected under lower temperatures, possibly facilitating pathogen control by heating.

Modeling the survival of two soilborne pathogens under dry structural solarization.

ABSTRACT Structural (space) solarization of a closed, empty greenhouse for sanitation involves dry heating to 60 degrees C and higher and low relative humidity (RH), under a fluctuating temperature and RH regime. Survival of inocula of Fusarium oxysporum f. sp. radicis-lycopersici and Sclerotium rolfsii during structural solarization was studied for 4 years (total of 12 experiments) in an attempt to develop a dynamic model for expressing the thermal inactivation of the pathogens. After 20 days of exposure, the populations of F. oxysporum f. sp. radicis-lycopersici and S. rolfsii were reduced by 69 to 95% and by 47.5 to 100%, respectively. The Weibull distribution model was applied to describe pathogen survival. The Weibull rate parameter, b, was found to follow an exponential (for F. oxysporum f. sp. radicis-lycopersici) and the Fermi (for S. rolfsii) functions at constant temperatures. To improve the applicability of the model, fluctuating conditions of both temperature and RH were utilized. The Weibull distribution derivative, expressed as a function of temperature and moisture, was numerically integrated to estimate survival of inocula exposed to structural solarization. Deviations between experimental and calculated values derived from the model were quite small and the coefficient of determination (R (2)) values ranged from 0.83 to 0.99 in 9 of 12 experiments, indicating that ambient RH data should be considered. Structural solarization for sanitation could be a viable component in integrated pest management programs.

Survival in Soil of Colletotrichum acutatum and C. gloeosporioides Pathogenic on Strawberry.

The survival ability in soil of different inocula of strawberry isolates of Colletotrichum gloeosporioides and C. acutatum was studied under laboratory and field conditions. Two isolates of each species used in this study were identified according to morphological characteristics and by molecular techniques. Conidia of all four isolates survived for up to 1 year in autoclaved soil, whereas viability declined rapidly in untreated soils at 22% soil moisture (field capacity), with a 95% reduction in population recorded within 4.0 to 9.8 days. In methyl bromide (MB)-treated field soil at field capacity, a 95% decline in the viability of conidia of the two species was recorded within 8.9 to 12.9 days. At 11% soil moisture content, the time required for a 95% population reduction of the isolates of C. gloeosporioides and C. acutatum conidia was 124.5 and 114.4, and 72.8 and 74.2 days, respectively. C. acutatum was not recovered from naturally infected crowns after burial for 5 months in MB-fumigated and untreated soils at 10- and 20-cm depths under field conditions, but the decline was slower in the MB-fumigated soil. However, recovery of the pathogen from artificially inoculated mummified fruit after 5 months of burial ranged from 15 to 39%. Soil solarization for 4 weeks and MB fumigation treatments eradicated the pathogen from buried, artificially inoculated fruits. Based on this study, the potential contribution of conidia as well as mummified fruits to disease epidemics should be considered.