Anaerobic Soil Disinfestation Efficacy Against Fusarium oxysporum Is Affected by Soil Temperature, Amendment Type, Rate, and C:N Ratio

Rhizosphere microbial community assembly as influenced by reductive soil disinfestation to resist successive cropping obstacle

BACKGROUND

Reductive soil disinfestation (RSD), which involves creating anaerobic conditions and incorporating large amounts of organic materials into the soil, has been identified as a reliable strategy for reducing soilborne diseases in successive cropping systems. However, limited research exists on the connections between soil microorganism composition and plant diseases under various types of organic material applications. This study aimed to evaluate the effects of distinct RSD strategies (control without soil amendment; RSD with 1500 kg ha-1 molasses powder; RSD with 3000 kg ha-1 molasses powder; RSD with 3000 kg ha-1 molasses powder and 37.5-41.3 kg ha-1 microbial agent) on the plant disease index, bacterial community composition and network structure in rhizosphere soil.

RESULTS

RSD treatments significantly reduced the occurrence of black shank disease in tobacco and increased soil bacterial diversity. High amounts of molasses powder in RSD treatments further enhanced disease inhibition and reduced fungal abundance and Shannon index. RSD also increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, while decreasing the relative abundance of bacterial phyla Chloroflexi and Acidobacteriota and fungal phylum Basidiomycota in rhizosphere soil. A multiple regression model identified bacterial positive cohesion as the primary factor influencing the plant disease index, with a greater impact than bacterial negative cohesion and community stability. The competition among beneficial bacteria for creating a healthy rhizosphere environment is likely a key factor in the success of RSD in reducing plant disease risk.

CONCLUSION

RSD, especially with higher rates of molasses powder, is a viable strategy for controlling black shank disease in tobacco and promoting soil health by fostering beneficial microbial communities. This study provides guidelines for soil management and plant disease prevention. © 2024 Society of Chemical Industry.

Unraveling the Interplay: Soil Biogeochemical Factors Shaping the Efficacy of Anaerobic Soil Disinfestation in Suppressing Fusarium Root Rot of Strawberry

Nontoxic alternatives to chemical soil fumigants for suppressing soilborne pathogens such as Fusarium oxysporum (Fo), one causative agent of strawberry black root rot complex prevalent in the Southeastern United States, are urgently needed. A promising alternative is anaerobic soil disinfestation, in which soil is amended with labile organic materials, irrigated to field capacity, and tarped to induce anaerobic fermentation for a brief period before planting. Pathogen-suppression mechanisms of anaerobic soil disinfestation include anaerobic conditions and generation of reduced metal cations (Fe2+ and Mn2+) and volatile fatty acids (VFAs; e.g., acetic, n-butyric, isovaleric, and others). However, little is known about how the interaction between VFAs, reduced metals, soil texture, and liming influences suppression of Fo. We investigated Fo suppression by VFAs and reduced metal cations in both aqueous and soil-based incubation trials. Inoculum containing Fo chlamydospores was added to aqueous medium containing either 5 or 10 mmol/liter VFAs and either 0.01 or 0.05% (wt/wt) reduced metals. In soil-based incubations, chlamydospore-containing inoculum was applied to sandy, sandy loam, and silty clay soil saturated by solutions containing 10 or 20 mmol/liter VFAs with or without 0.05% (wt/wt) reduced metals. VFAs, particularly in combination with Fe2+ in aqueous solutions and Mn2+ in soils, significantly reduced Fo viability. At the same time, liming and higher soil clay content reduced the effectiveness of VFAs and reduced metals for suppressing Fo, highlighting the influence of soil pH and soil texture on anaerobic soil disinfestation effectiveness.

Optimization of anaerobic soil disinfestation against Verticillium wilt in strawberry cultivation using local agrowastes as amendments

The study explores anaerobic soil disinfection as an alternative to soil fumigants for controlling Verticillium wilt in strawberry crops. For this purpose, two agrowastes close to the strawberry-growing areas of Huelva province were tested as potential amendments for the control of Verticillium wilt: rice bran and residual strawberry extrudate. Furthermore, two application rates were evaluated: 13.50 and 20.00 t/ha for the rice bran and 16.89 and 25.02 t/ha for residual strawberry extrudate. Amended and anaerobically disinfested soils were compared with a non-amended soil under anaerobic conditions, a soil treated with the chemical fungicide metam sodium and an untreated soil. One week before the start of disinfection treatment, these soils were artificially inoculated with 250 microsclerotia/g dry soil of Verticillium dahliae. After disinfestation treatments, pathogens were quantified, and strawberry plants were cropped in a growth chamber to further evaluate Verticillium wilt severity, which was measured with a symptom scale in the same potting soils. Measurements of the anaerobic condition, pH and microbial population densities were performed, and the results showed significant differences between the different amendments. In addition, the treatment with rice bran at 20 t/ha recorded the lowest population density of V. dahliae. Likewise, it was possible to achieve a reduction in foliar disease severity in all amended treatments in similar percentage to those obtained by chemical treatment. These results suggest potential application of this technique for the control of Verticillium wilt in the strawberry-growing area of Huelva, reducing the use of chemical fumigants.

Impacts of the Ban on the Soil-Applied Fumigant Methyl Bromide

The loss of the soil fumigant methyl bromide (MeBr) and adoption of soil fumigant alternatives has been challenging for farmers, particularly for those crops in which pathogens previously controlled by MeBr have emerged as significant problems, but it has resulted in some unanticipated benefits for the scientific community and the environment. Applauded as one of the most effective environmental agreements to date, the universally accepted Montreal Protocol on Ozone Depleting Substances has had a significant impact on the environment, reducing the release of halogenated compounds from anthropogenic sources enough to mitigate global warming by an estimated 1.1°C by 2021. The funding associated with various MeBr transition programs has increased collaboration across scientific disciplines, commodity groups, industry, and regulatory agencies. Chemical alternatives and improved application strategies, including the development of gas-retentive agricultural films, coupled with sound efficacy data and grower ingenuity have resulted in the sustained production of many of the impacted crops; although there has been some loss of acreage and value, particularly for Florida fumigated crops, for some, value has continued to increase, allowing production to continue. The loss of a single, broad-spectrum tool for pest control has led to a deeper understanding of the specific pest complexes impacting these at-risk crops, as well as the development of new, biologically based management tools for their control while increasing our understanding of the role of the soil microbiome in pest control and crop production.

Anaerobic Soil Disinfestation and Vermicompost to Manage Bottom Rot in Organic Lettuce

Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris [Frank] Donk) is an aggressive soilborne pathogen with a wide host range that survives saprophytically between crops, presenting a challenge for organic vegetable farmers who lack effective management tools. A 2-year field experiment was conducted at two organic farms to compare anaerobic soil disinfestation (ASD) and worm-cured compost (vermicompost) to manage bottom rot caused by R. solani subspecies AG1-IB in field-grown organic lettuce (Lactuca sativa). At each farm, four replicate plots of seven treatments were arranged in a randomized complete block design. Randomization was restricted by grouping treatments to evaluate ASD, and treatments to evaluate vermicompost in starter plugs. ASD experiment treatments were three different ASD carbon sources that are commonly used and widely available to local farmers in Vermont: compost, cover crop residues, and poultry manure fertilizer, as well as a tarped control. Vermicompost experimental treatments were vermicompost compared with two types of controls: a commercial biocontrol product (RootShield PLUS + G), and unamended (untarped control). This study demonstrated that the ASD method is achievable in a field setting on Vermont farms. However, neither ASD nor vermicompost produced significant disease suppression or resulted in higher marketable yields than standard growing practices. Given the laborious nature of ASD, it is likely more appropriate in a greenhouse setting with high-value crops that could especially benefit from being grown in plastic tarped beds (e.g., tomatoes and strawberries). This study is the first known attempt of field-implemented ASD for soil pathogen control in the northeastern United States.

Optimization of the Use of Industrial Wastes in Anaerobic Soil Disinfestation for the Control of Fusarium Wilt in Strawberry

Anaerobic soil disinfestation (ASD) is proposed as an alternative to the use of chemical fumigants against Fusarium wilt in strawberry crops. Different residual wastes (rice bran, fishmeal, and residual strawberry extrudate) were assessed as amendments for ASD. Two different concentrations and two incubation durations were tested in growth chamber trials. The abundance of several microbial groups was noted before and after the treatments. Strawberry plants were grown in the treated soils to record Fusarium wilt disease severity. The population density of F. oxysporum increased after ASD in most amendments with rice bran and residual strawberry extrudate. Changes in Trichoderma spp., copiotrophic bacteria, and Streptomyces spp. populations were observed after anaerobiosis treatments and plant trials. A reduction in the disease severity was achieved in ASD-treated soils with 20 t/ha of rice bran at both 25 and 60 days of incubation, but not when using a 13.5 t/ha dose. Similarly, treatments using 19.3 t/ha of fishmeal for both incubation durations were able to reduce disease severity. In contrast, a severity reduction was only obtained in soils treated with 25.02 t/ha of the residual strawberry extrudate and incubated for 60 days in anaerobic conditions. Two of the three by-products tested were able to reduce Fusarium wilt symptoms in strawberry plants after an ASD-treatment period of only 25 days. Accordingly, the technique seems promising for strawberry growers in Huelva, Spain, and highly sustainable by giving value to residues produced in surrounding areas.

Facilitating effects of the reductive soil disinfestation process combined with Paenibacillus sp. amendment on soil health and physiological properties of Momordica charantia

Reductive soil disinfestation (RSD) is an anaerobic and facultative anaerobic microbial-mediated soil management process. The extent of improvement of diseased soil properties by RSD relative to comparable healthy soil is, however, not well characterized. Importantly, how to promote the colonization efficiency of these facultative anaerobic functional species to ensure soil and plant health remain unknown. Here, Fusarium wilt-diseased soil of Momordica charantia grown under a plastic-shed field (PS-CK) was used to conduct molasses-RSD (MO-RSD) along with Paenibacillus sp. (a model of facultative anaerobic species) (MO_PA-RSD) treatment, and the soil from a nearby open-air paddy field was considered comparable healthy soil (OA-CK). Both RSD treatments significantly improved the properties of PS-CK soil, and the extent of improvement of soil pH, Fusarium oxysporum reduction efficiency (98.36%~99.56%), and microbial community and functional composition were higher than that achieved for OA-CK soil, which indicated that RSD-regulated most soil properties outperformed those of the comparable healthy soil. The disease incidence and ascorbic acid content of M. charantia in MO-RSD- and MO_PA-RSD-treated soils were considerably decreased, while the weight and soluble protein contents were correspondingly increased, as compared to those of M. charantia in PS-CK soil. Specifically, the changes in these physiological properties of M. charantia in MO_PA-RSD soil performed well than that in MO-RSD soil. The relative abundances of Cohnella, Effusibacillus, Rummeliibacillus, Oxobacter, Thermicanus, and Penicillium enriched in both RSD-treated soils were positively correlated with Paenibacillus and negatively correlated with F. oxysporum population and disease incidence (P < 0.05). Notably, the relative abundances of these potential probiotics were considerably higher in MO_PA-RSD-treated soil than in MO-RSD alone-treated soil. These results show that the RSD process with inoculation of Paenibacillus sp. could promote the colonization of this species and simultaneously stimulate the proliferation of other probiotic consortia to further enhance soil health and plant disease resistance.

Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition

Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.

Sunflower Seed Husk as Promising By-Product for Soil Biodisinfestation Treatments and Fertility Improvement in Protected Lettuce Crop

One of the major challenges in biodisinfestation treatments against soilborne pathogens is the selection of the proper organic amendments and mixture features. The use of agro-industrial by-products is a sustainable alternative with proven efficacy, but the availability has to be considered in terms of location and quantity. Sunflower seed is one of the five major oil crops widely cultivated and the husk constitutes a significant part that is discarded. This by-product brings together the features to be considered an interesting organic amendment in agricultural soils because of its lignocellulose content, but no references have been found in this field. In this study, sunflower seed husk was used with fresh cow manure in biodisinfestation treatments, alone or combined with other by-products (rapeseed cake, beer bagasse and wheat bran). The assay was performed in summer in a commercial greenhouse with significant yield losses in lettuce crops caused by the root-knot nematode Meloidogyne incognita. Four different amendment mixtures were applied which included 3kg/m2 cow manure, as common waste, and 1 kg/m2 of by-products (dry weight), considering 6mgC/g soil in all treatments but different C/N ratio (23, 29, 31, 34) and by-products. Data was collected in three moments: (i) before and (ii) after biodisinfestation treatments and (iii) after harvesting the first crop after biodisinfestations. Crop damage was assessed through root galling index and the number of eggs in roots. The effects on the pathogen population and the whole soil nematode community were assessed along with some physicochemical and soil microbiological variables (respiration rate, microbial organic C, water-soluble organic C and physiological profile of heterotrophic bacteria through Biolog Ecoplates™). All treatments reported effectiveness in disease control without significant differences among them, but among times. However, soil temperatures during biodisinfestations were higher at higher C/N ratios and fertility variables also increased in these cases, mainly in the treatment with husk as the only by-product. Sunflower seed husk proved to be an interesting source of organic C to improve both biodisinfestation treatments and soil fertility in humid temperate climate zones.

Mechanisms of Anaerobic Soil Disinfestation: Volatile Fatty Acids Reduce Viability of Athelia (Sclerotium) rolfsii Sclerotia in Acidic Soil Conditions and Have Limited Effects on Endemic Trichoderma spp

Volatile fatty acids (VFAs), such as acetic and n-butyric acid, released during anaerobic decomposition of organic soil amendments during anaerobic soil disinfestation (ASD) likely play a role in soilborne plant pathogen inoculum suppression. However, research is limited on the direct effects of soil VFA exposure on fungal plant pathogen inoculum, effects on pathogen antagonists such as Trichoderma spp., and the role of soil microbial VFA metabolism on reducing exposure effects. The present study addresses these limitations through a series of studies evaluating the effects of VFA (acetic or n-butyric acid), VFA concentration (4, 8, or 16 mmol/kg soil), soil sterilization by autoclaving, and soil amendment on the viability of Athelia rolfsii (Sclerotium rolfsii) sclerotia post VFA exposure, and soil populations of Trichoderma spp. HCl and water-only controls were included. After 4-days exposure in an acidic, anaerobic environment, sclerotial viability, and colonization by culturable fungi or bacteria were assessed with standard procedures. Greenhouse experiments were similarly conducted to evaluate endemic soil populations of Trichoderma spp. following soil exposure to VFAs and Trichoderma spp. populations assessed with standard soil dilution plating onto semi-selective medium. Sclerotial germination was generally reduced by soil exposure to acetic (35.1% germination) or n-butyric (21.9% germination) acids compared to water (74.3% germination) and HCl (62.7% germination). Germination was reduced as VFA concentration increased from 4 to 8 and 16 mmol/kg (39.5, 29.1, and 16.9%, respectively). In amended soils, there was no difference in sclerotial germination compared to non-amended soils, but in the greenhouse experiment there was a Trichoderma spp. population increase of over 300% in amended soil [3.4 × 106 colony forming units (CFU)/g soil] compared to the non-amended soil (9.6 × 105 CFU/g soil). Soil autoclaving had no effect on sclerotial germination at low VFA concentrations, but sclerotial germination was reduced at higher VFA concentrations compared to non-autoclaved soil. Our results suggest that VFAs contribute to sclerotial mortality in strongly acidic soil environments, and mortality is influenced by VFA components and environment. Antifungal activity is less for acetic acid than for n-butyric, and less in non-sterile soil environments more typical of field conditions than in sterile laboratory conditions.

Amendment Properties Affect Crop Performance, Leaf Tissue Nitrogen, and Soil Nitrogen Availability Following Soil Treatment by Anaerobic Soil Disinfestation

Efficacy of anaerobic soil disinfestation (ASD) for soilborne plant pathogen suppression is strongly influenced by soil environment and organic amendment attributes. At the same time, these factors influence soil nutrient availability, crop nutrition, and crop performance, but published information on ASD amendment property effects, including carbon to nitrogen (C:N) ratio and C substrate bioavailability, on crop performance and soil nutrient availability is limited. We evaluated ASD amendment effects on soil N availability, crop N status, and solanaceous crop performance in a series of trials: (1) greenhouse/growth chamber study of amendments (primarily molasses/soybean hulls and wheat bran) formulated at 10:1, 20:1, 30:1 and 40:1 C:N ratios (4 mg C g−1 soil), (2) field study with molasses/soybean hull-based amendments at equivalent C:N ratios/C rates (3) on-farm study with molasses/soybean hull-based amendments (4 mg C g−1 soil) compared to grower-standard control, and (4) field study of labile to recalcitrant amendment substrates at 30:1 C:N ratio (~3.4 mg C g−1 soil). ASD amendment C:N ratio strongly influenced soil inorganic N and the lowest (10:1) ratio was associated with highest soil inorganic N at ASD treatment termination in both trials 1 and 2, which often persisted into the cropping phase. Accordingly, the lowest amendment C:N ratio was also associated with the highest biomass (trail 1), leaf tissue N (trial 2), and crop yield (trials 1, 2) among treatments, even with application of recommended fertigation rates to all treatments in the field study. In trial 3, ASD treatment induced higher soil inorganic N and crop yield than the control, but no differences were observed in plant tissue N. In trial 4, more decomposable ASD substrates reduced soil inorganic N at ASD treatment termination, with the highest soil inorganic N associated with the most recalcitrant amendment, but there was no effect on crop yield. ASD amendment C:N ratio, and to a lesser extent, amendment decomposability, exert a strong influence soil inorganic N and crop performance. Optimization of ASD treatments for disease management will require simultaneous optimization of crop nutrition practices to facilitate more holistic, less confounded assessment of crop performance and to facilitate recommendations for grower adoption.

Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation

Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace soil fumigants to manage these serious diseases. Studies were conducted to discern whether Gramineae carbon input type, incubation temperature, or incubation duration influences the efficacy of this disease control tactic. In experiments conducted using 'low rate' amendment applications at moderate day/night temperatures (24/18 °C), and carbon inputs (orchard grass, wheat, and rice bran) induced an initial proliferation and subsequent decline in soil density of the Fusarium wilt pathogen. This trend coincided with the onset of anaerobic conditions and a corresponding generation of various anti-fungal compounds, including volatile organic acids, hydrocarbons, and sulfur compounds. Generation of these metabolites was associated with increases in populations of Clostridium spp. Overall, carbon input and incubation temperature, but not incubation duration, significantly influenced disease suppression. All Gramineae carbon inputs altered the soil microbiome and metabolome in a similar fashion, though the timing and maximum yield of specific metabolites varied with input type. Fusarium wilt and charcoal rot suppression were superior when anaerobic soil disinfestation was conducted using standard amendment rates of 20 t ha-1 at elevated temperatures combined with a 3-week incubation period. Findings indicate that anaerobic soil disinfestation can be further optimized by modulating carbon source and incubation temperature, allowing the maximum generation of antifungal toxic volatile compounds. Outcomes also indicate that carbon input and environmental variables may influence treatment efficacy in a target pathogen-dependent manner which will require pathogen-specific optimization of treatment protocols.