Suppression Of Soil-borne Diseases Research Articles

Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack.

The rhizosphere microbiome is critical to plant health and resistance. PGPR are well known as plant-beneficial bacteria and generally regulate nutrient utilization as well as plant responses to environmental stimuli. In our previous work, one typical PGPR strain, Pseudomonas chlororaphis IRHB3, isolated from the soybean rhizosphere, had positive impacts on soil-borne disease suppression and growth promotion in the greenhouse, but its biocontrol mechanism and application in the field are not unclear. In the current study, IRHB3 was introduced into field soil, and its effects on the local rhizosphere microbiome, disease resistance, and soybean growth were comprehensively analyzed through high-throughput sequencing and physiological and molecular methods. We found that IRHB3 significantly increased the richness of the bacterial community but not the structure of the soybean rhizosphere. Functional bacteria related to phosphorus solubilization and nitrogen fixation, such as Geobacter, Geomonas, Candidatus Solibacter, Occallatibacter, and Candidatus Koribacter, were recruited in rich abundance by IRHB3 to the soybean rhizosphere as compared to those without IRHB3. In addition, the IRHB3 supplement obviously maintained the homeostasis of the rhizosphere microbiome that was disturbed by F. oxysporum, resulting in a lower disease index of root rot when compared with F. oxysporum. Furthermore, JA-mediated induced resistance was rapidly activated by IRHB3 following PDF1.2 and LOX2 expression, and meanwhile, a set of nodulation genes, GmENOD40b, GmNIN-2b, and GmRIC1, were also considerably induced by IRHB3 to improve nitrogen fixation ability and promote soybean yield, even when plants were infected by F. oxysporum. Thus, IRHB3 tends to synergistically interact with local rhizosphere microbes to promote host growth and induce host resistance in the field.

Soil-borne disease suppressiveness after short and long term application of fermented, composted or fresh organic amendment treatments in arable soils

Soil-borne diseases can cause significant crop losses and should be tackled sustainably in agroecosystems. Increasing the capacity of soils to suppress the effects of soil-borne diseases (soil suppressiveness) is an important tool in sustainable crop production. Soil suppressiveness can be improved by adding organic amendments to the soil for multiple years, but the effects can vary greatly depending on the processing method of the organic amendment (composted, fermented, or fresh material) and the time since application. To test these impacts we conducted two bioassays using the Lepidium savitum (cress) – Pythium ultimum model system. We tested the disease suppression capacity of sandy arable soil from a field experiment where fresh plant material, compost, or Bokashi (fermented amendment), all originating from the same plant material had been applied for two consecutive years across 10 field sites subject to conventional farming. In addition, the effect of short term application on soil suppressiveness was tested right after applying the same organic amendments to control arable sandy soil from 2 sites from the field experiment. Field sites strongly differed in cress growth independent of the organic amendment treatments. Absence of field effects in the sterilized soil and their soil chemical characteristics suggested differences in inherent soil pathogen load between the field sites. Focussing on sites with low inherent pathogen load we found no significant impact of long term organic amendment application on either cress weight or soil suppressiveness. However, short term application of Bokashi did significantly promote soil suppressiveness. This effect can likely be attributed to the increased metabolic activity of the soil's microorganisms in response to Bokashi, which contains more easily decomposable compounds as compared to the other soil amendments, together with Bokashi microorganisms that survive the fermentation and are activated in the aerobic soil condition. Our results suggest that Bokashi could promote the suppression of soil-borne diseases by stimulating the locally adapted soil microbiome but the longevity of this effect requires further field tests.

Combination of biochar and PGPBs amendment suppresses soil-borne pathogens by modifying plant-associated microbiome

Consecutive monoculture regimes lead to the emergence of soil-borne diseases, which in turn impair plant growth and soil health, and restrict sustainable agricultural production. Biochar and plant growth-promoting bacteria (PGPBs) amendment in soil is considered a potential strategy for reducing soil-borne diseases. However, the combined effects of biochar and PGPBs on plant microbiomes and the subsequent consequences on plant performance remain largely unexplored. Here, we investigated the mechanisms on how biochar and biochar combined with a Bacillus synthetic community (SynCom) alleviated replant disease in Radix pseudostellariae by modulating rhizosphere soil protistan and plant microbial communities based on lab and field experiment. First, we found that biochar with Bacillus SynCom treatment increased the abundance of beneficial Bacillus spp. and Pseudomonas spp. after exposure to Fusarium oxysporum. Field experiments showed that biochar alone and combined with Bacillus SynCom improved the physiological traits and main components of Radix pseudostellariae. Besides, we found both two treatments increased Bacillus abundances in the root and soil, and significantly decreased Fusarium oxysporum density in the three compartments. Last, we validated that the combined treatment significantly decreased the relative abundance of pathogenic Ralstonia, promoted the abundance of Bacillus in the root and Paenibacillus in the leaf, and increased the abundance of the predatory protists Cercomonas and Paracercomonas in the soil. In addition, the combined amendment significantly increased the relative abundance of parasitic protists and decreased the plant pathogens. Meanwhile, the abundance of soil parasitic protists exhibited a significantly negative relationship with F. oxysporum density, and positive relationship with Bacillus density. Especially, soil pH and NO3−-N had a significantly indirect and positive effect on the parasitic protists and biomass by influencing bacterial richness of R. pseudostellariae leaf and root. Overall, our results revealed that amendment with combined biochar and Bacillus SynCom efficiently improved soil-borne disease suppression and plant physiological parameters by remodeling the plant and rhizosphere microbiome. This study provides a practical basis for more sustainable agriculture by promoting plant health through the modulation of plant and soil microbiomes.

Efficiency of some Organic Matter on Suppression of Soil-Borne Diseases of Tomato Plants under Organic Agriculture System

Efficiency of some Organic Matter on Suppression of Soil-Borne Diseases of Tomato Plants under Organic Agriculture System

More microbial manipulation and plant defense than soil fertility for biochar in food production: A field experiment of replanted ginseng with different biochars.

The role of biochar-microbe interaction in plant rhizosphere mediating soil-borne disease suppression has been poorly understood for plant health in field conditions. Chinese ginseng (Panax ginseng C. A. Meyer) is widely cultivated in Alfisols across Northeast China, being often stressed severely by pathogenic diseases. In this study, the topsoil of a continuously cropped ginseng farm was amended at 20 t ha-1, respectively, with manure biochar (PB), wood biochar (WB), and maize residue biochar (MB) in comparison to conventional manure compost (MC). Post-amendment changes in edaphic properties of bulk topsoil and the rhizosphere, in root growth and quality, and disease incidence were examined with field observations and physicochemical, molecular, and biochemical assays. In the 3 years following the amendment, the increases over MC in root biomass were parallel to the overall fertility improvement, being greater with MB and WB than with PB. Differently, the survival rate of ginseng plants increased insignificantly with PB but significantly with WB (14%) and MB (21%), while ginseng root quality was unchanged with WB but improved with PB (32%) and MB (56%). For the rhizosphere at harvest following 3 years of growing, the total content of phenolic acids from root exudate decreased by 56, 35, and 45% with PB, WB, and MB, respectively, over MC. For the rhizosphere microbiome, total fungal and bacterial abundance both was unchanged under WB but significantly increased under MB (by 200 and 38%), respectively, over MC. At the phyla level, abundances of arbuscular mycorrhizal and Bryobacter as potentially beneficial microbes were elevated while those of Fusarium and Ilyonectria as potentially pathogenic microbes were reduced, with WB and MB over MC. Moreover, rhizosphere fungal network complexity was enhanced insignificantly under PB but significantly under WB moderately and MB greatly, over MC. Overall, maize biochar exerted a great impact rather on rhizosphere microbial community composition and networking of functional groups, particularly fungi, and thus plant defense than on soil fertility and root growth.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BackgroundSoil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.ResultsWe found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil’s previous fumigation exposure.ConclusionsThe legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

Cover crop usage for the sustainable management of soilborne diseases in woody ornamental nursery production system

Cover crops represent a potential tool for suppression of soil borne diseases in woody ornamental nursery production, which can cause significant economic losses. Field experiments were conducted in 2019 and 2020 to explore the effects of a cover crop and the timing of cover crop disturbance on soilborne disease suppression. Soils from red maple (Acer rubrum ‘October Glory’) plantations grown with or without a cover crop [crimson clover (Trifolium incarnatum)] were sampled following senescence of the cover crop. Greenhouse bioassays were conducted using red maple cuttings on inoculated (with Rhizoctonia solani, Phytopythium vexans or Phytophthora nicotianae) and non-inoculated field soils. Plant height, total and root fresh weight were measured, and the roots were assessed for disease severity on a 0 to 100% root damage scale. Pathogen recovery was assessed by culturing root pieces (~1 cm length) on oomycetes or Rhizoctonia semi-selective media. Soil samples were analyzed for organic matter, nitrogen, phosphorus, potassium, pH and Pseudomonad population count. A minimal effect of cover crop disturbance timing (late fall or early spring) was found on disease suppression. Cover crop usage reduced disease severity and pathogen recovery in red maple field soils. Plants grown in cover cropped soil had greater total, root and aboveground fresh weight compared with those from non-cover cropped soil, but plant height was not affected. Cover crops increased soil organic matter and total nitrogen in 2020. Pseudomonad populations were higher when cover crops were used. The results suggest that cover crops can reduce soilborne disease in woody ornamentals.

POTENTIAL USE OF ANIMAL MANURES IN MANAGING PHYTOPHTHORA WILT OF CHILLI CAUSED BY PHYTOPHTHORA CAPSICI

Phytophthora wilt of chilli, caused by Phytophthora capsici, is a major concern for many growers because an effective management method has not been identified yet. In agriculture, animal manures have primarily been focussed on the supply of nutrients to the crops but their use for suppression of soil borne diseases is not well investigated and understood. In this study, we examined the efficacy of five different animal manures (poultry, cattle, goat, pig and sheep) at four levels (1, 5, 10 and 20% volume/volume) added to potting mix for management of Phytophthora wilt of chilli. The preliminary study revealed that the quantity of 5 g per pot (500 mL) of P. capsici-colonised millet-seed inoculum was effective for the development of Phytophthora wilt in chilli seedlings grown in coir-based potting media. The main greenhouse experiments were conducted in randomised complete design with five replications. The results showed that all types of manures were effective in increasing the survival rate of chilli by reducing the incidence of Phytophthora wilt. In the first planting all manures caused at least two-fold increase in plant survival compared to the inoculated control. The chilli plant survival was much higher in the second planting when seedlings were planted after six week of incorporation of manures and seven weeks after inoculation of potting mix. Among manures, the highest plant survival percentage at the final assessment was found in pots amended with 20% v/v poultry manure in both the first (66%) and the second (86%) plantings. For sustainable and effective management of Phytophthora wilt of chilli, this study recommends application of poultry manure to growing media two months before planting of chilli seedlings.

Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments.

Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.

The soil-borne ultimatum, microbial biotechnology and sustainable agriculture.

The soil-borne ultimatum, microbial biotechnology and sustainable agriculture.

Effect of inorganic fertilizer application on soil microbial diversity in an oil palm plantation

Excessive fertilizer applications in oil palm plantations are conventionally done to increase the oil yield, but they result in high production cost and environmental pollution. There have been only separate reports on the effects of fertilizer application on soil physical, chemical characteristics, and microbial biodiversity. Therefore, this study was conducted to determine the correlation between soil characteristics and soil microbial biodiversity in oil palm plantation after long-term frequent chemical fertilizer application compared with secondary soil, using molecular methods of polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and MiSeq. Secondary forest soil was chosen as the control. The results showed that after 25 years of fertilizer application, the total nitrogen and organic carbon contents decreased from low to very low scale, indicating soil infertility condition. Reduction of Firmicutes was related to suppression of soil borne diseases, and Bacteroidetes which is an indicator of soil health were both almost eliminated after 25 years of fertilizer application. In conclusion, long-term inorganic fertilizer application reduced the soil nitrogen, and organic carbon, altered beneficial microbes in the soil.

Composted Chicken Manure for Anaerobic Soil Disinfestation Increased the Strawberry Yield and Shifted the Soil Microbial Communities

Anaerobic soil disinfestation (ASD), as a bio-fumigation technology, has been developed to control soil-borne pests. There is increasing evidence showing that carbon sources and cover tarps play an important role in the ASD suppression of soil-borne pests, but little is known about the effect of composted chicken manure (CCM) and totally impermeable films (TIF) against soil-borne pests in the strawberry production system. In experiments, the colonies of Fusarium spp. and Phytophthora spp., which are recognized to cause strawberry soil-borne diseases, decreased significantly after ASD. The soil promoted a significant increase in ammonium nitrogen, nitrate-nitrogen and organic matter, but a decrease in oxidation-reduction potential after ASD. Besides, the strawberry plant height, stem thickness and yield were significantly higher than in the non-amended soil. Compared to the untreated control, ASD, both at 6 and 12 ton/ha of CCM, significantly (p = 0.05) increased strawberry marketable yield and income. The economic benefit could be due to the suppression of soil-borne diseases and the improvement of soil nutrition. The soil bacterial and fungal diversity and richness increased after soil fumigation. The increased presence of biological control agents led to the suppression of soil-borne pathogens. In summary, ASD with CCM amendments could be applied in pre-plant fumigation to control strawberry soil-borne pests, strengthen soil fertility, improve crop yield and increase growers’ income.

Phenolic Acids Released in Maize Rhizosphere During Maize-Soybean Intercropping Inhibit Phytophthora Blight of Soybean.

Interspecies interactions play a key role in soil-borne disease suppression in intercropping systems. However, there are limited data on the underlying mechanisms of soil-borne Phytophthora disease suppression. Here, a field experiment confirmed the effects of maize and soybean intercropping on Phytophthora blight of soybean caused by Phytophthora sojae. Experimentally, the roots and root exudates of maize were found to attract P. sojae zoospores and inhibit their motility and the germination of cystospores. Furthermore, five phenolic acids (p-coumaric acid, cinnamic acid, p-hydroxybenzoic acid, vanillic acid, and ferulic acid) that were consistently identified in the root exudates and rhizosphere soil of maize were found to interfere with the infection behavior of P. sojae. Among them, cinnamic acid was associated with significant chemotaxis in zoospores, and p-coumaric acid and cinnamic acid showed strong antimicrobial activity against P. sojae. However, in the rhizosphere soil of soybean, only p-hydroxybenzoic acid, low concentrations of vanillic acid, and ferulic acid were identified. Importantly, the coexistence of five phenolic acids in the maize rhizosphere compared with three phenolic acids in the soybean rhizosphere showed strong synergistic antimicrobial activity against the infection behavior of P. sojae. In summary, the types and concentrations of phenolic acids in maize and soybean rhizosphere soils were found to be crucial factors for Phytophthora disease suppression in this intercropping system.

The diversity of volcanic soils: focusing on the function of aluminum–humus complexes

ABSTRACT Andosols (or Andisols) are the typical soils developed from volcanoclastic materials. They possess several distinctive properties that are rarely found in other groups of soils. These properties are largely due to the dominance of short-range ordered minerals (allophane, imogolite, and ferrihydrite) and/or mineral–humus complexes (Al/Fe–humus complexes). In this review, I survey the diversity of volcanic soils mainly from the viewpoint of the function of Al–humus complexes. Specific topics include the role of Al–humus complexes in organic carbon accumulation, Al solubility and kinetics, Al phytotoxicity to plants, and the suppression of soil-borne diseases. It is shown that Al–humus complexes are heavily involved in the diversity of these properties of volcanic soils.

The hidden potential of saprotrophic fungi in arable soil: Patterns of short-term stimulation by organic amendments

Saprotrophic fungi are abundant in soils of (semi-)natural ecosystems, where they play a major role in ecosystem functioning. On the contrary, saprotrophic fungal biomass is remarkably low in intensively managed soils and this can have a negative impact on soil functioning. Nevertheless, arable soils harbour a diverse pool of fungi, which can be stimulated by organic amendments. Management targeted towards increasing soil organic matter often coincides with an increase of fungal biomass, but it can take years before effects are seen. However, a rapid stimulation of fungal biomass at the start of the growing season could immediately benefit crop production, by improving nutrient availability, soil structure and suppression of soil-borne diseases. The objective of this study is to realize a rapid increase of saprotrophic fungal biomass with organic amendments. In controlled pot experiments, dried and milled organic materials of different quality were added to an arable sandy soil. Ergosterol-based fungal biomass and ITS2-based fungal community structure were measured over a period of two months. Wood sawdust of deciduous tree species and paper pulp resulted in a high and lasting increase of fungal biomass, as opposed to transient effects given by cover crops and other non-woody plant materials. Little or no stimulation of fungi was seen for coniferous wood sawdust and agro-industrial by-products. Nitrogen immobilization induced by sawdust and paper pulp was compensated by supplementing mineral nitrogen, which enhanced the stimulation of saprotrophic fungi. The composition of the stimulated fungi was influenced by the quality of organic amendments. In particular, deciduous wood sawdust and paper pulp favoured saprotrophic ascomycete fungi (mainly Sordariomycetes), with no increment in potential plant-pathogenic fungi. Overall, our results point at a good perspective to use woody materials as sustainable soil improver via stimulation of saprotrophic fungi.

The potential of endophytic fungi isolated from cucurbit plants for biocontrol of soilborne fungal diseases of cucumber

The ability of endophytic fungi isolated from cucurbit plants to suppress soilborne diseases and the relationship between antagonism and disease suppression were studied. In dual culture tests of 1044 strains of 90 genera and three pathogenic fungi, 47.1 % of the endophytic fungal strains showed antagonistic effects on at least one pathogen; 186 strains against Rhizoctonia solani, 371 strains against Sclerotinia sclerotiorum, and 403 strains against Fusarium oxysporum f. sp. cucumerinum. The main antagonistic type of the strains of one genus generally was identical to one pathogen. In the pot experiment of cucumber inoculated with R. solani and endophytic fungi, 74.3 % and 33.3 % of 288 strains showed control efficacy of more than 50 % and more than 80 % on cucumber Rhizoctonia root rot respectively. These strains were mostly distributed in Fusarium, Chaetomium, Colletotrichum and Acrocalymma. There were some differences in the proportion of strains with better disease suppressive effects between strain sources. No significant correlation existed between the disease suppression of a strain in vivo and its antagonism against the pathogen in vitro. Most growth-promoting strains had good suppressive effects on cucumber Rhizoctonia root rot. In this study, 82 endophytic fungal strains had good disease suppressive effects and no obvious adverse effects on cucumber growth, and 35 of them showed obvious growth-promoting effects, which suggested that endophytic fungi from cucurbit plants have excellent potential for plant disease control.

Microbial Network and Soil Properties Are Changed in Bacterial Wilt-Susceptible Soil.

Bacterial wilt disease is a devastating disease of crops, which leads to huge economic loss worldwide. It is hypothesized that the occurrence of bacterial wilt may be related to changes in soil chemical properties and microbial interactions. In this study, we compared the soil chemical properties and microbial network structures of a healthy soil (HS) and a bacterial wilt-susceptible soil (BWS). The contents of available nitrogen, potassium, and phosphorus and the soil pH in the BWS were significantly lower than those in the HS. BWS showed nutrient deficiency and acidification in comparison with the HS. The structure and composition of the BWS network were quite different from those of the HS network. The BWS network had fewer modules and edges and lower connectivity than the HS network. The HS network contained more interacting species, more key microorganisms, and better high-order organization and thus was more complex and stable than the BWS network. Most nodes and module memberships were unshared by the two networks, while the ones that were shared showed different topological roles. Some generalists in the HS network became specialists in the BWS network, indicating that the topological roles of microbes were changed and key microorganisms were shifted in the BWS. In summary, the composition and structure of the microbial network of the BWS were different from that of the HS. Many microbial network connections were missing in the BWS, which most likely provided conditions leading to higher rates of bacterial wilt disease.IMPORTANCE Bacterial wilt disease is caused by the pathogen Ralstonia solanacearum and is a widespread devastating soilborne disease leading to huge economic losses worldwide. The soil microbial community is crucial to the capacity of soils to suppress soilborne diseases through complex interactions. Network analysis can effectively explore these complex interactions. In this study, we used a random matrix theory (RMT)-based network approach to investigate the changes in microbial network and associated microbial interactions in a bacterial wilt-susceptible soil (BWS) in comparison to a healthy soil (HS). We found that the structure and composition of the microbial network in BWSs were quite different from those of the HS. The BWS network had fewer modules, edges, and key microorganisms and lower connectivity than the HS network. In the BWSs, apparently the topological role of microbes was changed and key microorganisms were shifted to specialists.

Effect of Brassica crop-based biofumigation on soilborne disease suppression in woody ornamentals

Soilborne diseases are the most economically important problem for ornamental nursery producers in the southeastern United States. The use of cover crops selected based on their biofumigant activity to improve soilborne disease management in woody ornamental production was assessed. Replicated pot bioassays were established as greenhouse trials in sterilized clay loam soil which had pre-existing populations of Rhizoctonia solani or Phytophthora nicotianae. Selected Brassica crops were seeded directly into the soil and flowering cover crops were incorporated 15 cm deep into the same pots and covered with polyethylene for 2 or 4 weeks. Volatile compounds released during the biofumigation process were collected at different time intervals. Soil type and moisture affected ITC release. Hydrangea or viburnum rooted cuttings were grown in the biofumigated (2 or 4 weeks) and non-biofumigated control pots and root rot disease severity was evaluated at the end of each bioassay. Yellow mustard (Sinapis alba, ‘White gold’), turnip (Brassica rapa, ‘Purple top forage’), arugula (Eruca vesicaria ssp. sativa, ‘Astro’), Mighty mustard (B. juncea, ‘Pacific gold’), rape (B. napus, ‘Dwarf essex’), mustard green (B. carinata, ‘Amara’) and brown mustard (B. juncea, ‘Kodiak’) cover crops were effective in suppressing R. solani and P. nicotianae. Similar disease suppression was observed whether biofumigation was performed for 2 or 4 weeks. Phytotoxicity was not observed on viburnum and hydrangea woody ornamental plants after either the 2 or 4 weeks biofumigation period with any of the tested cover crops. Viburnum and hydrangea grown in mustard green-, arugula- and turnip-incorporated soil had significantly higher whole plant and root fresh weights compared with the inoculated, non-biofumigated control plants. Although mustard green and arugula are not used currently as commercial biofumigation cover crops, they also showed promise for controlling soilborne pathogens of woody ornamental plants under greenhouse conditions.

Fengycin produced by Bacillus subtilis NCD-2 is involved in suppression of clubroot on Chinese cabbage

Clubroot, caused by the obligate parasite Plasmodiophora brassicae, is one of the most important diseases of Brassicaceae family. Bacillus spp. that produce lipopeptide antibiotics are often used as biocontrol agents to suppress soilborne diseases. B. subtilis NCD-2 isolated from the cotton rhizosphere has been found to inhibit pathogenic fungi through the production of fengycin-type cyclopeptides. In this study, the biocontrol efficacy of B. subtilis NCD-2 against P. brassicae and the role of fengycin in disease suppression were evaluated on Chinese cabbage in glasshouse. B. subtilis NCD-2 reduced clubroot disease incidence and severity up to 47.7% and 51.6%, respectively, while the fengycin defective mutant ΔfenC and a PhoP/PhoR two-component regulatory system mutant, ΔphoP, were unable to prevent this disease. In vitro, P. brassicae resting spore cells were lysed when treated with standard fengycin and crude fengycin extracts of the wild type B. subtilis NCD-2, but not of its mutant ΔfenC. Moreover, the population dynamics of B. subtilis and P. brassicae was determined using quantitative real-time PCR (qPCR). The results were surprising that the wild type B. subtilis NCD-2 and its mutant ΔfenC colonized at similar rates in the rhizosphere, while levels of P. brassicae DNA in the rhizosphere and root tissue were reduced following B. subtilis NCD-2 treatment, but there was no effect of the mutant ΔfenC. Thus, the production of fengycins in B. subtilis NCD-2 may play a promising role in the suppression of P. brassicae in the rhizosphere and reduction of incidence of clubroot disease in Chinese cabbage.

Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness

The microbiome of grassland soils provides ecosystem services essential to plant health and productivity, including nutrient cycling and suppression of soil-borne diseases. Understanding how soil management practices affect soil microbial communities will provide opportunities by which indigenous soil microbes and their functions can be managed to sustain or promote plant growth and enhance disease suppressiveness. Here, we investigated the impact of 20 years of plant residue management in a long-term grassland field trial on soil chemical and (micro)biological properties, in particular the suppression of damping-off disease of kale caused by the fungal root pathogen Rhizoctonia solani AG 2–1. Plant residue management led to significant variation in the community structure of the bacterial genus Pseudomonas between treatments. Soil organic matter quality (inferred carbon recalcitrance) was responsible for 80% of the observed variation in Pseudomonas community structure. Furthermore, increased Pseudomonas species diversity (Shannon's index), microbial activity, soil organic matter content, and carbon availability distinguished suppressive (low disease) soils from conducive (high disease) soils. More specifically, Pseudomonas species diversity and richness (Margalef's) were identified as the primary parameters explaining the greatest proportion (>30%) of variation in the disease suppressive capacity of soils across treatments. Collectively, our results suggest that management-induced shifts in Pseudomonas community composition, notably species diversity and richness, provide a better indicator of disease conduciveness for a broad-host range fungal pathogen than soil chemical parameters. In conclusion, our study indicates that frequent addition of organic residues to agricultural grassland soils enhances the diversity and activity of plant-beneficial bacterial taxa.