Control of soil-borne pathogens with living bacteria and fungi: Status and outlook

Efficacy of Streptomyces murinus JKTJ-3 in Suppression of Pythium Damping-Off of Watermelon

Damping-off caused by Pythium aphanidermatum (Pa) is one of the most destructive diseases for watermelon seedlings. Application of biological control agents against Pa has attracted the attention of many researchers for a long time. In this study, the actinomycetous isolate JKTJ-3 with strong and broad-spectrum antifungal activity was screened from 23 bacterial isolates. Based on the morphological, cultural, physiological, and biochemical characteristics as well as the feature of 16S rDNA sequence, isolate JKTJ-3 was identified as Streptomyces murinus. We investigated the biocontrol efficacy of isolate JKTJ-3 and its metabolites. The results revealed that seed and substrate treatments with JKTJ-3 cultures showed a significant inhibitory effect on watermelon damping-off disease. Seed treatment with the JKTJ-3 cultural filtrates (CF) displayed higher control efficacy compared to the fermentation cultures (FC). Treatment of the seeding substrate with the wheat grain cultures (WGC) of JKTJ-3 exhibited better control efficacy than that of the seeding substrate with the JKTJ-3 CF. Moreover, the JKTJ-3 WGC showed the preventive effect on suppression of the disease, and the efficacy increased with increase in the inoculation interval between the WGC and Pa. Production of the antifungal metabolite actinomycin D by isolate JKTJ-3 and cell-wall-degrading enzymes such as β-1,3-glucanase and chitosanase were probably the mechanisms for effective control of watermelon damping-off. It was shown for the first time that S. murinus can produce anti-oomycete substances including chitinase and actinomycin D. This is the first report about S. murinus used as biocontrol agent against watermelon damping-off caused by Pa.

Caffeic Acid in Tobacco Root Exudate Defends Tobacco Plants From Infection by Ralstonia solanacearum

In rhizospheres, chemical barrier-forming natural compounds play a key role in preventing pathogenic bacteria from infecting plant roots. Here, we sought to identify specific phenolic exudates in tobacco (Nicotiana tobaccum) plants infected by the soil-borne pathogen Ralstonia solanacearum that may exhibit antibacterial activity and promote plant resistance against pathogens. Among detected phenolic acids, only caffeic acid was significantly induced in infected plants by R. solanacearum relative to healthy plants, and the concentration of caffeic acid reached 1.95 μg/mL. In vivo, caffeic acid at 200 μg/mL was highly active against R. solanacearum and obviously damaged the membrane structure of the R. solanacearum cells, resulting in the thinning of the cell membrane and irregular cavities in cells. Moreover, caffeic acid significantly inhibited biofilm formation by repressing the expression of the lecM and epsE genes. In vitro, caffeic acid could effectively activate phenylalanine ammonia-lyase (PAL) and peroxidase (POD) and promote the accumulation of lignin and hydroxyproline. In pot and field experiments, exogenous applications of caffeic acid significantly reduced and delayed the incidence of tobacco bacterial wilt. Taken together, all these results suggest that caffeic acid played a crucial role in defending against R. solanacearum infection and was a potential and effective antibacterial agent for controlling bacterial wilt.

Evaluation of the Antibacterial Effects and Mechanism of Action of Protocatechualdehyde against Ralstonia solanacearum

Protocatechualdehyde (PCA) is an important plant-derived natural product that has been associated with a wide variety of biological activities and has been widely used in medicine as an antioxidant, anti-aging and an anti-inflammatory agent. However, fewer reports concerning its antibacterial effects on plant-pathogenic bacteria exist. Therefore, in this study, protocatechualdehyde was evaluated for its antibacterial activity against plant pathogens along with the mechanism of its antibacterial action. PCA at 40 μg/mL was highly active against R. solanacearum and significantly inhibited its growth. The minimum bactericidal concentration and minimum inhibitory concentration values for PCA were 40 μg/mL and 20 μg/mL, respectively. Further investigation of the mechanism of action of PCA via transmission electron microscopy and biological assays indicated that the destruction of the cell structure, the shapes and the inhibition of biofilm formation were important. In addition, the application of PCA effectively reduced the incidence of bacterial wilt on tobacco under greenhouse conditions, and the control efficiency was as high as 92.01% at nine days after inoculation. Taken together, these findings suggest that PCA exhibits strong antibacterial activity against R. solanacearum and has the potential to be applied as an effective antibacterial agent for controlling bacterial wilt caused by R. solanacearum.

Characterization of novel Trichoderma spp. isolates as a search for effective biocontrollers of fungal diseases of economically important crops in Argentina

Monoconidial cultures of 33 isolates of Trichoderma from Buenos Aires Province, Argentina were characterized on the basis of twenty eight morphological, physiological and biochemical features. All of them were screened for proteinase, endochitinase and β-1,3 glucanase activity. Universally primed PCR (UP-PCR) and inter-simple sequence repeat (ISSR) techniques were used to examine the genetic variability among isolates, which resulted in 127 bands for the total number of isolates. These results were subjected to numerical analysis revealing 20 haplotypes grouped in five clusters. The ability of Trichoderma isolates to antogonize soil-borne fungal plant pathogens using a dual culture assay was done against five fungal species: Alternaria sp., Bipolaris sorokiniana, Fusarium graminearum, F. solani, and Pyricularia oryzae. The highest inhibition values (85% RI) were obtained against B. sorokiniana and P. oryzae. Three isolates of T. harzianum named as FCCT2, FCCT3 and FCCT9 were capable of causing a high growth inhibition on four of the fungal species assayed, which was in agreement with their higher extracellular hydrolytic activity. Our results suggest that these isolates have the potential to be effective agents for biocontrol of cereal and tomato fungal pathogens.

Citrus compost and its water extract for cultivation of melon plants in greenhouse nurseries. Evaluation of nutriactive and biocontrol effects

Two different types of citrus composts, and their water extracts, were tested with regard to their utilisations as partial substitutes for peat in growing media for melon seedlings in greenhouse nurseries. Both compost showed higher plant growth than peat. Compost composed by citrus waste and green residue (C2) showed greater plant growth than compost obtained from the same organic matrices mentioned above further the addition of sludge obtained from citrus industry (C1). Compost C2 showed a greater auxinic effect than C1 and it was the only one that showed cytokinic effect. Both composts also demonstrated a biocontrol effect against Fusarium oxysporum for melon plants: the effects were also higher in C2 than in C1. Higher number of isolated fungi was active against F. oxysporum in compost C2, than compost C1. No different bacterial biocontrol efficacy was observed between both composts. The water extracts of both composts gave lower plant yields than their solid matrices, their relative effects being similar to those of the solid composts (C2 extract gave higher plant yields than the extract from C1). The biocontrol effects of compost water extracts followed the same trend.

Effect of Repetitive Applications of the Biocontrol Bacterium Pseudomonas putida 06909-rif/nal on Citrus Soil Microbial Communities

ABSTRACT The effects of repetitive applications of Pseudomonas putida 06909-rif/nal on the resident microbial communities within a citrus orchard were studied with fatty acid methyl-ester (FAME) profiles and ribosomal intergenic spacer analysis. The data set from FAME was large and very complex, requiring 23 factors from principal component analysis to explain 91% of variability in the data. Spatial and temporal effects on variation within microbial communities were much greater than the effects of either yearly applications of Pseudomonas putida 06909-rif/nal, weekly repetitive applications of Pseudomonas putida 06909-rif/nal, or yearly applications of the fungicide metalaxyl and the nematicide phenamiphos. Multivariate analysis of covariance showed much of the variability between treatments could be accounted for by populations of Pseudomonas putida 06909-rif/nal. Soil fatty acids that showed significant changes between treatments were not related to fatty acids found in Pseudomonas putida 06909-rif/nal, suggesting applications of Pseudomonas putida 06909-rif/nal altered the soil microbial community.

Repetitive Applications of the Biocontrol Agent Pseudomonas putida 06909-rif/nal and Effects on Populations of Phytophthora parasitica in Citrus Orchards

ABSTRACT Pseudomonas putida 06909-rif/nal was applied repetitively during the irrigation season in two citrus orchards over 3 years. In a mature (50-yearold) commercial citrus orchard covering 2.02 ha, weekly applications of Pseudomonas putida 06909-rif/nal with an in-field fermentor resulted in soil populations that fluctuated between 2.83 log CFU + 1 per g of soil and 4.35 log CFU + 1 per g of soil. Resulting rhizosphere populations of Phytophthora parasitica were significantly reduced in 1999 but not 1997 or 1998. In a newly planted citrus orchard, yearly applications of Pseudomonas putida 06909-rif/nal at the beginning of the irrigation season resulted in high soil populations of Pseudomonas putida 06909-rif/nal that declined rapidly and never reduced the rhizosphere populations of Phytophthora parasitica. When Pseudomonas putida 06909-rif/nal was applied weekly, soil populations increased throughout the 1997 and 1998 irrigation seasons, reaching a maximum in 1998 and remained high throughout the 1999 irrigation season. Rhizosphere populations of Phytophthora parasitica were significantly reduced in 1998. Yearly applications of the fungicide metalaxyl and the nematicide phenamiphos reduced rhizosphere populations of Phytophthora parasitica in 1997 but not in 1998 or 1999. Pseudomonas putida 06909-rif/nal was uniformly distributed throughout the soil profile to a depth of 75 cm in both yearly and weekly applications. When applied through low-volume minisprinklers, Pseudomonas putida 06909-rif/nal was found in aerosols up to 3 m away.

Biological control of cucumber and sugar beet damping-off caused by Pythium ultimum with bacterial and fungal antagonists

AIMS

Five bacterial strains belonging to Bacillus subtilis, Pseudomonas fluorescens and Ps. corrugata and two fungal strains belonging to Trichoderma viride and Gliocladium virens were evaluated for their efficacy in controlling sugar beet and cucumber damping-off caused by Pythium ultimum.

METHODS AND RESULTS

The in vitro antagonistic activity of bacteria against various Pythium spp. was evaluated with dual cultures in various media. Pseudomonas strains inhibited the pathogen better than Bacillus strains. To identify potentially useful antagonist combinations, dual compatibility of antagonists was also evaluated, based on growth in two liquid media containing substrate previously used by other antagonists. Four pairs of bacteria were selected. Sugar beet damping-off biocontrol was attempted with bacterial seed treatments (individually and in pairs). Cucumber damping-off biocontrol was attempted with bacterial seed treatments and bacterial and fungal compost treatments. In sugar beet, satisfactory biocontrol was only achieved with Pseudomonas antagonists. Antagonist combinations did not show any superior biocontrol ability to individual antagonists and compatibility of bacteria in vitro did not correlate with compatibility in vivo. Bacterial seed treatments and fungal compost treatments failed to control cucumber damping-off. Better biocontrol in cucumber was achieved when bacterial antagonists were applied by drenching or by coating seed with bacteria in a peat carrier.

CONCLUSIONS

Pseudomonas antagonists were superior to Bacillus antagonists in controlling damping-off in cucumber and sugar beet. Pseudomonas peat inocula maintained a good shelf-life 2 years after preparation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Pseudomonas peat formulations have the potential for development into commercial biopesticides.

Evaluation of Continuous Application Technology for Delivery of the Biocontrol Agent Pseudomonas putida 06909-rif/nal

We evaluated a commercial field fermentor as a means of culturing and delivering a bacterial biocontrol agent, Pseudomonas putida 06909-rif/nal, through irrigation water. There was no evidence of contamination in 12-hour cultures produced by the fermentor. It produced 120 liters of inoculum at 5 × 10⁸ CFU/ml after 12-hour fermentations, allowing two applications per day. Dilutions up to 1:100,000 of inoculum of P. putida 06909-rif/nal produced by the fermentor allowed the biocontrol agent to effectively colonize soil in greenhouse trials. Bacteria produced in 19-hour fermentations colonized soil better than bacteria produced in 12-hour fermentations. Ten repetitive applications of P. putida 06909-rif/nal yielded soil population levels similar to those from a single application at 10-fold greater concentrations. Repetitive applications of lower concentrations may be a cost-effective method for delivering bacterial biocontrol agents to large acreages. This work suggests that the commercial field fermentor would be a viable instrument for delivering bacterial biocontrol agents for commercial-scale field applications.

Overproduction of an inducible extracellular serine protease improves biological control of Pythium ultimum by Stenotrophomonas maltophilia strain W81

Stenotrophomonas maltophilia W81 can protect sugar beet against PYTHIUM:-mediated damping-off disease through the production of an extracellular protease. Here, the proteolytic enzyme of W81 was purified by anion-exchange chromatography and characterized as a serine protease. The purified enzyme was fungicidal against PYTHIUM: ultimum in vitro. Its synthesis was inducible by casein in W81, and mutagenesis of this strain using the luciferase (luxAB) reporter transposon Tn5-764cd resulted in the isolation of two mutant derivatives (W81M3 and W81M4) capable of producing significantly increased levels of extracellular protease in the presence of casein. Strain W81M4 also exhibited increased chitinolytic activity. The luxAB fusions in strains W81M3 and W81M4 were highly expressed in the absence of casein but not in its presence, suggesting that the corresponding loci were involved in down-regulating extracellular protease production. Extracellular protease production in the W81 wild-type strain and protease overproduction in mutants W81M3 and W81M4 were also induced in the presence of the autoclaved fungal mycelium. In soil microcosms naturally infested by PYTHIUM: spp., inoculation of sugar beet seeds with W81M3 or W81M4 resulted in improved biocontrol of PYTHIUM:-mediated damping-off disease compared with W81, and the level of protection achieved was equivalent to that conferred by chemical fungicides. The wild-type W81 and its mutant derivatives did not differ in rhizosphere colonization. Therefore, the improved biocontrol ability of W81M3 and W81M4 resulted from their capacity to overproduce extracellular serine protease.

Plants genetically modified to produce N-acylhomoserine lactones communicate with bacteria

N-acylhomoserine lactones (AHLs) play a critical role in plant/microbe interactions. The AHL, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL), induces exoenzymes that degrade the plant cell wall by the pathogenic bacterium Erwinia carotovora. Conversely, the antifungal activity of the biocontrol bacterium Pseudomonas aureofaciens 30-84 is due (at least in part) to phenazine antibiotics whose synthesis is regulated by N-hexanoylhomoserine lactone (HHL). Targeting the product of an AHL synthase gene (yenI) from Yersinia enterocolitica to the chloroplasts of transgenic tobacco plants caused the synthesis in plants of the cognate AHL signaling molecules (OHHL and HHL). The AHLs produced by the transgenic plants were sufficient to induce target gene expression in several recombinant bacterial AHL biosensors and to restore biocontrol activity to an HHL-deficient P. aureofaciens strain. In addition, pathogenicity was restored to an E. carotovora strain rendered avirulent as a consequence of a mutation in the OHHL synthase gene, carI. The ability to generate bacterial quorum-sensing signaling molecules in the plant offers novel opportunities for disease control and for manipulating plant/microbe interactions.

Characterization of genes involved in biosynthesis of a novel antibiotic from Burkholderia cepacia BC11 and their role in biological control of Rhizoctonia solani

Genetic manipulation of fluorescent pseudomonads has provided major insight into their production of antifungal molecules and their role in biological control of plant disease. Burkholderia cepacia also produces antifungal activities, but its biological control activity is much less well characterized, in part due to difficulties in applying genetic tools. Here we report genetic and biochemical characterization of a soil isolate of B. cepacia relating to its production of an unusual antibiotic that is very active against a variety of soil fungi. Purification and preliminary structural analyses suggest that this antibiotic (called AFC-BC11) is a novel lipopeptide associated largely with the cell membrane. Analysis of conditions for optimal production of AFC-BC11 indicated stringent environmental regulation of its synthesis. Furthermore, we show that production of AFC-BC11 is largely responsible for the ability of B. cepacia BC11 to effectively control the damping-off of cotton caused by the fungal pathogen Rhizoctonia solani in a gnotobiotic system. Using Tn5 mutagenesis, we identified, cloned, and characterized a region of the genome of strain BC11 that is required for production of this antifungal metabolite. DNA sequence analysis suggested that this region encodes proteins directly involved in the production of a nonribosomally synthesized lipopeptide.

Biological control of Pythium ultimum by Stenotrophomonas maltophilia W81 is mediated by an extracellular proteolytic activity

Stenotrophomonas maltophilia strain W81, isolated from the rhizosphere of field-grown sugar beet, produced the extracellular enzymes chitinase and protease and inhibited the growth of the phytopathogenic fungus Pythium ultimum in vitro. The role of these lytic enzymes in the interaction between W81 and P. ultimum was investigated using Tn5 insertion mutants of W81 incapable of producing extracellular protease (W81M1), extracellular chitinase (W81M2) or the two enzymes (W81A1). Lytic enzyme activity was restored in W81A1 following introduction of a 15 kb cosmid-borne fragment of W81 genomic DNA. Incubation of P. ultimum in the presence of commercial purified protease or cell-free supernatants from cultures of wild-type W81, the chitinase-negative mutant W81M2 or the complemented derivative W81A1 (pCU800) resulted in hyphal lysis and loss of subsequent fungal growth ability once re-inoculated onto fresh plates. In contrast, commercial purified chitinase or cell-free supernatants from cultures of the protease-negative mutant WS1M1 or the chitinase- and protease-negative mutant W81A1 had no effect on integrity of the essentially chitin-free Pythium mycelium, and did not prevent subsequent growth of the fungus. In soil microcosms containing soil naturally infested by Pythium spp., strains W81, W81M2 and W81A1(pCU800) reduced the ability of Pythium spp. to colonize the seeds of sugar beet and improved plant emergence compared with the untreated control, whereas W81A1 and W21M1 failed to protect sugar beet from damping-off. Wild-type W81 and its mutant derivatives colonized the rhizosphere of sugar beet to similar extents, it was concluded that the ability of S. maltophilia W81 to protect sugar beet from Pythium -mediated damping-off was due to the production of an extracellular protease.

A full factorial analysis of nine factors influencing in vitro antagonistic screens for potential biocontrol agents

The effect of nine factors on the outcome of classic in vitro screens testing the antagonistic action of endophytic bacterial isolates from grape vines against virulent Agrobacterium vitis has been examined. These factors were (i) the strain of A. vitis, (ii) the strain of endophyte, (iii) the growth medium of the pathogen, (iv) the growth medium of the endophyte, (v) the temperature of growth of the pathogen, (vi) the temperature of growth of the endophyte, (vii) the pH of growth of the pathogen, (viii) the pH of growth of the endophyte, and (ix) the medium of the assay plate. Analyses of variance of the full factorial design incorporating main effects and two- and three-way interactions accounted for 66% of the variance. All nine factors had a significant effect on the diameter of inhibition zones (p < 0.001). An examination of the three-way interactions revealed that generalizations were difficult to draw; each target agrobacterium had a specific response to a given antagonistic isolate. It was possible to determine that the growth history of bacterial strains, before they were administered to an assay plate to test for antagonism (especially the composition of the growth medium and the temperature of growth), had a profound effect on the outcome of the test. Generally the more chemically defined media produced less inhibition whereas the lower growth temperature of 15 degrees C produced more inhibition. These findings could be relevant to in situ inhibitory activity. The method used to conduct the inhibitory screen (order of strain application and the medium of the assay plate) had a profound influence on the results. These influences add to the caution necessary in the use of in vitro antagonistic screens for finding successful biocontrol agents.