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Applied and Environmental Microbiology, June 2003, p. 3333-3343, Vol. 69, No. 6
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.6.3333-3343.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Tennessee 37996,1 Swiss Federal Research Station for Fruit, Wine, and Vegetable Production, Wädenswil, Switzerland CH-8820,2 Cereal Root Disease and Biological Control Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington 991643
Received 30 August 2002/ Accepted 10 March 2003
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The first objective of this study was to identify edaphic parameters that influenced, positively or negatively, the biocontrol activity of P. fluorescens. As a model, we selected biocontrol of take-all disease of wheat using P. fluorescens strain 2-79. Take-all, caused by the ascomycetous fungus Gaeumannomyces graminis var. tritici, is an important root and crown rot disease of wheat worldwide, particularly in relatively moist regions or under irrigation (5). Strain 2-79 was isolated from wheat roots grown in a take-all decline soil, one that develops natural disease suppressiveness after long-term wheat monoculture. Intensive study since the early 1980s has demonstrated that 2-79 aggressively colonizes wheat roots (43) and suppresses take-all disease in the field (46). However, as is typical for many biocontrol agents, the effectiveness of 2-79 in the field varies from location to location (45). Our second objective was to compare the effect of soil properties on the biocontrol activity of strains derived from 2-79, which differed in their ability to produce the antibiotic phenazine-1-carboxylate (PCA). In previous studies with 2-79, genetic analysis indicated that production of PCA in the rhizosphere is a primary mechanism of biocontrol accounting for up to 90% of disease suppression (38, 39, 40, 41), with other antifungal factors, including a fluorescent siderophore and anthranilic acid, making minor contributions to biocontrol activity (12). However, in other biocontrol systems, such as suppression of Fusarium wilts with fluorescent pseudomonads, siderophore-mediated iron competition in low-iron environments is an effective mechanism of disease control (22). Although a PCA-deficient, anthranilate-producing mutant (FM13) of the biocontrol strain P. aeruginosa PNA1 was not as effective as the parental strain in suppression of Fusarium wilt of chickpea, it was as effective as the wild-type strain in biocontrol of Pythium damping-off of bean (1). Our rationale for including several derivatives of 2-79 was to determine if the reduced effectiveness against take-all of mutants that could not produce PCA that was observed in previous studies would occur over a range of different soils. Our third objective was to determine if our insight regarding soil properties had practical applications for improving biocontrol. To do this we amended soil with zinc or organic matter, soil factors that were identified in our study as favorable and unfavorable for disease suppression, respectively, by strain 2-79.
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TABLE 1. P. fluorescens 2-79 and derivatives
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Pathogen inoculum.
G. graminis var. tritici (isolates R3-111a-1 and SCS) was prepared as described previously (10, 26) on autoclave-sterilized whole oat kernels (250 g of oats and 250 ml of deionized water per liter flask, 4 weeks in light at 21 to 25°C). Colonized oat grains were air dried, ground in a blender, and sieved. Particles of 0.25 to 0.5 mm were collected for use as inoculum. A mixture of the two virulent isolates of G. graminis var. tritici was used to minimize possible effects from differential sensitivity of the pathogen to the biocontrol agent (23).
Soils.
Ten soils representative of those in the wheat-growing region of the Pacific Northwest were included in this study. Quincy fine loamy sand and Larkin, Palouse, Puget, Ritzville, Thatuna, Walla Walla, and Woodburn silt loams were collected from sites in the state of Washington state near Pasco, Rockford, Pullman, Mt. Vernon, Lind, and Pullman and sites in Oregon near Pendleton and Corvallis, respectively. Shano silt loams were collected from two distinct sites in Washington state, Quincy and Moses Lake. For each soil, 28 chemical and physical characteristics were determined by the University of Idaho Soil Testing Laboratory, Moscow (Table 2). Soils were collected from the upper 30 cm of the profile, sieved (2.0-mm-pore-size mesh), steam treated (1 h at 95°C), and air dried on a bench top at room temperature before use. The take-all pathogen is sensitive to antagonism by a wide range of soil microorganisms (48); thus, soils were steamed to "normalize" the impact of biotic factors on take-all disease among the 10 soils tested.
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TABLE 2. Chemical and physical properties of soils
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The take-all suppression assay was arranged as a 10 x 8 factorial in a split-plot design with 10 soil treatments (main plot) and eight seed treatments (MC-treated control, 2-79RN10, and six mutant derivatives) (subplot). Each treatment was replicated five times with 20 seedlings per replicate. The main effects of soil and seed treatment and the interaction were analyzed for significance with the general linear models procedure of SAS (Statistical Analysis Systems Institute, Cary, N.C.). Significant effects were further analyzed with Fisher's-protected least-significant-difference test at P = 0.05.
Identification of soil properties involved in biocontrol of take-all.
Correlations between the 28 soil parameters measured and the disease suppressiveness of P. fluorescens 2-79 derivatives were determined using the SAS correlation procedure. Previously three metabolites (PCA, fluorescent siderophore, and anthranilic acid) were shown to have a role in the biocontrol activity of 2-79 (12). For this reason, data for derivatives with common phenotypes (i.e., all PCA+, all PCA- and siderophore+, and all PCA- and siderophore- were grouped for the analysis. Due to the primary role of PCA in biocontrol of take-all by 2-79 (12, 38), the relationship between the group of PCA+ derivatives and key soil factors correlated with their biocontrol activity was further analyzed using principal component factor (PCF) analysis with varimax rotation procedure of SAS. This analysis is an investigative tool useful for identifying patterns of interrelated variables with the aim of selecting a reduced number of variables for further study (19). Soil properties interrelated to take-all disease rating were selected with a preliminary PCF analysis. The selected properties were included in a final analysis to develop the principal component solution that best explained the covariance among take-all disease rating and the soil properties. Loading values greater than or equal to the absolute value of 0.35 indicated significant interrelationships among variables within a principal component. The number of soil properties influencing biocontrol by PCA+ strains was further narrowed using the step-wise regression analysis procedure of SAS to identify a model that included the least number of soil properties and that best described variation in disease rating (Cp statistic closest to the number of variables included in the model) (25).
Effect of soil amendments with zinc and organic matter on take-all severity and biocontrol.
The effects of zinc and organic matter amendments were evaluated in separate experiments. To determine the impact of zinc on biocontrol by 2-79RN10, Woodburn silt loam, the soil with the lowest natural level of zinc (Table 2), was sieved (2-mm-pore-size mesh), steam treated (1 h at 95°C), and air dried on a bench top at room temperature prior to addition of zinc amendments. Zinc was added as Zn-EDTA at 15 and 50 µg of zinc-EDTA/g of soil, based on soil dry weight. Control soil received no zinc amendment. Prior to filling plastic tubes, zinc-EDTA treatments were mixed with water and added to soil for a final soil moisture content of 20%. Water was added also to the control soil for a final soil moisture content of 20%. Seeds treated with 2-79RN10, 2-79-59.34, or MC were planted into pathogen-infested soil and evaluated for severity of take-all disease in tube assays as described above.
To determine the effect of organic matter on biocontrol by 2-79RN10, dried nontreated wheat straw collected from the field was ground in a blender, sieved (2-mm-pore-size mesh), and added to Ritzville and Shano (from Moses Lake, Wash.) silt loams, two soils with low organic matter content (Table 2). Separate experiments were conducted for each soil. Wheat straw was added to the soils at 1.25, 2.5, 5, and 10% (wt/wt) based on soil dry weight. The wheat straw-amended and control soils (no wheat straw added) were sieved (2-mm-pore-size mesh), treated with steam (1 h at 95°C), and air dried on a bench top at room temperature. Three seed treatments (MC, 2-79RN10, and 2-79.59.34) were planted into soil infested with G. graminis var. tritici and evaluated for take-all disease in tube assays as previously described.
Amendment experiments were arranged in a split-plot design with soil amendment as the main plot and seed treatment as the subplot. There were six replicates per treatment with 12 seedlings per replicate for the organic matter tests and five replicates per treatment with 18 seedlings per replicate for the zinc experiment. Disease severity was assessed as described above for the take-all suppression assay. Main effects and interactions were analyzed for significance with the SAS general linear models procedure. Significant effects of qualitative factors were further analyzed with a means comparison test (Fisher's protected least-significant-difference test at P values of
0.05), while significant effects of quantitative factors were evaluated with single-degree-of-freedom orthogonal polynomials.
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FIG. 1. Effect of seed treatment on take-all disease rating of wheat when data from all 10 soils were pooled. Disease was rated 3 weeks after planting on a scale of 0 to 8 (24). The effect of seed treatment was significant at a P value of 0.0001. Bars with the same letters are not significantly different according to a Fisher's protected least-significant-difference test at a P value of 0.05.
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FIG. 2. Effect of the interaction between soil and seed treatment on take-all disease rating. The soil-seed treatment interaction was significant (P 0.0001), and further analysis was performed on the response to soil. Within each soil (Larkin silt loam [A], Palouse silt loam [B], Puget silt loam [C], Quincy fine loamy sand [D], Ritzville silt loam [E], Shano silt loam #1 [F], Shano silt loam #2 [G], Thatuna silt loam [H], Walla Walla silt loam [I], and Woodburn silt loam [J]), bars with the same letter are not significantly different according to Fisher's protected least-significant-difference test at P = 0.05.
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TABLE 3. Correlations between soil properties and disease rating of plants treated with P. fluorescens 2-79RN10 and derivatives grouped by common phenotype
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Three linear combinations (termed principal components) were responsible for 87% of the covariation among soil properties and disease rating in the final PCF analysis (Table 4). Component 1 had a significant negative loading value for disease rating (-0.71), indicating that disease rating was deemphasized in Component 1. Conversely, component 2 had a significant positive loading (0.63) for disease rating, suggesting that disease rating is emphasized in this component. The loading value for disease rating was not significant (less than the absolute value of 0.35) for component 3 (Table 4).
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TABLE 4. Principal component factor analysis (varimax rotation) of disease rating of wheat treated with Phz+ derivatives of P. fluorescens 2-79 and soil propertiesa
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Regression analysis of soil characteristics associated with biocontrol of take-all by phenazine-producing strains.
The 16 soil properties identified with PCF analysis were further analyzed with step-wise least-squares regression. A model was identified (R2 = 0.96; Cp = 6.17) that included six key soil properties: ammonium-nitrogen, cation exchange capacity, iron, percent silt, soil pH, and zinc, to explain the variance in take-all disease rating of wheat treated with P. fluorescens 2-79RN10 and its PCA-producing derivatives.
Interactions among soil properties.
In addition to the influence of various soil properties selected by PCF analysis on take-all biocontrol, there were significant correlations among the selected soil properties. Correlations among soil properties are well known. For example, among the six soil properties identified by the regression model, cation exchange capacity was positively correlated with iron and percent silt and negatively correlated with soil pH and zinc (Table 5). Iron was positively correlated with percent silt and negatively correlated with soil pH. Percent silt was negatively correlated with soil pH and zinc, while ammonium-nitrogen was positively correlated with zinc.
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TABLE 5. Correlation coefficients among selected soil properties correlated with disease suppression by Phz+ strains of P. fluorescens 2-79a
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FIG. 3. Influence of organic matter amendment (percentage of wheat straw [wt/wt]) on biocontrol activity of 2-79 in Ritzville silt loam, which is normally low in organic matter (0.93% [Table 2]). (A) Values are the mean ± standard error. Within each seed treatment, each amendment treatment was compared with the 0% control using single-degree-of-freedom orthogonal contrasts. Significant differences are indicated by *, **, ***, and **** at P values of 0.05, 0.01, 0.001, and 0.0001, respectively. (B) Within each rate of organic matter amendment, bars with the same letter are not significantly different according to Fisher's protected least-significant-difference test at a P value of 0.05.
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FIG. 4. Influence of organic matter amendment (percentage of wheat straw [wt/wt]) on biocontrol activity of 2-79 in Shano silt loam #1, which is normally low in organic matter (1.13% [Table 2]). (A) Values are the mean ± standard error. Within each seed treatment, each amendment treatment was compared with the 0% control using single-degree-of-freedom orthogonal contrasts. Significant differences are indicated by *, **, ***, and **** at P values of 0.05, 0.01, 0.001, and 0.0001, respectively. (B) Within each rate of organic matter amendment, bars with the same letter are not significantly different according to Fisher's protected least-significant-difference test at P values of 0.05.
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FIG. 5. Influence of zinc amendment (Zn-EDTA, micrograms per gram of soil) on biocontrol activity of 2-79 in a low-zinc soil (Woodburn silt loam [Table 2]). (A) Values are the mean ± standard error. Within each seed treatment, each amendment treatment was compared with the 0% control using single-degree-of-freedom orthogonal contrasts. Significant differences are indicated by double asterisks at a P value of 0.01. (B) Within each rate of zinc amendment, bars with the same letter are not significantly different according to Fisher's protected least-significant-difference test at a P value of 0.05.
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Variability in biocontrol performance of P. fluorescens 2-79 in field studies has been reported numerous times (45). Although there are several factors that may impact biological control of root diseases, the influence of the abiotic soil environment is clearly significant. In the present study, under controlled conditions (pathogen density, photoperiod, soil moisture, and temperature), we investigated biocontrol of take-all by PCA-producing 2-79RN10 strains in 10 soils. Using interpretational multivariate PCF analysis, we identified soil properties that positively or negatively influenced take-all disease of wheat seedlings in the presence of PCA-producing strains. It is important to note that the soils studied were not deficient in any of the micro- and macroelements evaluated; the soils were steam treated to remove the influence of indigenous microflora and nontarget root pathogens; and soil properties were not significantly correlated with the take-all disease rating of seedlings treated with the MC sticker only (no bacteria).
We identified a negative interrelationship between ammonium-nitrogen, sulfate-sulfur, sodium (extractable and soluble), zinc, percent sand, soil pH, and take-all severity of plants treated with PCA-producing derivatives of 2-79 in the 10 soils. In contrast, cation exchange capacity, exchangeable acidity, percent silt, percent clay, percent organic matter, manganese, iron, and percent total carbon were positively interrelated with take-all severity in the presence of PCA-producing derivatives. In the final PCF analysis, a three-component solution, which included 16 soil properties, accounted for 87% of the variation in disease rating of wheat treated with the PCA-producing derivatives of 2-79. A regression model was developed that included the six soil variables, ammonium-nitrogen, cation exchange capacity, iron, percent silt, soil pH, and zinc, to explain the variance in take-all disease rating of wheat treated with P. fluorescens 2-79RN10 and its PCA-producing derivatives. Amendment studies with both organic matter and zinc further confirmed their negative and positive influence, respectively, on biocontrol of take-all with PCA-producing 2-79RN10 derivatives.
Some of the soil factors that we identified as having a significant influence on biocontrol of take-all by P. fluorescens 2-79 have been examined in earlier studies. For example, it is well known that ammonium forms of nitrogen can reduce the severity of take-all (3, 17, 24). Absorption of ammonium-nitrogen by wheat roots leads to excretion of corresponding H+ ions (33) and a corresponding reduction in rhizosphere pH (36). In slightly acidic to alkaline soils, suppression of take-all has been attributed to the combined effect of direct inhibition of ectotrophic hyphal growth of G. graminis var. tritici by low pH of the wheat root surface and to specific antagonism by fluorescent pseudomonads in the rhizosphere (34, 35). The decrease in rhizosphere pH associated with ammonium nitrogen also increases the availability of micronutrients, such as manganese (18), to the wheat plant, which is known to influence host susceptibility to take-all (16, 18).
The direct effect of pH on PCA accumulation by 2-79 was tested in liquid fermentation culture by Slininger and Shea-Wilbur (30). Production of PCA was diminished at pHs less than 6, optimal at pH 6 to 7, and declining at pH 7 to 8. In our previous study on the effects of in vitro and in situ pH on inhibition of G. graminis var. tritici by 2-79RN10, inhibition of hyphal growth by 2-79RN10 in vitro was least at pH 4.9 to 5.8, greatest at pH 6.0 to 6.6, and intermediate at pH 6.8 to 8.0 (26). However, in situ, 2-79RN10 significantly reduced take-all in a Ritzville silt loam adjusted to a range of pH values (4.9 to 8.0). In our present study, the pH of the 10 soils ranged from 5.17 to 8.53, and a decrease in pH was associated with an increased disease rating (diminished disease suppression).
In experiments on the effects of minerals on PCA production by P fluorescens 2-79 in defined liquid medium, PCA production increased as the concentration of zinc sulfate increased (29, 32). Accumulation of PCA in culture was maximal when a combination of high zinc sulfate (75 µM) and low iron sulfate (36 µM) was added. In the present study, both sulfate-sulfur and zinc were positively associated, while iron was negatively associated, with take-all suppression in soil in the presence of PCA-producing strains. The influence of zinc was further supported by our studies on zinc amendments to a Woodburn silt loam. Increased zinc had no effect on disease of seedlings treated with the MC sticker only, but take-all was significantly reduced in seedlings treated with PCA-producing 2-79RN10 strains in soil with the highest rate (50 µg of EDTA-Zn/g of soil) of zinc amendment.
Organic matter content and the amount and type of clay are the main factors that influence cation exchange capacity in soil. Clay and humus provide a large surface area with surface charges to which ions and water are attracted. These surfaces are the centers of activity for chemical reactions and nutrient exchange. In our study, CEC and percentages of clay and organic matter were negatively associated with disease suppression by PCA-producing 2-79 derivatives. To examine effects related to CEC, we manipulated organic matter content in two soils. As suggested by the PCF analysis, increasing the percentage of organic matter led to a corresponding decrease in suppression of disease by 2-79RN10 PCA producers in both soils. The bacteria were ineffective in suppressing take-all at higher rates of organic matter amendment (2.5% and above). At the highest rates, 10% in Ritzville silt loam and 5 and 10% in Shano silt loam, failure in biological control was partially due to an increase in disease because take-all was more severe in the "no bacteria" control at high rates of organic matter amendment. The mechanism(s) by which organic matter reduces biocontrol activity of strain 2-79 is a topic of future interest because there is increasing interest in the Pacific Northwest in direct seeding of wheat, which results in accumulation of straw in the field compared to conventionally cultivated fields.
The question remains of how these soil characteristics influence biocontrol activity by PCA-producing 2-79. Factors such as zinc availability and pH could act directly by enhancing production of PCA, while the negative influence of clay, organic matter, and CEC could be related to binding and inactivating PCA, or by adsorbing nutrients needed by the bacteria to effect biocontrol. Potential indirect effects of soil factors on biocontrol of root diseases are numerous. For example, soil factors are known to influence root colonization and survival of bacteria in natural soil (2, 4). Our study also underscores the need for a more complex analysis of the relative role of biocontrol mechanisms. In our study, PCA production was the primary mechanism responsible for take-all suppression by 2-79 in the 10 soils; however, it is possible that in other soil environments, such as those with low iron, mechanisms such as siderophores have a more important role than previously concluded (12). Besides their direct role in sequestering iron and other metals, siderophores may indirectly stimulate biosynthesis of other secondary metabolites involved in biocontrol by increasing the availability of these minerals to the producing bacteria (39). Antibiotics and siderophores may also function to induce local and systemic host resistance (21).
No soil factors were significantly interrelated with take-all severity of nonbacterized seedlings in our study, and there was a sufficiency of macro- and micronutrients in the 10 soils evaluated. However, soil factors can affect susceptibility of the host by altering host plant nutrition (15). Applications of NaCl and other Cl salts to soil infested with Rhizoctonia solani increased plant tissue levels of Cl and Mn and the subsequent yield of table beets (11). G. graminis var. tritici can reduce the availability of Mn in the rhizosphere of wheat through oxidation. Under Mn-deficient conditions, photosynthesis is reduced, metabolism of nitrogen is inefficient, and plant defense reactions against pathogens are limited (16). In the rhizosphere of wheat, biocontrol strains of Bacillus subtilis reduced Mn4+ to Mn2+, thus making it more available to the wheat plant. Corresponding decreases in take-all severity and increases in yield were reported with these bacteria (16). In contrast, P. fluorescens 2-79 can reduce and oxidize manganese (16). Bacteria that can do both may increase disease severity under conditions in which they oxidize Mn in the rhizosphere, thus decreasing availability to the plant. Alternatively, such bacteria may decrease disease if conditions favor Mn reduction, thus increasing its availability to the plant (15). In the present study, Mn was negatively correlated with disease suppression by 2-79; this may be related to the ability of 2-79 to either oxidize or reduce Mn under different soil conditions.
The interaction between a plant pathogen and a biocontrol agent (8) can be influenced by soil properties. Fusaric acid produced by the phytopathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici acts as a repressor of antibiotic production by the biocontrol bacterium P. fluorescens CHA0. In hydroponics culturing of tomatoes, addition of Zn reduced fusaric acid production by the pathogen. A concomitant increase in the antibiotic 2,4-diacetylphloroglucinol by CHA0 was reported, and biocontrol was improved (8). The aggressiveness of phytopathogens also can be affected by soil factors. Penetration of wheat roots by G. graminis var. tritici was greatly reduced when there was a sufficiency of Mn available to plant roots, compared to Mn-deficient conditions (49).
In addition to the many potential impacts of soil factors on a biocontrol system, there is potential for an indirect impact of interactions between factors. For example, soil pH plays an important role in the availability of various macro- and micronutrients. Soil properties that appear to influence disease suppression may not be directly related to biocontrol but may be associated due to strong correlations with other soil factors that are directly related to biocontrol by 2-79.
A practical application of this study and our previous report in which soil factors associated with take-all suppression by the fungal agent Trichoderma koningii were identified (10) is that it will provide a basis for customizing biological control treatments against take-all in different soil environments. This could be accomplished by targeting biocontrol agents for sites with favorable soil environments in which they can be expected to perform optimally or by developing formulations with mineral amendments that enhance biocontrol, as shown with zinc and 2-79. Through studies with liquid fermentation culture of 2-79, Slininger and colleagues (31) have developed formulations encapsulated on wheat seed that have improved viability, reduced phytotoxicity, and enhanced take-all suppression. Identification of soil factors that influence biological control will provide a biological basis for improved integration of biological controls with cultural practices that manipulate soil properties, with an aim toward improved disease control. The influence of soil factors on biological control is also an argument in support of incorporating a variety of biocontrol mechanisms in inoculants, perhaps through combinations of compatible organisms (27).
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