Efficacy of Bacterial Seed Treatments for Controlling Pythium Root Rot of Winter Wheat

Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural, or industrial settings, the organisms must be profiled at the species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760-nucleotide (nt) region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a 16-member Pseudomonas species mock community. All 16 species were correctly and semiquantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3-V4 amplicon sequencing only correctly identified one species. We analyzed the Pseudomonas profiles in 13 soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the 16S rRNA gene abundance, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and 10 from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD amplicon approach identified more species than were found by cultivation, including hard-to-culture nonfluorescent pseudomonads, as well as more than were found by 16S rRNA V3-V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large-scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method.

IMPORTANCE A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.

The Control of Panicle Blight Bacterial Pathogen on Rice Seeds Through In Vitro Treatments

Burkholderia glumae is a seed-borne pathogen of rice known to cause bacterial panicle blight disease. The lack of effective control methods makes seed treatment the alternative management approach. The aim of this research was to determine an effective seed treatments technique, using liquid smoke, clove oil, hot water and copper hydroxide fungicide treatment against bacteria B. glumae. The experiment used a complete randomized design with five treatments and three replications, including control, liquid smoke, clove oil, hot water, and copper hydroxide fungicide. The results showed the propensity for all treatments to reduce bacterial populations on rice seeds, while liquid smoke, clove oil, and fungicide did not reduce vigour and viability. Application of copper hydroxide fungicide 77% at concentration of 5% was recommended as the best treatment to control the bacterial pathogen. Keywords: Burkholderia glumae, clove oil, copper hydroxide fungicide, hot water, liquid smoke, rice

Harnessing Pseudomonas protegens to Control Bacterial Panicle Blight of Rice

Bacterial panicle blight of rice is a seedborne disease caused by the bacterium Burkholderia glumae. This disease has affected rice production worldwide and its effects are likely to become more devastating with the continuous increase in global temperatures, especially during the growing season. The bacterium can cause disease symptoms in different tissues and at different developmental stages. In reproductive stages, the bacterium interferes with grain development in the panicles and, as a result, directly affects rice yield. Currently, there are no methods to control the disease because chemical control is not effective and completely resistant cultivars are not available. Thus, a promising approach is the use of antagonistic microorganisms. In this work, we identified one strain of Pseudomonas protegens and one strain of B. cepacia with antimicrobial activity against B. glumae in vitro and in planta. We further characterized the antimicrobial activity of P. protegens and found that this activity is associated with bacterial secretions. Cell-free secretions from P. protegens inhibited the growth of B. glumae in vitro and also prevented B. glumae from causing disease in rice. Although the specific molecules associated with these activities have not been identified, these findings suggest that the secreted fractions from P. protegens could be harnessed as biopesticides to control bacterial panicle blight of rice.

Beneficial Bacteria Identified for the Control of Botrytis cinerea in Petunia Greenhouse Production

Botrytis cinerea infects most major greenhouse crops worldwide. With its increasing resistance to conventional fungicides and the movement of the greenhouse industry toward more sustainable production practices, alternative methods of control are needed. The objective of this study was to evaluate a collection of 60 bacterial strains through both a dual-culture assay and greenhouse trials to identify strains with biocontrol activity against B. cinerea. For the dual-culture assay, each bacterial strain was streaked on potato dextrose agar medium with B. cinerea. The B. cinerea growth reduction and the zone of inhibition were measured. Thirty-five strains reduced the growth of B. cinerea. All strains were also tested in an initial greenhouse trial in which Petunia × hybrida 'Carpet Red Bright' was sprayed and drenched with the bacteria biweekly for 6 weeks. All open flowers were tagged, and plants were inoculated with B. cinerea (1 × 10⁴ conidia per 1 ml). Disease severity indices calculated from the daily flower gray mold severity ratings of all tagged flowers were used to identify the seven top-performing strains. These seven strains were then evaluated in a greenhouse validation trial. The methods were similar to those of the initial greenhouse trials except that replicate numbers were increased. Three strains (Pseudomonas protegens AP54, Pseudomonas chlororaphis 14B11, and Pseudomonas fluorescens 89F1) were selected for the ability to reduce B. cinerea infection in a greenhouse production setting. These strains can be used in future studies to develop additional biocontrol products for the management of B. cinerea in floriculture crops.

Selection of an Endophytic Streptomyces sp. Strain DEF09 From Wheat Roots as a Biocontrol Agent Against Fusarium graminearum

Selection of biological control agents (BCA) profits from an integrated study of the tripartite interactions occurring among the BCA, the plant and the pathogen. The environment plays a crucial role in the efficacy of BCA, therefore, the selection process shall utmost mimic naturally occurring conditions. To identify effective biocontrol strains against Fusarium graminearum, the major cause of Fusarium head blight (FHB) in wheat and deoxynivalenol (DON) accumulation in grains, a workflow consisting of in vitro and in vivo assays was set up. Twenty-one Streptomyces strains, 16 of which were endophytes of different plants, were analyzed. In vitro and in vivo tests characterized their plant growth promoting (PGP) traits. Biocontrol activity against F. graminearum was firstly assessed with a dual culture assay. An in vivo germination blotter assay measured Fusarium foot rot and root rot symptoms (FFR-FRR) reduction as well as growth parameters of the plant treated with the Streptomyces strains. A selected subset of Streptomyces spp. strains was then assessed in a growth chamber measuring FFR symptoms and growth parameters of the wheat plant. The approach led to the identification of an effective Streptomyces sp. strain, DEF09, able to inhibit FHB on wheat in controlled conditions by blocking the spread of the pathogen at the infection site. The results were further confirmed in field conditions on both bread and durum wheat, where DEF09 decreased disease severity up to 60%. This work confirms that FRR and FFR pathosystems can be used to identify BCA effective against FHB.

From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms

Any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. Microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. This paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. In addition, we review some of the most effective microbial products on the market today, explore the reasons for their success and outline some of the major challenges involved in industrial production and commercialization of beneficial strains for widespread agricultural application. General processes associated with commercializing viable microbial products are discussed in two broad categories, biofertility inoculants and biocontrol products. Specifically, we address what farmers desire in potential microbial products, how mode of action informs decisions on product applications, the influence of variation in laboratory and field study data, challenges with scaling for mass production, and the importance of consistent efficacy, product stability and quality. In order to make a significant impact on global sustainable agriculture, the implementation of plant beneficial microorganisms will require a more seamless transition between laboratory and farm application. Early attention to the challenges presented here will improve the likelihood of developing effective microbial products to improve crop yields, decrease disease severity, and help to feed an increasingly hungry planet.

Effect of indigenous mycobiota on ochratoxin A production by Aspergillus carbonarius isolated from soil: ochratoxin in mixed cultures

This study determined the biotic interaction between 30 non-toxigenic indigenous strains of Aspergillus niger aggregate, Aspergillus flavus, Trichoderma spp., Mucor spp., Cladosporium spp., Ulocladium spp., Curvularia spp., Absidia spp., Geotrichum spp. and Acremonium spp., isolated from soil destined for maize crops, with respect to their ability to prevent ochratoxin A (OTA) production by A. carbonarius on "in vitro" assay, on liquid and solid medium. OTA production was completely inhibited when A. carbonarius was inoculated in a interactive mixed culture with all A. niger aggregate strains assayed, a 80 % of Trichoderma spp. strains, a 40 % of Cladosporium spp. strains, Acremonium spp and Geotrichum spp; only one strain of A. flavus tested was able to completely inhibit the mycotoxin accumulation. OTA production increased when A. carbonarius ACS 8 was growing on liquid interactive mixed culture with Mucor spp strains. These results demonstrated that OTA production by Aspergillua carbonarius strain was significantly influenced by the presence of different non-toxigenic fungal strains when growing together on paired cultures.

In vitro antagonists of Rhizoctonia solani tested on lettuce: rhizosphere competence, biocontrol efficiency and rhizosphere microbial community response

The rhizosphere competence of 15 in vitro antagonists of Rhizoctonia solani was determined 4 weeks after sowing inoculated lettuce seeds into nonsterile soil. Based on the colonization ability determined by selective plating, eight strains were selected for growth chamber experiments to determine their efficacy in controlling bottom rot caused by R. solani on lettuce. Although in the first experiment all antagonists colonized the rhizosphere of lettuce with CFU counts above 2 x 10(6) g(-1) of root fresh weight, only four isolates significantly reduced disease severity. In subsequent experiments involving these four antagonists, only Pseudomonas jessenii RU47 showed effective and consistent disease suppression. Plate counts and denaturing gradient gel electrophoresis (DGGE) fingerprints of Pseudomonas-specific gacA genes amplified from total community DNA confirmed that RU47 established as the dominant Pseudomonas population in the rhizosphere of inoculated lettuce plants. Furthermore, the DGGE fingerprint revealed that R. solani AG1-IB inoculation severely affected the bacterial and fungal community structure in the rhizosphere of lettuce and that these effects were much less pronounced in the presence of RU47. Although the exact mechanism of antagonistic activity and the ecology of RU47 remain to be further explored, our results suggest that RU47 is a promising agent to control bottom rot of lettuce.

Biological interactions to select biocontrol agents against toxigenic strains of Aspergillus flavus and Fusarium verticillioides from maize

Biological control represent an alternative to the use of pesticides in crop protection. A key to progress in biological control to protect maize against Fusarium verticillioides and Aspergillus flavus maize pathogens are, to select in vitro, the best agent to be applied in the field. The aim of this study was to examine the antagonistic activity of bacterial and yeast isolates against F.verticillioides and A. flavus toxigenic strains. The first study showed the impact of Bacillus amyloliquefaciens BA-S13, Microbacterium oleovorans DMS 16091, Enterobacter hormomaechei EM-562T, and Kluyveromyces spp. L14 and L16 isolates on mycelial growth of two strains of A. flavus MPVPA 2092, 2094 and three strains of F. verticillioides MPVPA 285, 289, and 294 on 3% maize meal extract agar at different water activities (0.99, 0.97, 0.95, and 0.93). From this first assay antagonistics isolates M. oleovorans, B. amyloliquefaciens and Kluyveromyces sp. (L16) produced an increase of lag phase of growth and decreased a growth rate of all fungal strains. These isolates were selected for futher studies. In vitro non-rhizospheric maize soil (centrally and sprayed inoculated) and in vitro maize (ears apex and base inoculated) were treated with antagonistics and pathogenic strains alone in co-inoculated cultures. Bacillus amyloliquefaciens significantly reduced F. verticillioides and A. flavus count in maize soil inoculated centrally. Kluyveromyces sp. L16 reduced F. verticillioides and A. flavus count in maize soil inoculated by spray. Kluyveromyces sp. L16 was the most effective treatment limiting percent infections by F. verticillioides on the maize ears.

Commercialization and implementation of biocontrol

Although the number of biocontrol products is increasing, these products still represent only about 1% of agricultural chemical sales. Yet these are important contributions because biocontrol agents offer disease management alternatives with different mechanisms of action than chemical pesticides. Trends in research include the increased use of biorational screening processes to identify microorganisms with potential for biocontrol, increased testing under semicommercial and commercial production conditions, increased emphasis on combining biocontrol strains with each other and with other control methods, integrating biocontrol into an overall system.

Screening procedures for selecting rhizobacteria with biocontrol effects upon Fusarium verticillioides growth and fumonisin B1 production

Screening is a critical step in the discovery of microbial agents that can exert biological control of Fusarium verticillioides at the root level. The objectives of this research were to determine the utility of a niche overlap index to realise the first screening of maize rhizobacterial isolates during different water activities. Studies were conducted to evaluate various methods for second screening with different modes of action. The antifungal activity of bacterial isolates through antibiosis assay was checked and the influence of different isolates on Fusarium verticilliodes growth and fumonisin B(1) was studied. Eleven competitive rhizobacterial isolates (Arthrobacter globiformis RC1, Azotobacter armeniacus RC2, A. armeniacus RC3, A. globiformis RC4, A. globiformis RC5, A. armeniacus RC6, Pseudomonas solanacearum RC7, Bacillus subtilis RC8, B. subtilis RC9, P. solanacearum RC10, B. subtilis RC11) were selected for the studies which followed. All bacteria were able to utilise the widest range of carbon sources and showed the highest niche overlap indices at the water activities tested. All bacterial antagonists reduced fumonisin B(1) production at all levels tested. Isolates belonging to Pseudomonas and Bacillus genera significantly inhibited fumonisin B(1) production, which ranged between 70 and 100%. Also, A. armeniacus RC2 caused important fumonisin B(1) reduction. The results of the present work suggest that A. armeniacus RC2, A. armeniacus RC3, B. subtilis RC8, B. subtilis RC9, B. subtilis RC11, P. solanacearum RC7, and P. solanacearum RC10 could have practical value in the control of F. verticillioides root colonisation. This paper is part of an on-going study to determine their application at the field level.

Evaluation of Adapted Wheat Cultivars for Tolerance to Pythium Root Rot

Genetic resistance in wheat (Triticum aestivum) against Pythium species would be an efficient means of control of this major root fungal pathogen, but so far no source has been identified. In addition, no long-term, sustainable options for controlling Pythium root rot are available; therefore, identifying and then incorporating genetic resistance into wheat cultivars would create an ideal method of control for this disease. The objective of this study was to examine the level of tolerance to Pythium root rot among a diverse set of wheat germ plasm collected from all major wheat production regions in the United States. Pythium debaryanum isolate 90136 and P. ultimum isolate 90038, previously identified as the most virulent Pythium isolates on wheat, were used to infest pasteurized soil, which was seeded with wheat genotypes and placed in a growth chamber maintained at a constant 16°C with a 12-h photoperiod and ambient humidity. Length of the first leaf and plant height measurements were recorded, and roots were digitally scanned to create computer files that were analyzed using WinRhizo software for length and number of tips. Significant (P < 0.05) differences in plant variables were detected among wheat genotypes in the presence of both Pythium species, and a significant (P < 0.0001) correlation between plant stunting and root loss was detected. Based on both shoot and root measurements, Caledonia, Chinese Spring, MN97695, and OR942504 appear to be highly susceptible to Pythium root rot, whereas genotypes KS93U161, OH708, and Sunco were the most tolerant to this disease.

Transformation of soil microbial community structure and rhizoctonia-suppressive potential in response to apple roots

ABSTRACT Changes in the composition of soil microbial communities and relative disease-suppressive ability of resident microflora in response to apple cultivation were assessed in orchard soils from a site possessing trees established for 1 to 5 years. The fungal community from roots of apple seedlings grown in noncultivated orchard soil was dominated by isolates from genera commonly considered saprophytic. Plant-pathogenic fungi in the genera Phytophthora, Pythium, and Rhizoctonia constituted an increasing proportion of the fungal community isolated from seedling roots with increasing orchard block age. Bacillus megaterium and Burkholderia cepacia dominated the bacterial communities recovered from noncultivated soil and the rhizosphere of apple seedlings grown in orchard soil, respectively. Populations of the two bacteria in their respective habitats declined dramatically with increasing orchard block age. Lesion nematode populations did not differ among soil and root samples from orchard blocks of different ages. Similar changes in microbial communities were observed in response to planting noncultivated orchard soil to five successive cycles of 'Gala' apple seedlings. Pasteurization of soil had no effect on apple growth in noncultivated soil but significantly enhanced apple growth in third-year orchard block soil. Seedlings grown in pasteurized soil from the third-year orchard block were equal in size to those grown in noncultivated soil, demonstrating that suppression of plant growth resulted from changes in the composition of the soil microbial community. Rhizoctonia solani anastomosis group 5 (AG 5) had no effect on growth of apple trees in noncultivated soil but significantly reduced the growth of apple trees in soil from third-year orchard soil. Changes in the ability of the resident soil microflora to suppress R. solani AG 5 were associated with reductions in the relative populations of Burkholderia cepacia and Pseudomonas putida in the rhizosphere of apple.