Agroecological factors correlated to soil DNA concentrations of Rhizoctonia in dryland wheat production zones of Washington state, USA

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.

Population Dynamics of Wheat Root Pathogens Under Different Tillage Systems in Northeast Oregon

No-till or direct seeding can be described as seeding directly into the crop stubble from the previous season without use of tillage. A reduction in tillage can result in many benefits, including increased soil organic matter, increased water holding capacity, and reduced fuel costs. However, the effect of no-till and reduced tillage on crop root disease profiles is poorly understood. To study the effect of tillage on disease dynamics, soil samples were collected from commercial wheat fields representing a wide range of tillage strategies in fall 2016 and fall 2017. Because precipitation might affect soilborne diseases, wheat fields located across a diverse gradient of precipitation zones of the dryland Pacific Northwest were selected. Fusarium spp., Pythium spp., and Rhizoctonia spp. were quantified from soil samples using soil dilution plating and quantitative PCR (qPCR) assays. Results of dilution plating showed that the colony counts of Fusarium, Pythium, and Rhizoctonia at the genus level were negatively associated with tillage. However, the same patterns were not observed when specific causal agents of Fusarium, Pythium, and Rhizoctonia that are known to be pathogenic on wheat were quantified with qPCR. Furthermore, precipitation affected the population density of some fungal pathogens (F. culmorum, P. ultimum, and R. solani AG 8). Within the scope of inference of this study, results of this study indicate that the benefits of adopting reduced tillage likely outweigh potential risk for increased root disease.

Antagonistic Activity of Chilean Strains of Pseudomonas protegens Against Fungi Causing Crown and Root Rot of Wheat (Triticum aestivum L.)

Seed treatments with antagonistic bacteria could reduce the severity of crown and root rot diseases in wheat crops. The objective of this study was to evaluate the potential antagonistic activity of a bacterial consortium of three Chilean strains of Pseudomonas protegens against the wheat crown and root rot pathogens Gaeumannomyces graminis var. tritici, Rhizoctonia cerealis, and Fusarium culmorum. Two field experiments were carried out on artificially infested soil during two consecutive seasons (2016-2017 and 2017-2018) in an Andisol soil of southern Chile. Control treatments (not inoculated with fungi) were also included. Each treatment included a seed treatment of spring wheat cv. Pantera-INIA with and without the bacterial consortium. Both phytosanitary damage (incidence and severity) and agronomic components were evaluated. Bacterial populations with the phlD+ gene in the wheat plant rhizosphere during anthesis state (Z6) were also quantified. In both seasons, infection severity decreased by an average of 16.8% in seeds treated with P. protegens consortium, while yield components such as spikes m^-1 and number of grains per spike increased. The use of antagonistic bacteria resulted in a total yield increase only during the first experimental season (P < 0.05). In general, accumulated rainfall influenced the antagonistic effect of the consortium of P. protegens strains, accounting for the differences observed between the two seasons. The results suggest that this P. protegens consortium applied on seeds can promote plant growth and protect wheat crops against crown and root rot pathogens in Southern Chile under field conditions.

Pseudomonas synxantha 2-79 Transformed with Pyrrolnitrin Biosynthesis Genes Has Improved Biocontrol Activity Against Soilborne Pathogens of Wheat and Canola

A four-gene operon (prnABCD) from Pseudomonas protegens Pf-5 encoding the biosynthesis of the antibiotic pyrronitrin was introduced into P. synxantha (formerly P. fluorescens) 2-79, an aggressive root colonizer of both dryland and irrigated wheat roots that naturally produces the antibiotic phenazine-1-carboxylic acid and suppresses both take-all and Rhizoctonia root rot of wheat. Recombinant strains ZHW15 and ZHW25 produced both antibiotics and maintained population sizes in the rhizosphere of wheat that were comparable to those of strain 2-79. The recombinant strains inhibited in vitro the wheat pathogens Rhizoctonia solani anastomosis group 8 (AG-8) and AG-2-1, Gaeumannomyces graminis var. tritici, Sclerotinia sclerotiorum, Fusarium culmorum, and F. pseudograminearum significantly more than did strain 2-79. Both the wild-type and recombinant strains were equally inhibitory of Pythium ultimum. When applied as a seed treatment, the recombinant strains suppressed take-all, Rhizoctonia root rot of wheat, and Rhizoctonia root and stem rot of canola significantly better than did wild-type strain 2-79.

Sensitivity of Rhizoctonia Isolates to Phenazine-1-Carboxylic Acid and Biological Control by Phenazine-Producing Pseudomonas spp

Rhizoctonia solani anastomosis groups (AG)-8 and AG-2-1 and R. oryzae are ubiquitous in cereal-based cropping systems of the Columbia Plateau of the Inland Pacific Northwest and commonly infect wheat. AG-8 and R. oryzae, causal agents of Rhizoctonia root rot and bare patch, are most commonly found in fields in the low-precipitation zone, whereas R. solani AG-2-1 is much less virulent on wheat and is distributed in fields throughout the low-, intermediate-, and high-precipitation zones. Fluorescent Pseudomonas spp. that produce the antibiotic phenazine-1-carboxylic acid (PCA) also are abundant in the rhizosphere of crops grown in the low-precipitation zone but their broader geographic distribution and effect on populations of Rhizoctonia is unknown. To address these questions, we surveyed the distribution of PCA producers (Phz⁺) in 59 fields in cereal-based cropping systems throughout the Columbia Plateau. Phz⁺ Pseudomonas spp. were detected in 37 of 59 samples and comprised from 0 to 12.5% of the total culturable heterotrophic aerobic rhizosphere bacteria. The frequency with which individual plants were colonized by Phz⁺ pseudomonads ranged from 0 to 100%. High and moderate colonization frequencies of Phz⁺ pseudomonads were associated with roots from fields located in the driest areas whereas only moderate and low colonization frequencies were associated with crops where higher annual precipitation occurs. Thus, the geographic distribution of Phz⁺ pseudomonads overlaps closely with the distribution of R. solani AG-8 but not with that of R. oryzae or R. solani AG-2-1. Moreover, linear regression analysis demonstrated a highly significant inverse relationship between annual precipitation and the frequency of rhizospheres colonized by Phz⁺ pseudomonads. Phz⁺ pseudomonads representative of the four major indigenous species (P. aridus, P. cerealis, P. orientalis, and P. synxantha) suppressed Rhizoctonia root rot of wheat when applied as seed treatments. In vitro, mean 50% effective dose values for isolates of AG-8 and AG-2-1 from fields with high and low frequencies of phenazine producers did not differ significantly, nor was there a correlation between virulence of an isolate and sensitivity to PCA, resulting in rejection of the hypothesis that tolerance in Rhizoctonia spp. to PCA develops in nature upon exposure to Phz⁺ pseudomonads.

iTRAQ-based proteomic analysis of defence responses triggered by the necrotrophic pathogen Rhizoctonia solani in cotton

The soil-borne necrotrophic pathogen fungus Rhizoctonia solani is destructive, causing disease in various important crops. To date, little is known about the host defence mechanism in response to invasion of R. solani. Here, an iTRAQ-based proteomic analysis was employed to investigate pathogen-responsive proteins in the disease tolerant/resistant cotton cultivar CRI35. A total of 174 differentially accumulated proteins (DAPs) were identified after inoculation of cotton plants with R. solani. Functional categorization analysis indicated that these DAPs can be divided into 12 subclasses. Notably, a large portion of DAPs are known to function in reactive oxygen species (ROS) metabolism and the expression of several histone-modifying and DNA methylating proteins were significantly induced upon challenge with the fungus, indicating that the redox homeostasis and epigenetic regulation are important for cotton defence against the pathogen. Additionally, the expression of proteins involved in phenylpropanoid biosynthesis was markedly changed in response to pathogen invasion, which may reflect a particular contribution of secondary metabolism in protection against the fungal attack in cotton. Together, our results indicate that the defence response of cotton plants to R. solani infection is active and multifaceted and involves the induction of proteins from various innate immunity-related pathways.

SIGNIFICANCE

Cotton damping-off is a destructive disease caused by the necrotrophic fungus Rhizoctonia solani. To date, the host defence mechanism involved in the disease protection remains largely unknown. Here, we reported the first proteomic analysis on cotton immune responses against R. solani infection. Employing iTRAQ technique, we obtained a total of 174 differentially accumulated proteins (DAPs) that can be classified into 12 functional groups. Further analysis indicated that ROS homeostasis, epigenetic regulation and phenylpropanoid biosynthesis were tightly associated with the innate immune responses against R. solani infection in cotton. The obtained data provide not only important information for understanding the molecular mechanism involved in plant-R. solani interaction but also application clues for genetic breeding of crops with improved R. solani resistance.

Rapid Quantification of Soilborne Pathogen Communities in Wheat-Based Long-Term Field Experiments

Rainfed experiments operated continuously for up to 84 years in semiarid eastern Oregon are among the oldest agronomic trials in North America. Disease incidence and severity had been quantified visually but quantification of inoculum density had not been attempted. Natural inoculum of 17 fungal and nematode pathogens were quantified for each of 2 years on eight trials using DNA extracts from soil. Crop type, tillage, rotation, soil fertility, year, and their interactions had large effects on the pathogens. Fusarium culmorum and Pratylenchus thornei were more dominant than F. pseudograminearum and P. neglectus where spring crops were grown, and the opposite species dominances occurred where winter wheat was the only crop. Bipolaris sorokiniana and Phoma pinodella were restricted to the presence of spring cereals and pulse crops, respectively. Helgardia spp. occurred in winter wheat-fallow rotations but not in annual winter wheat. Gaeumannomyces graminis var. tritici was more prevalent in cultivated than noncultivated soils and the opposite generally occurred for Rhizoctonia solani AG-8. Densities of Pythium spp. clade F were high but were also influenced by treatments. Significant treatment effects and interactions were more prevalent in two long-standing (>50-year) annually cropped experiments (29%) than two long-standing 2-year wheat-fallow rotations (14%). Associations among pathogens occurred mostly in an 84-year-old annual cereals experiment. This survey provided guidance for research on dynamics of root-infecting pathogens of rainfed field crops and identified two pathogens (Drechslera tritici-repentis and P. pinodella) not previously identified at the location.

Molecular Characterization, Morphological Characteristics, Virulence, and Geographic Distribution of Rhizoctonia spp. in Washington State

Rhizoctonia root rot and bare patch, caused by Rhizoctonia solani anastomosis group (AG)-8 and R. oryzae, are chronic and important yield-limiting diseases of wheat and barley in the Inland Pacific Northwest (PNW) of the United States. Major gaps remain in our understanding of the epidemiology of these diseases, in part because multiple Rhizoctonia AGs and species can be isolated from the same cereal roots from the field, contributing to the challenge of identifying the causal agents correctly. In this study, a collection totaling 498 isolates of Rhizoctonia was assembled from surveys conducted from 2000 to 2009, 2010, and 2011 over a wide range of cereal production fields throughout Washington State in the PNW. To determine the identity of the isolates, PCR with AG- or species-specific primers and/or DNA sequence analysis of the internal transcribed spacers was performed. R. solani AG-2-1, AG-8, AG-10, AG-3, AG-4, and AG-11 comprised 157 (32%), 70 (14%), 21 (4%), 20 (4%), 1 (0.2%), and 1 (0.2%), respectively, of the total isolates. AG-I-like binucleate Rhizoctonia sp. comprised 44 (9%) of the total; and 53 (11%), 80 (16%), and 51 (10%) were identified as R. oryzae genotypes I, II, and III, respectively. Isolates of AG-2-1, the dominant Rhizoctonia, occurred in all six agronomic zones defined by annual precipitation and temperature within the region sampled. Isolates of AG-8 also were cosmopolitan in their distribution but the frequency of isolation varied among years, and they were most abundant in zones of low and moderate precipitation. R. oryzae was cosmopolitan, and collectively the three genotypes comprised 37% of the isolates. Only isolates of R. solani AG-8 and R. oryzae genotypes II and III (but not genotype I) caused symptoms typically associated with Rhizoctonia root rot and bare patch of wheat. Isolates of AG-2-1 caused only mild root rot and AG-I-like binucleate isolates and members of groups AG-3, AG-4, and AG-11 showed only slight or no discoloration of the roots. However, all isolates of AG-2-1 caused severe damping-off of canola, resulting in 100% mortality. Isolates of Rhizoctonia AG-8, AG-2-1, AG-10, AG-I-like binucleate Rhizoctonia, and R. oryzae genotypes I, II, and III could be distinguished by colony morphology on potato dextrose agar, by PCR with specific primers, or by the type and severity of disease on wheat and canola seedlings, and results of these approaches correlated completely. Based on cultured isolates, we also identified the geographic distribution of all of these Rhizoctonia isolates in cereal-based production systems throughout Washington State.

Predicting Cereal Root Disease in Western Australia Using Soil DNA and Environmental Parameters

Root diseases have long been prevalent in Australian grain-growing regions, and most management decisions to reduce the risk of yield loss need to be implemented before the crop is sown. The levels of pathogens that cause the major root diseases can be measured using DNA-based services such as PreDicta B. Although these pathogens are often studied individually, in the field they often occur as mixed populations and their combined effect on crop production is likely to vary across diverse cropping environments. A 3-year survey was conducted covering most cropping regions in Western Australia, utilizing PreDicta B to determine soilborne pathogen levels and visual assessments to score root health and incidence of individual crop root diseases caused by the major root pathogens, including Rhizoctonia solani (anastomosis group [AG]-8), Gaeumannomyces graminis var. tritici (take-all), Fusarium pseudograminearum, and Pratylenchus spp. (root-lesion nematodes) on wheat roots for 115, 50, and 94 fields during 2010, 2011, and 2012, respectively. A predictive model was developed for root health utilizing autumn and summer rainfall and soil temperature parameters. The model showed that pathogen DNA explained 16, 5, and 2% of the variation in root health whereas environmental parameters explained 22, 11, and 1% of the variation in 2010, 2011, and 2012, respectively. Results showed that R. solani AG-8 soil pathogen DNA, environmental soil temperature, and rainfall parameters explained most of the variation in the root health. This research shows that interactions between environment and pathogen levels before seeding can be utilized in predictive models to improve assessment of risk from root diseases to assist growers to plan more profitable cropping programs.