R. James Cook

Bacillus sp. L324-92 for biological control of three root diseases of wheat grown with reduced tillage.

ABSTRACT Strain L324-92 is a novel Bacillus sp. with biological activity against three root diseases of wheat, namely take-all caused by Gaeumannomyces graminis var. tritici, Rhizoctonia root rot caused by Rhizoctonia solani AG8, and Pythium root rot caused mainly by Pythium irregulare and P. ultimum, that exhibits broad-spectrum inhibitory activity and grows at temperatures from 4 to 40 degrees C. These three root diseases are major yieldlimiting factors for wheat in the U.S. Inland Pacific Northwest, especially wheat direct-drilled into the residue of a previous cereal crop. Strain L324-92 was selected from among approximately 2,000 rhizosphere/rhizoplane isolates of Bacillus species isolated from roots of wheat collected from two eastern Washington wheat fields that had long histories of wheat. Roots were washed, heat-treated (80 degrees C for 30 min), macerated, and dilution-plated on (1)/(10)-strength tryptic soy agar. Strain L324-92 inhibited all isolates of G. graminis var. tritici, Rhizoctonia species and anastomosis groups, and Pythium species tested on agar at 15 degrees C; provided significant suppression of all three root diseases at 15 degrees C in growth chamber assays; controlled either Rhizoctonia root rot, takeall, or both; and increased yields in field tests in which one or more of the three root diseases of wheats were yield-limiting factors. The ability of L324-92 to grow at 4 degrees C probably contributes to its biocontrol activity on direct-drilled winter and spring wheat because, under Inland Northwest conditions, leaving harvest residues of the previous crop on the soil surface keeps soils cooler compared with tilled soils. These results suggest that Bacillus species with desired traits for biological control of wheat root diseases are present within the community of wheat rhizosphere microorganisms and can be recovered by protocols developed earlier for isolation of fluorescent Pseudomonas species effective against take-all.

Insights into the prevalence and management of soilborne cereal pathogens under direct seeding in the Pacific Northwest, U.S.A.

Direct seeding or no-till leaves the soil undisturbed, except where the seed is planted and the soil fertilized. It offers several advantages in small-grain cereal production, including reduction in labor and other operating costs, reduction of soil erosion, and improvement of soil quality. However, only about 10% of small grains in the U.S.A., and 6% of the small grains in the Pacific Northwest region of the U.S.A. are currently direct seeded. Root diseases are major constraints to adoption of direct seeding; they increase because of lack of tillage, increased crop residue left on the surface, and typically cooler and wetter soil conditions in the spring. This review covers some recent research on the four most important root diseases of cereals in the Pacific Northwest and their causal agents. These diseases are rhizoctonia root rot and bare patch [Rhizoctonia solani AG-8, Rhizoctonia oryzae], pythium damping-off and root rot [Pythium spp.], take-all [Gaeumannomyces tritici var. tritici], and fusarium foot rot [Fusarium pseudograminearum and Fusarium culmorum] We discuss how these diseases are affected by direct seeding and the impact of management strategies, including crop rotation, residue management, control of inoculum from volunteers and weeds, fertilizer placement, genetic tolerance, biological control, development of natural suppressiveness, and prediction of risk through DNA-based detection methods.Key words: soilborne pathogens, cereal, direct seeding, management strategies, no-till.

Take-all of wheat

Take-all, caused by the soilborne fungus Gaeumannomyces graminis var. tritici, is arguably the most-studied root disease of any crop, yet remains the most important root disease of wheat worldwide. S. D. Garrett launched the study of root diseases and soilborne pathogens as an independent field of science starting in the middle of the 20th century, inspired by and based in large part on his research on take-all during the first half of the 20th century. Because there has been neither a source of host plant resistance nor an effective and economical fungicide for use against this disease, the focus for nearly a century has been on cultural and biological controls. In spite of the intensive and extensive works towards these controls, with mostly site-or soil-specific success, the only broadly and consistently effective controls require either crop rotation (break crops), or the converse, wheat monoculture to induce take-all decline. Take-all decline has become the model system for research on biological control of plant pathogens in the rhizosphere and provided the first proof to the scientific world after decades of debate that antibiotics are both produced in soils and play a role in the ecology of soil microorganisms. On the other hand, even the best yields following take-all decline are rarely equal to those achieved with crop rotation. Because of this, the continuing trends globally to shorten rather than lengthen the rotations in wheat-based cropping systems, and the growing use of direct-seed (no-till) trashy systems to reduce costs and protect soil and water resources, new methods to control take-all are needed more than ever. With high resolution maps of the genomes of cereals and other grasses now available, including a complete sequence of the rice genome, and the interesting differences as well as striking similarities among the genomes of cereals and related grasses, gene transfer to wheat from oats, rice, maize and other grass species resistant to G. graminis var. tritici should be pursued.

Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances

The aim of the present study was to assess possible adverse effects of transgene expression in leaves of field-grown barley relative to the influence of genetic background and the effect of plant interaction with arbuscular mycorrhizal fungi. We conducted transcript profiling, metabolome profiling, and metabolic fingerprinting of wild-type accessions and barley transgenics with seed-specific expression of (1,3-1, 4)-β-glucanase (GluB) in Baronesse (B) as well as of transgenics in Golden Promise (GP) background with ubiquitous expression of codon-optimized Trichoderma harzianum endochitinase (ChGP). We found more than 1,600 differential transcripts between varieties GP and B, with defense genes being strongly overrepresented in B, indicating a divergent response to subclinical pathogen challenge in the field. In contrast, no statistically significant differences between ChGP and GP could be detected based on transcriptome or metabolome analysis, although 22 genes and 4 metabolites were differentially abundant when comparing GluB and B, leading to the distinction of these two genotypes in principle component analysis. The coregulation of most of these genes in GluB and GP, as well as simple sequence repeat-marker analysis, suggests that the distinctive alleles in GluB are inherited from GP. Thus, the effect of the two investigated transgenes on the global transcript profile is substantially lower than the effect of a minor number of alleles that differ as a consequence of crop breeding. Exposing roots to the spores of the mycorrhizal Glomus sp. had little effect on the leaf transcriptome, but central leaf metabolism was consistently altered in all genotypes.

Rhizoctonia root rot and take-all of wheat in diverse direct-seed spring cropping systems

The percent area of patches of wheat plants stunted by Rhizoctonia solani AG8 in years 3 and 4 of a direct seed (no-till) cropping systems study conducted under dryland conditions of Washington state was the same for continuous spring wheat (Triticum aestivum) (no crop rotation), spring wheat after spring barley (Hordeum vulgare), or first- or second-year spring wheat after consecutive crops of safflower (Carthamus tinctorius) and yellow mustard (Brassica hirta). Similar percent area of patches occurred in plots sown to spring barley after spring wheat and in the safflower and yellow mustard. Greenhouse studies confirmed that safflower and yellow mustard as well as several other broadleaf crops are susceptible to R. solani AG8. Between years 3 and 4, some patches increased in size, some new patches formed, and a few patches present in year 3 were not present in year 4. Seventy to 80% of the wheat plants sampled in year 4 of the study had at least 10% roots with take-all caused by Gaeumannomyces graminis var. tritici, including wheat after back-to-back safflower and yellow mustard (not susceptible to this pathogen). A one-time application of zinc at 1.1 kg/ha at planting provided no visual response of the stunted plants where the application passed through one side of a patch. The effect of crop rotation on grain yield of spring wheat related to water supply, with lower yield after the broadleaf crops because they extract more water (leaving less water for the next crop) than either wheat or barley.

Yield Responses of Direct-Seeded Wheat to Rhizobacteria and Fungicide Seed Treatments

Field trials were conducted with winter and spring wheat in eastern Washington and northern Idaho over several years to determine the benefit, as measured by grain yield, of seed treatments with rhizobacteria and formulated fungicides in cropping systems favorable to root diseases. The trials were conducted with wheat direct-seeded (no-till) in fields with a history of intensive cereals and one or more of the root diseases: take-all caused by Gaeumannomyces graminis var. tritici, Rhizoctonia root rot caused by Rhizoctonia solani AG8 and R. oryzae, and Pythium root rot caused mainly by Pythium irregulare and P. ultimum. The seed treatments included Bacillus sp. L324-92, Pseudomonas fluorescens Q69c-80, Pseudomonas fluorescens Q8r1-96, difenoconazole + metalaxyl (Dividend + Apron), difenoconazole + mefenoxam (Dividend + Apron XL = Dividend XL), tebuconazole + metalaxyl (Raxil XT), and tebuconazole + thiram (Raxil-thiram). Controls were nontreated seed planted into both nontreated (natural) soil and soil fumigated with methyl bromide just prior to planting. Although the data indicate a trend in higher wheat yields with two rhizobacteria treatments over the nontreated control (171 and 264 kg/ha, respectively), these higher yields were not significantly different from the nontreated control (P = 0.06). Fungicide seed treatments alone similarly resulted in yields that were 100 to 300 kg/ha higher than the nontreated control, but only the yield responses to Dividend on winter wheat (289 kg/ha) and Dividend + Apron on spring wheat (263 kg/ha) were significant (P ≤ 0.05). The greatest yield increases over the nontreated control occurred with certain rhizobacteria-fungicide combinations, with three treatments in the range of 312 to 486 kg/ha (6.1 to 17.7%; P ≤ 0.05). Some rhizobacteria-fungicide combinations brought average yields to within 85 to 90% of those obtained with soil fumigation. Only soil fumigation produced a measurable reduction in the incidence of take-all and Rhizoctonia root rot, as assessed on washed roots. No reliable method exists for visual quantification of Pythium root rot on wheat.

Population Dynamics of Bacillus sp. L324-92R12 and Pseudomonas fluorescens 2-79RN10 in the Rhizosphere of Wheat

ABSTRACT Bacillus sp. L324-92 is suppressive to three root diseases of wheat, namely take-all caused by Gaeumannomyces graminis var. tritici, Rhizoctonia root rot caused by Rhizoctonia solani AG8, and Pythium root rot caused by several Pythium species. Populations of strain L324-92R(12), a rifampicin-resistant mutant of L324-92 applied as a seed treatment, were monitored in the rhizosphere and spermosphere of wheat and compared with populations of Pseudomonas fluorescens 2-79RN(10), a known, rhizosphere-competent, biocontrol agent. In growth chamber studies, the population sizes of L324-92R(12) on roots of wheat were approximately 1,000-fold smaller than those of 2-79RN(10) at 5 days after planting, but, thereafter, they increased while those of 2-79RN(10) decreased until the two were equal in size at 45 days after planting. In the field with winter wheat, the population sizes of L324-92R(12) on roots were at least 10-fold smaller than those of 2-79RN(10) during the fall (November 1993) and early spring (March 1994). Thereafter, the population of L324-92R(12) remained constant or increased slightly, while the population of 2-79RN(10) decreased until the two were roughly the same at 10(4) to 10(5) CFU/plant over the period of 150 days (April 1994) until 285 days (harvest) after planting. In growth chamber studies, strain L324-92R(12) remained confined to root sections within 3.5 cm below the seed, whereas 2-79RN(10) was recovered from all root sections ranging from 0.5 to 6.5 cm below the seed. In the field on winter wheat, both strains were recovered from root sections down to 5.0 to 6.5 cm below the seed at 75 days after planting (mid December), but only 2-79RN(10) was recovered at this depth at 90 days after planting. Both strains were recovered from the seed remnants 6 months after planting in the field. Both strains also were recovered from inside the roots and shoots, but population sizes of strain 279RN(10) were greater than those of L324 92R(12).

Management of wheat and barley root diseases in modern farming systems

Root diseases, namely take-all and Rhizoctonia, Pythium and Fusarium root rots, are so widespread and occur so uniformly within fields of wheat and barley in the U.S. Pacific Northwest (PNW) that we have come to accept these crops with these diseases as normal ‘healthy’ crops. The main reasons for the expanding range and increasing prevalence of root diseases on wheat and barley in this and many other cereal-growing areas of the world are two-fold: increased frequency of cereals in the rotation and the use of less, or no, tillage. Both trends are here to stay because of their economic advantages and environmental benefits. Managing these diseases in these modern farming systems is no small challenge since, unlike most leaf diseases of these crops, all cultivars of wheat and barley are more or less equally susceptible to all four root diseases. Through a combination of cultural practices, the severity of these diseases can at least be limited to ‘chronic’, while ‘acute’ outbreaks or what growers call ‘wrecks’, are relatively rare. These practices are timely and effective management of volunteer and grass weed hosts before planting; placement of fertiliser, especially phosphorus, beneath the seed within easy access of diseased roots; soil disturbance below the seed; trash removal from within the seed row; pairing the row for a more open canopy to favour warming and drying of soil beneath the crop residue; and the use of fresh seed and treatment of the seed with a combination of fungicides for improved seedling vigour. No equivalent effort has been made in any other crop to manage a disease complex without the benefit of host plant resistance. In spite of this, these practices, together with take-all decline, only elevate yields to about 80% of the potential as revealed by fumigated (methyl bromide) check plots. Future research must concentrate on the development of host plant resistance, including host plant resistance with transgenes.

Management of resident plant growth-promoting rhizobacteria with the cropping system: a review of experience in the US Pacific Northwest

In view of the inconsistent performance of single or mixtures of plant growth-promoting rhizobacteria (PGPR) strains formulated for commercial use, and the high cost of regulatory approval for either a proprietary strain intended for disease control or a crop plant transformed to express a disease-suppressive or other growth-promoting PGPR trait, management of resident PGPR with the cropping system remains the most practical and affordable strategy available for use of these beneficial rhizosphere microorganisms in agriculture. A cropping system is defined as the integration of management (agricultural) practices and plant genotypes (species and varieties) to produce crops for particular end-uses and environmental benefits. The build-up in response to monoculture cereals of specific genotypes of Pseudomonas fluorescens with ability to inhibit Gaeumannomyces graminis var. tritici by production of 2,4-diacetylphoroglucinol (DAPG), accounting for take-all decline in the US Pacific Northwest, illustrates what is possible but apparently not unique globally. Other crops or cropping systems enrich for populations of the same or other genotypes of DAPG-producing P. fluorescens or, possibly and logically, genotypes with ability to produce one or more of the five other antibiotic or antibiotic-like substances inhibitory to other soilborne plant pathogens. In the U.S Pacific Northwest, maintenance of threshold populations of resident PGPR inhibitory to G. graminis var. tritici is the centerpiece of an integrated system used by growers to augment take-all decline while also limiting damage caused by pythium and rhizoctonia root rot and fusarium root and crown rot in the direct-seed (no-till) cereal-intensive cropping systems while growing varieties of these cereals (winter and spring wheat, barley and triticale) fully susceptible to all four root diseases.

Characterization of Rhizoctonia Isolates, Disease Occurrence and Management in Cereals

Cereal crops are susceptible to infection by several species and inter- and intraspecific groups of Rhizoctonia. Symptoms caused by these pathogens are diverse and include preemergence damping-off, root rot, foliar blight, hypocotyl rot and sheath blight. Root diseases are the most damaging to cereals, and therefore, are the primary focus of this paper. In addition, although all cereals are susceptible to infection by Rhizoctonia spp., diseases of wheat and barley are emphasized due to the limited number of reports on the diseases and species of Rhizoctonia that affect other cereal crops. Diseases of rice caused by Rhizoctonia spp. are discussed in the chapter by T. Hashiba.