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Fungi (17 species), oomycetous organisms (four species of Pythium) and a plasmodiophorid (Polymyxa graminis) were recorded in wheat roots analysed by cloning of the total ITS1/2 rDNA and sequencing of representative clones. Roots of a fourth successive wheat crop were inhabited mostly by fungal pathogens including Gaeumannomyces graminis var. tritici, Monographella nivalis var. nivalis, Ophiosphaerella sp. and Helgardia anguioides. Roots of a first wheat crop were inhabited mostly by P. graminis and saprotrophic Pythium species. Results on fungal diversity and density were compared with those obtained by pure culture isolation and morphotyping. Only M. nivalis var. nivalis and H. anguioides were identifed in wheat roots by both the molecular and the pure culture isolation methods. New and additional evidence for the ecological roles of the species recorded is discussed. Take-all

Relationships between the incidence and severity of brown foot rot and of pathogenic fungi, determined by diagnostic and quantitative PCR, were investigated during the growth of nine winter wheat crops in three cropping seasons. Microdochium nivale vars nivale and majus were the only brown foot rot pathogens present in significant amounts. Relationships between disease symptoms and amounts of pathogen DNA were often weak in early spring (when shoot-base symptoms are usually most difficult to ascribe to particular pathogens by visual examination) because of indistinct symptoms and small amounts of pathogen. Relationships were strongest during stem elongation. The amount of M. nivale in the tissues tended to decline in the summer as the plants matured, apparently disappearing partially from necrotic lesions to which it contributed, resulting in a weakened relationship between symptoms and pathogen DNA. Regression analyses of brown foot rot on amounts of M. nivale DNA for different wheat cultivars generally produced lines with similar slopes but were often most significant for the cultivar with most eyespot resistance (i.e. with least confounding eyespot) or most apparently genuine brown foot rot. DNA of Fusarium spp. was rarely present in amounts sufficient to quantify.

Effects of regular treatments with the fungicides carbendazim and prochloraz applied to whole plots divided into subplots with different initial population mixtures of carbendazim-sensitive or carbendazim-resistant Tapesia yallundae or T acuformis were studied in successive crops of winter wheat from 1984/85 to 1999/2000. In unsprayed and carbendazim-sprayed whole plots, a stable coexistence of about 50% each of T yallundae and T acuformis developed within five seasons, but in whole plots sprayed with prochloraz or prochloraz plus carbendazim, the proportion of T acuformis increased to > 80%. A discrete time difference equation model was derived from knowledge of the biology of eyespot and competition theory to describe the population changes. The model was fitted to the data from treatments where coexistence occurred [subplots in unsprayed (1985-92) and carb endazim-sprayed (1985-89) whole plots], using nonlinear least squares regression. The optimized value of the resource overlap coefficient was small, suggesting niche differences between the two species. Populations were nearly 100% carbendazim-resistant in carbendazim-sprayed whole plots by July 1985 (one season) and in whole plots sprayed with prochloraz plus carbendazirn by July 1986 (two seasons). In prochloraz-sprayed whole plots, the proportion of carbendazim-resistant isolates decreased more rapidly than in unsprayed whole plots in the 1980s, but by July 1992 a shift in populations in unsprayed and prochloraz-sprayed whole plots towards predominantly carbendazim-resistant strains had occurred.

A reservoir of infection of Tapesia yallundae may exist after harvest in bases of cereal stems due to the presence of apothecia capable of discharging infective ascospores. Apothecia of T. yallundae developed in a seasonal pattern on winter barley inoculated with the pathogen, with maximum numbers of apothecia produced on stubble 5-7 months after harvest. A similar pattern of development was observed on infected winter wheat. However, the peak in numbers of mature apothecia was observed 2 months later than in winter barley. Apothecia capable of discharging ascospores were present for up to 6 months on stubble. Apothecia of T. acuformis were not detected on spring or winter barley, or spring or winter wheat stubble, despite inoculation of growing crops with isolates of compatible mating type.

Isolates of Fusarium avenaceum, mostly from crops of white lupin or wheat, were tested for pathogenicity on white lupin and wheat plants and compared by DNA tests and, in a limited study, vegetative compatibility. Most of the 80 isolates were pathogenic on both plant species after inoculation on shoot bases. Disease severity was greater at higher incubation temperatures that ranged from 15/10 degrees C to 25/20 degrees C (day/night temperatures). Isolates from lupin crops tended to be more pathogenic, on average, on lupins than on cereals. Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the internal transcribed spacer region of the rDNA distinguished two groups of isolates that occurred in different proportions among isolates from lupins and cereal crops. Random amplified polymorphic DNA (RAPD)-PCR analyses indicated considerable genetic variation among isolates, but there was some similarity among groups of isolates from populations in the same field. Genetic diversity was confirmed by a high degree of vegetative incompatibility among 20 isolates using nitrate nonutilizing mutants. There were no relationships among pathogenicity, RFLP group, RAPD group and vegetative compatibility group.

Communities of fungi on roots increased in diversity between second and third cereals, and were more diverse on winter wheat than on winter barley in a field experiment conducted over 3 years. Seed treatment with formulations containing fluquinconazole or fluquinconazole plus prochloraz had little effect on these communities, which include potentially beneficial, antagonistic fungi. Seed treatment decreased take-all and increased yield of wheat, especially in the second wheat in which take-all was building up, and in the third wheat when take-all was at its peak. It was less effective in the fourth wheat when take-all appeared to be in decline in plots that had no seed treatment throughout the experiment, and in barley, in which take-all was usually less severe. Take-all increased in untreated fourth wheat crops grown after third wheat crops that had been treated, suggesting that treatment had delayed take-all build-up and eventual progress into take-all decline.

Diagnostic and quantitative polymerase chain reaction (PCR) provided clarification of the causes of symptoms and the extent of infection by eyespot (Tapesia spp.) and sharp eyespot (Rhizoctonia cerealis) on winter wheat at early growth stages. Disease assessments made before stem extension, when decisions to apply fungicides are usually made, often did not agree with the pathogen diagnoses using PCR, suggesting that such early visual diagnoses may be unreliable. Visual and PCR diagnoses made on stems in summer generally supported each other, but there were often discrepancies in relating disease severity to amounts of pathogen present when determined by regression analyses of incidence or severity of symptoms on amount of pathogen DNA. Mixed symptoms caused by different pathogens may sometimes have been confounded. Relationships between symptoms and DNA of eyespot pathogens were less clear on some cultivars, often those with least disease. Sharp eyespot symptoms had a stronger relationship to DNA of its pathogen. Significant regressions often accounted for a small percentage of the variance, suggesting either that pathogens not assayed were contributing to symptoms or that lesions were in some cases persisting longer into the season than pathogen DNA. The frequency of pathogen detection before stem extension was a poor predictor of the amounts of pathogen DNA measured later in the season.