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Organic farming (OF) has significantly increased in importance in recent decades. Disease management in OF is largely based on the maintenance of biological diversity and soil health by balanced crop rotations, including nitrogen-fixing and cover crops, intercrops, additions of manure and compost and reductions in soil tillage. Most soil-borne diseases are naturally suppressed, while foliar diseases can sometimes be problematic. Only when a severe disease outbreak is expected are pesticides used that are approved for OF. A detailed overview is given of cultural and biological control measures. Attention is also given to regulated pesticides. We conclude that a systems approach to disease management is required, and that interdisciplinary research is needed to solve lingering disease problems, especially for OF in the tropics. Some of the organic regulations are in need of revision in close collaboration with various stakeholders.

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Soil suppressiveness to Fusarium disease was induced by incubating sandy soil with debris of wild rocket (WR; Diplotaxis tenuifolia) under field conditions. We studied microbial dynamics in the roots of cucumber seedlings following transplantation into WR-amended or nonamended soil, as influenced by inoculation with Fusarium oxysporum f. sp. radicis-cucumerinum. Disease symptoms initiated in nonamended soil 6 days after inoculation, compared with 14 days in WR-amended soil. Root infection by F. oxysporum f. sp. radicis-cucumerinum was quantified using real-time polymerase chain reaction (PCR). Target numbers were similar 3 days after inoculation for both WR-amended and nonamended soils, and were significantly lower (66%) 6 days after inoculation and transplanting into the suppressive (WR-amended) soil. This decrease in root colonization was correlated with a reduction in disease (60%) 21 days after inoculation and transplanting into the suppressive soil. Fungal community composition on cucumber roots was assessed using mass sequencing of fungal internal transcribed spacer gene fragments. Sequences related to F. oxysporum, Fusarium sp. 14005, Chaetomium sp. 15003, and an unclassified Ascomycota composed 96% of the total fungal sequences in all samples. The relative abundances of these major groups were highly affected by root inoculation with F. oxysporum f. sp. radicis-cucumerinum, with a 10-fold increase in F. oxysporum sequences, but were not affected by the WR amendment. Quantitative analysis and mass-sequencing methods indicated a qualitative shift in the root's bacterial community composition in suppressive soil, rather than a change in bacterial numbers. A sharp reduction in the size and root dominance of the Massilia population in suppressive soil was accompanied by a significant increase in the relative abundance of specific populations; namely, Rhizobium, Bacillus, Paenibacillus, and Streptomyces spp. Composition of the Streptomyces community shifted significantly, as determined by PCR denaturing gradient gel electrophoresis, resulting in an increase in the dominance of a specific population in suppressive soils after only 3 days. This shift was related mainly to the increase in Streptomyces humidus, a group previously described as antagonistic to phytopathogenic fungi. Thus, suitable soil amendment resulted in a shift in the root's bacterial communities, and infection by a virulent pathogen was contained by the root microbiome, leading to a reduced disease rate.

We studied the effect of water salinity on the incidence and severity of crown and root rot disease of tomato, as well as on the pathogen and on the plant's response to the pathogen. Irrigation with saline water significantly increased disease severity in tomato transplants inoculated with Fusarium oxysporum f. sp. radicis-lycopersici, and mineral fertilization further increased it. In one field experiment, disease incidence in plots irrigated with saline water (electrical conductivity [EC] = 3.2 +/- 0.1 dS m(-1)) and in those irrigated with fresh water (EC = 0.4 +/- 0.1 dS m(-1)) was 75 and 38%, respectively. Disease onset was earlier and yield was lower in plots irrigated with saline water. In a second field experiment, final disease incidence 250 days after planting, was 12% in plants which had been irrigated with saline water (EC = 4.6 +/- 0.1 dS m(-1)) and 4% in those irrigated with fresh water (EC = 1.2 +/- 0.1 dS m(-1)). Irrigation of tomato transplants with 20 mM NaCl did not inhibit plant development, but partial inhibition was observed at higher NaCl concentrations. Growth of the pathogen in culture or survival of conidia added to soil were not affected by saline water. Plants which were preirrigated with saline water were more severely diseased than those preirrigated with tap water. It was concluded that disease increases effected by saline water are associated with the latter's effect on plant response.