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Worldwide, growing concern about the harmful effects of pesticides on humans and non-target organisms has resulted in an increasing demand from international markets for fruit that is produced using sustainable management systems. This study measured the effects of fungicides on population density and species richness of phylloplane microorganisms in apple orchards under different management systems. A secondary objective was to identify one or a few microorganisms that could be easily recognised by colony morphology and be used as bioindicators of sustainable orchard management. During the 1998/1999 season, a sampling, isolation and enumeration method was developed that determined the amount of natural variation in microorganism populations among trees, among locations within trees and between spring and autumn, in an unsprayed orchard. The results showed that during spring, the variation among trees, locations within trees, and dilution plates were responsible for 49, 39 and 12 percent, respectively, of the total variation. During autumn, the variation among trees, locations within trees, shoots, and dilution plates were responsible for 34,0,49 and 17 percent, respectively of the total variation. The information gained from the first study was used to modify the methods, which were used in a second study in 1999/2000, to compare microorganism populations from apple orchards under different management systems, at four times during the season. Three orchards followed ENZA-IFP (Integrated Fruit Production) requirements for export, three produced for the local market (IFP-local market) and two produced apples organically, complying with BIO-GRO standards. An unsprayed orchard was also included in the study. The results showed that populations increased during the season, by factors of 11, 47, 774 and 80 for bacteria, 'smooth yeasts', Aureobasidium spp. and filamentous fungi, respectively. Throughout the season, population densities of bacteria and 'smooth yeasts' were similar in all orchards (1 x 10⁵ to 1 X 10⁶ colony forming units per leaf [CFU/leaf]), whereas those of Aureobasidium spp. and filamentous fungi were lower in IFP orchards (about 1 x 10³ and 1 x 10⁴ CFU/leaf respectively) than in BIO-GRO and unsprayed orchards (3 x 10⁴ and 1 x 10⁵ CFU/leaf respectively). The mean species richness (number of recognisable taxonomic units per sample [RTU/sample]) varied from 5.3 in IFP orchards to 6.6 in the BIO-GRO and unsprayed orchards, but species richness was lower in IFP orchards (5) than in BIO-GRO and unsprayed orchards (13) during spring, and it increased during the season and became similar to that of BIO-GRO orchards in autumn. In a third study, the direct effects were determined of the fungicides, captan, copper hydroxide, myclobutanil, dodine, inorganic sulphur and a fish-based foliar fertiliser, on phylloplane microorganism populations. Products were sprayed four times during the 1999/2000 season, and the microorganism populations assessed immediately before treatment and at 1, 3 and 7 days after treatment. With all microorganisms combined there were significant differences (P≤0.05) in the level of increase or decrease in microorganism populations among the four treatment dates, but differences among products were only significant at P≤0.l. 'Smooth yeasts', filamentous fungi and species richness, showed significant (P≤0.05) changes in population densities due to foliar treatments. Although this trend was observed only in a few (3/60) cases, this indicates that a single isolated foliar application of a chemical product can affect microbial population densities and species richness. The effect of repetitive fungicide applications, different products and product combinations and insecticide use on non-target microorganism as applied in commercial situations requires further investigation. During the second and third study, Cladosporium spp. were identified as having potential to be suitable indicators of sustainable orchard management, because they were present in most orchards, during most of the growing season, and most often showed a significant response to orchard management systems and fungicide treatments.