AbstractWorldwide, coffee (Coffea arabica) is an economically important crop. In the mountainous zone of Puerto Rico this crop is planted alone or as an intercrop forming an economically and ecologically important agroecosystem. Xylella fastidiosa Wells et al., an endophytic bacteria, causes coffee leaf scorch, which is a serious threat to the crop. Most endophytic bacteria colonize an ecological niche similar to that of phytopathological organisms, thus, some strains of these bacteria could potentially be biological control agents. This study aimed to isolate and characterize endophytic colonizing bacteria in coffee trees under shade and sun, during the rainy and dry seasons. During two years, on coffee farms of Adjuntas, Jayuya, Las Marias and Yauco, we evaluated the effect of season, location, shade and year on the amount and diversity of endophytic bacteria associated with coffee. To contrast endophytic bacterial populations, we analyzed colonyforming units (CFU/mL) and the number of phenotypically different strains (strain diversity) isolated from leaf veins and branches of coffee trees. Higher bacterial populations were observed on branches versus leaf veins (P menor que 0.0001); therefore, in order to obtain a higher number of bacterial diversity, isolations should be performed from branches instead of leaf veins. The interaction of shade type with season was the most common statistically significant interaction, indicative that the effect of the season depends on the type of shade used. During the dry season, statistical differences in the shade and location were found (P menor que 0.05) for leaf veins and branches. In the rainy season, statistical differences were found in the number of strains per tree in shade from leaf veins and tree samples. In general, a high number of bacteria in a location, season or type of shade management was associated with a high degree of strain diversity. Certain endophytic strains might interact in an antagonist manner to Xylella fastidiosa, representing an alternative for controlling the disease.
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