Microbial Ecology provides a dedicated international forum for the presentation of high-quality scientific investigations of how microorganisms interact with their biotic and abiotic environments, with each other as well as with their neighbors and hosts, to carry out their diverse functions. Microbial ecology lies at the heart of functioning for almost every ecosystem on the planet, from the deep-sea vents and subsurface systems to human and animal well-being from pristine marine and terrestrial environments to industrial bioreactor functioning. This is the first quantitative comparison of epiphytic and endophytic fungal floras in any plant, and the first to examine endophytic fungi or epiphytic fungi in leaves of coffee, one of the world's most valuable crops. Significant correlations between occurrence of fungal morphospecies suggested that fungi may have positive or negative effects on their neighbors. Thus epiphytic and endophytic communities differed greatly on a single leaf, despite living only millimeters apart, and both communities differed from site to site. Differences among sites in number of fungi per plant were significant. Suprisingly, more morphospecies occurred as endophytes than as epiphytes. Of the most common genera, Pestalotia and Botryosphaeria were significantly more common as epiphytes Colletotrichum, Xylaria, and Guignardia were significantly more common as endophytes. The taxonomic affinities of the four most common nonsporulating fungi were determined by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region: two grouped with Xylaria and one each with Botryosphaeria and Guignardia. A total of 821 colonies were isolated and grouped into 131 morphospecies. Epiphytic and endophytic fungi were isolated by placing leaf pieces on potato dextrose agar without and with surface sterilization, respectively. Leaves of naturalized coffee plants were collected from six sites in Puerto Rico. We asked whether the dominant fungi are the same in both communities, whether endophyte and epiphyte communities are equally diverse, and whether epiphytes and endophytes exhibit similar patterns of spatial heterogeneity among sites. We compared epiphytic and endophytic fungal communities associated with leaves of coffee (Coffea arabica) in Puerto Rico. Fungi are known to occur both on plant surfaces (epiphytes) and inside plant tissues (endophytes), but the two communities have rarely been compared. Plants harbor diverse communities of fungi and other microorganisms.
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