Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil - 36570-000.
Can J Microbiol. 2013 Apr;59(4):221-30. doi: 10.1139/cjm-2012-0674. Epub 2013 Jan 22.
The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction - denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.
与咖啡植株相关的微生物群可能在咖啡品质的最终表现中发挥关键作用。然而，咖啡樱桃中的微生物多样性仍未得到充分描述。在这里，我们通过使用非培养方法研究了阿拉比卡咖啡樱桃中的内生多样性，以鉴定相关微生物，最终更好地了解它们的生态学及其在确定咖啡品质方面的潜在作用。特定于群体的 16S rRNA 和 26S rRNA 基因聚合酶链反应-变性梯度凝胶电泳和克隆文库测序表明，内生群落由生命的 3 个域的成员组成。与培养和未培养细菌具有高度相似性的细菌序列属于β变形菌门、γ变形菌门和厚壁菌门。来自厚壁菌门的克隆序列的系统发育分析表明，大多数序列属于芽孢杆菌属、葡萄球菌属和类芽孢杆菌属 3 个主要属。古菌序列显示存在属于广古菌门和泉古菌门的分类单元。内生酵母的序列没有被回收，但发现了各种与丝状真菌具有高度同源性的不同序列。微生物组成与咖啡植物的品种或地理位置之间没有明显的相关性。据我们所知，这是首次报道成员古菌定植在植物果实的内部组织中。虽然在咖啡樱桃中发现古菌小亚基 rRNA 不足以表明它们作为活跃内生菌的作用，但肯定拓宽了我们的视角，将该领域的成员视为潜在的内生微生物。
