Endophyte microbiome of banana roots reveals high diversity and potential for agricultural uses

Similar to humans, plants are populated with different sets of microorganisms with potential roles on host and ecosystem functions. Endophytic microorganisms colonize root tissues inter- and/or intracellularly producing a wide range of compounds useful for plants growth as well as for protection against biotic and abiotic stresses. Clonally propagated crops such as banana are frequently multiplied by using tissue culture techniques in order to get uniform, pathogen-free plants. This process, however, also eliminates the endophyte beneficial microbiota and might have their fitness altered. To understand the microbial functional diversity of Musa spp., and its potential application in banana production systems, root-associated endophytic microorganisms (360 bacteria and 143 fungal) were isolated from 20 Musa spp. genotypes of the ex situ collection in CORBANA, Guapiles, Costa Rica. Analyses of specific genome regions (16S rDNA for bacteria and tefa-1á or ITS for fungi) revealed 21 different bacterial genera, with Klebsiella, Enterobacter, Bacillus, Acinetobacter and Burkholderia as the most frequent. Trichoderma spp. and Fusarium oxysporum prevailed among the 12 genera of fungi identified. Most isolates are known to be associated with banana, but genera such as Sphingobacterium, Grimontella, Providencia, Pleosporaceae have not been reported previously. Microorganisms with no significant similarities to the analysed database (04 bacteria and 03 fungi) were found and will probably constitute new descriptions. Some endophytes were more frequent or uniquely found on certain banana genotypes, but endophyte-host specificity needs to be further verified. Partial characterisation of the collection showed that T. asperellum isolates from cv. Yangambi Km5 (AAA) can significantly inhibit (up to 80.5 %) the mycelial growth of the banana pathogen Fusarium oxysporum f. sp. cubense. When a set of selected bacteria was inoculated in the tissue culture plants of the commercial cultivar Cavendish, three bacterial isolates (Bacillus aryabhattai, Burkloderia spp. and unknown) significantly increased the dry root weight. These results revealed a high and multifunctional diversity of culturable endophytes from Musa spp. roots, with a strong potential for new product developments and methods to enhance productivity in banana. Opportunities also exist to explore Musa genotypes in their native habitat and to characterise non-culturable microorganisms.