TY - JOUR T1 - The cycad coralloid root contains a diverse endophytic bacterial community with novel biosynthetic gene clusters unique to its microbiome JF - bioRxiv DO - 10.1101/121160 SP - 121160 AU - Pablo Cruz-Morales AU - Antonio Corona-Gómez AU - Nelly Selem-Mójica AU - Miguel A. Perez-Farrera AU - Francisco Barona-Gómez AU - Angélica Cibrián-Jaramillo Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/03/27/121160.1.abstract N2 - Cycads are the only gymnosperms and ancient seed plants that have evolved a specialized coralloid root to host endophytic bacteria. There are no studies exploring the taxonomic, phylogenetic and functional diversity of the bacterial endophyte microbiome of this 300 million-year old symbiosis. We provide a genomic characterization of the cycad coralloid root microbiome of the Mexican cycad Dioon merolae collected from their natural environment. We employed a co-culture-based metagenomics experimental strategy jointly with phylogenomic analyses to reveal both predominant and rare bacteria, to capture biological diversity, and also the presence of biosynthetic gene clusters associated with specialized metabolites. Most taxa were identified as diazotroph plant endophytes that include undescribed taxa and at least 27 genera belonging to 17 bacterial families in addition to Cyanobacteria. Three cyanobacteria genomes obtained from our samples formed a monophyletic group, suggesting a level of specialization characteristic of co-evolved symbiotic relationships. This contrasted with our finding of their large genome sizes and their broad biosynthetic potential, distinctive of facultative endosymbionts of complex alternative lifestyles. Nine out of 23 novel biosynthetic gene clusters identified after detailed genome mining are specific to these coralloid root endophytes, including a NRPS system predicted to direct the synthesis of nostoginins, protease inhibitors whose biosynthetic pathway remains to be discovered. Combined, our results show that the highly diverse taxonomic composition of the coralloid root and its biosynthetic repertoire, correlate more with a degree of specificity to the cycad plant host than to other closely related plant endosymbionts or to the environment. We support the growing notion that plant-bacteria relations occur under heavy influence of chemical and genomic interactions, and we add to the understanding of the evolution of cycad-bacteria microbiome, with a bearing on bioprospecting of natural products for drug discovery and other applications. ER -