Cycad coralloid roots contain bacterial communities including cyanobacteria andCaulobacterspp that encode niche-specific biosynthetic gene clusters

Abstract

Cycads are the only early seed plants that have evolved a specialized coralloid root to host endophytic bacteria that fix nitrogen for the plant. To provide evolutionary insights into this million-year old symbiosis, we investigate the phylogenetic and functional diversity of its endophytic bacterial community, based on the (meta)genomic characterization of the coralloid root of Dioon merolae collected from natural populations. We employed a co-culture-based metagenomics experimental strategy, termed EcoMining, to reveal both predominant and rare bacteria that were analyzed through phylogenomics and detailed metabolic annotation. Most of the characterized bacteria were identified as diazotrophic plant endophytes belonging to at least 18 different bacterial families. The draft genomes of three Cyanobacteria strains were obtained, and after whole-genome inferences they were found to form a monophyletic group, suggesting a level of specialization characteristic of co-evolved symbiotic relationships. In agreement with their large size over 8 Mbp, the draft genomes of these organisms were found to encode for biosynthetic gene clusters predicted to direct the synthesis of specialized metabolites present only in these symbionts. Overall, we provide a new notion of the composition and evolution of the cycad coralloid root that contributes to studies on phylogenetic and functional patterns in plant-bacteria symbiotic systems.

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

“…Endophytes associated with cycad coralloid roots have been studied for more than a century mostly by methods that underestimated or did not aim to measure the non-cyanobacterial bacterial diversity present inside the root. Our study supports very early studies [4,8,9], and two more recent studies, the 16S rRNA-based Zheng et al [17] and the metagenomic-based Gutiérrez-García et al [18], that report a diverse bacterial microbiome beyond cyanobacteria.…”

“…We also found the 14 other most abundant families from C. bifida that are present in our Dioon samples. In the Gutiérrez-García et al [18] study, the authors used shotgun metagenomics to characterize co-cultures from an inoculum of the coralloid root endosphere from D. merolae and found 51 families and 76 bacterial genera, of which 34 and 33 respectively, were present in our amplicon data. Nine families were shared between these two studies and ours, including Nostocaceae, Rhizobiaceae, Pseudonocardiaceae, Mycobacteriaceae, Hyphomicrobiaceae, Bacillaceae, Bradyrhizobiaceae that were abundant in our data, suggesting these may constitute a taxonomic core for cycads in general.…”

“…interacting Nostoc-Caulobacter in other Dioon species adds to this possibility [18]. These hypotheses require appraisal based on a wider sampling of Mexican cycad species and functional studies of the main groups we identified here.…”

“…Zheng et al [17] found significant differences in the abundance of some bacterial families compared to regular cycad roots, with a dominance of cyanobacteria in the coralloid roots [17]. Likewise, Gutiérrez-García et al [18] sampled the bacterial coralloid microbiome of Dioon edule using complete genomes and shotgun metagenomes from axenic cultures and liquid co-cultures that aim to describe the functional diversity of the endophytic microbiome [19], and also found several bacterial groups in addition to cyanobacteria endophytes. There appears to be a broad spectrum of noncyanobacteria inside the coralloid root, which we are only beginning to explore.…”

Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen

“…We also note that recent work (e.g., Gutiérrez-García et al, 2018;Zheng, Chiang, Huang, & Gong, 2018; Suarez-Moo, Vovides, Griffith, Barona-Gomez, & Cibrian-Jaramillo, 2019) has revealed additional taxonomic diversity in coralloid roots beyond the dominant cyanobacterial strains that are typically described (i.e., Nostoc and Calothrix), including other diazotrophic bacteria such as rhizobia.…”