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

Abstract

Cycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from seven Dioon species and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species of Dioon that we evaluated, suggesting a recent divergence of Dioon populations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched with Nostoc spp and Calothrix spp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

Crop Management Impacts the Soybean (Glycine max) Microbiome

“…In terms of alpha diversity, there was not a consistent difference between organic and conventional management systems, a pattern that was also observed for corn . Alpha diversity results were consistent with studies that have demonstrated the highest alpha diversity of both Fungi and Prokaryotes in the soil (Lebreton et al, 2019;Suárez-Moo et al, 2019). Additionally our results were consistent with previous results from the same site which demonstrated that the highest within plant alpha diversity for Prokaryotes could be found in the roots, but for Fungi the root alpha diversity was similar to that of the leaves (Gdanetz and Trail, 2017).…”

Specialized bacteriome uncovered in the coralloid roots of the epiphytic gymnosperm, Zamia pseudoparasitica

“…The cyanobacterial sequences from Panamanian Zamia belong to a single clade based on rb-cL-rbcX. Our study is in line with findings in the Mexican cycad genus Dioon where cyanobionts were also monophyletic using 16S rRNA (Gutiérrez-García et al, 2018;Suárez-Moo et al, 2019).…”

“…Our results support the suggestion that there may exist some specialization for symbiosis in the Nostoc taxa inhabiting the coralloid roots of cycads (Cuddy et al, 2012;Suárez-Moo et al, 2019;Zimmerman & Rosen, 1992) or perhaps a biogeographical structure may be present in cycads.…”

“…Zheng et al, 2002) cyanobacterial taxonomic units could simultaneously inhabit the same coralloid root. Metagenomics now demonstrates that there is indeed a diverse bacteriome within coralloid roots, including hundreds of taxonomic units (this paper;Suárez- Moo et al, 2019;Zheng et al, 2018) (Table 1).It is worth noting that 2,405 out of 2,570 ASVs (93.6%) were found in single-root samples. If we include the number of ASVs found in >25% of the samples, then we found 48 ASVs(47 Nostocalesand 1 Rhizobiales); in >50% of the samples, we found 46 ASVs (all Nostocales), and in >75% of the samples, we found 27 ASVs (all Nostocales).…”

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, ; Zheng, Chiang, Huang, & Gong, ; Suarez‐Moo, Vovides, Griffith, Barona‐Gomez, & Cibrian‐Jaramillo, ) 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. While it is not known whether these other taxa contribute significant amounts of nitrogen to the host plant, our coupled pure culture and foliar δ 15 N dataset suggests that any additional nitrogen supply to cycad tissues has an isotopic composition similar to that of the cyanobacterial isolates.…”