Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China

Abstract

Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.

Keywords: Cycas; Desmonostoc; Exophiala; coralloid root; core microbiome.

Figure 1

The coralloid roots of Cycas under ex situ protection in Kunming Botanical Garden, Yunnan, China: (a) morphology of the whole root of Cycas; (b) growing status of cycad coralloid root; (c) cross sectional illustration of coralloid root; (d) longitudinal illustration of coralloid root.

Figure 2

The comprehensive experimental design.

Figure 3

The structure of endophytic bacteria and fungal communities in mature coralloid roots of Cycas: bacterial (a–c) and fungal (e–g) α-diversity measured across different sections at the genus level; different letters were used to indicate the significance of the difference (alpha = 0.05). (d) principal coordinate analysis of the bacterial community at the genus level; (h) principal coordinate analysis of the fungal community at the genus level; (i) modular co-occurrence of endophytic bacteria at the family level; (j) co-occurrence network of phyla in the endophytic bacteria community at the family level; (k) modular co-occurrence of endophytic fungi at the genus level; (l) co-occurrence network of phyla in the endophytic fungi community at the genus level. Larger nodes indicate more connections to other nodes. Wider line segments indicate stronger correlations between connected nodes.

Figure 4

Communities of bacteria and fungi in four sections of Cycas: (a–d) the comparison of endophytic communities across different sections of Cycas based on 16s rRNA (a,b) and ITS sequences (c,d) at the genus or family level; (e–g) taxonomical composition of coralloid root endophytic bacteria at the genus level (e) and fungi (f,g) at the genus or family level in different Cycas species; (h,i) microbiome dynamic balance of coralloid root endophytes at the genus (h) and family (i) level. Taxa are labelled with an identifiable taxonomic level if they failed to be assigned at the genus or family level.

Figure 5

Phylogenetic tree of abundant bacterial (left panel) and fungal (right panel) species colonizing cycad oralloid roots: (a) unrooted tree of all endophytic bacteria; the different genera of Nostocaceae highlighted in red; (b) clustering of fungal genera with abundance higher than 2%, where the abundance of genera were shown in the right panel; (c) clustering of Nostocaceae ASVs with the abundance of ASVs displayed in the right panel. For (b,c), family-level classification was used if the genus was unknown. Taxa are labelled with an identifiable taxonomic level if they could not be assigned at the genus or family level. Relative abundances were aggregated at the family (or genus) level and are depicted with circles.

Figure 6

The functional prediction of the fungal community and its core microbiome with high-abundance functional components. (a) Functional heatmap displaying the top 30 abundantly functional components in the fungal community; (b) species heatmap illustrating the top 30 abundant species with high functionality (proportion of abundance > 20%). Family-level or order-level classification was utilized when the genus was unknown.