Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae)

Abstract

As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.

Keywords: coralloid root; core microbes; cyanobacteria; endophyte.

Figure 1

The geographic distribution of sampling sites (blue triangle) in China; the capital letter represents the abbreviation of sampling localities.

Figure 2

Principal co-ordinates analyses results of bacteria community composition among different sample types of Cycas revoluta at ASV level. (a) Community in coralloid roots; (b) community in coralloid roots after removing cyanobacteria; (c) community between coralloid roots and bulk soils; (d) community in bulk soils.

Figure 3

Taxonomic composition of bacteria in coralloid roots (a) and bulk soils (b) of Cycas revoluta from different sampling localities. Phyla with relative abundance less than 0.01% are merged into “others”.

Figure 4

Extended error bar plot of bacterial communities in coralloid roots and bulk soils. The COG functions are listed to the left.

Figure 5

Core microbes in coralloid roots of C. revoluta at the genus level. (a) Flower plot demonstrated the endophytic bacteria shared among 11 sites; (b) correlation co-occurrence network of endophytic bacteria from C. revoluta coralloid root. Nodes represent genera; node size represents degree; node color represents the belonged phylum of genus; edges represent Spearman’s correlation (R > 0.6, p < 0.05).