Assembly of bacterial symbionts for rhizosphere soil under host plants
Numerous Frankia ASVs were detected from both rhizosphere and riparian soils while the number of ASVs from root nodules was limited (Fig. S1). Frankia communities were more diverse in the rhizosphere than in the communities in nodules and in riparian soils even when Frankia sequences were separated by OTUs (Fig. 1). This finding indicated that phylogenetically distant genotypes were assembled in host rhizosphere soil.
The higher Frankia diversity in rhizosphere soils compared to riparian soils can be explained by the occurrence of hosts. In rhizosphere soil, free-living Frankia obtains carbon sources from plant root exudates (Chaia et al., 2010; Rönkkö et al., 1993; Samant et al., 2015; 2016; Smolander et al., 1990; Valdés, 2008). In addition, secondary metabolites, such as flavonoids, in root exudates act as signals during the development of plant-microbe symbiosis associations, including actinorhizal symbioses (Hughes et al., 1999; Perrine-Walker et al., 2011; Steinkellner et al., 2007). These chemical compounds in the host’s root exudates may promote the local assembly of Frankia in the host’s rhizosphere, regardless of infective or non-infective types. Also, the genetic community compositions of Frankia in the host’s rhizosphere were affected by the soil environment (Table 1). This result suggests that conspecific host individuals might be exposed to different genotypes of bacterial symbionts in natural environments. Soil conditions, such as soil pH and nutrients, are important drivers to shape rhizospheric microbial community structure in nature (Fierer et al., 2012; Wei et al., 2017). However, the knowledge of rhizobial communities in soil, including non-infective strains, is still limited. Future studies should pay attention to the assembly processes of rhizobial communities in soil to understand how interacting bacterial members are determined in a natural ecosystem.