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.