Root exudation activity in the apical zone of the EF host
potentially contributed to forming the features of its endophyte
microbiome
Root exudation activity in the apical zone of the EF host potentially
contributed to forming the features of its endophyte microbiome. As
rhizosphere microbiome was largely determined by the background
microbiota of bulk soil (R2=0.81, Table 1), the root
exudation effect was relatively minor. The endosphere microbiome was a
sub-population of the rhizosphere microbiome based on the two-step
selection model (Bulgarelli et al., 2013), and was affected by the
genotype (R2=0.24, Table 1), to a greater extent than
soil type (R2=0.6, Table 1) in our study. Therefore,
the effect of genetic variation in root exudation on the endophyte
assembly is the focus of the present study. Compared with the LF
genotypes, the EF host secreted a specific composition of metabolites
from the apical zone, with more carboxylates and amino acids,
especially, propionic acid, benzoic acid, and phenylalanine. The
resulting acidic microhabitat and metabolites can facilitate nutrient
availability and mobilization for microbial utilisation, and stimulated
the activity of particular microbial taxa, such as the enrichment ofBurkholderia species in the low-pH rhizosphere of white lupin
(Lupinus albus ) cluster roots (Weisskopf et al., 2011).
Interestingly, one core ASV colonising apical root of EF genotype was
also in Burkholderiaceae group (Fig. 4a).
The EF-enriched benzoic acid and phenylalanine observed in the present
study are associated with biosynthesis of benzoxazinoids (BX) and
salicylic acid (SA) in plants (Kudjordjie et al., 2019; de Vries et al.,
2020). The effect of excreting BX and SA on the root microbiome have
been thoroughly examined using genetic mutations (Lebeis et al., 2015;
Cotton et al., 2019; Kudjordjie et al., 2019; Veach et al., 2019). A
study on maize determined that the main role of BX-dependent metabolites
was to stimulate methylophilic bacteria (Cotton et al., 2019). Notably,
we also identified one endophytic core ASV belonging toMethylotenera genus in the apical zone of EF genotype (Fig. 4a),
possibly due to the strong exudation of benzoic acid in the microsite.
Although the early flowering genotype was able to module the microbiome
by root exudation activity, we cannot ignore the converse effect that
the root-associated microbiome could alter plant flowering time. For
example, the EF genotype had 5 core endophytes in the basal roots with
higher relative abundance than the LF genotypes, while no compounds
secreted from the basal root were enriched/depleted by EF genotypes. So
the microbes differentially colonising the EF genotype might promote
early flowering. Previous studies using a multi-generation experimental
system found that the inoculation of selected early- or late-flowering
microbiomes can shift the flowering time of Arabidopsis, and the key
members in the early-flowering microbiome were from the family
Methylobacterium and Pseudomonadaceae (Panke-Buisse et al., 2015; Lu et
al., 2018), these two families also contain the enriched core endophytes
(Methylotenera and Rhizobacter ) of the EF genotype in
present study.