Genetic variation in phenology of host plants characterised
microbiota inhabiting the seedling root
Compared with the LF genotypes, the EF host was characterised by a
distinct microbial community in the endosphere of the apical root. More
importantly, the phenomenal assemblage of endophytes at EF genotype’s
root apex, and its differentiation from the LF genotypes were conserved,
and consistent across diverse soil types. Our results demonstrate that
the apical segment of the root system exerted a strong selection force
on the soil microbiome, and the structured microbiota was potentially
contributing to the plant’s adaptation to the oncoming harsh
environment, e.g. , by promoting early maturity.
We have identified three important features of the endophytic microbiome
established at the root apical zone of the EF host. Firstly, within the
root system of the EF genotype, there was a homogeneous structure of the
endosphere microbiome between the apical and basal zone, indicated by
the high similarity of composition and diversity (Fig. 1b, c, 3b). In
contrast, the apical and basal zones had divergent endophyte communities
in the LF genotypes. Although the sampled apical fraction was only one
day old in our experiment, the root apex of the EF genotype was able to
rapidly select and assemble its endophyte microbiome with a similar
composition to its 15-day old basal zone of the same root, which was
presumably associated with its early maturity trait through this rapid
development of an associated microbiome. Endophyte colonisation in the
basal root tissues of the EF host was also more stable than in LF
plants, as indicated by lower variation across soil types (Fig. 1d).
Secondly, the root of the EF genotype housed a greater diversity of the
endophyte community in both the apical zone and basal zone, as indicated
by a higher Shannon index than in LF plants (Fig. 3b). More diverse
microbial communities also have a greater diversity of functions due to
the functional differences between species (Jousset et al., 2017). A
previous study has demonstrated that root-associated microbes modulated
host flowering time by producing indole acetic acid and altering
plant-available N source (Lu et al., 2018).
Thirdly, microbes closely colonising the root apex of the EF host served
roles that potentially enhance plant growth. For example,Rhizobacter and Methylotenera microbes consistently
enriched the apical zones of the EF genotype. Rhizobacter has
been identified as a root endophytic bacteria in a diverse range of
species (Pelletier et al., 2020), particularly in legumes (Hu et al.,
2019; Brown et al., 2020), and was able to rescue growth inhibition
induced by root-inhabiting fungi (Durán et al., 2018). The genusMethylotenera is a group of putative methylotrophic bacteria
firmly interacting with plant growth as they are capable of utilizing
one carbon source from the decomposition of the soil organic matter and
the cell wall (Martin et al., 2020). Methylotenera can survive in
low pH habitats (Kumar et al., 2019), hence might adapt to the apical
zone of the DR genotype with more carboxylates secreted (as discussed
below).
Chickpea has a quite limited genetic variation (Varshney 2013), and its
wild progenitor (C. reticulatum ) is a rare species with a narrow
distribution in a small area of SE Turkey (Abbo et al., 2002). The
previous studies screening the collection of Australian chickpea
cultivars found that only one genotype (the genotype EF used here) is
able to keep early flowering across diverse environments, and flowering
time is the most important trait to differentiate the genotype EF from
genotypes LF1 and LF2 based on the previous morphological, physiological
and genomic comparison (Sadras et al., 2016; Kaloki et al., 2019).
Therefore, the differentiation in the root microbiota among the three
genotypes in present study was mainly attributed to their phenotypical
and genetic variation in flowering phenology, although only one EF
genotype was used.