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.