Deterministic processes of longitudinal niche differentiation shaped rhizosphere and endosphere microbiome
Our five soils with different physical and chemical properties generated diverse communities of indigenous microbes. For the rhizospheric microbiome, soil type was the key driver influencing the composition and diversity, to a greater extent than other plant-associated attributors (Table 1, and Fig. 1a, d), which was in line with previous observations in legumes using fewer soil types (Brown et al., 2020; Han et al., 2020). However, we also found that deterministic processes of longitudinal niche differentiation acted to select for certain rhizobacteria, e.g., two core ASVs (both belonging to Micrococcaceae) exceptionally enriched in the basal rhizosphere, independently of the host genotypes and soil types (Fig. 4). The rhizosphere microbiome in the root tip was variable and stochastic across different soils, possibly because the soil residence time of the sampled apical root was too short (only one day) to modulate its rhizosphere microbiome. Only one core ASV (annotated as Bacillus ) was in the apical rhizosphere, which is in line with the previous finding thatBacillus was able to colonise Arabidopsis root tip rapidly by excluding the other competing bacteria (Massalha et al., 2017).
The recruitment of endophytic microbiota was governed by the host plant (including both genotype and its longitudinal niche effects), independent of the microbiome source (soil type). However, according to the sample-to-sample variation in the single soil, previous reports indicated that the assemblage of root microbiota was stochastic at root tips, and then stabilised in the mature sections (Thiergart et al., 2019). Nevertheless, our findings, based on diverse soils, demonstrated that endophyte colonisation was conserved at the root apex compared with the basal root, as indicated by the larger number of core ASVs (Fig.4 ) and higher compositional similarity among soil sources (Fig.1d ). Our observation was possibly attributed to the more active metabolism in the root tip of chickpea, especially secreting more carboxylates than at the basal zone (Fig. 5). Previous studies (Ross-Elliott et al., 2017; Canarini et al., 2019) revealed that the phloem (part of the endosphere) of the root tip was the location unloading most of the primary metabolites released by the roots, which potentially explains our finding that the recruitment effect of the root tip on endophyte acquisition exceeded the effect of soil type.