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.