Legume symbiotic rhizobia and total bacteria number
The rhizotron experiment lasted for 15 days. As this was not long enough
for chickpea plants to form visible nodules, an additional pot
experiment was established using the same chickpea genotypes and soils.
Nodules were collected and cleaned after 5 weeks growth. We performed
16S rRNA gene amplicon shotgun sequencing of chickpea clean nodules and
found ASV29417 consistently accounted for 90%-95% relative abundance
in all the samples and considered it as the chickpea symbiotic rhizobia
ASV (ASVcsr).
For the abundance of ASVcsr relative to the bulk soil, interactions
between soil and other factors were not detected (Table 1). The
enrichment of ASVcsr in the endosphere was greater than in the
rhizosphere (P < 0.01, 4.02 vs 0.67 log2 fold changes to bulk
soil, Fig. 3c). In the rhizosphere of the apical root, no variation of
ASVcsr abundance among host genotypes was observed, while the EF
genotype had more ASVcsr at the rhizosphere of basal zone than LF2 did.
In the apical root endosphere, the genotype LF2 was colonised by the
highest abundance of ASVcsr (82 vs 3.2-5.5 based on log2 FC to bulk
soil), while this large genotypic difference was minimal in the basal
zone. It should be noted that the ASVcsr was one of the core ASVs at the
endosphere of LF2 apical roots, but not the core ASV in other niches or
genotypes (Fig. 4b).
Bacterial number was estimated by the copy number of bacterial 16S rRNA
genes using qPCR. In the endosphere, there was a significant interaction
between genotype and longitudinal root segment (P < 0.01,
Table S2); the root tip of EF genotype was colonised by more bacteria
than the LF genotypes (Fig. 3d), while genotypic variation in the basal
zone was not observed. In contrast, bacterial number in the rhizosphere
was only influenced by soil type (P < 0.01, Table S2 and Fig.
S5).