The composition and diversity of the root-associated microbial
community
We analysed all the experimental factors and their interactions on
microbial community composition. Permutational multivariate analyses of
variance (PERMANOVA) showed that rhizocompartment and soil type
explained the largest percentage of data variation, with 16% and 18%,
respectively (P < 0.01, Table 1). Therefore, microbiome
structure in the rhizosphere and endosphere were analysed individually.
For rhizosphere microbiome composition, soil type accounted for most of
the variation (about 80%, P < 0.01 based on PERMANOVA, Table
1), although the effects of root segment, genotype and their
interactions were all significant (P < 0.01, Table 1). The
biplot of non-metric multidimensional scaling (NMDS) based on
Bray-Curtis distance showed that the samples clustered by soil type, and
there was a high overlap between Soil-A and Soil-C (Fig. 1a). By
contrast, the effects of root segment and host genotype were greater
than soil type in determining the endosphere microbiome (11%-24% vs
6% PERMANOVA test, Table 1). In the NMDS biplot exploring root
endophyte profiles, communities from the root apical and basal zone were
clearly separated based on NMDS1, independently of different soil types
(Fig. 1b, and Fig S4). Interestingly, endophyte composition in apical
and basal root of the genotype EF overlapped considerably in the biplot
(Fig. 1b). Consequently, we calculated the Bray-Curtis distance of
microbiota composition between apical and basal root within each
treatment and confirmed that this distance for the EF genotype was only
half of the LF genotypes (LF1 and LF2) in the endosphere (P <
0.01, Table 1 and Fig. 1c). In addition, the variability of endophytic
colonization across different soils was more stable in apical roots of
all the genotypes, and in the EF basal root than other niches, as
indicated by the shorter Bray-Curtis distance (P < 0.05, Table
1 and Fig. 1d).
At the phylum level, we analysed the taxonomic composition of the
microbiome in each of the studied niches (Fig. 2). Proteobacteria and
Actinobacteria were the dominant phyla in all the samples, accounting
for 47% - 93% of the microbial consortia. A compensatory trend was
observed in which the relative abundance of Proteobacteria increased,
but Actinobacteria decreased from rhizosphere to endosphere, as well as
from apical root to basal root, except for the EF genotype’s basal root
tissue, which harboured an unaltered phylum composition relative to its
apical zone, with less Proteobacteria but more Actinobacteria than the
other two LF genotypes (FDR-adjusted P < 0.01).
Shannon index was used to estimate alpha diversity of the microbial
community in each of the sampled niches. The magnitude of
rhizocompartment effects on Shannon index was the greatest, indicated by
the largest F value (P < 0.01, Table 1), and, on average,
Shannon index was about 10 times higher in rhizosphere than endosphere
samples (Fig. 3a and b). In the rhizosphere, the genotypic variation in
the Shannon index was strongly dependent on the soil type and the
longitudinal root fraction (Fig. 3a). While in the endosphere
microbiome, the diversity of the EF genotype was greater than the two LF
genotypes, and this observation was consistent in apical roots and basal
roots in all soil types (Fig. 3b).