Results
This study examined the interactions of root longitudinal segments (apical and basal zones), rhizocompartment (rhizosphere and endosphere), chickpea genotype, and soil type on the assemblage of the prokaryotic microbiome by sequencing 16S rRNA genes. We used three chickpea genotypes, including one early flowering (EF) and two late flowering (LF1 and LF2), based on previous long-term and multi-environmental field evaluations. Thermal time to flowering of EF, LF1, and LF2 were 962 ± 21.5 ºCd, 1041 ± 27.4 ºCd, and 1124 ± 29.2 ºCd, respectively (Sadras et al., 2016). Genomic analysis confirmed that genotype EF carried a mutated form of the gene Efl1 with 11-bp deletion compared with genotype LF1 and LF2 (Fig. S2). The 11-bp deletion of Efl1 was associated with early flowering in the global chickpea germplasm (Ridge et al., 2017).
Five soils were collected from rainfed cropping lands with contrasting physical, chemical and biological properties (Table S1). Using the rhizotron system with a removable transparent side, root longitudinal segments of apical zone and basal zone in the same chickpea plant were sampled, based on the rapid establishment of root microbiome reported previously (DeAngelis et al., 2009; Edwards et al., 2015). Each of the sampled longitudinal zone had the same root-soil contact period (1 day) from different soils and genotypes. We measured the length of sampled apical roots or basal roots, and the rooting depth at harvest under different soil types and genotypes, and found the interactions between soil type and genotype were significant, but genotypic variation of sampled root length or rooting depth was not associated with flowering time (Fig. S3). As root elongation rate differs among genotypes and soil types, our rhizotron system can ensure that the sampled apical / basal zone was at the same soil residence period across different treatments.