Introduction
In his book “The Power of Movement in Plants” (Darwin, 1897) Charles Darwin postulated the “Root-Brain” hypothesis, where he identified similarities between the plant root tip and the simple brain of lower metazoans, including sensory perception of external stimuli and physiological responses. The root apex is currently attracting both intensive and extensive attention related to plant signalling and development, as it is the zone for root elongation, cell division, and hormone crosstalk, triggered by sensing diverse physical and chemical gradients and/or thresholds such as gravity, moisture, mechanical resistance, light, and inorganic nutrients (Benizri et al., 2001; Baluška et al., 2010).
The apical zone of a root plays a greater role than the basal zone in coordinating the formation of root-associated microbiota. Firstly, a plant can manipulate the soil microbiome by secreting root exudates as substrates to direct the microbial life close to the root (Sasse et al., 2017; Zhou et al., 2020). Most of these exudates arise from the zone just behind the root tip, due to the absence of an apoplastic barrier (i.e., Casparian strip, suberin or schlerenchyma) which favours passive diffusion of compounds through the plasma membrane (Canarini et al., 2019). Additionally, the root tip is the first tissue to contact soil - the ‘seed bank’ of any plant microbiome. Soil microbes may penetrate into the central cell layers of the root tip, prior to differentiation of the endodermis, which later forms a thick-walled boundary in the mature zone (Reinhold-Hurek and Hurek, 1998). Changes in the patterns of microbiome assemblages between the root tip and the basal root within the same root system were found in Avena fatua (DeAngelis et al., 2009), Brachypodium distachyon (Kawasaki et al., 2016), maize (Rüger et al., 2021), wheat, and rice (Kawasaki et al., 2021b; Kawasaki et al., 2021a). However, the previous evaluation of root microbiomes at longitudinal niches has only considered a single soil type, host genotype, or rhizocompartment (rhizosphere or endosphere), and failed to provide deeper insights into the complexity of these interactions in structuring root microbiota.
The specific length of the root region is generally defined as apical or basal root for microbiome analysis (DeAngelis et al., 2009; Kawasaki et al., 2016; Kawasaki et al., 2021b; Kawasaki et al., 2021a; Rüger et al., 2021). This length-based definition might lead to different soil residence times for the apical or basal root segments when growing under different environments, because the elongation rate of the plant root varied under different soil types and for different plant genotypes. Microbiome assembly in roots is rapid (e.g., 24 h, Edwards et al., 2015) and sensitive to the soil residence period (Dombrowski et al., 2017), so root segments with the same soil residence time should be sampled to compare their microbiomes under different soils or for different host genotypes, which has not been considered in previous studies.
Plant phenology is an important trait for crop domestication and improvement and has strong interactions with the root-associated microbiome. Root microbiomes of the perennial plant Arabis alpinawas influenced by soil residence periods, but microbiomes were indistinguishable between the nonflowering wild type and the early flowering mutant (Dombrowski et al., 2017). For annual rice genotypes, both the developmental rate and soil residence time determined the microbiota assembly through the life cycle (Edwards et al., 2018). A recent mode showed that the flowering time of Arabidopsis was driven by rhizosphere microbes that were modulated by root exudates (Lu et al., 2018). As there was spatial variation of root exudates within a root system, microbiome acquisition along the longitudinal root axis after a short soil-residence time might indicate the genetic variation of host plant phenology.
Chickpea (Cicer arietinum L.) originated from a small area in southeast Turkey (Von Wettberg et al., 2018). The selection in chickpea’s domestication focuses on photoperiod-responsive and vernalization-insensitive genotypes to ensure the life cycle completed before the summer heat and drought (Abbo et al., 2002). The genomic analysis revealed that an 11-bp deletion in the early flower geneELF3 was associated with early flowering among chickpea cultivars (Ridge et al., 2017). In addition, chickpea is characterised by late lateral root initialisation, acidic root exudates (Wang et al., 2016; Zhou et al., 2020), and specific symbiosis with Mesorhizobium ciceri (Greenlon et al., 2019). The objectives of our study were to (1) identify longitudinal niche differentiation of the root-associated microbiome, and its interactions with soil type, genotype, and rhizocompartments from the exterior to the interior of the root (Expt 1), and (2) investigate the mechanisms that structure the root microbiome, and modulate root exudation and rhizosphere soil architecture associated with genetic variation in flowering phenology (Expt 2-4).