The Triticum and Aegilops ancestors of bread wheat (Triticum aestivum) and durum wheat (Triticum durum) underwent hybridization, as well as polyploidization events (Haberer et al., 2016) involving genomes A, S, B and D (Figure 2A). The A and S genomes arose by divergence from a common ancestor circa 7 million years Before Present (BP) (Pont et al., 2019). D genome might have originated from homoploid hybrid speciation of A and S genomes, 5–6 million years BP (Glémin et al., 2019). Two wild diploid wheats (2n = 14), i.e., Triticum urartu (AA genome) and a close descendant of Aegilops speltoides (BB genome) (Pont et al., 2019), hybridized about 500,000 years BP and gave a tetraploid wild wheat (2n = 28) termed Triticum dicoccoides (wild emmer wheat; AABB genome) (Pont et al., 2019). A second hybridization took place about 10,000 years BP, between domesticated emmer and a direct ascendant of the current diploid species Aegilops tauschii (DD genome), giving rise to a wild hexaploid wheat (2n = 42; AABBDD genome) at the origin of domesticated T. aestivum. Hexaploid wheat might have arisen from more than one crossing event (Dvorak et al., 1998). In both hybridization events, the seven chromosomes of each genome (A, B, or D) could not pair for subsequent mitosis, which resulted in chromosome doubling and thus allopolyploidy (Glover, 2016). On one hand, hybridization can lead to a loss of genetic diversity, since only a limited number of individuals of each species is involved in the crossing. On the other hand, polyploidy may lead to particular gene expression patterns, and probably also to particular properties in terms of root exudation, root uptake, etc. (Saia et al., 2019; Iannucci et al., 2021), which can be expected to impact on microorganisms.

Wheat has undergone several domestication events. The wild einkorn Triticum monococcum subsp. beoticum (genomically close to T. urartu; Fricano et al., 2014) was domesticated and gave T. monococcum subsp. monococcum, a crop seldom cultivated nowadays (Salamini et al., 2002) (and therefore is not portrayed in Figure 2A). The wild emmer wheat T. dicoccoides (AABB genome) gave rise to the domesticated emmer wheat T. dicoccon (perhaps on several independent occasions (Özkan et al., 2011)), which later evolved into durum wheat T. durum (Figure 2A). The cross between wild emmer and the ascendant of A. tauschii (DD genome) either (i) resulted in an unknown hexaploid wild wheat, from which derived the domesticated wheat T. aestivum (Salamini et al., 2002), or (ii) was concomitant with the domestication event itself. Agronomic traits of wheat changed gradually upon domestication. As for other Poaceae, domesticated wheat presents bigger grains and higher seed number per spike (Salamini et al., 2002). Wheat domestication resulted also in lower root biomass (Waines and Ehdaie, 2007), with more fine roots and a shallower root system (Roucou et al., 2018), and with more seminal roots (Golan et al., 2018), but these traits display heterogeneity at inter and infra-species levels. Domestication represents a genetic bottleneck, with an estimated 50–60% reduction of wheat genetic diversity (Bonnin et al., 2014).

Nowadays, wild wheat habitats are still located in the area that was 10,000 years ago the Fertile Crescent (Supplementary Figure 1), and where T. urartu, T. beoticum, T. dicoccoides, A. speltoides, and A. tauschii can be found. Beyond the Fertile Crescent, wild wheats grow mainly in temperate climates between latitudes 30°N and 40°N, but they may occur also within the Arctic Circle and to higher elevations near the equator (Haas et al., 2019). Therefore, wild wheats grow under a wide range of pedoclimatic conditions, which means they may encounter different types of soil microbial communities.

Whereas wild wheats are mostly winter type, domesticated wheat can be either winter or spring type (i.e., does not need vernalization), which enables to find domesticated wheat in a larger range of climatic zones (and soil conditions). In comparison with spring wheat, winter wheat is sown in the autumn, which means the root system develops and interact with soil microorganisms over a much longer duration in the year. Domesticated wheats (both durum and bread wheats) are found in a broad range of areas and climates, and are present on all continents (Di Paola et al., 2018; Mideksa et al., 2018; Dong et al., 2019; Tidiane Sall et al., 2019). They are therefore likely to be included in a diversity of cropping systems and farming practices (i.e., regarding tillage, fertilizers, etc.) in contrasted conditions of soil and climate, which means exposure to very different types of soil microbial communities (Chaudhary et al., 2017; Dong et al., 2017; Gajda et al., 2017; Somenahally et al., 2018; Wang et al., 2018).

Growth of domesticated wheats in diverse environments and climatic conditions required local adaptations (Dwivedi et al., 2016). Farmers, through mass selection, led to the creation of particular, still genetically heterogeneous (Bonjean, 2001) wheat genotypes (called landraces) well-adapted to local environments (Kiszonas and Morris, 2018) and to specific stresses (Feldman and Kislev, 2007). Thus, the growth of landraces results in stands consisting of mixtures of many different closely related genotypes. Considering features important for plant-microbe interactions, this means an expected heterogeneity in terms of root system traits, plant physiology, rhizodeposition patterns and rhizosphere chemistry within a given plot.

Modern breeding aimed at higher yield. Genealogical selection (Gayon and Zallen, 1998) resulted into (i) limited plant-to-plant genetic heterogeneity within these cultivars, (ii) preferential allocation of N and C compounds to shoots rather than roots, probably leading to reduced rhizodeposition for microorganisms (Lindig-Cisneros et al., 1997), (iii) enhanced mineral uptake (Zhang et al., 2020; Cantarel et al., 2021), and (iv) particularities in root functioning and rhizosphere chemistry (George et al., 2014).

During the Green Revolution (from 1950 to late 1960s), crosses with semi-dwarf varieties were implemented (Brancourt-Hulmel et al., 2003). Hybrids were produced (Šramková et al., 2009). Chromosome engineering methodologies have been employed to transfer specific disease genes from other members of the tribe Triticeae into wheat, conferring new immune system defenses against phytopathogens (Rong et al., 2000; Niu et al., 2011). More recently, molecular markers and quantitative trait loci (QTLs) (Peng et al., 2003; Pestsova et al., 2005; Peleg et al., 2011) have been used successfully to facilitate breeding, whereas CRISPR-Cas9 (Kiszonas and Morris, 2018) and genome sequencing (Trebbi et al., 2011; Jia et al., 2013; Ling et al., 2013; Maccaferri et al., 2014; Soriano et al., 2016; International Wheat Genome Sequencing Consortium [IWGSC], Appels et al., 2018) open new perspectives, with potentially an impact on wheat-microbe interactions.

Soil type (Donn et al., 2015; Simonin et al., 2020) as well as cultivation history (Hilton et al., 2018) and practices (e.g., tillage, soil amendments) are the main factors shaping wheat root microbiota (Ahlawat et al., 2018; Kavamura et al., 2018). The second most important factor is the wheat genotype, both at the species and intra-species (varieties) levels (Mahoney et al., 2017; Stromberger et al., 2017; Ellouze et al., 2018; Naz et al., 2018; Kinnunen-Grubb et al., 2020; Iannucci et al., 2021). Growth stage and plant physiology matter less (Houlden et al., 2008; Donn et al., 2015), despite significant shifts after tillering (Wang J. et al., 2016) and when heading starts (Hilton et al., 2018).

In the case of wheats (Triticeae tribe), most work on rhizosphere and root microbiomes has focused on bread wheat T. aestivum, whereas durum wheat T. durum has received little attention (Figure 2B). Therefore, knowledge on other Triticum species and Aegilops species is very incomplete (Özkurt et al., 2020; Tkacz et al., 2020).

Other species of the Triticeae tribe have been considered mostly for comparison with T. aestivum and T. durum, to decipher the impact of domestication and selection on the wheat microbiome (Golan et al., 2018; Roucou et al., 2018; Meziani et al., 2019) (Figure 2B). For instance, the interactions with Glomeromycota fungi have been compared between wild (T. urartu, A. speltoides, etc.) and domesticated wheats (T. aestivum, etc.) (Kapulnik and Kushnir, 1991; Hetrick et al., 1992).

Microorganisms are subjected to stronger plant selection in the root endosphere than the rhizosphere (Compant et al., 2010; Fitzpatrick et al., 2018), including in the case of wheat. This materializes by greater dominance effects in the wheat endosphere, i.e., with fewer taxa but in greater relative abundance, both for bacteria and fungi (Lu et al., 2018; Özkurt et al., 2020; Tkacz et al., 2020; Prudence et al., 2021). While the rhizosphere was extensively studied, fewer studies have focused on the root endosphere of wheats (Germida and Siciliano, 2001; Bokati et al., 2016; Özkurt et al., 2020; Tkacz et al., 2020). In addition, the bacterial community has been more investigated than the archaeal and fungal communities. Information about the archaeal community of wheat rhizosphere and root endosphere exists almost only for T. aestivum, and this community has been documented by culture-independent methods only (Fan et al., 2018; Szoboszlay et al., 2019; Tkacz et al., 2020; Prudence et al., 2021), archaea being difficult to isolate with methods routinely used in rhizosphere ecology. Very few studies have focused on fungi in the root endosphere, whether with culture-dependent (Bokati et al., 2016) or culture-independent methods (Bokati et al., 2016; Ofek-Lalzar et al., 2016; Özkurt et al., 2020). It must be kept in mind that the various root-associated compartments, i.e., root endosphere, rhizoplane and rhizosphere, are not always straightforward to distinguish from one another from an experimental point of view, which complicates comparisons between studies.

Microorganisms play key roles in the biogeochemical cycles of carbon, nitrogen, sulfur, etc. (Philippot et al., 2013; Louca et al., 2016; Figure 1B). In root environments, the plant is the major provider of organic C and stimulate microorganisms, leading to the synthesis of various microbial metabolites, many of them with feed-back effects on the plant (Raaijmakers et al., 2009; Compant et al., 2010; Vacheron et al., 2013). The range of possible interactions between microorganisms and plant host is very broad (Figure 1B), from parasitism and competition to commensalism and mutualism (Lambers et al., 2009; Newton et al., 2010). Root-associated microorganisms also interact with one another, which modulates their own interactions with the plant (Raaijmakers et al., 2009; Huang et al., 2012). Due to the importance of root metabolism and rhizodeposition, it can be expected that exudate differences between wheat genotypes have the potential to materialize in significant differences in the implementation of biogeochemical cycles and biotic interactions in the root zone, but this possibility remains poorly documented.

Microbial functioning involves a complex network of elementary transformations (e.g., the conversion of N₂ into NH₃) or interactions (e.g., the inhibition mediated by a given antibiotic), each corresponding to a particular function. Each individual microorganism is endowed with many of these functions, and typically each function is common to different strains and species, leading to functional redundancy in the microbial community (Louca et al., 2016). All microorganisms participating to the same function form a functional group, and therefore each organism is likely to belong to several functional groups (Louca et al., 2016). For root-associated microorganisms, the context of the holobiont adds a supplementary dimension when considering microbial functioning (Vandenkoornhuyse et al., 2015; Lemanceau et al., 2017; Hassani et al., 2020). Whereas taxonomic variation within individual functional groups does not seem to fluctuate extensively with soil and other environmental conditions, the functional potential of the microbiota is thought to be strongly linked to environmental conditions (soil physico-chemistry, plant genotype, and growth stage) (Louca et al., 2016; Lemanceau et al., 2017; Guo et al., 2018). Accordingly, similar environments should promote similar microbial functional communities, while allowing for taxonomic variation inside an individual functional group.

The emergence of metagenomics has made it possible to glimpse the global functional and metabolic capacities of a microbiota. The assessment of the rhizosphere metagenome of T. durum showed an overrepresentation of two categories of microbial functions (Ofek-Lalzar et al., 2016; Ofaim et al., 2017). A first category corresponded to basic metabolism, important for root colonization (Santi et al., 2013; Vacheron et al., 2013), such as chemotaxis, lipopolysaccharide metabolism, nitrogen metabolism, pentose and glucoronate interconversions, starch, and sucrose metabolism. The second category was related to secondary metabolism, e.g., anthocyanin production or xenobiotic metabolism (Ofaim et al., 2017; Lu et al., 2018). Whether metagenome differences occur between wheat species or lines of individual wheat species remains to be determined. Despite methodological limitations, functional metagenome predictions from metabarcoding-based OTU datasets did suggest microbial differences between wheat lines (Mahoney et al., 2017). These predictions differed also according to T. aestivum growth stage (Kavamura et al., 2018). Energy metabolism dominates in the rhizosphere microbiota during early wheat development, vs. degradation of complex organic compounds with older, photosynthetically active plants. A similar rhizosphere acclimatization was found with oat (Nuccio et al., 2020). Metatranscriptomic analysis of the rhizosphere of one T. aestivum genotype revealed metabolic capabilities for rhizosphere colonization, including cellulose degradation and methylotrophy (Turner et al., 2013).

Metagenomic or metatranscriptomic studies have been useful to describe global metabolic activity in root environments, but they have not been implemented yet to compare different wheat species or lines. Therefore, it remains difficult to assess the impact of intra-species variation, domestication and hybridization of wheats on global microbial functioning in the root zone, and this is a topic in strong need of research attention.

Rhizosphere microorganisms develop deleterious, beneficial or neutral interactions with one another (Figure 1B). The extent of these interactions, and the density and complexity of the resulting interaction network depend on taxa richness, microbial abundance and activity levels (Finlay et al., 1997; Torsvik and Øvreås, 2002; Fuhrman, 2009). Wheat root system architecture and rhizodeposition traits determine the root surface that can be colonized and the amount of root exudates. Since these characteristics were affected by domestication and subsequent crop selection (Waines and Ehdaie, 2007; Shaposhnikov et al., 2016; Iannucci et al., 2021), wild wheats, landraces and modern cultivars probably display different patterns of microbial colonization and of microbial interactions in their roots and rhizosphere. Microbial interactions and competition can also be modulated by predators (nematodes and protozoa), which thrive to different extents in the rhizospheres of oat, pea and wheat (Turner et al., 2013), and perhaps also in the rhizosphere of different wheat genotypes. Microbiota network analysis of T. aestivum rhizosphere revealed the co-occurrences of cercozoa (protozoa), bacterial and fungal taxa, reminiscent of a predator-prey system (Rossmann et al., 2020). Co-occurrence levels were higher and trophic networks more entangled with landraces than modern cultivars, which suggests a higher level of microbial interactions in the rhizosphere of landraces.

Pathogens infecting wheat roots cause significant damage, including the take-all fungus Gaeumannomyces graminis var. tritici (Wilkinson et al., 1985), Rhizoctonia spp. causing root rot or damping-off (Ingram and Cook, 1990), and Pythium species leading to root rot (Wiese, 1987; Ingram and Cook, 1990). Differences in sensitivity to root pathogens exist according to wheat genotype. A. speltoides and T. durum are more sensitive than T. monococcum to G. graminis var. tritici (McMillan et al., 2014), whereas inter-cultivar variability of resistance to this pathogen is high within T. aestivum (Golizadeh et al., 2017). Susceptibility to Rhizoctonia was similar for T. monococcum and T. durum, as well as certain T. aestivum cultivars, whereas other cultivars of T. aestivum were more sensitive (Oros et al., 2013). Differences in tolerance to G. graminis (Golizadeh et al., 2017), root-infecting Fusarium graminearum (Wang et al., 2018), foot, crown and root rot-causing Fusarium culmorum (Erginbaş Orakcı et al., 2018) and Pythium (Higginbotham et al., 2004) occurred among T. aestivum cultivars. Wheat is also affected by parasitic nematodes, with cultivar-level differences in susceptibility of T. aestivum to cereal cyst nematodes Heterodera spp. (Cui et al., 2016) and root-lesion nematode Pratylenchus curvicauda (Begum et al., 2020). Apart from differences in disease sensitivity, modern T. aestivum cultivars tend to be more colonized by Fusarium, Neoascochyta and Microdochium root pathogens compared with landraces (Kinnunen-Grubb et al., 2020).

Wheat cultivars might rely on specific microbial populations for phytoprotection, which may entail pathogen inhibition (via competition or antagonism) or systemic induction of plant defense pathways. Fluorescent Pseudomonas inhibit Pythium, Rhizoctonia and G. graminis (Weller and Cook, 1986; Mavrodi et al., 2013), using 2,4-diacetylphloroglucinol (DAPG), hydrogen cyanide (HCN), or phenazines (Keel et al., 1992; Kwak and Weller, 2013; Mavrodi et al., 2013; Imperiali et al., 2017). The diversity of bacterial populations producing these compounds and rhizosphere expression of the corresponding genes depend on plant host genotype (Latz et al., 2015). DAPG and HCN-producing microorganisms can be studied via the marker genes phlD and hcnABC, respectively (Supplementary Table 2), and DAPG-producing microorganisms associated with different wheat genotypes have been well-studied in comparison with the case of other antagonistic compounds (Table 4). Modern cultivars of T. aestivum differentially select for and benefit from DAPG-producing Pseudomonas species in resident soil populations (Berg et al., 2002; Mazzola et al., 2004; Meyer et al., 2010). Cultivar differences were evidenced in the interaction with DAPG-producing P. brassicacearum in soil suppressive to take-all (Yang et al., 2018). Suppression of Rhizoctonia root rot and take-all is cultivar-dependent, through enhanced recruitment of specific Pseudomonas populations by cultivars less affected by disease (Mazzola et al., 2004; Yang et al., 2018). Phytopathogens may also be inhibited by other saprophytic microorganisms, including bacteria and fungi (Barnett et al., 2017), and for the latter the ability to colonize wheat roots can depend on the cultivar (Osborne et al., 2018). In addition, Arbuscular Mycorrhizal (AM) fungi (division Glomeromycota) also inhibit wheat pathogens via competition (Ganugi et al., 2019) or production of cellulases and chitinases, which may affect pathogen cell wall and provide wheat protection (Pérez-de-Luque et al., 2017), but the significance of wheat genotypes is not documented. Induced resistance is poorly documented in monocots, including wheat (Balmer et al., 2013). Induced Systemic Resistance (ISR), which involves jasmonate and ethylene signaling, is triggered in wheat by certain Pseudomonas strains (Balmer et al., 2013). Similarly, saprophytic fungi from Aspergillus, Penicillium and Trichoderma genera and protecting against Rhizoctonia wilt trigger ISR in wheat (El-Maraghy et al., 2020). Mycorrhizae also induce systemic plant resistance, termed Mycorrhiza-Induced Resistance (MIR) (Mustafa et al., 2016), which is reminiscent of ISR (Balmer et al., 2013) but displays also features of Systemic Acquired Resistance (SAR), especially the priming of salicylic acid-dependent genes (Pérez-de-Luque et al., 2017). Thus, MIR by the AM fungus Funneliformis mosseae upregulated several defense genes in wheat, and protected wheat from the powdery mildew pathogen Blumeria graminis f. sp. tritici (Mustafa et al., 2016). In addition, Bacillus velezensis CC09 stimulated SAR pathways, inducing PR1 genes and enhancing lignin accumulation, and protected wheat from take-all (Kang et al., 2018). Little has been done to compare induced resistance in different wheat genotypes (Table 4). The two cultivars studied in Pérez-de-Luque et al. (2017) displayed different levels of systemic priming for chitosan-induced callose after co-inoculation with Pseudomonas putida and Rhizophagus irregularis. One of the two cultivars showed higher level of callose deposition after co-inoculation than inoculation of P. putida or R. irregularis alone, suggesting additive or synergistic effects in some but not all genotypes, probably linked to cultivar differences in the signaling pathway leading to systemic immune priming (Haichar et al., 2016). Root expression of defense gene homologs induced by P. brassicacearum Q8r1-96 differed between the three wheat cultivars analyzed (Okubara et al., 2010). Since wheat species and varieties differ in their abilities to recruit microbial taxa containing strains with induced resistance potential, especially AM fungi (Figure 2A), it raises the possibility that some varieties are more prone to be protected by ISR. If so, this might explain some of the differences in sensitivity to diseases observed among cultivars.

Apart from plant protection, several microbial functional groups present in the rhizosphere are beneficial, by ensuring better plant growth (Vacheron et al., 2013; Lemanceau et al., 2017). However, information about their abundance and activity according to wheat genotype is scarce, even for the best described functional groups. Mineral nutrition of wheat can be promoted by different functional groups directly affecting nutrient bioavailability or stimulating plant development through microbial modulation of its hormonal balance (Finkel et al., 2017). Wheat growth can be promoted by microorganisms that produce phytohormones, such as Indole-3-Acetic Acid (IAA) (Spaepen et al., 2007), cytokinins and gibberellin, or secondary metabolites interfering with auxin, such as DAPG (Landa et al., 2003) and nitric oxide (NO) (Molina-Favero et al., 2008). Inoculation with different P-solubilizing, IAA-producing strains of Azotobacter chroococcum carried out on three cultivars of T. aestivum showing contrasted P responses resulted in enhanced N, P, K uptakes, probably as a consequence of phytohormone effects, but without difference between wheat genotypes (Narula et al., 2000). In contrast, cultivar differences were found following Azospirillum inoculation, when considering phenotypic traits such as root system architecture or plant height, especially during early growth phases, but without an effect on grain yield (Kazi et al., 2016). Using the Opata × synthetic mapping population, one QTL region on chromosome 1A was identified for Azospirillum adhesion to wheat roots (Díaz De León et al., 2015). DAPG, at low concentration, induces the plant’s auxinic pathways, which stimulates root exudation and branching (Brazelton et al., 2008; Combes-Meynet et al., 2010). Application of wheat root exudates to a soil modified the composition of the DAPG-producing community in a cultivar-specific manner (Gu and Mazzola, 2003). The activity of DAPG-producing Pseudomonas in the rhizosphere and DAPG accumulation on the rhizoplane of T. aestivum is influenced by specific cultivar-bacterial strain associations (Bergsma-Vlami et al., 2005; Okubara et al., 2010). Variability is also observed between old and modern cultivars, as colonization by P. ogarae F113 and expression of phl genes (coding for DAPG production) are higher for ancient genotypes of T. aestivum (Valente et al., 2020). Not much data is available on the effect of wheat genotype on the abundance or activity of other phytohormone-producing microorganisms (Table 4). 1-aminocyclopropane-1-carboxylate (ACC) is the precursor of ethylene in plants and more ACC is produced in case of stress, which may have deleterious effects on plant growth (Glick, 2014). ACC deaminase activity, which catalyzes the cleavage of ACC into ammonium and alpha-ketobutyrate (Glick, 2005, 2014), is found in many microorganisms living in the rhizosphere (Bouffaud et al., 2018). This activity can improve the growth and yield of T. aestivum under salt stress and drought conditions, acting as an ACC sink that lowers ethylene level without stopping stress-induced reactions (Zahir et al., 2009; Shakir et al., 2012; Hassan et al., 2014). The abundance of microorganisms with ACC deaminase activity in the rhizosphere varies with plant genotype (Bouffaud et al., 2018), and the abundance, composition and activity of the corresponding functional group depends also on T. aestivum cultivar (Stromberger et al., 2017). Under drought or well-watered conditions, the response of T. aestivum to inoculation with ACC deaminase-producing bacteria is genotype dependent, as some cultivars showed higher root length while others had increased above-ground biomass (Salem et al., 2018). The ability of these bacteria to promote drought resistance may depend on wheat genotype (Stromberger et al., 2017). The significance of ACC deaminase activity has not been studied for wheat species other than T. aestivum (Figure 2A). Pseudomonas producing phenazine (usually studied for its antimicrobial properties) are thought to be involved in drought resistance as well. Indeed, when inoculated, their presence on roots (at population levels that are wheat cultivar dependent; Mahmoudi et al., 2019) leads to added protection of seedlings against drought in cultivars that are genetically drought resistant (Mahmoudi et al., 2019). Moreover, Pseudomonas producing phenazine were shown to be abundant in non-irrigated soil (Mavrodi et al., 2012, 2013). Furthermore, resistance to drought (along with other abiotic stress like salinity or metals; Seguel et al., 2016; Aguilera et al., 2018; Ganugi et al., 2019) may be conferred by AM fungi following the induction of particular metabolomic responses in wheat roots (Bernardo et al., 2019). This protection varies with T. aestivum cultivars and QTLs have been identified, especially on chromosomes 3D and 7D (Lehnert et al., 2017). More generally, genome-wide association studies for the establishment of AM symbiosis have highlighted QTL regions on chromosomes 3A, 4A, and 7A in T. aestivum inoculated with Rhizophagus intraradices, Claroideoglomus claroideum and Claroideoglomus etunicatum (Lehnert et al., 2017) and on chromosomes 1A, 2B, 5A, 6A, 7A, and 7B for T. durum when inoculated individually with Funneliformis mosseae or Rhizoglomus irregulare (De Vita et al., 2018). Depending on the species (T. aestivum or T. durum), changes in rhizosphere microbiota traits due to drought will differ, suggesting that different wheat genotypes recruit their own specific microbiota to help alleviate abiotic stresses (Azarbad et al., 2018, 2020).

The rhizosphere is characterized by the release of organic exudates and other rhizodeposits, and the uptake of mineral nutrients by roots (Figure 1B). The biogeochemical cycles of carbon, nitrogen and phosphorus are well-understood, and several primers are available to target microbial markers associated with these cycles (Supplementary Table 2). However, microbial activities involved in other important cycles such as those of potassium, sulfur or iron are less described in the wheat root and rhizosphere (Narula et al., 2000; Sheng and He, 2011; Jacoby et al., 2017; Kumar et al., 2018).