An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness

Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root-soil-microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype. and the host plant in previous These findings


INTRODUCTION
Plants, as sessile organisms, have evolved strategies to successfully address the challenges they face from a changing and unpredictable environment. In particular, plants need to mine the soil for resources such as water and nutrients, whose distribution is patchy and changes dynamically. Plants do so by modulating their root system architecture and root anatomy in response to environmental clues to explore different soil horizons and detect and exploit water and nutrient-rich patches (recently reviewed in Morris et al., 2017 andLynch, 2019). Besides these, plants have evolved mechanisms to modify soil physicochemical properties and microbial communities under the influence of roots (the rhizosphere) to improve their foraging activities (York et al., 2016). Reciprocally, soil microbes that live on and/or in the plant root together with the changes in soil properties caused by the root, trigger important functional adjustments in the plant such as modification of root development and physiology. This dynamic interplay in the rootsoil-microbiome interactions creates emerging properties that impact plant nutrition and health.
In this review, we will consider three habitats as integral parts of the rhizosphere continuum: the rhizospheric soil, the rhizoplane and the root endosphere (see York et al., 2016 for terms definition), as the apoplastic spaces in the root cortex (root endosphere) form a continuum of microbial colonization with the surrounding soil and the root surface (rhizoplane). Due to the properties of the rhizosphere that are largely influenced by the plant genotype, this could be regarded as an 'extended root phenotype' as defined by Dawkins (1982) i.e. a manifestation of the effects of plant genes on their environment inside and/or outside the organism. This extended root phenotype has a profound impact on plant fitness and is likely to be under strong selection (Pérez-Jaramillo et al., 2016, Schmidt et al., 2016. Hence, a better understanding of the principles that govern the formation of the rhizosphere, critical in the interaction with the soil and the microbiota, could contribute to the development of more resilient crop varieties and the optimization of agricultural practices. However, while root architecture and anatomy traits are starting to become an integral target of crop breeding programmes (Wissuwa et al., 2016, Lynch 2019, root-soil-microbiome interactions that configure rhizosphere traits are not yet considered. The delay in the use of these new root-soil-microbiome traits is due to two major factors: a) the majority of the root microbiome research has focused on characterising only one side of the interaction, the microbiota structure or the impact of edaphic factors on plant-microbe interaction, without paying attention to how plants shape these complex microbial communities, soil properties, their feedbacks on plant fitness, and ultimately, on agronomy; b) the methods that fully capture and measure the impact of roots on plant-soil-microbiome interactions are not well developed yet as it mobilizes knowledge from multiple disciplines (soil biogeochemistry, plant biology, microbial ecology). This bottleneck limits our ability to define corresponding plant root ideotypes.
Here, we review our current knowledge on how plants (focusing on annual plants) create an extended phenotype by changing rhizosphere traits through root-soil-microbiome interactions and the benefits it confers to plant fitness. While the rhizosphere is shaped by many others factors including the physicochemical properties of the soil and the environmental changes, in this review we only consider the influence of the plant on the rhizosphere formation and dynamic. We also highlight open questions and future challenges to be addressed (Box2) in order to reap the benefits of these extended root phenotypes.

Root development changes the physical properties of the surrounding soil
Root growth in a new region of the soil contributes mechanically to the formation of a rhizosphere (Bengough et al., 2011, Jin et al., 2013, Kolb et al., 2017. Growing roots displace soil particles in the vicinity of the root surface as the axial and radial growth pressures exerted at the root tip overcome the impedance of the surrounding soil. The recent advances in non-invasive techniques for soil and plant imaging opened new avenues for the study of soil-root interactions in natural soils at very fine (micron scale) resolution. For instance, X-ray computed tomography (XRCT) allowed in vivo dynamic visualisation and quantification of soil deformation around a growing root tip (Keyes et al., 2016). It showed that soil particles displacement at the root tip occurs approximately perpendicular to the root surface. XRCT was also used recently to explore the interaction among root growth, soil structure, and soil porosity in different plant species (Helliwell et al., 2017;Helliwell et al., 2019). These studies revealed the formation of a gradient of soil porosity from the proximity of the root surface, with high presence of pores, to a dense soil area a few millimetres away from the root (Helliwell et al., 2017;Helliwell et al., 2019). The size of the soil densification zone varies according to plant species and soil structure, but is independent of root thickness.
Likewise, root hairs influence rhizosphere porosity depending on soil texture. In coarse textured soils with heterogeneous pore size distribution, root hairs favour large pores formation in the vicinity of the root surface. This is particularly evident in dry soils (Koebernick et al., 2017). Surprisingly, root hair formation has no effect on finer textured soils with a more homogeneous pore structure (Koebernick et al., 2019). Therefore, root hairs tend to influence soil inter-aggregates rather than intra-aggregates arrangement in the formation of soil pores in the vicinity of the roots.
These changes in soil density and porosity have a strong impact on plant water and nutrient accessibility and on soil microbial community composition. Indeed, Kravchenko et al., 2019 using X-ray microtomography combined with micro-scale enzyme mapping have demonstrated that the soil pore formation driven by the plant is the main factor modulating carbon storage in soil. These pores define regions with high microbial activity related to carbon turnover and sequestration. Hence, root development modifies soil structure around the root and thus contributes to the formation of the rhizosphere (Figure 1).

Rhizodeposition: plants invest carbon to shape the rhizosphere physicochemical properties
Living roots release a wide range of organic compounds to the soil (i.e. rhizodeposits) that transform the physicochemical properties of the rhizosphere (Hinsinger et al., 2009, Sasse et al., 2018 Figure 1).
Rhizodeposits include primary and secondary metabolism products, volatile organic carbon compounds, cells debris derived from the root cap (i.e. border cells) and metabolites originating from senescence of root epidermal cells as well as root turnover (Nguyen 2003, Jones et al., 2009, Oburger and Jones, 2018. Therefore, rhizodeposition leads to a net carbon flux from the plant root into the soil estimated at 15% of the total plant belowground carbon allocation which may range between 17% and 40% of the total photosynthetically fixed carbon (Nguyen 2003, Badri andVivanco 2009;Sasse et al., 2018, Pausch andKuzyakov, 2018). The quantity and composition of rhizodeposits vary considerably depending on the diversity of plant communities, plant species, genotypes, plant age and growing conditions (Hütch et al., 2002, Nguyen 2003, Chaparro et al., 2013, Oburger and Jones, 2018. Root tips are the first plant tissue sensing new soil environments and are major hotspots for exudation in diverse ways. Primary and secondary plant-derived metabolites either diffuse or are actively transported from root cells to soil. Low molecular weight compounds such as sugar, amino and organic acids flow out from root cells to the rhizosphere driven by concentration gradients. The absence of an apoplastic barrier (i.e. Casparian strip, suberin or schlerenchyma) in undifferentiated root tip tissues favours passive diffusion of hydrophilic compounds through the plasma membrane, as well as being mediated by specific transporters. Exudation of high molecular weight compounds such as polysaccharides, proteins, alkaloids and phenolics requires transmembrane primary active transporters (ATP-dependent transporters) such as ABC transporters or secondary active transporters (coupled with H+ pumps). Other complex molecules such as mucilage (polymerized sugars) are actively excreted from root cap cells, forming a gelatinous layer around the root tip which, together with root cap morphology, are major drivers defining root-soil mechanical interaction and consequently root tip penetration ability (Oleghe et al., 2017;Keyes et al., 2017). Root exudation mechanisms and the key transporters involved have recently been exhaustively reviewed (Canarini et al., 2019;Sasse et al., 2018).
Exudates and mucilaginous polymers released by plant roots (mucilage) and root associated microorganisms (mucigel) impact the mechanical stability and hydraulic processes in the rhizosphere. The intricate interplay between the physical properties of the secreted mucilage (high viscosity, low surface tension and capacity to adsorb water) and the porosity and texture of the granular media defines the spatial configuration and connectivity of the liquid phase in the rhizosphere (Carminati et al., 2017, Kroener et al., 2018, Benard et al., 2019a. Water retention capacity and nutrient diffusion in the soil-root interface is defined by this complex interaction and it becomes particularly important in dry soils where the mucilage network reinforce the soil matric potential around the root, helping to keep the rhizosphere wet and preventing sudden drops in water flow particularly around the root tip (Carminati et al., 2013 and2016). Techniques such as neutron radiography have been used to monitor the changes in rhizosphere water content at the whole root system level (Carminati et al., 2010). Furthermore, this technique in combination with experimental systems using chia seed mucilage combined with diverse soil mixtures aid to reproduce rhizosphere analogues where the dynamics of biophysical processes in response to changes in water content can be assessed at smaller scale. In this regard, recent work suggests that the increased water retention associated with mucilage secretion sustains higher soil enzymatic activity and the diffusion of the rhizospheric solutes in dry soils (Zarebanadkouki et al., 2019). Importantly, the mucilage life-span extends significantly in response to low water availability ensuring a source of carbon that preserves the necessary microbial activity in the rhizosphere (Ahmed et al., 2018, Benard et al., 2019b. The exudation of organic acid anions such as malate, citrate and oxalate, change the redox state and pH of the soil. This has strong repercussion for instance on the mobilisation of inorganic phosphorus (P) from P deprived soils. These organic acids may also act as chelates to improve aluminium toxicity tolerance in acid soils (Chen et al., 2016). Fluctuation in the amount of rhizodeposition to the rhizosphere responds to changes in soil properties. For instance, amino acids exudation is influenced by the nitrogen concentration in the plant-soil interface and it is the signal for root N uptake (Kiba andKrapp, 2016, Canarini et al., 2019). Similarly, rhizosphere acidification is tightly controlled by A. thaliana in response to phosphate limitation (increased acidification associated to miR156 gene, Lei et al., 2016) or lead toxicity (reduced acidification linked to nitrate transporter NTR1.1, Zhu et al., 2019).
Altogether, rhizodeposition has a profound effect on the physicochemical properties of the rhizosphere.

The rhizobiome: plant roots influence microbial communities
Roots influence soil microbial communities leading to a very specific rhizosphere microbiome characterized in general by a larger active microbial community, but exhibiting reduced diversity compared to bulk soil (Alegria Terrazas et al., 2016, Lopes et al., 2019. This microbial rhizosphere assembly is extremely dynamic and is mostly influenced by rhizodeposits that can act as major carbon sources for microbes, signalling molecules or antimicrobial agents ( Figure 1 Microbial colonisation along growing roots is shaped by differential exudation patterns, that change the distribution of microbial biomass along the root, and the kinematics of root tip growth through soil profiles (Lugtenberg and Kamilova, 2009;Compant et al., 2010;Dupuy and Silk, 2016). Chemotaxis towards root secreted signalling molecules attracts microbes to the proximity of root surfaces whilst root elongation rate influences the dynamics of root surface adhesion and longitudinal transport along elongating roots. Generally, larger and varied number of active bacteria tends to accumulate around the root tip whereas fewer microbial taxa are associated with the root elongation zone (Watt et al., 2006;Massalha et al., 2017). Bacterial density decreases progressively from the elongation zone towards mature root zone. This is likely to reflect the rapid expansion in root epidermal cell size (up to thirty times in six hours as cells transit the elongation zone) which will, in effect, 'dilute' microbial cells resident on the root surface until they divide and create a continuous biofilm in the maturation zone. Dispersion of rhizosphere bacteria and chemotactic movements may also govern the shifts in rhizosphere communities favouring the occurrence of bacterial decomposers (DeAngelis et al., 2009;Dupuy and Silk, 2016;Massalha et al., 2017).
Additionally, plant life cycle imposes a temporal pattern in exudates secretion that sculpts the dynamics of root associated microbiota. For instance, recent studies have investigated the distinctive root microbiota associated with early and late stages of plant development in Arabidopsis (Chaparro et al., 2013), rice (Edwards et al., 2018) and oats (Zhalnina et al., 2018). In oats, the increased abundance of sucrose at the seedling stage has been suggested to facilitate the establishment of symbiotic interactions with soil microorganisms, whereas shifts to aromatic compounds and amino acids during the vegetative phase may reflect enhanced plant defence responses. Cumulative secretion of amino acids in Arabidopsis has been suggested to be crucial for bacterial root colonisation (Chaparro et al., 2013). These studies suggest the important coordination between plant developmental stage and changes in root associated microbiota to counterbalance plant immunity and nutrition needs. While many studies indicate a strong interdependence between plant genotype and rhizosphere microbiome composition (Jacoby et al., 2017), very little is known about the plant genes underlying this process. In the study of Mwafulirwa et al., (2016), closely related barley genotypes from a biparental cross between an elite and a wild accession were found to greatly differ in rhizosphere microbial activity as a consequence of genotypic variation in rhizodeposition. This study not only provided evidence of plant genetic control and heritability of the barley root microbiome, but also revealed the large potential of untapped exotic germplasm to contribute to enhanced plant-soil interactions. In addition, an interesting recent study using Avena barbata revealed that the fluctuations in chemical composition of root exudates during plant growth respond to the substrate metabolite preferences of rhizosphere associated microorganisms (Zhalnina et al., 2018). The authors highlight the significant role of organic acids (and genes controlling their transport) in the establishment of the rhizosphere microbiome. Studies comparing current crops with landraces and its wild relatives highlight the risks that domestication and breeding programs have had on rhizosphere functions and diversity (Mwafulirwa et al., 2016;Pérez-Jaramillo et al., 2016). Domestication of crops and intensive agricultural practices have altered the plant carbon source and sink dynamics to favour aboveground allocation of photo-assimilates in the form of yield. This process has impacted the extended root phenotype by altering plant-soil feedbacks including plastic responses to reveal clear shifts in rhizosphere bacterial community composition and assembly between the two genepools. In barley, introducing genetic variation from wild accession into a modern cultivar promoted beneficial plant -soil interactions associated with soil carbon dynamics (Mwafulirwa et al., 2016). These studies not only demonstrate the genetic basis underpinning root microbiome assembly but also the potential genetic loss in modern cultivars for beneficial associations in plant -root microbial communities for particular habitats.

BENEFITS OF THE EXTENDED ROOT PHENOTYPE
Plants invest carbon and energy in building a belowground niche, essentially because it comes with a large number of benefits for its overall fitness, and it facilitates plant's adaptation to a changing environment (Turner et al., 2013). The description of the rhizosphere effect on plant fitness is not new, and it is intuitive to assume that the specific conditions that the rhizosphere provides (e.g. higher soil moisture or organic matter content and microbial activities or biomass) are beneficial for plant fitness. However, the mechanisms operating at finer scales in close proximity to the root and the strength of the relationships among the rhizosphere traits and plant fitness remains in large part unknown. This section describes the current relations that have been established between the extended root phenotype and plant health and productivity ( Figure 2).

Physicochemical changes linked to the extended root phenotype impact plant fitness
As described in detail above, plants act as ecosystem engineers that modify the physical and chemical  Rabbi et al., (2018) found that a drought-tolerant chickpea variety had a greater rhizosphere moisture storage linked to larger rhizosheaths resulting from greater mucilage exudation.
Also, rhizosheath formation was related with increased water stress levels in foxtail millet and enhanced exploration of deeper soil horizons to access water (Liu et al., 2019). Similarly, larger rhizosheath formation was found to correlate with greater shoot biomass in wheat and suggested to respond to an improved water uptake regardless of the nutrient stress imposed in the experiment (James et al., 2016).
Soil aggregation in the rhizosphere is highly variable between plant genotypes (Ndour et al., 2017) and represents a rhizosphere emerging property crucial for plant water and nutrient uptake on which crop varieties could be selected.
Additionally, the modification of soil pH in the rhizosphere induced by root exudation and (micro)organisms' respiration (1-2 pH units above or below the bulk soil) influences soil nutrient availability (Neumann and Römheld, 2012). Rhizosphere acidification potential differs between species and genotypes and thus represents a currently neglected trait to consider in the context of crop breeding or crop rotation and intercropping to improve nutrient acquisition or pollution resistance.
Similarly, the role of genes controlling the expression of transport channels involved in the efflux of root exudates should be considered as significant targets for sustainable breeding programmes. In recent field evaluations, alleles conferring Al-tolerance were found concomitantly associated with a yield QTL displaying additive effect on grain yield in acid soils. The absence of yield penalties in non-stress conditions highlights the breeding value of the locus for improving sorghum grain yield on acid soils (Carvalho et al., 2016). The rhizosphere is a unique biophysical and biogeochemical environment shaped by plant evolution to maximize plant fitness and more attention should be given to rhizosphere abiotic traits (e.g. acidification, aggregation, rhizosheath mass) to improve crop selection and production.

Role of the rhizosphere microbiome for plant nutrition and water uptake
Endosymbioses -Plants have evolved mechanisms to interact and support the growth of large numbers of beneficial microbial taxa that live in the proximity of the root or inside the root tissues. The nature of the beneficial root-microbial interactions ranges from symbiotic to commensalistic, and they are critical for plant nutrition. Two of these interactions have been thoroughly mechanistically explored: plant association with symbiotic mycorrhizal fungi (e.g. arbuscular mycorrhiza, ectomycorrhiza) and with nodule forming nitrogen-fixing bacteria (e.g. Rhizobium, Frankia).
Mycorrhizal fungi form symbiotic associations with almost all land plants, with current estimates of 50 000 fungal species forming associations with 250 000 plant species (van der Heijden et al., 2015), with the most common association being established with arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota, 74% of all land plants, Smith and Read 2008). AMF symbiosis plays a key role in plant P nutrition through a more efficient solubilization and uptake of orthophosphate (i.e. only form available to plants) by the extended fungal network that can contribute to up to 90% of plant P uptake (Ferrol et al., 2019). This symbiotic interaction is especially relevant in ecosystems with low soil nutrient availability.
Although, the abundance of AM fungi is often reduced in heavily managed agroecosystems due to fertilization and soil perturbation, most of the crops can form symbiotic associations with AM fungi (e.g. cereals, legumes, potato, tomato) with a significant impact on crop productivity. Experiments using a set of maize mutants able to establish a beneficial relationship with AM fungi but deprived of the mycorrhizaspecific orthophosphate transporter presented large decreases in aboveground biomass and reduced grains production when grown in agroecosystems with low phosphorus availability (Willmann et al., 2013).
AMF influences plant nitrogen nutrition at a lower extent than phosphorus, and it is highly context dependent (van der Heijden et al., 2015). Plants associated with AMF present a higher water uptake and more effective scavenging for water in soil micropores. AMF network also promote a higher moisture retention and aggregation in soils (Augé, 2001;Augé, 2004), that sometimes are combined to a higher plant water-use efficiency (Birhane et al., 2012). Indeed, AMF influence maize plant aquaporins activity resulting in higher water transport under water deficit that led to an improved photosynthetic capacity in the shoots (Quiroga et al., 2019). Overall, these combined nutritional and non-nutritional effects of AMF generate increases in plant yield and seed protein mass in greenhouse and field conditions that has justified the use of AMF inocula in agriculture for decades (Berruti et al., 2016).

Legume plants (family Fabaceae) and the so-called actinorhizal plants (orders Fagales, Rosales,
Curbitales) rely on their associations with nitrogen fixing microorganisms (e.g. Rhizobium, Bradyrhizobium, Frankia) for nitrogen nutrition. The association between plants and nitrogen fixers microbes are characterized by the formation of specialized root organs called nodules colonized by the nitrogen-fixing microbes where the atmospheric nitrogen is converted into a reduced nitrogen form and become available for the host plant (Masson-Boivin and Sachs, 2018). In this symbiosis, the plant provides the nitrogen fixers bacteroids with dicarboxylates (e.g. l-malate, succinate, fumarate), used as energy and carbon sources by the microorganism, and in return, bacteroids provide ammonium to the plant (Poole et al., 2018). Across many plant hosts and Rhizobium symbionts a clear fitness alignment exists between the two members of the symbiotic relationship with a robust positive correlations between plant aboveground biomass and the number of nodules or nodules biomass (Friesen, 2012).
Additionally, as these symbiotic species always evolve in complex microbial communities with which they strongly interact, sometimes the establishment of a functional symbiosis may require the presence of other symbionts or microbial helpers present in the rhizosphere (Frey-Klett et al., 2007). For instance, it has been reported in soybean that AMF inoculation improved both nodulation and nitrogen-fixation, especially because nodulation requires high phosphorus demand that can be addressed by an established symbiosis with AMF (Meena et al., 2018). Also, nitrogen-fixing symbioses for legume trees from the and siderophore production (Vacheron et al., 2013). Many bacteria (e.g. Pseudomonas, Bacillus) and fungi (e.g. Penicillium, Aspergillus) are able to solubilize soil mineral phosphate through excretion of organic acids (e.g. oxalic acids, citric acids) causing a local acidification or the chelation of the cations to which phosphate is bound (Richardson et al., 2009). Additionally, a large diversity of microorganisms (e.g. Proteobacteria, AMF, ectomycorrhizal fungi), through extracellular phosphatase activities, can mineralize soil organic phosphorus and make it available for the plant (Spohn et al., 2015;Menezes-Blackburn et al., 2018). Rhizospheric microorganisms also contribute to plant iron uptake through the production of siderophores, small organic molecules, that chelate the ferric form of iron, normally not bioavailable, and make it absorbable by the plants (Saha et al., 2013). Other microbial mechanisms modulate plant nutrition indirectly by the microbial production of phytohormones and other signals that stimulate lateral root branching and root hair growth, maximizing the soil exploratory capacity of the plant (Vacheron et al., 2013).
The microorganisms harbouring these beneficial functions are known as Plant Growth Promoting (PGP) microbes and some culturable species are used as biofertilizers (e.g. Pseudomonas fluorescens, Azospirillum brasilense). Microorganisms harbouring the same PGP functions (e.g. phosphate solubilization, siderophore production) can be categorized as functional groups that can be studied together and not as single strains using sequencing and qPCR on functional genes or high-throughput cultivable approaches (Vacheron et al., 2013). These PGP functional groups can be seen as biotic traits of the extended root phenotype that when better characterized (e.g. size, composition, structure, activity of the group) could help us understand the importance of these functions under variable environmental conditions (e.g. low nutrient availability, soil or climatic disturbance, plant life stage). These approaches have been well developed to characterize the nitrogen-fixer functional group in the rhizosphere using the nifH gene (Tan et al., 2003;Coelho et al., 2009;Bouffaud et al., 2016) but it needs to be developed for other important microbial functions performed by rhizospheric microorganisms.
Currently, this field of research is transitioning from studying a single PGP strain inoculated alone on the plant, in axenic conditions or on the field, to testing the effects of an assemblage of PGP strains (Vorholt et al., 2017, Finkel et al., 2017. The goal is to determine if complex inocula with diverse or redundant functions provide more efficient plant growth promotion and improve our understanding of the collective effects of the hundreds of PGP microorganisms that live and interact naturally in the rhizosphere. Some studies that inoculated a consortium of PGP strains reported higher increases in crop biomass and yield as compared with a single strain inoculum, suggesting additive or synergistic effects associated to microbial interactions and niche complementarity (Nain et al., 2010;Lally et al., 2017).
However, in other studies strain consortia performed similarly or worse than single strains (Lampis et al., 2015) or even caused bacterial community collapse and a loss of plant protection (Becker et al., 2012).
These findings highlight the necessity to develop a better understanding of microbe-microbe interactions in complex communities to design efficient microbial-based solutions for agriculture.
Microbiome level -Overall at the rhizosphere microbiome level, rhizodeposition stimulates the growth of hundreds of heterotrophic microbial species. These microbes do not necessarily harbour PGP traits but contribute in making the rhizosphere a nutrient hotspot for the plant through the degradation of soil organic matter (e.g. litter degradation). The definition and interpretation of the overall impact these microbes have on plant nutrient acquisition and use is challenging. It requires the development of synthetic plant microbiomes, that through the assemblage of multiple microbial strains simulate realistic rhizosphere microbial communities. Reductionist approaches based on synthetic plant microbiomes offer incredible opportunities to establish causality between microbiome characteristics (e.g. structure, composition, functions) and plant phenotypes under variable biotic and abiotic conditions (Vorholt et al., 2017). Pioneering work on rice synthetic microbiomes reveals bacterial consortia enriched in the indica genotypes contribute to higher nitrogen use efficiency than in japonica genotypes and also resulting in higher growth rates (Zhang et al., 2019).  (Finkel et al., 2019). These findings demonstrate that many rhizospheric microorganisms can either have beneficial or detrimental effects on plant fitness depending on the dynamic of multiple biotic and abiotic parameters that remain to be uncovered (Haney et al., 2015;Hacquard et al., 2017).

Role of the rhizosphere microbiome for abiotic and biotic stress tolerance
Plants face multiple abiotic and biotic stressors during their lifetime and they use a large repertoire of mechanisms to mitigate the effects on their fitness. Emerging evidence suggests that rhizospheric microbiota can enhance plant tolerance to drought, salt stress, pollutants, pathogen outbreak, herbivory or competition with other plants. In this section, we will detail how root-associated microbes and their functions provide a diverse arsenal to help the plant survive under stressful conditions and act as an extended immunity.
Tolerance to abiotic stressors (drought, salinity, pollution...) A large number of studies on stress tolerance mediated by the rhizosphere microbiome focused on drought stress that is one of the most destructive abiotic stressors for plants in both natural and agricultural ecosystems. PGP microbes are known to play a role in drought stress alleviation for various crops through the production of exopolysaccharides, different phytohormones, 1-aminocyclopropane-1-carboxylate (ACC) deaminase or volatile compounds (reviewed in Naylor and Coleman-Derr, 2018). At the microbiome level, it was found that an increase in endospheric Actinobacteria and especially of the Streptomycetaceae family was associated to higher drought tolerance across 30 phylogenetically diverse host plant species in a common garden experiment (Fitzpatrick et al., 2018).
Hence, the presence of specific PGP microbes or families can lead to higher drought tolerance but these beneficial effects are dependent on different historical factors, like previous exposure to drought or the host plant. Lau and Lennon (2012) demonstrated that adaptive plant responses to drought were mainly driven by the responses of soil microbiomes and highlighted that microbial communities pre-adapted to drought maintained a higher fitness for Brassica rapa in a mesocosm experiment. This is consistent with the finding that soil microbiomes from more constant environments are more sensitive to change and have a poorer functional acclimatisation compared to microbiomes from more fluctuating environments (Hawkes and Keitt, 2015). Additionally, Zolla et al. (2013) demonstrated that microbiomes historically exposed to the host plant (i.e. sympatric communities) provided higher drought tolerance than microbiomes previously exposed to other plant species. The presence of these sympatric microbiomes reduced the expression of drought response marker genes in the host plant and plant biomass was significantly increased compared to non-sympatric microbiomes conditions. These results highlight that plants benefit from their associated microbiomes to resist drought stress, especially when the microbial communities have been pre-exposed to this stressor and the host plant in previous seasons. These findings encourage more research to determine the adaptive potential of plants and their microbiomes to rapid changing climates but also in agriculture in the context of transition to new cropping systems or rotations.
Another abiotic stress that plants face frequently is soil salinity, especially in arid or coastal areas, that leads to large decreases in plant growth and yield. Some halotolerant PGP microbes, like Halomonas strains have been shown to promote plant growth under salt stress (Mapelli et al., 2013) and this higher salt tolerance was often linked to the bacterial production of ACC deaminase or volatile organic compounds (VOC) that helps the plant determine its sodium homeostasis (Yang et al., 2009;Siddikee, 2010). Additionally, anthropogenic activities are causing a large release of organic and metallic pollutants in the atmosphere and in soils that can cause oxidative stress in plants and decrease their fitness. Many rhizospheric microorganisms are able to accumulate or detoxify heavy metals and are playing a crucial role for the management of heavy metal stress in plants (Mishra et al., 2017). In particular, mycorrhizal fungi through their hyphal networks and the secretion of organic acids (e.g. oxalic acid, citric acid, gluconic acid, acetic acid) can solubilize, chelates and absorb heavy metals in soil and reduce their bioavailability for plants (Gube, 2016).
In conclusion, rhizosphere microorganisms are able to enhance plant tolerance to a wide array of abiotic stressors and to illustrate this phenomenon the umbrella concept of Induced Systemic Tolerance (IST) was proposed to describe all physical and chemical changes induced in plants by microorganisms that result in higher abiotic stress tolerance (Yang et al., 2009).

Rhizosphere microbiomes provide an extended immunity against biotic stressors
The commensal and mutualistic microorganisms of the rhizosphere also provide an extended immunity to the plant when exposed to biotic stressors, like pathogens, parasites or herbivores. In particular, many studies are available on the role of plant microbiota in mediating disease resistance (Vannier et al., 2019).
For instance, it was demonstrated that the resistance of a tomato variety to the soil borne pathogen Ralstonia solanacearum was driven by a native bacterial strain affiliated to the genus Flavobacterium (Kwak et al., 2018). Interestingly, for the same pathogen it was also demonstrated that the pathogen success was influenced by the microbial network structure, particularly when communities presented a higher stability and niche overlap with the pathogen (Wei et al., 2015). These two examples highlight that microbiota-mediated disease resistance operate at multiple levels in the microbiome, from single strains to emerging properties at the community level. This can be explained by the fact that microbiomes provide an extended immunity to their hosts through multiple mechanisms. Microorganisms can stimulate the plant innate immunity through a mechanism called induced systemic resistance (ISR) or priming, which is dependent of jasmonic acid and ethylene signalling (Pieterse et al., 2014). Recent studies show that plants modify their exudation pattern when exposed to pathogens as a "call for help" that enable the recruitment of beneficial ISR-inducing bacteria Yuan et al., 2018). Second, the plant microbiota can decrease pathogen success through direct microbial competition that complement plant innate immunity (Vannier et al., 2019). Native microorganisms can decrease pathogen invasion and fitness through resource and space competition, the production of antimicrobial compounds or hyperparasitism. Several studies show that the entire microbial community or the presence of a microbial consortium can act collectively as a barrier to pathogen invasion or emergence that are at the origin of disease-suppressive soils (Yin et al., 2013;Santhanam et al., 2015;Hacquard et al., 2017). Hence, some studies encourage to apply well established ecological theory to plant microbiome research on the relationships between biodiversity and ecosystem functioning that suggest that resistance to pathogen invasion increases with species diversity (i.e. diversity-resistance relationship, Hu et al., 2016;Mallon et al., 2015;Mallon et al., 2018). For instance, Hu et al., (2016) showed in simplified conditions that pathogen density and disease incidence decreased with increasing Pseudomonas diversity due to an intensification of resource competition and interference with the pathogen. Additionally, pioneer work considering multi-kingdom microbial consortia shows that A. thaliana survival in agar-based growth medium depends on the presence of a community of bacteria with redundant biocontrol traits to protect against fungi and oomycetes that are not kept at bay by the plant immune system alone (Durán et al., 2018). Thus, plant microbiota plays a crucial role for plant fitness during pathogen invasion and emergence through competitive exclusion that constitutes the first barrier for pathogens to circumvent and then through a modulation of plant immunity.
Similar findings on the role of plant-associated microorganisms for the suppression of aboveground insect pests through direct (e.g. pathogenicity against herbivores) and indirect mechanisms (e.g. microbial ISR against insects, modification of the leaf metabolome) are currently emerging (Pineda et al., 2017).
For instance, the root-endophytic fungus Trichoderma atroviride can induce resistance in maize against the herbivore insect Spodoptera frugiperda through an activation of plant defence responses and the production of volatile terpenes that reduces foliar consumption (Contreras-Cornejo et al., 2018). At the microbiome level, a study that performed inoculations of contrasted soil microbiomes on the roots of A.
thaliana showed that most microbiomes induced inhibition of Trichoplusia ni larvae herbivory compared to non-inoculated plants, that was likely associated with changes in the leaf metabolome (Badri et al., 2013). Altogether, these findings show that plants can survive to diverse biotic stressors with the help of their associated microbiomes harbouring a large repertoire of protective mechanisms that offers promising research perspectives to improve plant protection.

Rhizosphere microbiomes influence plant phenology
The association of plants with microorganisms starts as soon as seed formation and germination. The composition of the seed microbiome can impact seed viability and this has been particularly well studied in the context of negative impacts of seed pathogens on germination and emergence. In contrast, limited work has been conducted to investigate the beneficial role of seed microbiota on germination rates and seedling growth, despite potential important implications for agricultural production (Truyens et al., 2015;Shade et al., 2017;Lamichhane et al., 2018). For instance, quinoa seeds harbour consistently Bacillus endophytes that have high catalase activities and superoxide contents that help the host during cell expansion and induce a priming of the immune system. This association with Bacillus strains helps to explain in part the incredible capacities of quinoa seeds to germinate in minutes under hostile conditions, to regenerate when broken or even resuscitate (Pitzschke, 2016). Yet, despite these promising findings, to date no experimental evidence using seed microbiome manipulations (e.g. synthetic communities) has been performed to assess the influence of seed microbiota on seed germination rates or seedling emergence (Lamichhane et al., 2018). Hence, exciting research perspectives exist to determine the influence of seed microbiota on plant phenology during these critical stages of the plant's life cycle that can have profound impacts on plant health and productivity.
The impact of rhizospheric microbes on plant flowering has been more extensively studied on various plant species and environmental conditions (e.g. soil types, drought, plant competition). Using natural soil microbial communities or manipulated communities inoculated into different sterile soils, several studies demonstrated that soil microbiota can alter flowering time of A. thaliana or Boechera stricta by 1 to 5 days (Lau and Lennon, 2012;Wagner et al., 2014;Lu et al., 2018;Fitzpatrick et al., 2019). In addition, Panke-Buisse et al., (2015) provided an elegant demonstration using a multi-generation experiment with A. thaliana that specific soil microbiomes can induce earlier or later flowering times. The inoculation of these microbiomes to the soil of different A. thaliana genotypes or Brassica rapa led to similar changes in flowering time, indicating that microbiome effects on plant fitness can be reproducible across plant hosts. These results demonstrate that microbiomes at different stages of the plant life play a role in the phenotypic plasticity of their host and thus contribute to their rapid adaptation to new colonized environments or local disturbed conditions.

Conclusion/perspectives/future directions
Plant roots are constantly interacting with the soil they grow in and the complex biodiversity it harbours. Plants have therefore evolved mechanisms to shape this environment to increase their foraging capacity and control bioagressors. This extended root phenotype provides the plants with new functions or redundant functions (additive effects), and can have priming effects.
Much more research is needed to characterize the genetic control of the extended root phenotype such as soil acidification or soil aggregation that represent emerging properties resulting from the complex abiotic and biotic transformations operating in the rhizosphere impacting plant fitness under different environmental conditions. This requires researchers to bridge soil sciences, plant sciences and microbial ecology to fully understand the rhizosphere, a complex and dynamic environment. For instance, the majority of the rhizosphere microbiome, and its contribution to the extended root phenotype of the host, is not well defined. Important components of the rhizosphere biodiversity (e.g. protists, viruses) are also currently largely overlooked while they could have large contributions to microbiome structure and function (Henkes et al., 2018;Kuppardt et al., 2018;Pratama and van Elsas, 2018;Gao et al., 2019;Roossinck, 2019).
Importantly, the microbiome is strongly influenced by the plant genome and may be considered as an extension to form a second genome or collectively to form a pan-genome (Turner 2013). We need to better characterize the extra functions provided by the rhizosphere and under which conditions they are expressed to improve plant fitness. Currently, very few studies have uncovered the links between rhizosphere traits and plant fitness, yield, stress tolerance or disease resistance and this constitutes a major knowledge gap in our understanding of plant biology and ecology. Future research should address these gaps and aim at quantifying the cumulative effects of this extended root phenotype on plant fitness to determine the most crucial functions to select for. Altogether, the consideration of the rhizosphere as an extended root phenotype could lead to a completely new paradigm in sustainable agriculture.

Box 1: Summary
• The rhizosphere is a unique biophysical and biogeochemical environment shaped by plant roots in their interdependent and dynamic interaction with soil microbial communities.
• Plants genotype influence root biomechanical interactions with the soil and rhizodeposition and thus, the rhizosphere physico-chemical properties mediating root growth and access to soil resources.
• Beneficial root-microbial interactions range from symbiotic to commensalistic and are critical not only for plant nutrition and water acquisition but also confer plant with an extended immunity • Rhizosphere microbiota play a role in the phenotypic plasticity of their host and contribute to their adaptation to new environments or locally disturbed conditions • The genetics controlling extended root phenotype remain as a huge untapped genetic resource that needs to be explored in the transition to more sustainable production systems

Box 2: Open Questions
• What is the best strategy to quantify and rank the relative contribution of each rhizosphere trait to a specific plant phenotype?
• What are the key evolutionary trade-offs faced by plants during rhizosphere niche construction that ultimately drives the variability observed between genotypes?
• How do rhizosphere viruses and protists influence the structure and function of the rhizosphere microbiome and plant fitness?
• Can plant breeding based on rhizosphere traits (soil aggregation, acidification, exudation profiles, microbiome structure) improve crop productivity and resistance to biotic and abiotic stressors?
• What are the most efficient solutions to manipulate the rhizosphere microbiome to improve plant productivity and health?

DATA STATEMENT
All relevant data can be found within the manuscript and its supporting materials.