<figure><img src="image_1.png" /></figure>

HAL
open science

# Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health

Morgane Duret, Adrian Wallner, Marc Buée, Aziz Aziz

► To cite this version:

Morgane Duret, Adrian Wallner, Marc Buée, Aziz Aziz. Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health. Microbiological Research, 2024, 287, pp.127860. 10.1016/j.micres.2024.127860. hal-04795658

HAL Id: hal-04795658

https://hal.inrae.fr/hal-04795658v1

Submitted on 21 Nov 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health

Morgane Duret<sup>a</sup>, Adrian Wallner<sup>a</sup>, Marc Buée<sup>b</sup>, Aziz Aziz<sup>a,*</sup>

<figure><img src="image_3.png" /></figure>

## ARTICLE INFO

**Keywords:**

Microbiome
Ligneous plant
Perennial
Plant health

## ABSTRACT

Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.

## 1. Perennial ligneous plant microbiome as a key to harness its full potential to promote plant health

The plant microbiota represents a reservoir of extended functions for its host and is recognized as contributing to plant growth and health. The composition of the recruited community depends largely on the initial microbial pool in the plant's surroundings, the soil being its principal reservoir. The plant exerts on these populations a filtering selection through the secretion of root exudates and the production of specific organic matter, which is highly dependent on multiple parameters such as the host's genetics and the microbial population dynamics, biotic and abiotic parameters (Trivedi et al., 2020). Despite these multiple factors, recent studies suggest the existence of core microbiomes, represented by a plant's typical assemblage of microorganisms. For example, the grapevine's rhizospheric core microbiome would be mainly composed of *Proteobacteria*, *Actinobacteria* and *Acidobacteria* (Bettenfeld et al., 2021), resembling to the poplar (Beckers et al., 2017), citrus (Xu et al., 2018; Zhang et al., 2021), oak (Uroz et al., 2010), beech and Norway spruce (Uroz et al., 2016) rhizospheric core microbiome. Moreover, the specific

recruitment of microbes by the plant is influenced by microbial traits involved in plant colonization and by the host selection pressure towards beneficial traits involved in tolerance process to biotic and abiotic stresses (Park et al., 2023). In line with the functional redundancy concept, the cumulative effect of these traits constitutes the functional core of a population and is independent on the taxonomic core, as different members of the community can perform the same functions for the plant (Lemanceau et al., 2017).

The relationship between plants, microbial communities and pathogens is still unclear (Berg et al., 2021; Ginnan et al., 2020; Lee et al., 2020). Understanding the structure and dynamic of microbial communities during the onset of plant-pathogen interaction is fundamental to determining the beneficial microbial composition to improve plant health. To date, such attempts were mainly performed on annual or biannual herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only a few studies have focused on the microbial compositions, dynamics and their drivers in ligneous perennial plants (Cazorla and Mercado-Blanco, 2016). Factors associated with longevity and aging, the presence of hardwood tissues, root and shoot

<footnote><sup>a</sup> Université de Reims Champagne-Ardenne, INRAE, RIBP, USC 1488, UFR Sciences, Reims 51100, France</footnote>

<footnote><sup>b</sup> Centre INRAE Grand Est-Nancy, UMR Interactions Arbres-Microorganismes, Champenoux 54280, France</footnote>

<footnote>* Corresponding author.</footnote>

<footnote>E-mail address: aziz.aziz@univ-reims.fr (A. Aziz).</footnote>
architectures, phenology and seasonality that affect plant physiology should have a considerable impact on interactions with surrounding microbes as a potential biocontrol tool (Fig. 1) (Cazorla and Mercado-Blanco, 2016). The specificities of ligneous and perennial plants raise new problematics and perspectives in the endeavor to untangle the role played by microorganisms in plant health.

While most crops are annuals, such as rice, corn and wheat, perennials account for more than 13 % of cultivated areas worldwide (Migicovsky and Myles, 2017). Recently, a perennial rice variety was generated offering the same yield levels as elite annual varieties while integrating the benefits of sustainable crops (Zhang et al., 2022). As a perennial crop, specific problematics associated to its life cycle may arise, requiring increased attention to the functional role of microbial communities in plant health and longevity.

This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate their microbial communities, structure and dynamic in the rhizosphere, thus affecting plant health. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.

## 2. The ontogeny of perennial ligneous plants is accompanied by a temporal succession of rhizosphere microbiota with an enrichment of beneficial populations

Succession of plant associated microbes is a "directional change in the composition, relative abundance and spatial pattern of species comprising communities" (Frankland, 1992). Indeed, the physiological and molecular processes involved in aging are important drivers of microbial variation that could affect the recruitment and enrichment of the root and rhizospheric microbiota over time (Bond, 2000; Wagner et al., 2016). Root structural changes and root-derived exudates associated with plant aging are known to be responsible for microbial diversity and assembly in the rhizosphere (Fig. 2). Furthermore, enrichment of beneficial populations can be associated with increased pathogenic microbes. For instance, in the apple bark, age was shown to influence both pathogenic (Alternaria, Diaporthe, Diplodia and Phom) and potential beneficial microbes including fungi (Aureobasidium, Cryptococcus, Filobasidium, Rhodotorula, Sporobolomyces) and bacteria (Methylobacterium, Nocardioides and Sphingomonas) (Arrigoni et al., 2020). A comparison of Eucalyptus species at different developmental stages highlighted a decrease of the phylum WPS-2, the order of Shingomanaicales, the Arthrobacter and Sinomonas genera, while the order GP6 increased in older plants, which may result from a reduction of root exudation and allelopathic effects limiting carbohydrate availability in the rhizosphere (Qu et al., 2020). The predictive functions also suggest a

<figure><img src="image_4.png" /><figcaption>**Fig. 1.** Some characteristics differentiating annual cultivated plants from perennial ligneous at the rhizosphere level. Ligneous plants can reach different microbial populations through root depth and may exhibit specific colonization patterns due to their characteristics including higher genetic diversity or the presence of fibrous and pioneer roots with different constituents, such as defense molecules, lignin, etc. Moreover, their microbiome may also be influenced by cultural practices (pruning, grafting, long-term cultivation, etc.), the growth-dormancy cycles and aging process. These factors may also modulate plant immune responses and are not considered enough in the outcome of plant-microbiome-pathogen relationship, and in the creation of biocontrol products. -, =, +: lower, same or higher amount of microbes following the depth; AMF: arbuscular mycorrhizal fungus; EMF: ectomycorrhizal fungus; arrow: root exudates associated to recruited microbes (shared color).</figcaption></figure>
<figure><img src="image_5.png" /><figcaption>**Fig. 2.** Relationship between aging of perennial plants and the recruitment of microbes in the rhizosphere. Along the plant's growth, the physiological changes may impact the root exudates composition, thereby modifying the microbial populations attracted by the plant through the years. In particular, changes in water fluxes in aged plants have been suggested as inducing ABA production (Munné-Bosch, 2007), which is associated to the root colonization by arbuscular mycorrhizal fungi and can be perceived by specific microbial populations (ex. *Rhodococcus*, *Novosphingobium...*) (Eichmann et al., 2021). Arrows: root exudation. Each color corresponds to a specific kind and amount of exudates. These changes in microbial populations may be related to an evolution from carbon-cycling to nitrogen and sulfur-cycling metabolism (Qu et al., 2020).</figcaption></figure>

metabolic shift within the microbiome during the aging process, transitioning from carbon-utilizing bacteria in younger plants to bacteria involved in nitrogen and sulfur cycling for older plants (Qu et al., 2020). The changes in nutrient acquisition strategy through plant aging, as seen in Korean pine (*Pinus koraiensis*), spruce (*Picea koraiensis*) or smelly fir (*Abies nephrolepis*) may cause this microbial metabolic shift (Ren et al., 2023). For root-associated fungi, the diversity of mycorrhizal fungi is lower in young forest stands than in older stands, as illustrated for arbuscular mycorrhizal fungal (AMF) communities associated with *Artocarpus altilis*, a long-lived perennial breadfruit (Hart et al., 2014), or ectomycorrhizal fungi (EMF) in Douglas-fir forests with fungal diversity and composition stabilizing at 26 and 65 years old, respectively (Twieg et al., 2007). However, young annual plants are shown to be more prone to forming mycorrhizal associations, although it depends on species, and are often used as bait in field studies for monitoring soil diversity (Smilauer et al., 2021). As they age, woody perennial plants will also modify the soil parameters, such as pH and C/N ratio (Frankland, 1992; Peltoniemi et al., 2004). These modifications will strongly structure the soil microbial and rhizosphere communities, which in turn will impact plant growth and health (plant-soil feedback).

The increased changes in the microbial communities, which could be dependent on the time of conditioning of plant-soil microbe exchange, may impact their functions and effects on plant fitness (Ke et al., 2021). During the plant ontogeny, intrinsic modifications can influence its microbiota. Phytohormones play a key role in the plant aging and in the assembly of plant microbiomes, and both microbes and plants use the same hormones in different functions and adaptive strategies (Khan et al., 2013). Specific phytohormones can be exuded into the rhizosphere and exert fine-tuning selection on plant-interacting microbes in the rhizosphere (Liu et al., 2020). For example, abscisic acid was shown

to be involved in the interaction with AMF and can also be perceived by other members of the rhizosphere and even used as a carbon source by some rhizobacteria like *Rhodococcus* and *Novoshingobium* (Eichmann et al., 2021). Other phytohormones including cytokinins, gibberellic acid, strigolactones and brassinosteroids have been shown to be involved in rhizobia and AMF associations (Carvalhais et al., 2019; Liu et al., 2020; Yu et al., 2018), whereas auxins can be used as a carbon source and triggers metabolic changes in the rhizosphere promoting antimicrobial activity of some members of Streptomycetaceae (Eichmann et al., 2021). Similarly, transcriptomic analyses showed an upregulation of SA pathway-related genes in 1-year-old ginkgo (*Ginkgo biloba*) plants and a downregulation JA pathway-related genes in older ones (Wang et al., 2022). These signaling pathways, which are involved in plant defense regulation at the systemic scale, may also play an important role in the structure, assembly and recruitment of microbial communities (Carvalhais et al., 2015; Lebeis et al., 2015; Eichmann et al., 2021).

Although microbial diversity recruitment seems to be dependent on the plant age (Berlanas et al., 2019), the long-term growth legacy in grapevine plants seems more important than the aging in shaping the rhizospheric microbiota (Manici et al., 2017). The microbiota assembly in perennial plants may result from a selection pressure exerted by the plant depending on its susceptibility to environmental stresses (Kristy et al., 2022). This may be close to the soil-borne legacy hypothesis in annual plants (Bakker et al., 2018). In line with the "cry for help" strategy (Liu et al., 2024), the growth of successive plant generations subjected to the same stress can shape the recruitment of beneficial microorganisms through specific exudates, thereby priming plant for enhanced systemic resistance (Vismans et al., 2022; Yuan et al., 2018). In perennial plants, the microbiome dynamic under a long-lasting stress
period remains to be explored. One example of the prairie grass (Andropogon gerardii) grown under arid conditions for ten years showed significant differences in bacterial root communities, without significant change in fungal communities between different ecotypes (Sarkar et al., 2022). It is also known that young vineyards are more susceptible to black foot and Petri diseases, while Esca complex, Botryosphaeria, and Eutypa diebacks usually occur in mature vineyards (Gramaje et al., 2018). Despite a lower microbial diversity and richness in declined grapevines, symptomatic rhizosphere was enriched in beneficial microbes, which could be involved in grapevine protection against trunk diseases (Darriaut et al., 2024). Investigating plant microbiome for a long-lasting stress period could provide clues on the existence of shaped communities that could modulate the plant health and aging process.

### 3. Heterozygosis in perennial ligneous plants may provide a wide range of functions through the microbiota

In animals, it was shown that heterozygosity of the major histocompatibility complex loci, in contrast to the homozygous one, is correlated with positive diversification of the gut microbiome's functionalities and an enhancement of microbial network connectivity (Wadud Khan et al., 2019). It resulted in a functional diversification associated with an improved host health (Wadud Khan et al., 2019). In plants, surrounding microbes are detected by cognate pattern recognition receptors localized at the cell surface. Their exact role in the differentiation of beneficial from pathogenic bacteria is still under investigation in both herbaceous and ligneous plants (Héloir et al., 2019; Huang and Joosten, 2024; Zhang and Kong, 2022). We could hypothesize that plant's heterozygosity could play a critical role in tremendous diversity of plant immune receptors, thus increasing the diversity and functionality of their microbiomes.

Perennial ligneous plants have a longer juvenile period, which has limited their number of generations compared to annuals and the subsequent loss of allelic diversity through directed selection. Single nucleotide polymorphism and microsatellite analyses of grapevine and apple genomes suggest a limited erosion of genetic diversity between cultivated varieties and their wild progenitors (Cornille et al., 2012; Miginovsky and Myles, 2017; Myles et al., 2011). Compared to the annual crops, perennials are mainly heterozygous, although heterozygosity and accelerated varietal selection exist in perennial crops. This heterozygosity is maintained through clonal propagation, even if this cultivation method introduces genetic homogeneity at the population scale for cultivated ligneous plants (Gaut et al., 2015). However, these genetically fixed perennial crops are more susceptible to diseases (Myles, 2013). Their heterozygotic genomes might drive higher microbial diversity and functionality of their microbiomes, despite being associated to a higher disease susceptibility in the case of clonal propagated crops. Recently, a correlation between microbial abundance in roots and heritable loci responsible for variations in PAMPs triggered immunity (PTI) was reported in switchgrass (Panicum virgatum) (Edwards et al., 2023). Thus, the higher genetic diversity commonly observed in perennial plants may contribute to shaping microbial diversity and presumably activating PTI through multiple signaling pathways.

### 4. Seasonality influences root colonization through plant metabolic change

Herbaceous and ligneous perennial plant are punctuated by seasonal environmental variations that affect their phenology (Friedman, 2020). These cycles induce changes in the metabolic activity of plants over the course of the seasons in response to climatic constrains. Climatic parameters and plant phenology could have a direct impact on the soil microbiome, leading to changes in the rhizospheric sub-populations. The work carried out in two *Populus* spp. from the leaf endosphere, root endosphere and rhizosphere revealed variations across seasons and

years (Argiroff et al., 2024). Together with climatic variations, specific seasonal patterns were observed each year (Argiroff et al., 2024). Similarly, Nakayama and Tateno (2023) reported important seasonal variations in the relative abundance of EMF species in a hardwood forest, with a reduced occupancy in the dormant seasons. In addition, bacterial populations in forests displayed similar abundance before and after winter, with a change in species diversity (Kubiak et al., 2018, 2017). Growth-dormancy cycles are associated with variations in carbon metabolism, affecting carbon availability for rhizospheric microbe during winter (Esperschütz et al., 2009) and symbiotic fungal partners (Nakayama and Tateno, 2023). In the beech rhizosphere, the reduction of photosynthetic activity associated to the dormancy process and subsequent rhizospheric carbon transfer correlates with an increase in microbial cyclopropyl fatty acids (Esperschütz et al., 2009). The enhanced accumulation of these fatty acids, as starvation indicators (Guckert et al., 1986), suggests a functional role of the dormancy-associated reduction in nutrient availability shaping the microbiome.

Mature ligneous plants may have more carbon to allocate as root exudate, which could in turn result in stronger effects on its rhizospheric microbiome during the dormancy process. For instance, a strong increase of belowground flux of photosynthate in boreal pine (*Pinus sylvestris*) forests between June and August was attributed to the end of the growing season (Högberg et al., 2010; Prescott, 2022). This suggests that growth-dormancy cycles could differently impact microbial communities of mature and juvenile plants. It has been reported that microbial community can tolerate changes in carbon allocations while maintaining its structure through modulation of carbon needs (Cesarz et al., 2013; Sommer et al., 2017). This is supported by the presence of intra-annual shifts in the microbiota composition, as shown with the endophytic root populations of two grapevine cultivars (Biget et al., 2023a).

The dormancy shift is often accompanied by a storage of photosynthesates in parenchyma or ray cells, as well as in roots (Dominguez and Niittylä, 2022). As some roots are preserved during this process in ligneous plants, the onset of dormancy should have an impact on the rhizospheric, endophytic and epiphytic microbial populations. The chemical changes in root composition before dormancy may induce a tissue spreading of endophytes, as they require a specific chemical environment for their growth and metabolic activities (Compant et al., 2021). De novo colonization events could thus result in activation of new plant defense responses at the tissue level (Chuberre et al., 2018). Some microbes could spend winter in perennial roots, as the case of the endophytes in seeds (Cheplick, 2017). Roots can also host various strains, which may originate from different simultaneous or successive colonization events. For example, Olive (*Olea europaea* L.) root hairs with established populations of a *Pseudomonas* strain allows the attachment and penetration by other bacteria from the same genus (Prieto et al., 2011). An established endophytic microbiome would then initiate waves of root colonization, promoting plant immune system and interactions between colonizing microbes (Fig. 3) (Hafiz et al., 2022; Pérez-De-Luque et al., 2017). This is consistent with the fact that AMF, as a part of the endospheric microbiota, were reported to induce reprogramming the root primary and secondary metabolite production (Kaur and Suseela, 2020). This could modify the issues of further symbiotic interactions (Kaur and Suseela, 2020). During growth-dormancy states, the occurring colonization events could increasingly support various ecological niches, contributing to the genotype-effect described above. Thus, exploring rhizospheric microbiome before and after dormancy could shed light on the relationships between physiological state and microbial-mediated metabolic change and plant immunity.

### 5. Specific cultural practices can contribute to microbial diversity shaping in perennial plants

The grafting of a scion on a rootstock is a common practice in ligneous crop cultivation for enhancing resistance to soil diseases and
<figure><img src="image_6.png" /><figcaption>**Fig. 3.** Change in epiphytic and endophytic microbial populations through the growth-dormancy transitions. The chemical changes in root composition during growth and dormancy states may influence the epiphytic and endophytic microbial populations through different steps. Epiphytic and endophytic microbial populations may colonize the perennial and non-perennial roots during the initial growth stage (1), thus promoting plant immune system (2). Following the shift to a dormancy state, root endophytic microbes can move to different tissues (3) (Compant et al., 2021; Dominguez and Niittylä, 2022). This tissue colonization could contribute to the modulation of plant systemic immunity (4) (Chuberre et al., 2018). By the end of the dormancy state, the endophytic microbes may recolonize their initial environment (5). The presence of these established microbes may further facilitate the root colonization by other microbes (5) (Prieto et al., 2011). The appearance of new or older roots may constitute a communication network between the plants and specific populations of their microbiome (5), thus modulating plant systemic immunity (6). Big arrows: plant immune response. Small arrows: microorganisms' movement across the tissues. Each color for the arrows corresponds to specific microorganisms at their origin. Numbers: events order.</figcaption></figure>

improving physiological traits (Tedesco et al., 2022; This et al., 2006; Wang et al., 2017). Grafting often combines compatible scions and rootstocks of different ages, offering the opportunity to explore the mechanisms behind the aging process in perennial plants. Grafting can influence phenotypic traits of grafted plants through various molecular signals exchanged between scion and rootstock (for a review see Wang et al., 2017). The grafting of *Pinus* sp. scions from old donors on young rootstocks impacts branching patterns, leaf morphology and growth period of dormant buds (Mencuccini et al., 2014; Velisevich et al., 2021). As shoot meristems respond to signals at a systemic scale, the scion could also modulate root system architecture and root meristem activity, thereby shaping their microbial communities. The meristematic zone of the root tip is the most active in terms of root exudate production and, as such, plays a key role in the selective process of the rhizomicrobial community (Tian et al., 2020). In addition, epigenomic and transcriptomic analyses showed that grafted plants inherited part of the rootstock's epigenomic characters, resulting in the activation of various genes at systemic level, including photosynthesis-related genes (Perrin et al., 2020). This underlines the important role of grafting process in improving photosynthetic activity, triggering root exudation and shaping microbial communities in the rhizosphere.

In grafted plants, the rootstock can modulate rhizomicrobial
composition, while the effect of scion seems to be dependent on the
microbial community in the rhizosphere and root compartments
(Darriaut et al., 2022; Lailheugue et al., 2024). However, in grapevine,
although the rootstock was shown to influence the taxonomy, structure,
and network properties of the root bacterial community, their impact on
microbial functional traits remains controversial (Marasco et al., 2018;
Zuzolo et al., 2023). In cacao (*Theobroma cacao* L.), unlike the rootstock,
the scion has shown only slight impact on the rhizomicrobiota (Schmidt
et al., 2021). Some of the recruited bacterial taxa by the rootstocks might

be related to the plant nutrition status (Schmidt et al., 2021). However, interactive effects of scion and rootstock genotypes resulted in different microbial diversities (ex. α- or β-diversity), suggesting that specific combinations could affect the plant's ability to recruit specific microbial functional diversity (Vink et al., 2021). The cross talks between rootstocks and scions are not well understood yet, but involve activation of phytohormone pathways, epigenetic changes, and small RNA long-distance signaling, processes that would also be involved in shaping and recruitment of microbiota (Habibi et al., 2022). Biget et al. (2023b) used several grafted grapevines to formally evaluate the hologenome concept. The authors showed that both scions and rootstocks are significant drivers of the shaped microbiome from endosphere, especially regarding the β-diversity, the rootstock effect being the stronger.

Pruning of ligneous crop plants may also contribute to shaping rhizosphere microbiota but remains poorly elucidated. If not removed, pruned shoots and leaves become a source for soil nutrients and lead to an accumulation of allelochemicals such as polyphenols, flavonoids and alkaloids, which ultimately lead to changes in soil microbial activity and biogeochemical cycling (Arafat et al., 2020; Oo et al., 2018). In tea (*Camellia sinensis*) plantations, where pruning is a common practice, it seems difficult to replant young plants, as leftover soil chemicals could negatively affect root architecture, root hair development, and apex swelling (Pham et al., 2019). Over the long term, pruning is correlated with a reduction in microbial abundance and richness (Bora et al., 2022). Nevertheless, the microbiota of pruned plants showed a higher proportion of bacteria with beneficial functions for plant growth and survival under stress conditions, like *Pseudomonas*, *Solibacter*, *Rhodopseudomonas* and *Nitrobacter* sp. In terms of functions, there was an enrichment in stress-responsive metabolic pathways, especially those related to carbohydrates and amino-acids. The stressful pruning practice
can therefore contribute to the shaping of a microbial community, which
can prime plants to cope with subsequent stresses (Bora et al., 2022).

Replanting perennial plants could also have a significant impact on microbial communities in the rhizosphere. In grapevines, short-term replanting increased the abundance of beneficial bacteria and damaging fungi, while long-lasting replanting resulted in a less complex microbiota (Liu et al., 2021). This imbalance could be related to secreted autotoxins by roots into the rhizosphere, since the autotoxin p-hydroxybenzoic acid (4-HBA) secreted by grapevine roots can trigger mitigation of beneficial bacteria belonging to *Gemmatimonas*, *Streptomyces*, and *Bacillus* genera and spreading of pathogenic fungi, such as *Fusarium*, *Neocosmospora*, *Gibberella*, and *Fusicolla* (Guo et al., 2015; Liu et al., 2022). These effects could be due to the 4-HBA-enhanced exudation of amino acids and secondary metabolites and reduced amount of organic acids in the rhizosphere (Liu et al., 2022). Moreover, the exudation of phloridzin by apple was positively correlated with the abundance of *Actinomycetes*, *Bacillus subtilis* and *Pythium intermedium*, which are considered as indicators of apple replant disease (Hofmann et al., 2009). However, the rhizosphere of disease-tolerant rootstocks displayed an enrichment in *Burkholderia cepacia* as a beneficial bacteria, which is completely absent from the disease-susceptible rootstock environment (Laurent et al., 2010).

**6. Root architecture, deepness and composition are key factors of microbial colonization and pathogen control**

Recent review (Fleishman et al., 2022) highlighted that 92 % of 377
studies on rhizospheric microbiota did not take into account the func-
tional properties and root architecture. Perennial plants display a more
complex root architecture, with functional variation at a same root

branching order i.e., pioneer roots and fibrous roots which differ in
morphology, lifespan and functions (Polverigiani et al., 2011; Zadworny
and Eissenstat, 2011). Pioneer roots are composed of more tracheary
elements and hypodermal layers, with less passage cells than fibrous
roots (Bagniewska-Zadworna et al., 2012; Zadworny and Eissenstat,
2011). They also enhance moist soil sections and are less prone to the
fungal colonization involved in nutrient acquisition (Polverigiani et al.,
2011; Zadworny and Eissenstat, 2011). Pioneer roots are also less sus-
ceptible to pathogen colonization than fibrous roots. This could be due
to the differential microbial colonization and accumulation of antimi-
crobial compounds, as well as to the expression of plant defense re-
sponses, including accumulation of phenolic compounds (Emmett et al.,
2014). It has been suggested that the allocation of defense molecules is
different in pioneer roots, compared to first order fine-feeder roots,
resulting in different outcomes against pathogens (Zadworny and Eis-
senstat, 2011) (Fig. 4).

The presence of additional hypodermal layers and less passage cells in pioneer roots could make them difficult to be colonized by beneficial or pathogenic microbes (Bagniewska-Zadworna et al., 2012; Emmett et al., 2014; Zadworny and Eissenstat, 2011). Nevertheless, pioneer roots could provide a perennial ecological niche for colonizing microorganisms (Polverigiani et al., 2011; Zadworny and Eissenstat, 2011). Although fibrous roots are more likely to produce higher concentrations of exudates, the attracted bacteria could only have a transient effect due to the short lifespan of the roots. However, endophytic bacteria could enter fibrous roots and then migrate through the conductive tissues towards more perennial parts. As fibrous roots have a shorter life cycle and are generated throughout a plant's lifetime, they could attract similar bacteria at each growth cycle, resulting in a priming state of plants (Conrath et al., 2015). More investigations are still needed to understand

<figure><img src="image_7.png" /><figcaption>**Fig. 4.** Root characteristics of perennial plants and their potential link with root colonization by microorganisms through the years. Two kinds of roots are retrieved in woody perennial plants: the fibrous roots, more abundant in the topsoil layer, and pioneer roots, more abundant in the subsoil layer. Each root system exhibits specificities that may impact their colonization, such as a gradient of plant defense molecules (ex. phenolic compounds) (blue arrows and blue gradient), more abundant in fibrous roots and in low root order (1–4), or the presence of more passage cells (purple cells) and less tracheary elements and hypodermal layers in fibrous roots (Bagniewska-Zadworna et al., 2012; Zadworny and Eissenstat, 2011). Moreover, pioneer roots are more likely to be preserved through the years, which maintain microbial populations through the years (green microbes). The fibrous roots may be at the origin of repeated contacts with microbes (red microbes) through the years following their growth, thus resulting in the induction of plant defense responses (Polverigiani et al., 2011; Zadworny and Eissenstat, 2011).</figcaption></figure>
the relationships between the root architecture of ligneous plants, their microbiota, and their immune system.

Trees and shrubs have the capacity to extend deeper in the soil than herbaceous plants (Schenk and Jackson, 2002). Microbial communities can therefore vary in size and diversity depending on the soil physico-chemical properties, which vary tremendously across soil layers (Steenwerth et al., 2008). In vineyard, when the rhizospheric soil samples from surface horizons were compared with two-meters depth, there was no significant difference in the relative abundance of Gram-positive bacteria and Actinomycetes, but a decrease in Gram-negative bacteria and an increase in fungal abundance were observed (Steenwerth et al., 2008). These shifts in soil microbial communities could be due to soil resource availability, root distribution and exudate gradient (Tückmantel et al., 2017). The fungal communities in eucalyptus (Eucalyptus grandis) roots were dominated by EMF at more than 4 m depth, particularly by Pisolithus genus, which represented 90 % of the sequences analyzed by Robin et al., (2019). This ECM genus is characterized by a mycelial structure favoring long-distance soil exploration (Agerer, 2001). The reach of deep soil layers by the roots or ECM fungi provides multiple benefits including nutrient and water uptake (Agerer, 2001). This can also be increased by hydraulic lift, with a water transfer through the roots from deep to topsoil layers (Maeght et al., 2013), thereby inducing change in microbial metabolism (Bian et al., 2022).

The deep rhizospheric microbiota may also influence the communities above through change in pattern of root exudation at the systemic level (Fig. 5). For instance, local colonization of tomato roots triggers a systemically induced root exudation of metabolites (SIREM), including acylsucrose, steroidal glycoalkaloids, lignans, hydroxycinnamic acids, which are accumulated in lateral root tips or root hairs (Korenblum et al., 2020). Glycosylated azelaic acid, known to be involved in systemic acquired resistance (SAR) signaling, was also found in SIREM of

<figure><img src="image_8.png" /><figcaption>**Fig. 5.** Root colonization waves by specific microbial species may be influenced by deeper microbial populations. The contact of plant with new microorganisms can trigger (1) a systemically induced root exudation of metabolites (SIREM) (Korenblum et al., 2020), then recruit new microorganisms at various depths (2). New colonization waves by beneficial microorganisms may occur (3). - , =, +: lower, same or higher amount of microbes following the depth. Small arrows: exudates; Big arrows: induction of SIREM. Each color corresponds to specific microorganisms and the root exudates.</figcaption></figure>

tomato following a local colonization by *Bacillus* genus (Korenblum et al., 2020). However, this process has not been described so far in ligneous plants.

## 7. Root cell wall constituents are involved in microbial colonization and persistence

Root colonization by the microbiome is a critical step in establishing molecular dialogue considered as a key determinant of plant health and resilience. Due to their numerous traits, plant roots are able to selectively shape the microbiome in the rhizosphere, rhizoplane and endosphere (Edwards et al., 2015). This could have considerable impact on microbial colonization and function. Root colonization is influenced not only by their exudated chemical profile, but also by root cell wall composition (Beckers et al., 2016; Zhou et al., 2022). It has been reported that larger roots have an increased cellulose content and less lignin in Chinese pine (*Pinus tabulaeformis*), Douglas fir (*Pseudotsuga menziesii* [Mirb.] Franco) and European beech (*Fagus sylvatica* L.) (Thomas et al., 2014; Zhang et al., 2014).

The root's chemical composition is also dependent on the root order. *Quercus alba* and *Quercus rubra* exhibit an overall lower lignin content in the distal roots of both first and second order (Suseela et al., 2020). Still, distal roots have a higher content of guaiacyl lignin and bound phenolics which increase the intertwining of the lignocellulosic matrix, and thus ensure greater tissue integrity (Suseela et al., 2020). In peach tree (*Prunus persica* L.), fine roots, compared to medium and large ones, harbor a higher microbial diversity and a higher abundance of beneficial taxa (*Bradyrhizobium*, *Pseudomonas*, *Streptomyces*, *Burkholderia* and *Sphingomonas*), involved in soil disease suppressiveness, plant growth, nutrient fixation, solubilization and cycling (Pervaiz et al., 2020). Similar patterns have been observed with AMF and EMF associated trees by comparing five root orders (King et al., 2021). Thus, the colonization efficiency of ligneous plants could be primarily directed by the capacity of some microbes to perceive and degrade the root components and to cross their physical barriers (Debois et al., 2015; Hoff et al., 2021; Wu et al., 2015). For instance, *Bacillus velezensis* is sensing the host pectic homogalacturonans through two conserved pectinolytic enzymes, which contribute to the production of biofilm and surfactant metabolites needed to the bacterium establishment and its persistence in the roots (Beauregard et al., 2013; Boubsi et al., 2023; Wu et al., 2015). The colonization efficiency could be in favor of microorganisms with functional traits involved in the degradation of cellulose and lignocellulose in first and second root order, and of lignin in higher root orders (Suseela et al., 2020). It has also been reported that a strong colonization of *Quercus alba* fine roots by EMF under water deficit stress is associated with a decrease in ellagitannin content, and an increase of fiber-bound condensed tannins in fine root orders (Suseela et al., 2020). As ellagitannins have antimicrobial properties, their decrease could be related to an adaptive response to promote symbiotic associations.

## 8. Mycorrhizal fungi and microbial interactions in ligneous plants

Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants (Brundrett, 2002; Hoeksema et al., 2018). AMF and ECM are the most common and widespread symbionts found in the rhizosphere of various ligneous plants, including wild and cultivated grapevines (Kocsis and Szalanski, 2011; Radić et al., 2018, 2021; Trouvelot et al., 2015). However, ericoid mycorrhizal fungi (ErMF) are other endosymbionts restricted to Ericaceae (Vohník et al., 2013). Besides their role in plant nutrition and plant health, EMF could provide a wider range of benefits directly, as demonstrated for AMF or through their interaction with microbial community associated with the host plant (Dreischhoff et al., 2020; Terhonen et al., 2019). It has been demonstrated that AMF inoculation resulted in a shift in the root bacterial and fungal communities
(Solís-Domínguez et al., 2011). Some bacterial genera are more associ-
ated with AMF-colonizing roots, while others are more frequent in the
roots colonized by EMF. For example, the bacterial genera *Flavisolibacter*
and *Phenylobacterium* are more commonly found in roots colonized by
EMF, whereas *Rudrobacter* and *Gemmata* were more abundant in plants
colonized by AMF (Toju et al., 2019). However, in non-mycorrhized
plants *Ferrimicrobium*, *Mycobacterium* and *Nocardioides* were more
abundant (Toju et al., 2019). A comparison of the bacteriome of roots
and mycosphere of *Pinus sylvestris* and three ericoids revealed that the
ErMF colonization is also associated to a different microbiome in the
plants surrounding soil (Timonen et al., 2017). Moreover, their relative
abundance increases with plant's age, as shown in rabbiteye blueberries
(Vaccinium ashei Reade) (Che et al., 2022). Although this phenomenon
can be partially explained by the influence of a mycorrhizal coloniza-
tion, it also seems to be linked to specific interactions between the
microbiota and mycorrhizal fungi (Liu et al., 2018; Scheublin et al.,
2010). Some bacteria are able to colonize hyphae and feed on
fungal-derived nutrients (Toju et al., 2019). Other bacteria are consid-
ered as mycorrhiza helpers, facilitating plant mycorrhization (Deveau
and Labbé, 2016). The association of mycorrhiza with beneficial bac-
teria is frequently observed in AMF colonizing herbaceous plants, with a
transport of the functional bacteria along the surface of their extra-
radical hyphae (Jiang et al., 2021). EMF could be also involved in the
root recruitment of long distant beneficial bacteria through transfer of
plant-derived carbon (Gorka et al., 2019) (Fig. 6). However, the soil of
some AMF-associated trees is likely colonized by pathogenic microbes,
which are not completely counteracted by the AMF (Kadowaki, 2024).
Thus, the symbiotic AMF-tree associations are tending towards negative
plant-soil feedback, while the EMF-trees are tending towards a positive

<figure><img src="image_9.png" /><figcaption>Fig. 6. Hypothetical changes in microbial populations during pathogen attack in mycorrhized perennial woody plants. Following pathogen attack (1; yellow dots), plant immune response (yellow arrows) is systemically expressed, and systemic signals could be transduced to neighboring plants through EMF (2) (Song et al., 2015). Some microbes are able to move along fungal hyphae (Jiang et al., 2021), and contribute to microbial transfer between the plants (3; red microbes). These microbes could then colonize roots of the attacked plants (pink stars). The enhanced immune response (4; pink arrows) could help the plant to defend itself against pathogen (5). The Hartig net can also contribute to the plant protection against soil pathogens (green microbes), while EMF themselves may provide specific beneficial microbes (purple microbes).</figcaption></figure>

one (Kadowaki, 2024).

EMF are able to build a network of intruding hyphae in the apoplast
of the root cortex layers, known as Hartig net. The resulting root cracks
could be used by bacteria to enter and colonize roots (Nurmiaho-Lassila
et al., 2011). In addition, EMF form a dense mantle at the root surface
that provides physical protection against root pathogens (Branzanti
et al., 1999; Marx, 1972; Ross, 1972). The mantle also provides shelter
for a number of bacteria that stimulate mycelial growth (Garbaye and
Bowen, 1989). Mantle formation by EMF, as opposed to AMF, can
further influence ligneous plant diversity in forests. The presence of EMF
associations results in less species diversity, which could be due to an
increased seedling survival promoting the spread of a dominant species
(Bennett et al., 2017). Similarly, EMF dominated stands were exhibiting
less prokaryotic diversity, as well as saprophytic and pathogenic fungi,
compared to combined EMF-AMF stands. Moreover, the fungal com-
munities were more homogeneous in this last condition (Edwards et al.,
2024).

9. Concluding remarks

Microbial assembly in the rhizosphere of annual and ligneous plants is controlled by various intrinsic and environmental drivers. In this review we highlighted the specificities of ligneous plants in shaping their microbiome, including their aging processes, physiological and molecular status associated to their seasonality and their high heterozygosis, root architecture and deepness, root components and colonization process, complex microbial interactions in the rhizosphere, and cultural practices. All or part of these drivers would have a considerable impact in improving plant growth and health directly or indirectly through the recruitment and shaping functional microbiome. Furthermore, perennial plants can harbor certain populations of microorganisms exhibiting specific functions necessary to maintain the structure and role of the whole rhizomicrobiome. Furthermore, the mechanisms associated with microbial signal transduction and plant physiological state in a holobiont context remain to be elucidated. Thus, characterizing microbial assemblages in the rhizosphere to predict plant health is a fundamental issue for anticipating the outcomes of plant-microbiome interactions. To this end, research efforts should be devoted to the microbiome evolution through the years and the plants development stages by increasing sampling size. This would provide an insight into the mechanisms of the ligneous plant-microbe interactions, as a holobiont, by including deeper bacterial and fungal populations. Further investigation would also involve extended sampling site to include the mycosphere of mycorrhizal fungi. More emphasis should be placed on understanding the effects the terroir and sustainable practices (e.g., intercropping, cover crops, microbiome inoculation) on the outcome of plant-microbiome relationships, plant health and resilience to climatic events.

CRediT authorship contribution statement

**Aziz Aziz:** Writing – review & editing, Validation, Supervision, Resources, Project administration, Investigation, Funding acquisition, Formal analysis, Conceptualization. **Marc Buée:** Writing – review & editing, Formal analysis. **Adrian Wallner:** Writing – review & editing, Investigation, Formal analysis, Conceptualization. **Morgane Duret:** Writing – original draft, Investigation, Formal analysis, Conceptualization.

Declaration of Competing Interest

The authors declare that the research was conducted in the absence
of any commercial or financial relationships that could be construed as a
potential conflict of interest.
# Data availability

No data was used for the research described in the article.

# Acknowledgements

This work was funded by the French National Research Agency through the PRIMA-MiDiVine project 1564.

# References

Agerer, R., 2001. Exploration types of ectomycorrhizae: A proposal to classify ectomycorrhizal mycelial systems according to their patterns of differentiation and putative ecological importance. *Mycorrhiza* 11, 107–114. https://doi.org/10.1007/S005720100108/METRICS.

Arafat, Y., Din, Ud, Tayyab, I., Jiang, M., Chen, Y., Cai, T., Zhao, Z., Lin, H., Lin, X., Lin, S., W., 2020. Soil sickness in aged tea plantation is associated with a shift in microbial communities as a result of plant polyphenol accumulation in the tea gardens. *Front. Plant Sci.* 11, 601. https://doi.org/10.3389/FPLS.2020.00601/BIBTEX.

Argiroff, W.A., Carrell, A.A., Klingeman, D.M., Dove, N.C., Muchero, W., Veach, A.M., Wahl, T., Lebreux, S.J., Webb, A.B., Peyton, K., Schadt, C.W., Cregger, M.A., 2024. Seas. longer-Term. Dev. Gener. Tempo Dyn. *Popul.* Micro mSystems 9. https://doi.org/10.1128/MSYSTEMS.00886-23/SUPPL_FILE/MSYSTEMS.00886-23-S0001.DOCX.

Arrigoni, E., Albanese, D., Longa, C.M.O., Angeli, D., Donati, C., Ioriatti, C., Pertot, I., Perazzolli, M., 2020. Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees. *Environ. Microbiol.* 22, 2080–2093. https://doi.org/10.1111/1462-2920.14963.

Bagniewska-Zadworna, A., Byczyk, J., Eissenstat, D.M., Oleksyn, J., Zadworny, M., 2012. Avoiding transport bottlenecks in an expanding root system: Xylem vessel development in fibrous and pioneer roots under field conditions. *Am. J. Bot.* 99, 1417–1426. https://doi.org/10.3732/AJB.1100552.

Bakker, P.A.H.M., Pieterse, C.M.J., de Jonge, R., Berendsen, R.L., 2018. The Soil-Borne Legacy. Cell 172, 1178–1180. https://doi.org/10.1016/j CELL.2018.02.024.

Beauregard, P.B., Chai, Y., Vlamakis, H., Losick, R., Kolter, R., 2013. *Bacillus subtilis* biofilm induction by plant polysaccharides. *Proc. Natl. Acad. Sci. U. S. A.* 110, E1621–E1630. https://doi.org/10.1073/PNAS.1218984110/SUPPL_FILE/PNAS.201218984110.SI.

Beckers, B., Beeck, De, Weyens, M.O., Acker, N., Van, Montagu, R., Van, M., Boerjan, W., Vangronsveld, J., 2016. Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome. *Proc. Natl. Acad. Sci. U. S. A.* 113, 2312–2317. https://doi.org/10.1073/PNAS.1523264113-/DCSUPPLEMENTAL.

Beckers, B., De Beeck, M.O., Weyens, N., Boerjan, W., Vangronsveld, J., 2017. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. *Microbiome* 2017 51 5, 1–17. https://doi.org/10.1186/S40168-017-0241-2.

Bennett, J.A., Maherali, H., Reinhart, K.O., Lekberg, Y., Hart, M.M., Klironomos, J., 2017. Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics. *Science* 355, 181–184. https://doi.org/10.1126/SCIENCE.AAI8212/SUPPL_FILE/BENNETT_AAI8212_DATABASE-S1.XLSX.

Berg, G., Kusstatscher, P., Abdelfattah, A., Cernava, T., Smalla, K., 2021. Microbiome modulation—Toward a better understanding of plant microbiome response to microbial inoculants, 0 Front. Microbiol. 803. https://doi.org/10.3389/FMICB.2021.650610.

Berlanas, C., Berbegal, M., Elena, G., Laidani, M., Cibriain, J.F., Sagües, A., Gramaje, D., 2019. The fungal and bacterial rhizosphere microbiome associated with grapevine rootstock genotypes in mature and young vineyards. *Front. Microbiol.* 10, 1142. https://doi.org/10.3389/fmicb.2019.01142.

Bettenfeld, P., Cadena i Canals, J., Jacquens, L., Fernandez, O., Fontaine, F., van Schaik, E., Courty, P.-E., Trouvelot, S., 2021. The microbiota of the grapevine holobiont: a key component of plant health. *J. Adv. Res.* https://doi.org/10.1016/J.JARE.2021.12.008.

Bian, H., Li, C., Zhu, J., Xu, L., Li, M., Zheng, S., He, N., 2022. Soil moisture affects the rapid response of microbes to labile organic C addition. *Front. Ecol. Evol.* 10, 857815. https://doi.org/10.3389/FEVO.2022.857815/BIBTEX.

Biget, M., Wang, T., Mony, C., Xu, Q., Lecoq, L., Chable, V., Theis, K.R., Ling, N., Vandenkoornhuyse, P., 2023b. Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants. *iScience* 26, 106031. https://doi.org/10.1016/j.iscience.2023.106031.

Biget, M., Mony, C., Wang, T., Ling, N., Miteul, A., Jambon, O., Causse-Védrines, R., Michon-Coudouel, S., Hervé, M., Chable, V., Pernet, S., Vandenkoornhuyse, P., 2023a. Intra- and inter-annual changes in root endospheric microbial communities of grapevine are mainly deterministic. *Plant Soil.* https://doi.org/10.1007/S11104-023-06262-6.

Bond, B.J., 2000. Age-related changes in photosynthesis of woody plants. *Trends Plant Sci.* 5, 349–353. https://doi.org/10.1016/S1360-1385(00)01691-5.

Bora, S.S., Hazarika, D.J., Gogoi, R., Dullah, S., Gogoi, M., Barooah, M., 2022. Long-term pruning modulates microbial community structure and their functional potential in Tea (*Camellia sinensis*) L.) soils. *Appl. Soil Ecol.* 176, 104483 https://doi.org/10.1016/j.APSOIL.2022.104483.

Boubsi, F., Hoff, G., Arias, A.A., Steels, S., Andrić, S., Anckaert, A., Roulard, R., Rigolet, A., Wuytswinkel, O., van, Ongena, M., 2023. Pectic homogalacturonan

sensed by *Bacillus* acts as host associated cue to promote establishment and persistence in the rhizosphere. iScience 26, 107925. https://doi.org/10.1016/J. ISHL2023.107925.

Branzanti, M.B., Rocca, E., Pisi, A., 1999. Effect of ectomycorrhizal fungi on chestnut ink disease. *Mycorrhiza* 9, 103–109. https://doi.org/10.1007/S005720050007/METRICS.

Brundrett, M.C., 2002. Coevolution of roots and mycorrhizas of land plants. N. Phytol. 154, 275–304. https://doi.org/10.1046/j.1469-8137.2002.00397.X.

Carvalhais, L.C., Dennis, P.G., Badri, D.V., Kidd, B.N., Vivanco, J.M., Schenk, P.M., 2015. Linking Jasmionic acid signaling, root exudates, and rhizosphere microorganisms. Mol. Plant-Microbe Inter. 28, 1049–1058. https://doi.org/10.1094/MPMI-01-15-0016-R/ASSET/IMAGES/LARGE/MPMI-01-15-0016-R.F5.JPEG.

Carvalhais, L.C., Rincon-Florez, V.A., Brewer, P.B., Beveridge, C.A., Dennis, P.G., Schenk, P.M., 2019. The ability of plants to produce strigolactones affects rhizosphere community composition of fungi but not bacteria. *Rhizosphere* 9, 18–26. https://doi.org/10.1016/J.RHISPH.2018.10.002.

Cazorla, F.M., Mercado-Blanco, J., 2016. Biological control of tree and woody plant diseases: an impossible task? *BioControl* 61, 233–242. https://doi.org/10.1007/s10526-016-9737-0.

Cesarz, S., Fender, A.C., Beyer, F., Valtanen, K., Pfeiffer, B., Gansert, D., Hertel, D., Polle, A., Daniel, R., Leuschner, C., Scheu, S., 2013. Roots from beech (*Fagus sylvatica* L.) and ash (*Fraxinus excelsior* L.) differentially affect soil宏organisms and carbon dynamics. Soil Biol. Biochem. 61, 23–32. https://doi.org/10.1016/J.SOILBIO.2013.02.003.

Che, J., Wu, Y., Yang, H., Wang, S., Wu, W., Lyu, L., Li, W., 2022. Long-term cultivation drives dynamic changes in the rhizosphere microbial community of blueberry. *Front. Plant Sci.* 13, 962759 https://doi.org/10.3389/FPLS.2022.962759/BIBTEX.

Cheplick, G.P., 2017. Persistence of endophytic fungi in cultivars of Lolium perenne grown from seeds stored for 22 years. Am. J. Bot. 104, 627–631. https://doi.org/10.3732/AJB.1700030.

Chuberre, C., Plancot, B., Driouich, A., Moore, J.P., Bardor, M., Gügi, B., Vicré, M., 2018. Plant immunity is compartmentalized and specialized in roots. *Front. Plant Sci.* 9 https://doi.org/10.3389/FPLS.2018.01692.

Comptant, S., Cambon, M.C., Vacher, C., Mitter, B., Samad, A., Sessitsch, A., 2021. The plant endosphere world - bacterial life within plants. *Environ. Microbiol.* 23, 1812–1829. https://doi.org/10.1111/1462-2920.15240.

Conrath, U., Beckers, G.J.M., Langenbach, C.J.G., Jaskiewicz, M.R., 2015. Priming for enhanced defense. https://doi.org/10.1146/annurev-phyto-080614-120132 53, 97–119. https://doi.org/10.1146/ANNUREV-PHYTO-080614-120132.

Cornille, A., Gladieux, P., Smulders, J.M.J., Roldán-Ruiz, I., Laurens, F., Le Cam, B., Nersesyan, A., Clavel, J., Olonova, M., Peugey, L., Gabrielyan, I., Zhang, X.G., Tenaillon, M.I., Giraud, T., 2012. New insight into the history of domesticated apple: secondary contribution of the european wild apple to the genome of cultivated varieties. *PLOS Genet* 8, e1002703. https://doi.org/10.1371/JOURNAL.PGEN.1002703.

Darriaut, R., Lailheugue, V., Masneuf-Pomarède, I., Marguerit, E., Martins, G., Comptant, S., Ballestra, P., Upton, S., Ollat, N., Lauvergeat, V., 2022. Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture. Hortic. Res. 9. https://doi.org/10.1093/HR/UHAC019.

Darriaut, R., Marzari, T., Lailheugue, V., Tran, J., Martins, G., Marguerit, E., Masneuf-Pomarède, I., Lauvergeat, V., 2024. Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions. *Front. Plant Sci.* 15 https://doi.org/10.3389/FPLS.2024.1358213.

Debois, D., Fernandez, O., Franzil, L., Jourdan, E., de Brogniez, A., Willems, L., Clément, C., Dorey, S., De Pauw, E., Ongena, M., 2015. Plant polysaccharides initiate underground crosstalk with bacilli by inducing synthesis of the immunogenic lipopeptide surfactin. *Environ. Microbiol.* Rep. 7, 570–582. https://doi.org/10.1111/1758-2229.12286.

Deveau, A., Labbé, J., 2016. Mycorrhiza helper bacteria. Mol. Mycorrhizal Symbiosis 437–450. https://doi.org/10.1002/9781118951446.CH24.

Dominguez, P.G., Niitylä, T., 2022. Mobile forms of carbon in trees: metabolism and transport. *Tree Physiol.* 42, 458–487. https://doi.org/10.1093/TREEPHYS/TPAB123.

Dreischhoff, S., Das, I.S., Jakobi, M., Kasper, K., Polle, A., 2020. Local responses and systemic induced resistance mediated by ectomycorrhizal fungi. *Front. Plant Sci.* 11, 1908. https://doi.org/10.3389/FPLS.2020.590063/BIBTEX.

Edwards, J.A., Saran, U.B., Bonnette, J., MacQueen, A., Yin, J., Nguyen, T. uyen, Schmutz, J., Grimwood, J., Pennacchio, L.A., Daum, C., Glavina del Rio, T., Fritschi, B.L., Lowry, D.B., Juenger, T.E., 2013. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. *e6 Curr. Biol.* 33, 1926–1938. https://doi.org/10.1016/j.CUB.2023.03.078.

Edwards, J.D., Krichels, A.H., Seyfried, G.S., Dalling, J., Kent, A.D., Yang, W.H., 2024. Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests. *Mycorrhiza* 34, 95–105. https://doi.org/10.1007/S00572-023-01134-4/FIGURES/4.

Edwards, J., Johnson, C., Santos-Medellín, C., Lurie, E., Podishetty, N.K., Bhatnagar, S., Eisen, J.A., Sundaresan, V., Jeffery, L.D., 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. *Proc. Natl. Acad. Sci. U. S. A.* 112, E911–E920.

Eichmann, R., Richards, L., Schäfer, P., 2021. Hormones as go-betweens in plant microbiome assembly. *Plant J.* 105, 518–541. https://doi.org/10.1111/TPJ.15135.

Emmett, B., Nelson, E.B., Kessler, A., Bauerle, T.L., 2014. Fine-root system development and susceptibility to pathogen colonization. *Planta* 239, 325–340. https://doi.org/10.1007/S00425-013-1989-7/FIGURES/7.

Esperschütz, J., Buegger, F., Winkler, J.B., Munch, J.C., Schloter, M., Gattinger, A., 2009. Microbial response to exudates in the rhizosphere of young beech trees (*Fagus*
sylvatica L.) after dormancy. Soil Biol. Biochem. 41, 1976-1985. https://doi.org/10.1016/J.SOLIBIO.2009.07.002.

Fleishman, S.M., Eissenstat, D.M., Bell, T.H., Centinari, M., 2022. Functionally-explicit sampling can answer key questions about the specificity of plant-microbe interactions. Environ. Microbiomes 17, 1-8. https://doi.org/10.1186/S40793-022-00445-X/TABLES/1.

Frankland, J., 1992. Mechanisms in fungal succession. The Fungal Community: its organization and role in the ecosystem. (eds. D.T. Wicklow and G.e. Carroll). 2nd edn. Marcel Dekker Press, New York: 403-426.

Friedman, J., 2020. The evolution of annual and perennial plant life histories: ecological correlates and genetic mechanisms. Annu. Rev. Ecol. Evol. Syst. 51, 461-481. https://doi.org/10.1146/ANNUREV-ECOLSYS-110218-024638/CITE/REFWORKS.

Gaut, B.S., Díez, C.M., Morrell, P.L., 2015. Genomics and the contrasting dynamics of annual and perennial domestication. Trends Genet 31, 709-719. https://doi.org/10.1016/J.TIG.2015.10.002.

Ginnan, N.A., Dang, T., Bodaghi, S., Ruegger, P.M., McCollum, G., England, G., Vidalakis, G., Borneman, J., Rolshausen, P.E., Caroline Roper, M., 2020. Disease-induced microbial shifts in citrus indicate microbiome-derived responses to huanglongblight across the disease severity spectrum. Phytopobiomes J. 4, 375-387. https://doi.org/10.1094/PBIOMES-04-20-0027-R/ASSET/IMAGES/LARGE/PBIOMES-04-20-0027-RF6.JPEG.

Gorka, S., Dietrich, M., Mayerhofer, W., Gabriel, R., Wiesenbauer, J., Martin, V., Zheng, Q., Imai, B., Prommer, J., Weidinger, M., Schweiger, P., Eichorst, S.A., Wagner, M., Richter, A., Schintlmeister, A., Woebken, D., Kaiser, C., 2019. Rapid transfer of plant photosynthesates to soil bacteria via ectomycorrhizal hyphae and its interaction with nitrogen availability. Front. Microbiol. 10, 168. https://doi.org/10.3389/FMICB.2019.00168/BIBTEX.

Gramaje, D., Urbez-Torres, J.R., Sosnowski, M.R., 2018. Managing grapevine trunk diseases with respect to etiology and epidemiology: Current strategies and future prospects. Plant Dis. 102, 12-39. https://doi.org/10.1094/PDIS-04-17-0512-FE/ASSET/IMAGES/LARGE/PDIS-04-17-0512-FE_BIO3.JPEG.

Guckert, J.B., Hood, M.A., White, D.C., 1986. Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of *Vibrio cholerae*: increases in the trans/cis ratio and proportions of cyclopropyl fatty acids. Appl. Environ. Microbiol. 52, 794. https://doi.org/10.1128/AEM.52.4.794-801.1986.

Guo, X.W., Wang, B., Li, K., Liu, Z.D., Han, X., Xu, S.J., Guo, Y.S., Xie, H.G., 2015. Effect of 4-hydroxybenzozoic acid on grape (*Vitis vinifera* L.) soil microbial community structure and functional diversity. Biotechnol. Biotechnol. Equip. 29, 637-645. https://doi.org/10.1080/13102818.2015.1037348.

Garbaye, J., Bowen, G.D., 1989. Ectomycorrhizal infection of Pinus radiata by Rhizopogon luteolus is stimulated by microorganisms naturally present in the mantle of ectomycorrhizas. New Phytol. 112, 383-388.

Habibi, F., Liu, T., Folta, K., Sarkhosh, A., 2022. Physiological, biochemical, and molecular aspects of grafting in fruit trees. Hortic. Res. 9 https://doi.org/10.1093/HR/UHAC032.

Hafiz, F.B., Moradtalab, N., Goertz, S., Rietz, S., Dietel, K., Rozhon, W., Humbeck, K., Geistlinger, J., Neumann, G., Schellenberg, I., 2022. Synergistic effects of a root-endophytic *Trichoderma* fungus and *Bacillus* on early root colonization and defense activation against *Verticillium longisporum* in rapeseed. Mol. Plant-Microbe Inter. 35, 380-392. https://doi.org/10.1094/MPMI-11-21-0274-R/ASSET/IMAGES/LARGE/MPMI-11-21-0274-RF5.JPEG.

Hart, M.M., Gorzelak, M., Ragone, D., Murch, S.J., 2014. Arbuscular mycorrhizal fungal succession in a long-lived perennial1. Botany 92, 313-320. https://doi.org/10.1139/CJB-2013-0185/SUPPL_FILE/CJB-2013-0185SUPPL.DOC.

Héloir, M.C., Adrian, M., Brulé, D., Claverie, J., Cordelier, S., Daire, X., Dorey, S., Gauthier, A., Lemaître-Guillier, C., Negrel, J., Trdá, L., Trouvelot, S., Vandelle, L., Poinsot, B., 2019. Recognition of elicitors in grapevine: From MAMP and DAMP perception to induced resistance. Front. Plant Sci. https://doi.org/10.3389/fpls.2019.01117.

Hoeksema, J.D., Bever, J.D., Chakraborty, S., Chaudhary, V.B., Gardes, M., Gehring, C.A., Hart, M.M., Housworth, E.A., Kaonongbua, V., Klironomos, J.N., Lajeunesse, M.J., Meadow, J., Milligan, B.G., Piculell, B.J., Pringle, A., Rúa, M.A., Umbanhowar, J., Viechtbauer, W., Wang, Y.W., Wilson, G.W.T., Zee, P.C., 2018. Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism, 2018 11 Commun. Biol. 1, 1-10. https://doi.org/10.1038/s42003-018-0120-9.

Hoff, G., Arias, A.A., Boubsi, F., Pršić, J., Meyer, T., Ibrahim, H.M.M., Steels, S., Luzuriaga, P., Legras, A., Franzil, L., Lequart-Pillon, M., Rayon, C., Osorio, V., de Pauw, E., Lara, Y., Deboever, E., de Coninck, B., Jacques, P., Deleu, M., Petit, E., van Wuytswinkel, O., Ongena, M., 2021. Surfactin stimulated by pectin molecular patterns and root exudates acts as a key driver of the *Bacillus*-plant mutualistic interaction. MBio 12. https://doi.org/10.1128/MBIO.01774-21.

Hofmann, A., Wittenmayer, L., Arnold, G., Schieber, A., Merbach, W., 2009. Root exudation of phloridzin by apple seedlings (Malus x domestica Borkh.) with symptoms of apple replant disease. undefined.

Högberg, M.N., Briones, M.J.I., Keel, S.G., Metcalfe, D.B., Campbell, C., Midwood, A.J., Thornton, B., Hurry, V., Linder, S., Näsholm, T., Högberg, P., 2010. Quantification of effects of season and nitrogen supply on tree below-ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest. New Phytol. 187, 485-493. https://doi.org/10.1111/j.1469-8137.2010.03274.X.

Huang, W.R.H., Joosten, M.H.A.J., 2024. Immune signaling: receptor-like proteins make the difference. Trends Plant Sci. 0 https://doi.org/10.1016/J.TPLANTS.2024.03.012.

Jiang, F., Zhang, L., Zhou, J., George, T.S., Feng, G., 2021. Arbuscular mycorrhizal fungi enhance mineralisation of organic phosphorus by carrying bacteria along their extraradical hyphae. New Phytol. 230, 304-315. https://doi.org/10.1111/NPH.17081.

Kadowaki, K., 2024. Forest tree community ecology and plant-soil feedback: Theory and evidence. Ecol. Res. 39, 257-272. https://doi.org/10.1111/1440-1703.12445.

Kaur, S., Susela, V., 2020. Unraveling arabusclor mycorrhiza-induced changes in plant primary and Secondary metabolome. Metabolites 10, 1-30. https://doi.org/10.3390/METABO10080335.

Ke, P.J., Zee, P.C., Fukami, T., 2021. Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time. N. Phytol. 231, 1546-1558. https://doi.org/10.1111/NPH.17420.

Khan, M., Rozhon, W., Poppenberger, B., 2013. The Role of Hormones in the Aging of Plants - A Mini-Review. Gerontology 60, 49-55. https://doi.org/10.1159/000354334.

King, W.L., Yates, C.F., Guo, J., Fleishman, S.M., Trexler, R.V., Centinari, M., Bell, T.H., Eissenstat, D.M., 2021. The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering, 2021 41 Commun. Biol. 4, 1-9. https://doi.org/10.1038/s42003-021-01988-4.

Kocsis, L., Szálanski, W., 2011. Grape phylloxera development on potted grapevine treated with ectomycorrhizal fungi. Acta Hortic. (904), 117-122. https://doi.org/10.17660/ACTAHORTIC.2011.904.16.

Korenblum, E., Dong, Y., Szymanski, J., Panda, S., Jozwiak, A., Massalha, H., Meir, S., Rogachev, I., Aharoni, A., 2020. Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling. Proc. Natl. Acad. Sci. U. S. A. 117, 3874-3883. https://doi.org/10.1073/pnas.1912130117.

Kristy, B., Carrell, A.A., Johnston, E., Cumming, J.R., Klingeman, D.M., Gwinn, K., Syring, K.C., Skalla, C., Emrich, S., Cregger, M.A., 2022. Chronic drought differentially alters the belowground microbiome of drought-tolerant and drought-susceptible genotypes of *Populus trichocarpa*. Phytopobiomes J. 6, 317-330. https://doi.org/10.1094/PBIOMES-12-21-0076-R/ASSET/IMAGES/LARGE/PBIOMES-12-21-0076-RF6.JPEG.

Kubiak, K., Damszel, M., Sikora, K., Przemieniecki, S., Malecka, M., Sierota, Z., 2017. Colonization of fungi and bacteria in stumps and roots of Scots pine after thinning and treatment with Rotstop. J. Phytopathol. 165, 143-156. https://doi.org/10.1111/JPH.12534.

Kubiak, K., Wrzosek, M., Przemieniecki, S., Damszel, M., Sierota, Z., 2018. Bacteria inhabiting wood of roots and stumps in forest and arable soils 319-342. https://doi.org/10.1007/978-3-319-89833-9_14.

Lailheugue, V., Darriaut, R., Tran, J., Morel, M., Marguerit, V., Lauvergeat, V., 2024. Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact. Environ. Micro 19, 1-21. https://doi.org/10.1186/S40793-024-00566-5/FIGURES/8.

Laurent, A.S., Merwin, I.A., Fazio, G., Thies, J.E., Brown, M.G., 2010. Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil. Plant Soil 337, 259-272. https://doi.org/10.1007/S11104-010-0522-Z.

Lebeis, S.L., Paredes, S.H., Lundberg, D.S., Breakfield, N., Gehring, J., McDonald, M., Malfatti, S., Rio, T.G., del, Jones, C.D., Tringe, S.G., Dangl, J.L., 2015. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Sci. (80-). J., 349, 860-864. https://doi.org/10.1126/SCIENCE.AAA8764.

Lee, S.-M., Kong, H.G., Song, G.C., Ryu, C.-M., 2020. Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. ISME J. 2020 151 15, 330-347. https://doi.org/10.1038/s41396-020-00785-x.

Lemanceau, P., Blouin, M., Muller, D., Moënne-Loczoz, Y., 2017. Let the Core Microbiota Be Functional. Trends Plant Sci. 22, 583-595. https://doi.org/10.1016/J.TPLANTS.2017.04.008.

Liu, F., Rice, J.H., Lopes, V., Grewal, P., Lebeis, S.L., Hewezi, T., Staton, M.E., 2020. Overexpression of stigrolactone-associated genes exerts fine-tuning selection on soybean rhizosphere bacterial and fungal microbiome. Phytopobiomes J. 4, 239-251. https://doi.org/10.1094/PBIOMES-01-20-0003-R/ASSET/IMAGES/LARGE/PBIOMES-01-20-0003-RF9.JPEG.

Liu, Q., Wang, S., Li, K., Qiao, J., Guo, Y., Liu, Z., Guo, X., 2021. Responses of soil bacterial and fungal communities to the long-term monoculture of grapevine. Appl. Microbiol. Biotechnol. 2021 10518 105, 7035-7050. https://doi.org/10.1007/S00253-021-11542-1.

Liu, Q., Zhang, L., Wang, L., Wu, Q., Li, K., Guo, X., 2022. Autotoxin affects the rhizosphere microbial community structure by influencing the secretory characteristics of grapevine roots. Front. Microbiol. 0, 2834. https://doi.org/10.3389/FMICB.2022.953424.

Liu, Y., Sun, Q., Li, J., Lian, B., 2018. Bacterial diversity among the fruit bodies of ectomycorrhizal and saprophytic fungi and their corresponding hyphosphere soils. Sci. Rep. 2018 81 8, 1-10. https://doi.org/10.1038/s41598-018-30120-6.

Liu, Y., Zhang, H., Wang, J., Gao, W., Sun, X., Xiong, Q., Shu, X., Miao, Y., Shen, Q., Xun, W., Zhang, R., 2024. Nonpathogenic *Pseudomonas syringae* derivatives and its metabolites trigger the plant "cry for help" response to assemble disease suppressing and growth promoting rhizomicrobiome. Nat. Commun. 2024 151 15, 1-14. https://doi.org/10.1038/s41467-024-46254-3.

Maeght, J.L., Rewald, B., Pierret, A., 2013. How to study deep roots-and why it matters. Front. Plant Sci. 4, 56547. https://doi.org/10.3389/FPLS.2013.00299/BIBTEX.

Manici, L.M., Saccà, M.L., Caputo, F., Zanzotto, A., Gardiman, M., Fila, G., 2017. Long-term grapevine cultivation and agro-environment affect rhizosphere microbiome rather than plant age. Appl. Soil Ecol. 119, 214-225. https://doi.org/10.1016/j.apsoil.2017.06.027.

Marasco, R., Rolli, E., Fusi, M., Michoud, G., Daffonchio, D., 2018. Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Microbiome 6, 1-17. https://doi.org/10.1186/s40168-017-0391-2.
Marx, D.H., 1972. Ectomycorrhizae as biological deterrents to pathogenic root infections. Annu. Rev. Phytopathol. 10, 429–454. https://doi.org/10.1146/ANNUREV.PY.10.090172.002241.

Mencuccini, M., Óñate, M., Peñuelas, J., Rico, L., Munné-Bosch, S., 2014. No signs of meristem senescence in old Scots pine. J. Ecol. 102, 555–565. https://doi.org/10.1111/1365-2745.12219.

Migicovsky, Z., Myles, S., 2017. Exploiting wild relatives for genomics-assisted breeding of perennial crops. Front. Plant Sci. 8, 460. https://doi.org/10.3389/FPLS.2017.00460/BIBTEX.

Munné-Bosch, S., 2007. Aging in Perennials. CRC. Crit. Rev. Plant Sci. 26, 123–138. https://doi.org/10.1080/07352680701402487.

Myles, S., 2013. Improving fruit and wine: what does genomics have to offer? Trends Genet 29, 190–196. https://doi.org/10.1016/J.TIG.2013.01.006.

Myles, S., Boyko, A.R., Owens, C.I., Brown, P.J., Grassi, F., Aradhya, M.K., Prins, B., Reynolds, A., Chia, J.M., Ware, D., Bustamante, C.D., Buckler, E.S., 2011. Genetic structure and domestication history of the grape. Proc. Natl. Acad. Sci. U. S. A. 108, 3530–3535. https://doi.org/10.1073/PNAS.1009363108/SUPPL_FILE/SAPP.PDF.

Nakayama, M., Tateno, R., 2023. Shift in the rhizosphere microbial communities between growing- and low-temperature dormant seasons in a northern hardwood forest. Plant Soil 1–17. https://doi.org/10.1007/S11104-023-06391-Y/FIGURES/7.

Nurmiaho-Lassila, E.L., Timonen, S., Hahtela, K., Sen, R., 2011. Bacterial colonization patterns of intact Pinus sylvestris mycorrhizomes in dry pine forest soil: an electron microscopy study. https://doi.org/10.1139/m97-147 43, 1017–1035. https://doi.org/10.1139/M97-147.

Oo, A.Z., Sudo, S., Win, K.T., Shibata, A., Sano, T., Hirono, Y., 2018. Returning tea pruning residue and its biochar had a contrasting effect on soil N2O and CO2 emissions from tea plantation soil. Atmos 2018 Vol. 9, 109. https://doi.org/10.3390/ATMOS9030109.

Park, I., Seo, Y.S., Mannaa, M., 2023. Recruitment of the rhizo-microbiome as a key to unlocking plant potential. Front. Microbiol. 14, 1163832. https://doi.org/10.3389/FMICB.2023.1163832/BIBTEX.

Peltoniemi, M., Mäkipää, R., Liski, J., Tamminen, P., 2004. Changes in soil carbon with stand age – an evaluation of a modelling method with empirical data. Glob. Chang. Biol. 10, 2078–2091. https://doi.org/10.1111/J.1365-2486.2004.00881.X.

Pérez-De-Luque, A., Tille, S., Johnson, I., Pascual-Pardo, D., Ton, J., Cameron, D.D., 2017. The interactive effects of arbuscular mycorrhizae and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogen. Sci. Rep. 7, 1–10. https://doi.org/10.1038/s41598-017-16697-4.

Perrin, A., Daccord, N., Roquis, D., Celton, J.M., Vergne, E., Bucher, E., 2020. Divergent DNA methylation signatures of juvenile seedlings, grafts and adult apple trees. Epigenomes 2020 Vol. 4, 4. https://doi.org/10.3390/EPIGENOMES401004.

Pervaiz, Z.H., Contreras, J., Hupp, B.M., Lindenberger, J.H., Chen, D., Zhang, Q., Wang, C., Twigg, P., Saleem, M., 2020. Root microbiome changes with root branching order and root chemistry in peach rhizosphere soil. Rhizosphere 16, 100249. https://doi.org/10.1016/J.RHISPH.2020.100249.

Pham, V.T.T., Ismail, T., Mishyna, M., Appiah, K.S., Oikawa, Y., Fujii, Y., 2019. Caffeine: The allelochemical responsible for the plant growth inhibitory activity of vietnamese tea (*Camellia sinensis*) L. Kuntze). Agron. 2019 Vol. 9, 396. https://doi.org/10.3390/AGRONOMY9070396.

Polverigiani, S., McCormack, M.L., Mueller, C.W., Eissenstat, D.M., 2011. Growth and profits of olive pioneer and fibrous roots to soil moisture deficits. Tree Physiol. 31, 1228–1237. https://doi.org/10.1093/TREEPHYS/TPR110.

Prescott, C.E., 2022. Sinks for plant surplus carbon explain several ecological phenomena. Plant Soil 476, 689–698. https://doi.org/10.1007/S11104-022-05390-9/FIGURES/1.

Prieto, P., Schilirò, E., Maldonado-González, M.M., Valderrama, R., Barroso-Albarracín, J.B., Mercado-Blanco, J., 2011. Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microb. Ecol. 62, 435–445. https://doi.org/10.1007/S00248-011-9827-6/FIGURES/3.

Qu, Z., Liu, B., Ma, Y., Sun, H., 2020. Differences in bacterial community structure and potential functions among Eucalyptus plantations with different ages and species of trees. Appl. Soil Ecol. 149, 103515 https://doi.org/10.1016/J.APSOIL.2020.103515.

Radić, T., Hancević, K., Likar, M., Regvar, M., Zdunić, G., 2018. High incidence of arbuscular mycorrhizal fungi in rare and endangered wild grapevine. https://doi.org/10.1080/11263504.2017.1415994 152, 1075–1078. https://doi.org/10.1080/11263504.2017.1415994.

Radić, T., Likar, M., Hancević, K., Regvar, M., Čarija, M., Zdunić, G., 2021. Root-associated community composition and co-occurrence patterns of fungi in wild grapevine. Fungal Ecol. 50, 101034 https://doi.org/10.1016/J.FUNECO.2020.101034.

Ren, H., Gao, G., Ma, Y., Li, Z., Wang, S., Gu, J., 2023. Shift of root nitrogen-acquisition strategy with tree age is mediated by root functional traits along the collaboration gradient of the root economics space. Tree Physiol. 43, 1341–1353. https://doi.org/10.1093/TREEPHYS/TPAD047.

Robin, A., Pradier, C., Sanguin, H., Mahé, F., Lambais, G.R., de Araujo Pereira, A.P., Germon, A., Santana, M.C., Tisseyre, P., Pablo, A.L., Heuillard, P., Sauvadet, M., Bouillet, J.P., Andreote, F.D., Plassard, C., de Moraes Gonçalves, J.L., Cardoso, E.J.B. N., Laclau, J.P., Hinsinger, P., Jourdan, C., 2019. How deep can ectomycorrhizas go? A case study on *Pisolithus* down to 4 meters in a Brazilian eucalypt plantation. Mycorrhiza 29, 637–648. https://doi.org/10.1007/S00572-019-00917-Y.

Ross, E.W., 1972. Susceptibility of Sand pine to *Phytophthora cinnamomi*. Phytopathology 62, 1197. https://doi.org/10.1094/PHYTO-62-1197.

Sarkar, S., Kamke, A., Ward, K., Rudick, A.K., Baer, S.G., Ran, Q., Feehan, B., Thapa, S., Anderson, L., Galliart, M., Jumpponen, A., Johnson, L., Lee, S.T.M., 2022. Bacterial but not fungal rhizosphere community composition differs among perennial grass ecotypes under abiotic environmental stress. Microbiol. Spectr. 10. https://doi.org/10.1128/SPECTRUM.02391-21/SUPPL_FILE/SPECTRUM.02391-21-S001.PDF.

Schenk, H.J., Jackson, R.B., 2002. Rooting depths, lateral root spreads and below-ground/above-ground allometries of plants in water-limited ecosystems. J. Ecol. 90, 480–494. https://doi.org/10.1046/j.1365-2745.2002.00682.X.

Scheublin, T.R., Sanders, I.R., Keel, C., Van Der Meer, J.R., 2010. Characterisation of microbial communities colonising the hypnym surfaces of arbuscular mycorrhizal fungi. ISME J. 2010 46 4, 752–763. https://doi.org/10.1038/ISMEJ.2010.5.

Schmidt, J.E., DuVal, A., Puig, A., Tempeleu, A., Crow, T., 2021. Interactive and dynamic effects of rootstock and rhizobiome on scion nutrition in cacao seedlings. Front. Agron. 3, 89. https://doi.org/10.3389/FAGRO.2021.754646/BIBTEX.

Smilauer, P., Košnar, J., Kotíłnek, M., Pecháčková, S., Smilauerová, M., 2021. Host age and surrounding vegetation affect the community and colonization rates of arbuscular mycorrhizal fungi in a temperate grassland. N. Phytol. 232, 290–302. https://doi.org/10.1111/NPH.17550.

Solís-Domínguez, F.A., Valentín-Vargas, A., Chorover, J., Maier, R.M., 2011. Effect of arbuscular mycorrhizal fungi on plant biomass and the rhizosphere microbial community structure of mesquite grown in acidic lead/zinc mine tailings. Sci. Total Environ. 409, 1009–1016. https://doi.org/10.1016/j.SITOTENV.2011.020.

Sommer, J., Dippold, M.A., Zieger, S.L., Handke, A., Scheu, S., Kuzyakov, Y., 2017. The tree species matters: Belowground carbon input and utilization in the mycorrhizosphere. Eur. J. Soil Biol. 81, 100–107. https://doi.org/10.1016/J.EJSOBI.2017.07.001.

Song, Y.Y., Simard, S.W., Carroll, A., Mohn, W.W., Zeng, R., Sen, 2015. Defoliation of interior Douglas-fir elicits carbon transfer and stress signalling to ponderosa pine neighbors through ectomycorrhizal networks. Sci. Rep. 5 https://doi.org/10.1038/SREP08495.

Steenwerth, K.L., Drenovsky, R.E., Lambert, J.J., Kluepfel, D.A., Scow, K.M., Smart, D.R., 2008. Soil morphology, depth and grapevine root frequency influence microbial communities in a Pinot noir vineyard. Soil Biol. Biochem. 40, 1330–1340. https://doi.org/10.1016/j.soilbio.2007.04.031.

Suseela, V., Tharayil, N., Orr, G., Hu, D., 2020. Chemical plasticity in the fine root construct of *Quercus* spp. varies with root order and drought. N. Phytol. 228, 1835–1851. https://doi.org/10.1111/NPH.16841.

Tedesco, S., Fevereiro, P., Kragler, F., Pina, A., 2022. Plant grafting and graft incompatibility: A review from the grapevine perspective. Sci. Hortic. (Amst.). 299, 111019 https://doi.org/10.1016/J.SCIENTA.2022.111019.

Terhonen, E., Blumenstein, K., Kovalchuk, A., Asiegbu, F.O., 2019. Forest tree microbiomes and associated fungal endophytes: functional roles and impact on forest health. For. 2019, Vol. 10, Page 42 10, 42. https://doi.org/10.3390/F10010042.

This, P., Lacombe, T., Thomas, M.R., 2006. Historical origins and genetic diversity of wine grapes. Trends Genet 22, 511–519. https://doi.org/10.1016/J.TIG.2006.07.008.

Thomas, F.M., Molitor, F., Werner, W., 2014. Lignin and cellulose concentrations in roots of Douglas fir and European beech of different diameter classes and soil depths. Trees - Struct. Funct. 28, 309–315. https://doi.org/10.1007/S00468-013-0937-2/FIGURES/2.

Tian, T., Reverdy, A., She, Q., Sun, B., Chai, Y., 2020. The role of rhizodeposits in shaping rhizomicrobiome. Environ. Microbiol. Rep. 12, 160–172. https://doi.org/10.1111/1758-2229.12816.

Timonen, S., Sinkko, H., Sun, H., Sietiö, O.M., Rinta-Kanto, J.M., Kiheri, H., Heinonsalo, J., 2017. Ericoid roots and mycospheres govern plant-specific bacterial communities in Boreal Forest Humus. Microb. Ecol. 73, 939–953. https://doi.org/10.1007/S00248-016-0922-6/TABLES/1.

Toju, H., Kurokawa, H., Kenta, T., 2019. Factors influencing leaf- and root-associated communities of bacteria and fungi across 33 plant orders in a grassland. Front. Microbiol. 10, 241. https://doi.org/10.3389/FMICB.2019.00241/BIBTEX.

Trivedi, P., Leach, J.E., Tringe, S.G., Sa, T., Singh, B.K., 2020. Plant-microbiome interactions: from community assembly to plant health, 2020 1811 Nat. Rev. Microbiol. 18, 607–621. https://doi.org/10.1038/s41579-020-0412-1.

Trouvelot, S., Bonneau, L., Redecker, D., van Tuinen, D., Adrian, M., Wipf, D., 2015. Arbuscular mycorrhiza symbiosis in viticulture: a review, 2015 354 Agron. Sustain. Dev. 35, 1449–1467. https://doi.org/10.1007/S13593-015-0329-7.

Tückmantel, T., Leuschner, C., Preusser, S., Kandeler, E., Angst, G., Mueller, C.W., Meier, I.C., 2017. Root exudation patterns in a beech forest: Dependence on soil depth, root morphology, and environment. Soil Biol. Biochem. 107, 188–197. https://doi.org/10.1016/J.SOILBIO.2017.01.006.

Twieg, B.D., Durall, D.M., Simard, S.W., 2007. Ectomycorrhizal fungal succession in mixed temperate forests. N. Phytol. 176, 437–447. https://doi.org/10.1111/j.1469-8137.2007.02173.X.

Uroz, S., Buée, M., Murat, C., Frey-Klett, P., Martin, F., 2010. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ. Microbiol. Rep. 2, 281–288. https://doi.org/10.1111/J.1758-2229.2009.00117.X.

Uroz, S., Oger, P., Tisserand, E., CéBron, A., Turpault, M.P., Bueé, M., De Boer, W., Leveau, J.H.J., Frey-Klett, P., 2016. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci. Rep. 2016 61 6, 1–11. https://doi.org/10.1038/srep27756.

Velisevich, S.N., Bender, O.G., Goroshkevich, S.N., 2021. The influence of scion donor tree age on the growth and morphogenesis of Siberian stone pine grafts. New 52, 473–491. https://doi.org/10.1007/S11056-020-09805-2/FIGURES/8.
Vink, S.N., Dini-Andreote, F., Höfle, R., Kicherer, A., Salles, J.F., 2021. Interactive effects of scion and rootstock genotypes on the root microbiome of grapevines (Vitis spp. L.), 2021 Appl. Sci. Vol. 11, 1615. https://doi.org/10.3390/APP11041615.

Vismans, G., Van Bentum, S., Spooren, J., Song, Y., Goossens, P., Valls, J., Snoek, B.L., Thiombiano, B., Schilder, M., Dong, L., Bouwmeester, H.J., Pétriacq, P., Pieterse, M. J., Bakker, P.A.H.M., Berendsen, R.L., 2022. Coumarin biosynthesis genes are required after foliar pathogen infection for the creation of a microbial soil-borne legacy that primes plants for SA-dependent defenses. Sci. Rep. | 12, 22473. https://doi.org/10.1038/s41598-022-26551-x.

Vohník, M., Mrnka, L., Lukešová, T., Bruzone, M.C., Kohout, P., Fehrer, J., 2013. The cultivable endophytic community of Norway spruce ectomycorrhizas from microhabitats lacking ericaceous hosts is dominated by ericoid mycorrhizal *Meliniomyces variabilis*. Fungal Ecol. 6, 281–292. https://doi.org/10.1016/J.FUNECO.2013.03.006.

Wadud Khan, M.A., Zac Stephens, W., Mohammed, A.D., Round, J.L., Kubinak, J.L., 2019. Does MHC heterozygosity influence microbiota form and function? PLoS One 14, e0215946. https://doi.org/10.1371/JOURNAL.PONE.0215946.

Wagner, M.R., Lundberg, D.S., Del Rio, T.G., Tringe, S.G., Dangl, J.L., Mitchell-Olds, T., 2016. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant, 2016 71 Nat. Commun. 7, 1–15. https://doi.org/10.1038/ncomms12151.

Wang, J., Jiang, L., Wu, R., 2017. Plant grafting: how genetic exchange promotes vascular reconnection. N. Phytol. 214, 56–65. https://doi.org/10.1111/NPH.14383.

Wang, Q., Jiang, Y., Mao, X., Yu, W., Lu, J., Wang, L., 2022. Integration of morphological, physiological, cytological, metabolome and transcriptome analyses reveal age inhibited accumulation of flavonoid biosynthesis in *Ginkgo biloba* leaves. Ind. Crops Prod. 187, 115405 https://doi.org/10.1016/J.INDCROP.2022.115405.

Wu, K., Fang, Z., Guo, R., Pan, B., Shi, W., Yuan, S., Guan, H., Gong, M., Shen, B., Shen, Q., 2015. Pectin enhances Bio-Control efficacy by inducing colonization and secretion of secondary metabolites by *Bacillus amyloliquefaciens* SQY 162 in the rhizosphere of tobacco. PLoS One 10, e0127418. https://doi.org/10.1371/JOURNAL.PONE.0127418.

Xu, J., Zhang, Y., Zhang, P., Trivedi, P., Riera, N., Wang, Y., Liu, X., Fan, G., Tang, J., Coletta-Filho, H.D., Cubero, J., Deng, X., Ancona, V., Lu, Z., Zhong, B., Roper, M.C., Capote, N., Catara, V., Pietersen, G., Vernière, C., Al-Sadi, A.M., Li, L., Yang, F.,

Xu, X., Wang, J., Yang, H., Jin, T., Wang, N., 2018. The structure and function of the global citrus rhizosphere microbiome. 2018 91 Nat. Commun. 9, 1–10. https://doi.org/10.1038/s41467-018-07343-2.

Yu, M.H., Zhao, Z.Z., He, J.X., 2018. Brassinosteroid Signaling in Plant-Microbe Interactions, 2018 Int. J. Mol. Sci. Vol. 19, 4091. https://doi.org/10.3390/JIMS19124091.

Yuan, J., Zhao, J., Wen, T., Zhao, M., Li, R., Goossens, P., Huang, Q., Bai, Y., Vivanco, J. M., Kowalchuk, G.A., Berendsen, R.L., Shen, Q., 2018. Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome 2018 61. https://doi.org/10.1186/s40168-018-0537-x.

Zadworny, M., Eissenstat, D.M., 2011. Contrasting the morphology, anatomy and fungal colonization of new pioneer and fibrous roots. N. Phytol. 190, 213–221. https://doi.org/10.1111/J.1469-8137.2010.03598.X.

Zhang, C.B., Chen, L.H., Jiang, J., 2014. Why fine tree roots are stronger than thicker roots: The role of cellulose and lignin in relation to slope stability. Geomorphology 206, 196–202. https://doi.org/10.1016/J.GEOMORPH.2013.09.024.

Zhang, M., Kong, X., 2022. How plants discern friends from foes. Trends Plant Sci. 27, 107–109. https://doi.org/10.1016/J.TPLANTS.2021.11.001.

Zhang, S., Huang, G., Zhang, Y., Lv, X., Wan, K., Liang, J., Feng, Y., Dao, J., Wu, S., Zhang, L., Yang, X., Lian, X., Huang, L., Shao, L., Zhang, J., Qin, S., Tao, D., Crews, T. E., Sacks, E.J., Lyu, J., Wade, L.J., Hu, F., 2022. Sustained productivity and agronomic potential of perennial rice. Nat. Sustain. 2022, 1–11. https://doi.org/10.1038/s41893-022-00997-3.

Zhang, Y., Trivedi, P., Xu, J., Caroline Roper, M., Wang, N., 2021. The citrus microbiome: From structure and function to microbiome engineering and beyond. Phytobiomes J. 5, 249–262. https://doi.org/10.1094/PBIOMES-11-20-0084-RVW/ASSET/IMAGES/LARGE/PBIOMES-11-20-0084-RVWF6.JPEG.

Zhou, Y., Wei, Y., Zhao, Z., Li, J., Li, H., Yang, P., Tian, S., Ryder, M., Toh, R., Yang, H., Denton, M.D., 2022. Microbial communities along the soil-root continuum are determined by root anatomical boundaries, soil properties, and root exudation. Soil Biol. Biochem. 171, 108721 https://doi.org/10.1016/J.SOILBIO.2022.108721.

Zuzolo, D., Ranauda, M.A., Maisto, M., Tartaglia, M., Prigioniero, A., Falzarano, A., Marotta, G., Sciarrillo, R., Guarino, C., 2023. The rootstock shape microbial diversity and functionality in the rhizosphere of *Vitis vinifera* L. cultivar Falanghina. Front. Plant Sci. 14, 1205451. https://doi.org/10.3389/FPLS.2023.1205451/BIBTEX.