Introduction
The rhizosphere, the narrow zone surrounding and influenced by plant
roots, harbors a plethora of microorganisms that can have deleterious or
beneficial effects on plant growth and health (Raaijmakers et al.2009; Mendes et al. 2011). Amongst the best-studied beneficial
rhizosphere microbes are the Plant Growth-Promoting Rhizobacteria
(PGPR). Their beneficial association is thought to be ancient and
presumably has been shaped by co-evolutionary processes in the long-term
interactions with their host plants (Lambers et al. 2009). PGPR
can enhance plant growth through direct and indirect mechanisms
(Lugtenberg & Kamilova 2009). The direct mechanisms involve
facilitation of nutrient acquisition and modulation of phytohormones,
whereas indirect effects involve suppression of biotic stress factors
through parasitism, antibiosis, competition and the induction of
systemic resistance (van Loon et al. 1998; De Vleesschauwer &
Höfte 2009; Van der Ent et al. 2009; Pineda et al. 2010;
Stringlis et al. 2018b).
PGPR can also have profound effects on the physiology and metabolism of
their host plants, not only by enhancing the production of known
secondary metabolites but also by inducing the biosynthesis of
yet-unknown compounds (van de Mortel et al. 2012; Etalo et
al. 2018). The plant secondary metabolites affected by PGPR reported to
date include, among others, polyphenols, flavonoids and glucosinolates
but also primary metabolites such as carbohydrates and amino acids
(Etalo et al. 2018). So far, only few studies have provided
mechanistic insights into the association between rhizobacteria-induced
biochemical changes and plant growth and defense (Walker et al.2011; Weston et al. 2012; van de Mortel et al. 2012; Etaloet al. 2018; Stringlis et al. 2018a; Hu et al.2018).
PGPR can prime plant defense against pathogens and insect herbivores and
at the same time promote plant growth. This is in contrast to the widely
accepted trade-off between plant defense and plant fitness in general
and plant growth in particular. Understanding the underlying plant
metabolic networks and unraveling their interactions is essential to
understand and optimize rhizobacteria-mediated growth promotion and ISR.
Although some reports indicated that rhizobacteria change specific
classes of plant metabolites (Mishra et al. 2006; Walker et
al. 2011; Chamam et al. 2013), their overarching effects on the
global metabolome of plants and in particular on core metabolite
pathways co-occurring with growth promotion across plant species are not
well understood. In this context, PGPR-mediated re-routing of the
plant’s metabolism could give insight into the metabolic interplay
between plant defense and growth. Furthermore, it is highly instrumental
to understand the organization of metabolite routes and how
rhizobacteria tilt a particular pathway towards a desired plant
phenotype or the enhanced production of high value plant compounds
(HVPC) (Etalo et al. 2018).
Here, we studied the impact of three strains of different rhizobacterial
genera on the phenotype and shoot metabolome of three plant species:Arabidopsis thaliana (model plant), Brassica olearaceavar. italica (crop) and Artemisia annua (medicinal plant). The
rhizobacterial strains Paraburkholderia graminis PHS1
(Pbg ) (Carrión et al. 2018) and Microbacterium EC8
(MB) (Cordovez et al. 2018) were originally isolated from the
rhizosphere of sugar beet (Beta vulgaris ). Pseudomonas
fluorescens SS101 (Pf SS101) was isolated from the wheat
rhizosphere (De Souza et al. 2003). These rhizobacteria showed
growth promoting and pathogen-protective effects in different plant
species (Tran et al. 2007; van de Mortel et al. 2012;
Cheng et al. 2017; Carrión et al. 2018; Cordovez et
al. 2018; Jeon et al. 2021). Here, our primary goal was to
identify core metabolic pathways that are targeted by rhizobacteria in
different plant species and to investigate the metabolomic changes
induced in rhizobacteria-plant interactions that lead to either plant
growth promotion (effective partnership) or growth reduction
(ineffective partnership). Integration of in vitro bioassays,
untargeted metabolomics and screening of pathways-specific mutants
showed that inoculation of the plant root system with each of the three
rhizobacterial genera induced substantial changes in the shoot
metabolome in a species-specific manner. The results pointed to the
phenylpropanoid pathway as a central plant metabolome response
associated with effective or ineffective partnerships. Subsequent
analysis of twelve Arabidopsis transparent testa (tt )
mutants defective in different branches of the flavonoid pathway,
revealed that the proanthocyanidin branch is key in
rhizobacteria-mediated plant growth promotion.