Metabolite signatures of Brassicaceae in effective and ineffective partnerships
The metabolome changes induced by the different rhizobacteria in the shoots of Arabidopsis and Broccoli were subjected to a comparative analysis as both plant species belong to the Brassicaceae family. Glucosinolates (GLS) are among the metabolites that showed alteration by rhizobacteria treatment. In Arabidopsis, the effective partnership withPf SS101 enhanced the relative levels of aliphatic long-chain GLS such as glucohirsutin and 8-methylthiooctyl glucosinolate, whereas the ineffective partnership between Pf SS101 and Broccoli was characterized by an increase in the levels of indolic GLS (i.e., glucobrassicin, desulfoglucobrassicin, 4-methoxyglucobrassicin and neoglucobrassicin) and short-chain aliphatic GLS such as glucoibervirin. In contrast to the effective Pf SS101-Arabidopsis partnership, the ineffective Pbg -Arabidopsis partnership caused a drastic reduction of all detected aliphatic GLS, (i.e., glucohirsutin (8-methylsulfinyloctyl glucosinolate), glucolesquerellin (6-methylthiohexyl glucosinolate), 7-methylthioheptyl glucosinolate and 8-methylthiooctyl glucosinolate. In Broccoli, both the ineffective partnership with Pf SS101 as well as the effective partnership with Pbg caused significant increases of the indolic GLS glucobrassicin. Meanwhile, the effective MB-Arabidopsis partnership led to upregulation of glucohirsutin while this rhizobacterial strain barely influenced the level of GLS in Broccoli (Supplementary Material,Tables S4 and S7 ). Considering their inconsistent accumulation patterns in effective and ineffective partnerships, GLS seem not to be appropriate plant metabolic markers for discriminating between effective and ineffective partnerships.
On the other hand, alteration of a particular branch of the phenylpropanoid pathway showed co-occurrence with growth promotion (effective partnership) or lack of growth promotion/ growth reduction (ineffective partnership) in the different plant-rhizobacteria combinations tested. Higher accumulation of flavonoids was evident in the ineffective partnerships between Arabidopsis-Pbg and Broccoli-Pf SS101, while flavonoids showed no significant change in their abundance in the effective partnership between Arabidopsis-Pf SS101 (Figure 3 and Supplementary Material, Tables S4 and S7 ). Furthermore, in the ineffective partnerships between Arabidopsis-Pbg, indole-derived defensive compounds such as camalexin, β-d-glucopyranosyl indole-3-carboxylic acid and metabolites from the phenylpropanoid pathway (including anthocyanin and salicylic acid) showed higher accumulation (Figure 2a2 , Supplementary Material, Table S4 and Figure 3b ). Similarly, the ineffective partnership between Broccoli and Pf SS101 resulted in a significant accumulation of flavonoids and other defensive metabolites (Figure 2c2 , Supplementary Material, Table S7 ). The accumulation of these stress/defense-related metabolites in the aforementioned ineffective partnerships suggests that both Pbgand Pf SS101 may be perceived as a biotic stressor by Arabidopsis and Broccoli, respectively (Figure 2a2 and 3 ).