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Microbes living in plant tissues—endophytes—are mainly studied in crop plants where they typically colonize the root apoplast. Trees—a large carbon source with a high capacity for photosynthesis—provide a variety of niches for endophytic colonization. We have earlier identified a new type of plant–endophyte interaction in buds of adult Scots pine, where  Methylorubrum  species live inside the meristematic cells. The endosymbiont  Methylorubrum extorquens  DSM13060 significantly increases needle and root growth of pine seedlings without producing plant hormones, but by aggregating around host nuclei. Here, we studied gene expression and metabolites of the pine host induced by  M. extorquens  DSM13060 infection. Malic acid was produced by pine to potentially boost  M. extorquens  colonization and interaction. Based on gene expression, the endosymbiont activated the auxin- and ethylene (ET)-associated hormonal pathways through induction of  CUL1  and  HYL1 , and suppressed salicylic and abscisic acid signaling of pine. Infection by the endosymbiont had an effect on pine meristem and leaf development through activation of  GLP1-7  and  ALE2 , and suppressed flowering, root hair and lateral root formation by downregulation of  AGL8 ,  plantacyanin ,  GASA7 ,  COW1  and  RALFL34 . Despite of systemic infection of pine seedlings by the endosymbiont, the pine genes  CUL1 ,  ETR2, ERF3 ,  HYL ,  GLP1-7  and  CYP71  were highly expressed in the shoot apical meristem, rarely in needles and not in stem or root tissues. Low expression of  MERI5, CLH2 ,  EULS3  and high quantities of ononitol suggest that endosymbiont promotes viability and protects pine seedlings against abiotic stress. Our results indicate that the endosymbiont positively affects host development and stress tolerance through mechanisms previously unknown for endophytic bacteria, manipulation of plant hormone signaling pathways, downregulation of senescence and cell death-associated genes and induction of ononitol biosynthesis.

The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings