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The symbiotic nitrogen-fixing soil bacteriumSinorhizobium meliloticarries a large number of toxin–antitoxin (TA) modules both on the chromosome and megaplasmids. One of them, thevapBC-5module that belongs to the type II systems was characterized here. It encodes an active toxinvapC-5, and was shown to be controlled negatively by the complex of its own proteins. Different mutants of thevapBC-5genes exhibited diverse effects on symbiotic efficiency during interaction with the host plantMedicago sativa. The absence of the entirevapBC-5region had no influence on nodule formation and nitrogen fixation properties. The strain carrying an insertion in the antitoxin gene showed a reduced nitrogen fixation capacity resulting in a lower plant yield. In contrast, when the toxin gene was mutated, the strain developed more efficient symbiosis with the host plant. The nitrogen fixing root nodules had a delayed senescent phenotype and contained elevated level of plant-derived molecules characteristic of later steps of nodule development. The longer bacteroid viability and abundance of active nitrogen fixing zone resulted in increased production of plant material. These data indicate that modification of the toxin/antitoxin production may influence bacteroid metabolism and may have an impact on the adaptation to changing environmental conditions.