The partition function of a three-dimensional $mathcal{N} =2$ theory on the manifold $mathcal{M}_{g,p}$, an $S^1$ bundle of degree $p$ over a closed Riemann surface $Sigma_g$, was recently computed via supersymmetric localization. In this paper, we compute these partition functions at large $N$ in a class of quiver gauge theories with holographic M-theory duals. We provide the supergravity bulk dual having as conformal boundary such three-dimensional circle bundles. These configurations are solutions to $mathcal{N}=2$ minimal gauged supergravity and pertain to the class of Taub-NUT-AdS and Taub-Bolt-AdS preserving $1/4$ of the supersymmetries. We discuss the conditions for the uplift of these solutions to M-theory, and compute the on-shell action via holographic renormalization. We show that the uplift condition and on-shell action for the Bolt solutions are correctly reproduced by the large $N$ limit of the partition function of the dual superconformal field theory. In particular, the $Sigma_g times S^1 cong mathcal{M}_{g,0}$ partition function, which was recently shown to match the entropy of $AdS_4$ black holes, and the $S^3 cong mathcal{M}_{0,1}$ free energy, occur as special cases of our formalism, and we comment on relations between them.
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