The metacommunity framework has been rarely adopted to investigate the
underlying ecological mechanisms shaping microbial communities. With the
aid of advanced molecular techniques, we investigated sediment
communities of Fungi, Bacteria and Archaea in four Italian show caves
aiming to disentangle the effects induced by tourists on species
richness and composition from environmental filtering and dispersal
driven mechanisms. We modelled community changes against human
disturbance ---measured as the distance from the tourist
path---demonstrating that the presence of visitors in caves decreases
fungal species richness and causes species replacement in Bacteria and
Archaea. Environmental filtering affects species richness and
composition of Fungi and species richness of Archaea, while a minor role
was played by dispersal, influencing only species richness in Fungi. We
provide new perspectives on the dynamics of microbial communities under
human disturbance suggesting that a proper understanding of the
underlying selective mechanisms requires a comprehensive and
multi-taxonomic approach.