LAUSR

Abstract Salinity fluctuations constitute a well‐known high stress factor strongly shaping global biological distributions and abundances. However, there is a knowledge gap regarding how increasing saline stress affects microbial biological interactions. We applied the combination of a probabilistic method for estimating significant co‐occurrences/exclusions and a conceptual framework for filtering out associations potentially linked to environmental and/or spatial factors, in a series of connected ephemeral (hyper) saline lakes. We carried out a network analysis over the full aquatic microbiome—bacteria, eukarya, and archaea—under severe salinity fluctuations. Most of the observed co‐occurrences/exclusions were potentially explained by environmental niche and/or dispersal limitation. Co‐occurrences assigned to potential biological interactions remained stable, suggesting that the salt gradient was not promoting interspecific facilitation processes. Conversely, co‐exclusions assigned to potential biological interactions decreased along the gradient both in number and network complexity, pointing to a decrease of interspecies competition as salinity increased. Overall, higher saline stress reduced microbial co‐exclusions while co‐occurrences remained stable suggesting decreasing competition coupled with lack of stress‐gradient promoted facilitation in the microbiome of ephemeral saline lakes.