Running against the clock: describing microbial diversity in an extremely endangered microbial oasis in the Chihuahuan desert

Cuatro cienegas Basin (CCB) is an extraordinary diverse oasis that is dying in front of our eyes. The Churince system disappeared completely in 2016 and the poza named for its amazing diversity, Archaean Domes, disappeared in 2023. However, there could be groundwater water connections between sites, allowing to dispersal of taxa as well as the survival of microbial lineages in the deep aquifer Herein, we explore whether there is microbial connectivity across sites in the oasis of CCB, located in the Chihuahuan Desert, in the Northern state of Coahuila in Mexico. We focused first on two distinct aquatic system within CCB that are [~]4700 meters apart on the Eastern lobe of the basin: Pozas Rojas -a preserved system characterized by several unique ponds surrounding a deep lagoon, and the now extinct Archean Domes (AD)--noted for its extreme salinity, as well as anoxic and methane-rich conditions. We sequenced the hypervariable V4 region of the 16S rRNA gene from samples of Pozas Rojas (PR), and of two different features in AD: orange circles (C) and dome-shaped structures (D). Additionally, we utilized whole-genome metagenomic data from different samples from AD site (from the years 2016 to 2023). Second, we compared metagenomes obtained from the now extinct Churince (samples from 2012 to 2014) in the West lobe of the basin, with the Easter side. Our results revealed taxa common to different sites, including Halanaerobium sp. and Desulfovermiculus sp., that are prevalent across samples from PR and AD, and shared between AD and Churince, suggesting that those genera are core to the deep aquifer. Moreover, during the eight years of sampling, AD exhibited a substantial decline in microbial diversity. Possibly, this decline, as well as Churince demise, is due to anthropogenic disturbances of the deep aquifer due to overexploitation for alfalfa irrigation. Diversity in metagenome-assembled genomes (MAGs) decreasing from 125 MAGs in 2016 to only 22 in 2023. Our study supports the hypothesis of the importance of groundwater as a fundamental microbial reservoir and connector among CCB ponds. Therefore, the regulation of extraction of such aquifer is paramount.