The Hidden Guardians: From Active Cells to Spores in a 20-Year Journey into the Microbial Heart of a Drying Oasis

Abstract

The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, a Ramsar Wetland, is historically characterized by a unique network of pozas renowned for microbial diversity. Among them, the Churince hydrological system epitomized a delicate balance of endemic species, stable water regimes, and complex microbial assemblages. Over the last five decades, however, Churince underwent a catastrophic [~]99% water loss, primarily driven by intensive agricultural extraction. We showed that this desiccation not only caused hydrological collapse but also reshaped microbial physiology. Longitudinal records from 2007 to 2019, combining satellite imagery, piezometer data, and field observations, documented progressive declines beginning in 2011 and culminating in the complete desiccation of the Intermediate Lagoon by 2019. To track microbial responses, we employed a cultivation-based approach distinguishing vegetative cells from dormant spores, enabling direct physiological assessment of metabolic activity versus dormancy. As water diminished, spore abundance increased relative to vegetative forms, revealing a shift toward dormancy as a survival strategy under extreme desiccation. Complementary mesocosm experiments showed that reduced diversity further enriched for spores, illustrating how loss of community complexity accelerated dormancy and erosion of active assemblages. Together, these results demonstrated that habitat loss triggered microbial community change, which we frame as a microbial extension of the ecological concept of community disassembly. By combining two decades of hydrological evidence with microbial physiology, this study fills a critical gap in understanding how wetland drying selects for microbial dormancy. These findings underscore the urgent need for sustainable agriculture and integrated water management to preserve biodiversity and ecosystem function in threatened wetlands worldwide.