Prokaryotic Diversity in Flooded Karst Caves from the Northeastern Yucatan Peninsula, Mexico

Karst aquifers provide drinking water for nearly a quarter of the global population, with little information regarding their prokaryotic diversity in tropical regions. This study surveyed the prokaryotic communities in four flooded karst caves from the northeastern of the Yucatan Peninsula, –the largest tropical karst platform in Latin America–, using depth profiles. The studied systems were mainly anchialine, according to EC values and ion concentrations at different depths. The 16S rRNA gene metabarcoding approach showed that the freshwater layers had significantly lower values of the inverse Simpson index compared to the saline layers, which can be associated with the dominance of Burkholderiaceae (former Comamonadace) bacteria in 33-98% of relative abundance in the freshwater samples. In contrast, the saline water presented a higher prokaryotic diversity, with the presence of ammonia oxidizing archaea (Nitrosopumilaceae), and bacteria related to the S -cycle such as Thioglobaceae and some members of Desulfobacterota, including Desulfocapsaceae bacteria. The presence of marine taxa and a saline water layer declined with distance from the coast. Further, the composition and distribution of the prokaryotic communities was highly dependent of the sampled site, with unique ribotypes at each sampled cave, suggesting their role as hotspots of prokaryotic biodiversity.