Diversity and structure of prokaryotic assemblages in a thermally stratified tropical lake

The structure and diversity of prokaryotic assemblages in inland waters are strongly related to their habitat. Yet, there is a lack of integrative studies surveying them in different compartments in tropical lakes. This study estimated the diversity and composition of prokaryotic assemblages in sediments, microbialites, and water column in the tropical warm monomictic Lake Alchichica and identified the most representative phylotypes while thermally stratified. The 16S rRNA gene survey showed a distinctive prokaryotic assemblage for each compartment, with 60–78 % of the phylotypes being unique to each one. Sediments accounted for the major prokaryotic diversity in the lake, with chemoorganotrophic bacteria and sulphate reducers as major biogeochemical components. Microbialites showed a high abundance of oxygenic and anoxygenic phototrophs, as well as organotrophs. The prokaryoplancton in the water column was mainly composed of picocyanobacteria and Flavobacteria in the epilimnion, shifting to a high diversity of anaerobic microorganisms in the hypolimnion. These water column assemblages were significantly correlated to pH, ORP, DO, and nutrient concentration. This study shows an integral view of the prokaryotic assemblages in a deep tropical lake related to physicochemical characteristics, from their diversity to their biogeochemical implications, suggesting the role of lake sediments as a possible microbial seed bank.