This study is part of a comprehensive biodiversity and geochemistry study of Antartic lagoons microbial mat, from James Ross Archipelago

The James Ross Archipelago (JRA), located at the northeastern tip of the Antarctic Peninsula, is a climatically sensitive region where lakes on Marambio Island (MI) and Clearwater Mesa (CWM) provide unique environments for studying microbial life. Lakes from JRA are influenced by varying hydrological inputs, including meltwater from glaciers, precipitation, and permafrost thaw, leading to changes in their geochemical and physical properties. While previous studies have focused on specific microbial groups, comprehensive assessments of prokaryotic diversity and the structural dynamics of microbial mats from these lakes are still lacking in this region. This study aims to fill this gap by examining the prokaryotic communities in 15 lakes and assessing their environmental geochemical characteristics, diversity, spatial distribution, and response to environmental factors like hydrology, geomorphology, and climate change. Results highlight a strong environmental gradient shaping microbial diversity and structure, with significant variations between the two regions. MI lakes were characterised by saline, sulphur-rich conditions, and extreme acid drainage in Lake Chica, while CWM lakes were fresh, alkaline, and more favourable to microbial diversity. The study found a predominance of Proteobacteria and Bacteroidota across both regions, but the abundance of different families varied with local environmental factors such as pH, conductivity, and redox potential. Notably, sulphur-oxidising bacteria like Thiobacillus dominated in MI lakes with extreme conditions, while more diverse microbial communities, including cyanobacteria, were found in the CWM region. Alpha diversity was higher in CWM than MI lakes, which exhibited increased cyanobacterial diversity and higher species richness. This was contrasted with MI lakes, where environmental stressors such as high metal concentrations and acidic pH seemed to limit diversity. The findings emphasise that local environmental factors, rather than geographical proximity, are the primary drivers of microbial community structure in Antarctic lakes. This study suggests that climate change, which affects the geochemistry and hydrology of these systems, may cause significant shifts in microbial community composition. The unique microbial assemblages in certain lakes, particularly in lakes Chica and Katerina, indicate that these ecosystems may be particularly vulnerable to climate-driven changes. These results underscore the need for continued monitoring of Antarctic freshwater systems, which serve as sensitive indicators of broader environmental changes in Polar Regions.