Differences in Bacterial Communities of Deep and Shallow Subarctic Ice-Covered Lakes in the Northern Pole of Cold

The cold conditions of these habitats, as well as the morphometric features and origins of long-term ice-covered freshwater lakes, influence the structure and diversity of bacterial communities, which remain poorly understood. This study focused on long-term ice-covered lakes of contrasting origins (tectonic–glacial, glacial, and thermokarst), located in the highland subarctic region of Eastern Yakutia—an area that includes the Northern Hemisphere’s Pole of Cold, characterized by extremely low temperatures The differences in bacterial community diversity between deep lakes of tectonic–glacial origin and shallow lakes of glacial and thermokarst origin are shown by metabarcoding of the 16S rRNA gene. According to ANOVA, the water quality parameters were homogeneous between samples from the deep and shallow, and their effect on the bacterial community structure was insignificant. The deep lake communities were dominated by groups indicative of oligotrophic, stratified, and cold environments: Cyanobium_PCC−6307 (low-light picocyanobacteria), Methylacidiphilaceae (methanotrophs in oxygenated conditions), and the heterotrophic psychrotolerant genera Acinetobacter and Paenisporosarcina. Shallow lakes, by contrast, were enriched in taxa associated with high-light, well-mixed, and sediment-influenced conditions: SAR11 (Clade_III) (photoheterotrophic oligotrophs), Methylobacter (methanotrophs at neutral-pH), and taxa dominant in sediments (Gemmataceae и Terrimicrobium). The broadly distributed genera Candidatus_Planktophila, Ilumatobacter, and Polynucleobacter represent cosmopolitan freshwater generalists with diverse metabolic capabilities, explaining their consistent presence across both lake types. The novelty of this study lies in identifying a link between the structure of bacterial communities and the morphometric characteristics of lakes under conditions of homogeneous environmental parameters. Despite similar chemical compositions, opposite patterns were observed in deep and shallow lakes: in deep lakes, autochthonous taxa associated with stratification (low-light-tolerant cyanobacteria, aerobic methanotrophs) predominated, whereas sediment-associated and photoheterotrophic taxa dominated in shallow lakes, indicating a stronger connection between the benthos and the pelagic zone and a dependence on allochthonous carbon. Our results demonstrate that morphometry appears to be an important factor of the stability of microbial composition and carbon flux in permafrost regions. We revealed the heterogeneity of bacterial communities in subarctic lakes and identified dominant groups and key taxa, contributing to a better understanding of the ecological structure and functioning of lake ecosystems in cold regions and providing a basis for their monitoring.