Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, “ Candidatus Nitrosopumilus limneticus,” is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.

Abstract. This article reports the results of three field campaigns conducted in Lake Issyk-Kul in 2015, 2016, and 2017. During the campaigns, CTD profiling and water sampling were performed at 34 locations all over the lake. A total of 75 CTD profiles were obtained. Some biogeochemical and thermohaline parameters at the lake surface were also mapped at high horizontal resolution along the ship's track. In addition, thermistor chains were deployed at three mooring stations in the eastern littoral region of the lake, yielding 147-day-long records of temperature data. The measurements revealed that – while the thermal state of the active layer, as well as some biogeochemical characteristics, were subject to significant interannual variability mediated by atmospheric forcing – the haline structure of the entire lake was remarkably stable at the interannual scale. Our data do not confirm the reports of progressive warming of the deep Issyk-Kul waters as suggested in some previous publications. However, they do indicate a positive trend of salinity in the lake's interior over the last 3 decades. A noteworthy newly found feature is a weak but persistent salinity maximum below the thermocline at a depth of 70–120 m, from where salinity slightly decreased downwards. The data from the moored thermistor chains support the previously published hypothesis about the significant role of the submerged ancient riverbeds on the eastern shelf in advecting littoral waters into the deep portion of the lake during differential cooling period. We hypothesize that the less saline littoral water penetrating into the deep layers due to this mechanism is responsible for the abovementioned features of salinity profile, and we substantiate this hypothesis by estimates based on simple model assumptions.

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30In this study, we explored the diversity and community composition of bacteria along a 31 vertical gradient in Lake Issyk Kul, Kyrgyzstan, one of the largest and deepest brackish lakes 32 in in the world. We identified 4904 bacterial ASVs based on analysis of 16S rRNA gene 33 sequences and determined significant changes in the composition responding mainly to the 34 variables depth and salinity. A higher abundance of Proteobacteria and Bacteroidetes was 35 observed in the surface waters and the lake tributaries. Cyanobacteria were more abundant in 36 the deep chlorophyll maximum (28.5 to 128 m), while Planctomycetes and Chloroflexi were 37 dominant at depths between 128 to 600 m. According to our machine learning analysis used 38 for identifying the most critical environmental factors, depth and temperature revealed the 39 strongest effect on members of Proteobacteria, Planctomycetes, and Chloroflexi, while 40 oxygen is associated with the variations in Cyanobacteria. Also, a notable increase in alpha 41 diversity estimations was observed with increasing water depth. This work evidences 42 significant differences in the structure of bacterial communities along the depth gradient in 43 deep, transparent lake ecosystems. Notably, there is a dominance of Planctomycetes and 44

Abstract. This article reports the results of 3 field campaigns conducted in Lake Issyk-Kul in 2015, 2016, and 2017. Vertical CTD profiles were obtained and water samples collected at the total of 75 stations. Some biogeochemical and thermohaline parameters at the lake surface were also mapped at high horizontal resolution along the ship’s track. In addition, thermistor chains were deployed at 3 mooring stations in the eastern littoral region of the lake, yielding 147 days long records of temperature data. The measurements revealed that while the thermal state of the active layer, as well as some biogeochemical characteristics, were subject to significant interannual variability mediated by atmospheric forcing, the haline structure of the entire lake was remarkably stable at the interannual scale. Our data do not confirm the reports of progressive warming of the deep Issyk-Kul waters as suggested in some previous publications. However, they do indicate positive trend of salinity in the lake’s interior over the last 3 decades. A noteworthy newly found feature is a weak but persistent salinity maximum below the thermocline at the depth of 70–120 m, from where salinity slightly decreased downwards. The data from the moored thermistor chains support previously published hypothesis about significant role of the submerged ancient riverbeds on the eastern shelf in advecting littoral waters into the deep portion of the lake during differential cooling period. We hypothesize that the less saline littoral water penetrating into the deep layers due to this mechanism is responsible for the abovementioned features of salinity profile, and substantiate this hypothesis by estimates based on simple model assumptions.