###### Abstract  
Lake Alboraj, located in southeast Spain, was declared natural Microreserve and included into European Natura-2000 Network due to its contribution to environmental heritage. Unfortunately, the ecological status of the lake has changed dramatically, mainly due to the lowering of water table caused by groundwater abstractions for irrigation. It is a permanent small karstic lake whose surface has reduced in the last decades to nearly the third part of its historical water level. The water column shows a marked seasonal oxycline, that splits an aerobic upper layer (epilimnion) from an anaerobic layer below (hypolimnion). Sequencing 16S rRNA gene amplicons and applying chemical tools at epilimnion, hypolimnion and sediment, showed a clear gradient in the bacterial community structure, which support the co-existence of assimilatory and dissimilatory microbial mediated reactions. Results allows to infer that microbial stratification could provide various physical and chemical environments at different depths in the water column related to biogeochemical reactions providing N-S-C- recycling processes. Authorization, Species  
an important biodiversity heritage at local and national level [3]. Nevertheless, from the 80's of the past century to the present, the ecological status of the lake has changed dramatically mainly due to changes in land uses produced in the hydrogeological boundary of the \"Tobarra-Tedera-Pinilla\" groundwater body, which formerly contributed to the formation and maintenance of the lake. The most noticeable modifications include the changes from dry-extensive to irrigated-intensive croplands facilitated by groundwater pumping, which has leaded to a lowering of the lake water table. Even though some limnological approaches have been addressed on the Lake Alborraj [4; 5; 6; 7; 8], studies on stratification dynamics of the water column have recently started. Since 2017, a marked oxyline in the eutrophic lake has been observed [9; 10], which can constitute a biogeochemical interface by providing aerobic and anaerobic conditions. The dissolved oxygen stratification patterns may originate different conditions in the environment, at different depths in the water column, that lead to different rates in nutrient recycling. Specifically, the turnover of nitrogen in the water column is highly relevant for assessing eutrophication processes in surface water bodies. In this line, the lake became eutrophic from an initial oligotrophic state due to the overgrowth of benthic cyanobacterial mats, which promoted a progressive burial of its submerged macrophyteadows [10]. The multiple spatial variations in oxygen, N-species concentration, as well as land occupation, may act akin to dependent factors in the composition of bacterial communities and the processes they carry out [11]. Consequently, it affects the correct functioning of the aquatic ecosystem since it may be significantly altered by the activity of microorganisms. Despite bacteria can play an important role in the water column chemostrification, due to their close involvement in N-S-C speciation via redox interfaces, the study of bacterial populations through specific DNA applications in small lakes remain widely unaddressed [12]. Understanding environmental processes is the first step in forecasting lake evolution and, in the same way, a comprehension of the dynamics of stratification is required to prognosticate the past and the future of lakes [13]. The study of environmental DNA by culture-independent tools in Lake Alboraj represents a starting point for studying the microbial structure involved in the N-S-C cycles. In this sense, both the eutrophic character of the small lake and the persistence of an oxyline offer an opportunity for studying the bacterial structure changes across the water column in order to gain knowledge about the microorganisms involved in eutrophication processes as well as in greenhouse gas emissions (i.e., CO\({}_{2}\), N\({}_{2}\)O, CH\({}_{4}\)).