## 5 Conclusions  
The amplicon-based MiSeq Illumina sequencing allows obtaining a complete screening of the bacterial population inhabiting at different depths in the water column as well as in the sediment of Lake Alboraj. The composition of bacterial communities differs from the epilimnion to the hypolimnion, while the sediment holds a bacterial population different from those representing water samples. A greater abundance of bacteria families related to processes involved in the N-cycle was found in the sediment and hypolimnion layer (W4), although with different composition. A greater abundance of denitrifiers such as those belonging to families _Caulobacteraceae_, _Rhodobacteraceae_ and _Hydrogenophilaceae_ was detected in W4 samples, while in the sediment, members of the families _Pseudomonasaceae_ and _Burkholderiaceae_, related to processes that contribute to nitrogen turnover, were found. The higher presence of denitrifier bacteria in the deeper zones is consistent with the decrease in the concentration of NO3- detected. On the other hand, NH4+ concentration was higher in the hypolimnion. In this sense, a large group of bacteria capable to perform DNRA processes was found in the sediment, from facultative anaerbs such as _Enterobacteriaceae_, to aerobes such as _Pseudomonadaceae_ or others akin to those from the family _Desulfuronondaceae_. As regards S-cycle, the results obtained showed the presence of a variety of sulphur related bacteria in the water samples, which can perform coupled sulphate reduction-sulphide oxidation processes. The anoxic hypolimnion layer showed a greater abundance of S-cycle related bacteria, including those belonging to the families Desulfobulbaceae, _Rhodobacteraceae_, _Crocinitomicaceae_, which can perform sulphate-reducing processes to produce H2S. This H2S may be re-oxidised in the presence of oxygen by known sulphate-oxidising bacteria such as _Rhodobacteraceae_ and _Cyclobacteriaceae_ found in the epilimnion. This study has shed light on the bacterial community structure and its support to the co-existence of assimilatory and dissimilatory microbial mediated reactions. Differences in physico-chemical conditions in the water column are associated to a bacterial community structure adapted to the available nutrients. These dynamic biological processes might hold a key role in maintaining the ecological equilibrium of the aquatic ecosystem. Bacterial distribution points out that N-S-C biogeochemical cycles can be interconnected throughout interfaces: water-atmosphere, oxycline and water-sediment. Future work is needed to understand the temporal changes in the structure of the bacterial communities through detailed monitoring that matches the changes in oxygen stratification patterns during the year. Detailed exploration of microbial community structure variation over a non-stratified situation and oxygen dynamic states, in addition to their function adjustment relationship, will be essential to deepen into the knowledge of the ecosystem development. Moreover, an exploration of the remaining microbial processes is still needed to understand the lake functioning and thus the resilience to its ongoing deteriorated ecological status. The following are available online at [[https://www.mdpi.com/article/10.3390/app11146309/s1](https://www.mdpi.com/article/10.3390/app11146309/s1)]([https://www.mdpi.com/article/10.3390/app11146309/s1](https://www.mdpi.com/article/10.3390/app11146309/s1)), Figure S1: Observed OTUs alpha rarefaction curve, Figure S2: Non-metric multidimensional scaling (NMDS) analysis of the weighted UniFrac distance of water and sediment samples from Lake Alboraj. **Author Contributions:** Conceptualisation, Y.E., M.A.-O. and J.J.G.-A. ; methodology, Y.E., A.M. and D.S. ; formal analysis, Y.E. and A.M.; investigation, M.A.-O., J.A.F. and J.J.G.-A. ; resources, J.L.M. ; data curation, Y.E., A.M., J.L.M. and D.S. ; writing--original draft preparation, Y.E. ; writing--review and editing. J.L.M., D.S., J.A.F., M.A.-O. and J.J.G.-A. ; funding acquisition, Y.E., D.S.