## 3 Results
### Comparative Analysis of the Microbial Structure
#### 3.2.1 Water Associated Bacterial Communities  
Bacterial community structure in the water column was more diverse than in sediments; results also showed that there were not large differences between epilimnion and hypolimnion bacterial richness (Figure 3). The sequencing of W1 clustered into 22 phyla, 36 classes, 158 families and 155 genera, while W4 clustered a total of 23 phyla, 39 classes, 171 families and 160 genera. In both cases, more than one third of the genera were unknown or uncultured. Water samples shared >85% of the main phyla, comprising Proteobacteria (W1, 30%; W4, 51%), Cyanobacteria (W1, 27%; W4, 21%) and Bacteroidetes (W1, 27%; W4, 14%). In addition, with the presence of the phylum Verrucomicrobia, the spatial distribution of the bacterial population covered up to 96% in W1. On the other hand, W4 reached a 97% of total spatial distribution with Patesobacteria, Actinobacteria and Verrucomicrobia. Despite of the similarity in phyla distribution, the water strata become divergent at the family level.  
_Oxynphotobacteria_, the only family within Cyanobacteria, comprised 27% of relative abundance in W1, decreasing to 21% in W4. The second most abundant family was _Rubritalaceae_, within Verrucomicrobia, contributing 8% in W1. An environment of low oxygen availability such as W4 habitat drastically limits family development because of its mandatory aerobic chemoheterotrophic metabolism [23]. The _Bacteroidia_ relatives clustered mainly in _Saprospiraceae_, _Cyclobacteriaceae_, _Cryomorphaceae_, _Crocinitiomicaceae_ and _Flavobacteriaceae_ families, accounting a total of 23% over the bacterial population in W1 sample. It is a clade strongly dependent on the availability of organic matter, with complex organic carbon sources transformation and decomposition (i.e., _Flavobacteriaceae_), sapropytism of microorganisms--algae or bacteria--(i.e., _Saprospiraceae_) [24]. Moreover, the clade involves other families without any known function due to the difficulties in isolating their members (i.e., _Cryomorphaceae_). Members of the family _Splingomonadaceae_ also were present, although only represented a 2% of the total spatial bacterial distribution in W1 and was described as xenobiotic compounds transformation [25; 26].  
As regards W4 sample, Cyanobacteria continue to be among the most abundant taxa, representing 20% of total identified sequences. Contrary to W1 sample, _Gammaproteobacteria_ members as well as _Hydrogenophilaceae_ and _Saccharomyces_ families increased their representation accounting for 30%, 19% and 14%, respectively. Little is known about these families and their metabolic functions. _Hydrogenophilaceae_ had been poorly described as nitrogen fixers by Calvin-Benson cycle and reduced-sulphur compounds oxidisers [27]. Unknown family from the recent proposed lineage _Gracilobacteria_ (currently, included in Patescibacteria phylum) was identified in a 5% of relative abundance in W4. _Alphaproteobacteria_ clade was comprised mainly by _Terasakilaceae_, _Rhodobacteraceae_, _Talassobucaceae_ and _Caulobacteraceae_. Members of the family _Terasakilaceae_ and _Caulobacteraceae_ were documented to be nitrogen fixers [28] and denitrifiers through nitrate reducing pathway [29], respectively, and may be important for nitrogen natural regulation. Furthermore, _Rhodobacteraceae_ and _Desulgobulaceae_ families had been reported to play a key role in sulphur cycle. _Rhodobacteraceae_ acts as sulphur, sulphide, thiosulfphate or sulphate oxidiser to obtain carbon sources [30], while _Desulgobulaceae_ is a well-known sulphate-reducing bacteria family [31]. Finally, some members of the family _Microbacteriaceae_ (Actinobacteria) appeared in W4. This family has been found to be associated to saprophytic processes by degradation of organic matter. They are also associated to phosphorus extraction under aerobic and anaerobic conditions or recalcitrant xenobiotic degradation [32; 33].