## 3 Results
### Metagenomic Analysis
#### 3.1.3 Bacterial Communities  
Analysis of the bacterial communities, which dominated over the eukaryotic communities, revealed six main phyla, namely _Cyanobacteria_, _Actinobacteria_, _Proteobacteria_, _Bacteroidetes_, _Firmicutes_ and _Deinococcus-Thermus_, representing together on average 98% of the total bacteria, in addition to some other phyla, each representing less than 0.5% of the total bacterial community and marked as \"others\" in Figure 3.  
The most dominant phylum was _Actinobacteria_ (54-61.5% of bacteria), with the exception of sample Ezuz 1, which showed a massive dominance of the phylum _Cyanobacteria_ (68% of bacteria) and a lower proportion of _Actinobacteria_ (14% of bacteria). The second most abundant phylum was _Cyanobacteria_ in samples Avdat 1 and Avdat 3 (26-39% of bacteria), while in sample Ezuz 4, _Cyanobacteria_ represented only 0.6% of the bacterial community. The phylum _Proteobacteria_ was present with a relative high abundance (21% of bacteria) in Ezuz 4 and with lower proportions in the other samples (1-9%), followed by the phyla _Bacteroidetes_ (6-16% of bacteria) and _Firmicutes_ (0.5-2%). The last two phyla accounted for less than 0.5% in sample Avdat 1. The phylum _Deinococcus-Thermus_ was identified in very low proportions in all the samples, reaching more than 0.5% only in samples Avdat 3 and Ezuz 4 (0.5-0.8% of bacteria). In Supplementary Figure S2, the relative abundance of the bacterial communities at the class level is presented, while all the genera representing more than 0.5% of the total microbiome in each of the samples are summarized in the form of a heatmap in Figure 4. The heatmap shows the relative abundance of each genus in each sample, highlighting differences and similarities between them. Figure 3: Relative abundance of bacterial communities at the phylum level (cutoff 0.5%). Figure 2: Relative abundance of bacteria, eukaryotes and archaea in the microbiomes of the four samples analyzed. Within the phylum _Actinobacteria_, the dominant class was _Rubrobacteria_, with all the members identified belonging to the _Rubrobacter_ genus, present with a very high relative abundance (35-58% of total reads) in all the samples and a lower abundance in Ezuz 1 (8% of total reads) (Figure 4). Members of the class _Actinomyctia_ were detected in all the samples with low relative proportions (0.6-4% of bacteria), but _Streptomyces_ was the only genus present with more than 0.5% relative abundance in samples Avdat 1 and Avdat 3 (Figure 4). _Cyanobacteria_ were the second most represented phylum within the bacteria and the one with the highest biodiversity, except in Ezuz 4 where no genus of cyanobacteria was significantly abundant (above 0.5% of total reads). Inside this phylum, in samples AV1, AV2 and EZ1, members of the order _Nostocales_ were detected, such as the genus _Nostoc_, which was present with a relatively high abundance in samples AV1 and EZ1 (\(\sim\)10% of total reads) but was also relatively abundant in AV3 (4% of total reads); the genus _Calothrix_, present with a relative low abundance (1-2% of total reads), and the genera _Richelia_ and _Anabena_ were found solely in sample EZ1. Other members of the Nostocales, such as the genera _Fischerella_, _Tylopthrix_, _Rivularia_, and _Nodularis_ were also identified, but contributed less than 0.5% of the total reads. Among the Oscillatoriales, the genus _Crianlium_, was the most abundant (2-4% of total reads), followed by the genus _Allocoleopsis_ (0.5-2% of total reads)  
Figure 4: Heatmap displaying the relative abundance (%) of the total microbial community (bacteria and fungi) at the genus level in each sample; the genera represent an abundance greater than 0.5% in at least one sample. and the genus _Oscillatoria_, present only with low abundance in samples AV3 and EZ1 (~0.6% of total reads). Members of the order _Synechococcus_ were identified in low proportions only in two samples, being the genus _Synechocystis_ only present in AV1, and the genus _Synechococcus_ only present in EZ1.