## 2 Results and Discussion
### Transcriptomic Profile of Halomicronema sp. Next, to know more about the general gene expression profile of _Halomicronema_ sp., an RNA sequencing experiment was performed on the strain grown under control conditions. Here, about 20 million reads were obtained for each biological replicate with an average input read length of 292 bp and a mean quality score of 36 (Table S1). More than 76% of the reads aligned with the reference genome of _Halomicronema_ sp. CCY15110. More specifically, a total of 5492 different genes were detected, of which 1268 (23%) encode for proteins with unknown function (or defined as \"hypothetical proteins\"). The most abundant transcript (Table S2), which had a value of 1,283,853 reads, is that for transfer-messenger RNA (tmRNA or SsrA) (values were normalized for gene length and total reads abundance per sample). The tmRNA is a bacterial RNA molecule that functions as both transfer and messenger RNA. In fact, it possesses paired and structured ends similar to a tRNA molecule, capable of loading alanine, while the central sequence of the molecule contains a short ORF coding for about ten amino acids, including various alanines, and ends with a stop codon [41]. It forms a ribonucleoprotein complex (tmRNP) along with Small Protein B (SmpB), elongation factor EF-Tu, and ribosomal protein S1. The key role of tmRNA is to bind stalled ribosomes and add a tag to the C-terminus of the unfinished polypeptide, inducing its proteolysis. This process assures translational quality and optimal regulation of gene expression. This process is known as a trans-translation reaction [42]. Given its importance, tmRNA is conserved and it is one of the most abundant RNAs in all bacteria [43]. As expected, analyzing the most commonly present transcripts (at least 5000 reads) showed that they code for proteins playing a role in photosynthesis (photosystem I and II related proteins, cytochrome), and among them, there are also genes involved in the synthesis of  
Figure 3: Gene expression analysis of EPS-related genes from _Halomicronema_ sp, cells were grown in six different growing conditions: control, and in the presence of EDTA 250 \(\upmu\)M, or MgSO\({}_{4}\) 50 mM, NaCl 340 mM, NaCl 680 mM, and NaCl 1 M; expression is relative to the control condition using the 2\({}^{-\Delta\Delta}\)Ct method. Red line represents a 2 logfold increased expression, while the green line represents a 2 log-fold decrease in expression. Data outside these two boundaries were considered significant. The data represent the mean and the standard deviation of three independent biological replicates. phycobilisome, phycocyanin, and allophycocyanin. These proteins form elaborate antennae capturing sunlight and transferring the energy to the photosynthetic reaction systems [44]. These protein complexes are located on the thylakoid and exhibit different abundance during their biogenesis and under light-activated heterotrophic growth [45; 46]. Genes coding for transporters of iron, phosphate, and ammonium are also highly represented (Table S2). This is not surprising since it is known that the availability of those components can be a bottleneck for the growth of cyanobacteria in various ecosystems [47; 48; 49]. Interestingly, growth as entangled filaments (a phenotype seen in _Halomicronema_ sp., see Figure 1) in _Trichdoesmium_ has been linked to an enhanced capacity to acquire iron from particulate sources such as dust, a physical structure that can facilitate the growth of a complex bacterial community [49; 50]. Similarly, it is possible that _Halomicronema_ sp. plays a similar role in the microbial mat where it was isolated. Finally, among the most abundant transcripts, we find genes coding for regulators of protein synthesis (sigma factors, elongation factors, and ribosomal proteins), other transcripts are linked to the production of ABC transporters and metalloproteinases. In addition, there are numerous transcripts coding for transcription factors, transposases, methyltransferases, and various transporters.