184 Chapter 6 Multi-omics analysis reveals retention and adaptation of “Ca. Methanoperedens” in the microbial community at increased salinities Sequences affiliated to “Ca. Methanoperedens” dominated the enrichment culture with adjusted salinities ranging from freshwater to 1.5%, as 75% to 80% of the metagenomes data reads mapped to the top recovered MAGs (Fig. 1B and Supplementary Table 6). Sequences associated to the dominant species MAG “Ca. Methanoperedens Vercelli Strain 1” retained its dominance at marine salinities (40-60% relative abundance) (Fig. 1B and Supplementary Fig. 4). Similarly, six archaeal 16S rRNA gene ASVs classified as “Ca. Methanoperedens”; ASV_1 being the most dominant (~ 97% of recovered total ASVs), followed by ASV_2 (~ 2%) (Supplementary Table 7). The bacterial 16S rRNA gene ASVs were dominated by Proteobacteria and Unclassified sequences (Supplementary Fig. 5). Bacterial ASVs decreased in abundance and diversity from 0% to 1.5% (Supplementary Fig. 6), with no clear physicochemical abundance-shift patterns (Supplementary Fig. 7). When assessing metagenome read-based “Ca. Methanoperedens” abundance at the three different salinities, we observed congruency with binning results, with read recruitment-percentages of 50%, 65%, and 45% at 0%, 1.5%, and 3% salinities, respectively (Supplementary Fig. 4A). “Ca. Methanoperedens” captured about 50% of metatranscriptome reads at freshwater salinity, whereas it dropped to below 25% of all TPM at 1.5% (Fig. 1B and Supplementary Table 8). In contrast, the metaproteome indicated that most proteins were mapped to “Ca. Methanoperedens” under both 0% and 1.5% salinities with more than 87% of all proteins assigned to this genus (Fig. 1B and Supplementary Table 9). N(ε)-acetyl-β-L-lysine accumulation by “Ca. Methanoperedens” To understand the metabolic response to salt stress of “Ca. Methanoperedens”, we performed non-targeted LC-MS metabolomics to search for compatible solutes accumulating at seven different salinities from 0% to 1.5%. Overall, we observed that metabolic profiles grouped samples from the range 0% to 0.5% and 0.75% to 1.5%, with distinct groupings in a Non-Metric Multidimensional Scaling (NMDS)-1 plot (Fig. 2A). To filter for osmolytes, we selected LC-MS features that increased to high intensities at higher salinities. This search revealed a top osmolyte candidate with a m/z of 189.125 [M+H]+. This feature ranked among the sixth most abundant
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