86 Chapter 3 Figure 4). The salinity increase (from 1% to 2%) in the last month of operation did not influence the brackish-acclimated microbiomes performance (Figure 2A-B and Supplementary Figure 4). We recovered a total of 452 bacterial and 17 archaeal metagenome-assembled genomes (MAGs) from the combined datasets (Supplementary Table 1). From these 469 MAGs, only 79 were highly curated bacterial and one archaeal (>90% complete and <5% contaminated) with > 1% of mapped reads for any bioreactor time point, excluding the inoculum sediment depths (Supplementary Figure 5). The single archaeal genome belonged to nitrate-dependent anaerobic methanotroph “Ca. Methanoperedens BLZ2” sp. (Supplementary Figure 5). The Gammaproteobacterial MAGs dominated both bioreactor systems, with 22/79 of the dominating and curated MAGs belonging to the group (Supplementary Figure 5). Moreover, the Gammaproteobacteria showed a high bacterial 16S rRNA gene amplicon read abundance (40-70%), while they were not so abundant in the inoculum (~ 10%) (Figure 2C and Supplementary Figure 6). In the eutrophic system, Campylobacterota increased in abundance over time in the planktonic biomass. A total of 70 ASVs were identified, representing five different species (counts in parenthesis): Sulfurimonas (39), Sulfurovum (16), Sulfuricurvum (3), Sulfurospirillum (2), Pseudarcobacter (5) and unknown (5). The overall diversity in the eutrophic biofilm did not change much during the reactor operation (Figure 2C). In both the planktonic and biofilm biomass of the oligotrophic system, the major phyla remained evenly represented after 2 months of operation. There was a higher abundance of “other” phyla compared to the eutrophic system (Figure 2C and Supplementary Figure 6).
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