235 Synthesis and discussion research. However, considerable variability still exists across laboratories, as different groups often employ unique bioinformatics approaches, complicating cross-study comparisons further. Applying both 16S rRNA gene amplicon sequencing and metagenomics resulted in good resolution of microbial diversity and metabolic potential, with the relative abundance recovered from both methods matching quite well in several chapters of this thesis. In Chapter 7, 16S rRNA gene Amplicon Sequencing Variants (ASVs) of SRB and “Ca. Methanoperedens” could be linked to full-length 16S rRNA genes resolved from the different MAGs recovered. In Chapter 6, we combined the high resolution of archaeal ASVs obtained to confirm the dominance of the two “Ca. Methanoperedens Vercelli Strain 1 and 2”. For the stable and less diverse co-cultures (Chapters 4 and 6) with fewer time points/conditions than the environmental studies (Chapters 2, 3 and 7), metagenomics were sufficient to properly represent the microbial diversity. The lower resolution metagenomes obtained with MiSeq Illumina Sequencing (Chapters 5 and 6) (2 Gbp/sample) were already adequate to characterize the most abundant microbial community shifts e.g. different “Ca. Methanoperedens” morphotypes. ‘still, this is not as powerful as the Illumina NovaSeq 6000 used for the rest of the metagenomes, which generates 10 Gbp/sample and allows for a better representation of the whole community, including the rare biosphere. In this dissertation, nanopore long-read sequencing was not employed but it would have been desirable to close the genome of “Ca. Methanoperedens BLZ2” (Chapter 5) and “Ca. Methanoperedens Vercelli Strain 1” (Chapter 6) and avoid losing key genes in the unbinned fraction (i.e. sulfite reductases in Chapter 5). Long sequencing has also been shown to be useful to retrieve extrachromosomal elements (ECEs) such as plasmids from both cultures studied in this PhD dissertation (Schoelmerich et al., 2022): the “Ca. Methanoperedens BLZ2” (Chapter 5) and Vercelli “Ca. Methanoperedens Vercelli” (Chapter 6) enrichments. 8
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