Bioinformatic analyses of species and intra-population diversity within Verrucomicrobiota populations

Marine microbes are central to global biogeochemical cycles, yet the functional roles and environmental dynamics of many microbial lineages remain poorly understood. In part, this is due to cultivation efforts which have failed to capture the full diversity of marine microbes, as made evident via amplicon and metagenomic sequencing studies. This thesis investigates the ecological dynamics, genomic adaptations, and evolutionary conservation of members of the phylum Verrucomicrobiota, a globally distributed group of bacteria with a capacity for degrading complex polysaccharides. While most research into this group focuses on Akkermansia muciniphila, a common member of gut microbiomes, the environmental Verrucomicrobiota have been under-studied. I employed cultivation-independent genomic and metagenomic approaches to examine Verrucomicrobiota across multiple biological scales. For this thesis, I utilized publicly available metagenome-assembled genomes (MAGs) from a variety of sources. In Chapters 2 and 3 I assess North Sea spring bloom Verrucomicrobiota populations, while I evaluate members of the same phylum from different sources and environments in Chapter 4.

In Chapter 2, I characterized the seasonal dynamics of Verrucomicrobiota populations over a ten-year period of recurring spring blooms in the North Sea. I focused on the previously under-described family MB11C04, which I reclassified as family Seribacteraceae, showing that this clade peaks in abundance during the late spring bloom. Genomic analyses revealed enrichment in genes involved in the degradation of fucose-rich sulfated polysaccharides (FCSPs), suggesting a specialized role in recycling complex organic matter released during bloom collapse. I formally described two novel genera, Seribacter and Chordibacter, and proposed the new family name in accordance with the SeqCode initiative, establishing a taxonomic framework for future research.

I expanded the aforementioned analyses to include the families Coraliomargaritaceae and Akkermansiaceae, revealing family-specific genomic strategies for substrate specialization, as detailed in Chapter 3. Comparative genomics showed that Seribacteraceae are enriched in sulfatases, whereas Coraliomargaritaceae and Akkermansiaceae possess broader repertoires of carbohydrate-active enzymes (CAZymes). Pangenome analyses and single-nucleotide variant (SNV) profiling indicated varying degrees of functional specialization, with evidence of adaptive fine-tuning in fucosidase genes, par-
ticularly in the Coraliomargaritaceae family. These results suggest ongoing evolutionary responses to fluctuating substrate availability.

Finally, in Chapter 4, I demonstrated that the glycan-utilization machinery of Akkermansiaceae is evolutionarily conserved across vastly different environments. Despite inhabiting marine, freshwater, and host-associated ecosystems, these lineages share a conserved molecular system for binding, importing, and degrading fucose-rich glycans. Using protein structure prediction, I revealed conserved active-site architectures in key enzymes, even in the absence of significant sequence identity. This mechanistic continuity supports the hypothesis that traits associated with host interaction in Akkermansia muciniphila are ancestral and ecologically relevant beyond the gut.

Together, these findings reveal that Verrucomicrobiota are not passive components of marine ecosystems but dynamic, specialized players in carbon cycling. Their success stems from niche partitioning through genomic innovation, evolutionary conservation, and fine-scale adaptation. While cosmopolitan in distribution, specific environmental conditions select for distinct functional adaptations. This thesis advances our understanding of the phylum as a whole and exemplifies how integrative, cultivation-independent approaches can link population dynamics to genomic potential and molecular mechanisms, providing a powerful framework for uncovering the ecological roles of microbial specialists in
complex ecosystems.