Sponges (phylum Porifera) are sessile, filter-feeding animals that are found in both marine and freshwater environments. They are known to be associated with highly diverse and stable microbial communities. The first component of this thesis presents a study on the diversity of the microbial communities associated with freshwater sponges collected from Lake Baikal, Baikalospongia intermedia profundalis (BIP) and Lubomirskia baicalensis (LB). Based on previous studies, microbial communities associated with freshwater sponges are not as diverse as those from marine sponges. However, one of the potential reasons for this observation is the limitation posed by conventional cloning and sequencing methods used in previous studies on freshwater sponges. To gain better insight into the diversity of the microbiome in freshwater sponges, we performed high-throughput sequencing of PCR-amplified 16S rRNA genes and of metagenome without prior amplification in two sponge species BIP and LB. Using techniques that involve greater sequencing coverage, we can observe that freshwater sponge microbiomes can be as diverse as marine sponge microbiomes. The microbial communities of the freshwater sponges were also compared using diversity indices and it was observed that the host sponge and collection depth can both influence the diversity of microbial associations in Lake Baikal sponges.

The availability and ease of access to cost-effective deep sequencing techniques yielded an increase in the number of completely sequenced genomes of organisms in three domains of life Archaea, Bacteria, and Eukarya. This increase in publicly available datasets led to an improved understanding on the general properties of proteins as well as their length distributions. The second component of this thesis presents a review of studies on protein length distribution and the observed differences in average protein length across all three domains of life. The review also discusses proposed explanations for why organisms maintain their protein size and presents some examples of proteins that defy constraints on protein size from literature and from genomes of sponges Amphimedon queenslandica, Oscarella carmela, and Baikalospongia intermedia.