Microalgal Microbiomes: Composition, Assembly, and Interactions

Microalgal microbiomes impact the growth and health of their microalgal hosts, which in turn impacts global biogeochemical cycles and biotechnological applications of microalgae. Residing in the phycosphere, the nutrient-rich diffusive boundary layer surrounding microalgae, the bacterial community making up microalgal microbiomes benefits from carbohydrates and other nutrients released by the microalgae. These associations cause a complex web of both inter-bacterial and algal-bacterial interactions to take place in the phycosphere, affecting both bacteria and microalgae in a variety of ways. However, factors shaping the composition of microalgal microbiomes are not well characterized, especially not across microalgal phyla, and only few interactions in the phycosphere have been characterized. Hence, the purpose of this thesis was to determine factors shaping composition and assembly of microalgal microbiomes across microalgal phyla and characterize interactions in the phycosphere.

In the present studies, we characterized three factors impacting microalgal microbiome compositions; microalgal host species, time, and DNA extraction protocol. Whereas DNA extraction protocol did impact analysis of compositions, it was overshadowed by the effect of microalgal host species as assessed at one time point. In further investigations, time did shape microalgal microbiomes compositions across 49 days, however, the same introduced natural seawater microbiome diverged over time according to host microalgae Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii (previously Thalassiosira), indicating a deterministic effect of host specificity on microalgal microbiome compositions. Further, host specificity was not only affecting taxonomic compositions of microbiomes, it also significantly shaped functional potential of microbiomes as assessed with shotgun metagenomics. Surprisingly, at higher taxonomic levels, microbiomes of T. suecica and C. weissflogii were both dominated by Rhodobacteraceae despite the distant phylogenetic relationships of the microalgal hosts, whereas I. galbana microbiomes were dominated by Flavobacteriaceae. Both bacterial families are common core microalgal microbiomes members, albeit with different carbohydrate degradation capabilities, and hence we hypothesize that the mixotrophic nature of I. galbana causes significant changes in carbohydrate exudates compared to photoautotrophic microalgae, which causes the difference in dominant microbiome members.

Further investigations of the interactions of Rhodobacteraceae and Flavobacteriaceae representatives, Yoonia sp. and Maribacter sp., respectively, with their microalgal hosts found that while Yoonia sp. does proliferate with I. galbana in a co-culture system, it resorts to anoxygenic photosynthesis for energy acquisition, possibly due to inavailability of carbohydrates degradable by this bacterium. Carbohydrate metabolism also shapes the interaction of Maribacter sp. with C. weissflogii, where Maribacter sp. upregulates its type IX secretion system genes along with several polysaccharide degradation genes encoding enzymes that are presumably secreted via the type IX secretion system. This is a testament to the versatile adaptations of core microalgal microbiome members to phycospheres of different microalgal hosts.

In conclusion, this thesis identifies host specificity as a major factor shaping microalgal microbiome compositions both taxonomically and functionally, underlining the adaptations of microalgal microbiome members to life in the phycosphere of specific hosts. Furthermore, the work provides insights into interactions between core microalgal microbiome members and microalgae, beginning to unravel mechanisms causing these commonly occurring associations. This knowledge lays the foundation for selecting microalgal microbiomes for specific hosts for purposes such as biotechnological ones in future research efforts.