Investigation of diatom-bacteria interactions with the model organism Thalassiosira rotula

Abstract

Marine microalgae are key primary producers responsible for more than 45% of global net primary production, fixing billions of tons of inorganic carbon each year. Diatoms constitute one of the most diverse and ecologically important group of microalgae. While diatom productivity and health are likely to be strongly governed by the structure and function of the diatom microbiome, we have little understanding which factors contribute to the microbiome assembly. In order to investigate the microbiome establishment on diatoms, an in vitro model system for reproducible laboratory studies was developed with the marine diatom Thalassiosira rotula. Thus, this thesis describes the isolation of diatoms and bacteria from the environment and the development of an in vitro model system for reproducible laboratory studies followed by the investigation of the microbiome assembling on the diatom T. rotula using co-culture experiments. In Chapter 2 diatoms and bacteria were co-isolated from a spring bloom in the German Bight of the North Sea. The isolation resulted in four different diatom species and 200 morphological different bacteria in culture. The marine diatom Thalassiosira rotula was selected as the model organism for the in vitro studies with diatoms and bacteria. Chapter 3 focused on the development of a co-culture to study mutualistic interactions between the diatom T. rotula and bacteria as well as the generation of an axenic (bacteria-free) culture of the diatom T. rotula. The experiments revealed that the diatom T. rotula is auxotroph for B-vitamins and that the bacterial community of T. rotula is able to maintain the growth of the vitamin-free diatom with the provision of vitamins. In Chapter 4 and 5 the microbiome assembling was investigated by exposing the vitamin-free and axenic diatom T. rotula to several bacterial source communities obtained from different diatom species. The co-culture experiments revealed that each of the newly established microbiomes on the T. rotula acceptor supports the growth of the diatom under vitamin absence, indicating that all microbiomes comprise bacteria capable for B-vitamin synthesis. To investigate the factors that contribute to the microbiome assembling, the bacterial community compositions of the different inoculated bacterial source communities and newly assembled acceptor microbiomes were analysed. The analysis revealed that the different inoculated bacterial source communities were highly different in their bacterial community composition and contained up to 4406 different operational taxonomic units (OTUs). On the contrary, the analysis of the newly established acceptor microbiomes revealed that all acceptor microbiomes were similar to each other in respect to their bacterial community composition and that they were more similar to the original T. rotula bacterial source community than to the donor cultures where the bacterial source communities were obtained from. The similarity of the acceptor microbiomes was most likely caused by 10 OTUs, which constituted for more than 80% of the total relative abundance of all acceptor microbiomes. Furthermore, these 10 OTUs were shown to be most responsible for the differences between acceptor microbiomes and bacterial source communities and were thus described as the core microbiome of the diatom T. rotula. Consequently, it was shown for the first time that the ecologically relevant diatom T. rotula establishes a robust and reproducible bacterial core microbiome of 10 OTUs if it is offered highly diverse and compositionally different bacterial source communities with up to 4406 OTUs. The results of the robust and reproducible microbiome composition on the diatom T. rotula suggest that host factors contribute more than the bacterial diversity in the environment to the shaping of the microbiome composition.