The influence of microbial secondary metabolites on microbial diversity and functionality in marine model systems

Bacterial secondary metabolites, which are produced by proteins encoded by biosynthetic gene clusters (BGCs), play a broad range of ecological roles in microbial communities, ranging from facilitators of cooperation to interference competition. As such, bacterial secondary metabolites mediated interactions may in part be responsible for shaping the composition and function of microbial communities. However, for decades secondary metabolites have primarily been studied for their antimicrobial qualities, and the ecological significance of secondary metabolites in natural microbial communities is therefore not elucidated. Furthermore, natural microbial communities are biologically and chemically complex, thus deciphering the role of secondary metabolites can be challenging. Fortunately, using ecologically relevant and well-designed model systems have lately proved to assist in understanding the establishment and dynamics of microbial communities. The purpose of this PhD project was to develop and use marine microbial model systems to allow studies of microbial secondary metabolites influence on marine microbial communities.

The BGC potential of microbial communities has predominantly been assessed at a single timepoint; however, microbial communities are compositionally and functionally dynamic due to community intrinsic processes. We developed an in situ model system in which we over four months followed the development of a marine microbial biofilm community. Using both amplicon and metagenomic sequencing, we determined that the BGC potential of the microbial community was dynamic over time and depended on the community phase. During the biofilm development we observed that only a minority of the microbial community carried the majority of the BGC potential and using untargeted metabolomics we found that the secondary metabolites pseudanes were present, but only in a limited time period. These findings demonstrates that the BGC potential and secondary metabolites changes during the development of microbial communities, thus only have a playing a role in specific periods. This outcome may assist in future discovery of novel secondary metabolites, by guiding scientist to select the right timepoint for mining for novel secondary metabolites.

Abiotic and biotic cues are vital for secondary metabolite production and function; however, the ecology is often neglected when exploring secondary metabolites, as witnessed for the multifunctional metabolite tropodithietic acid (TDA) produced by marine roseobacters. We designed an ecological appropriate model system – that is, a non-axenic microalgae community, to explore the temporal influence of a TDA-producer, Phaeobacter inhibens, and a TDA-deficient isogenic mutant on the microbial community composition. We found that presence of the TDA-producing bacteria influenced bacterial strain dynamics and led to the disappearance of an indigenous Phaeobacter from the community. We were not able to chemically detect TDA in the system, however, we did detect transcripts from one of the genes (tdaC) involved in the biosynthesis of TDA, underlining the ecological relevance of the system. Based on these findings, we concluded that TDA producing Phaeobacter compete with closely related strains in natural niches and thereby can alter the strain dynamics within microbial communities. Secondary metabolite detection under natural conditions is difficult, yet essential when attempting to examine the function and role of these metabolites. Motivated by this, we sought for a new ecological relevant model system that could sustain the production of TDA. We found that Conopeum seurati, a marine bryozoan, contained a natural high relative abundance of Phaeobacter sp. and tdaC genes, essential for the production of TDA. Conclusively, this invites for a future model system to study the ecological role and spatial distribution of TDA.

This thesis concludes that model systems designed on ecological principles, with a longitudinal design and high taxonomic/functional resolution of bacterial community members, provide the suitable frame for studying the influence of secondary metabolites in marine microbial communities. The work in this thesis also provides novel insight into the dynamics and ecological influence of secondary metabolites and their producers in marine microbial communities, which contributes to our understanding of the true ecological significance of secondary metabolites in nature.