PhD Defense Pernille Kjersgaard Bech
01 Dec 2022
The potential of microbial secondary metabolites in marine systems and their influence on microbial diversity
Supervisor
Professor Lone Gram, DTU Bioengineering
Co-supervisors
Associate professor Mikael L. Strube, DTU Bioengineering
Associate professor Mikkel Bentzon-Tilia, DTU Bioengineering
Examiners
Professor Lars Jelsbak, DTU Bioengineering
Senior scientist Antje Wichels, AWI Alfred-Wegener-Institute
Professor Andreas Schramm, Aarhus University
Chair
Professor Ákos T. Kovács, DTU Bioengineering
Professor Lone Gram, DTU Bioengineering
Co-supervisors
Associate professor Mikael L. Strube, DTU Bioengineering
Associate professor Mikkel Bentzon-Tilia, DTU Bioengineering
Examiners
Professor Lars Jelsbak, DTU Bioengineering
Senior scientist Antje Wichels, AWI Alfred-Wegener-Institute
Professor Andreas Schramm, Aarhus University
Chair
Professor Ákos T. Kovács, DTU Bioengineering
Microbial secondary metabolites have been predominantly for their antibiotic properties, due to their history of being used to treat infectious human pathogens. However, much less is known about their actual functions and role(s) as well as their producers in the natural environment. Antibiotic secondary metabolites can be mediators of microbial competition, why they are considered to play important
roles in microbial interactions. Nonetheless, we still do not understand how these compounds affect the assembly and development of microbial communities in nature, where their ecological role might expand much beyond microbial antagonism.
The purpose of this PhD project was to explore the genetic secondary metabolite diversity of marine microbial communities and unravel if and how microbial secondary metabolism can shape microbial communities.
In the first paper, an amplicon-based sequencing approaches was used as a proxy for the genetic secondary metabolite potential in marine environmental samples. Targeted sequencing of conserved adenylation (AD) and ketosynthase domains within biosynthetic gene clusters (BGCs) encoding nonribosomal peptides synthetases (NRPS) and polyketide synthases (PK), respectively, revealed that
seawater, and particularly sandy sediments hold a high and distinct genetic potential for secondary metabolite production relative to that of soil microbiomes. In the second paper, we constructed a semi-natural model system to study the possible impact of an antibiotic secondary metabolite producing marine bacteria on the assembly dynamics of marine microbial communities. Specifically, we focused on the marine biofilm forming and Phaeobacter inhibens with the capability to produce
the antibiotic tropodithietic acid (TDA) and a mutant incapable of TDA production. We show that especially the relative abundance of Bacteriodetes peaked during the biofilm succession in the model system with the WT P. inhibens relative to the mutant and control system. Finally, in the third paper, we studied the temporal patterns of a natural biofilm succession in seawater conducted in situ.
Findings from multi-omics approaches (16S- 18S- and AD amplicon sequencing, genome resolved metagenomics and metabolomics) to track the taxon, BGCs and metabolome dynamics of surface
associated communities during marine biofilm succession suggested that the early marine biofilm formation favoured bacterial community members with higher BGC potential. This early phase of the biofilm succession, where furthermore associated with more metabolic features, while the later phase was dominated by multicellular eukaryotes and a reduction in microbial BGC potential.
In conclusion, this work has contributed to the understanding of microbial community assembly, highlighting the importance of temporal studies to display dynamic changes of the genetic microbial secondary metabolite potential and thus the possible production of secondary metabolites and their impact on microbial community succession.
roles in microbial interactions. Nonetheless, we still do not understand how these compounds affect the assembly and development of microbial communities in nature, where their ecological role might expand much beyond microbial antagonism.
The purpose of this PhD project was to explore the genetic secondary metabolite diversity of marine microbial communities and unravel if and how microbial secondary metabolism can shape microbial communities.
In the first paper, an amplicon-based sequencing approaches was used as a proxy for the genetic secondary metabolite potential in marine environmental samples. Targeted sequencing of conserved adenylation (AD) and ketosynthase domains within biosynthetic gene clusters (BGCs) encoding nonribosomal peptides synthetases (NRPS) and polyketide synthases (PK), respectively, revealed that
seawater, and particularly sandy sediments hold a high and distinct genetic potential for secondary metabolite production relative to that of soil microbiomes. In the second paper, we constructed a semi-natural model system to study the possible impact of an antibiotic secondary metabolite producing marine bacteria on the assembly dynamics of marine microbial communities. Specifically, we focused on the marine biofilm forming and Phaeobacter inhibens with the capability to produce
the antibiotic tropodithietic acid (TDA) and a mutant incapable of TDA production. We show that especially the relative abundance of Bacteriodetes peaked during the biofilm succession in the model system with the WT P. inhibens relative to the mutant and control system. Finally, in the third paper, we studied the temporal patterns of a natural biofilm succession in seawater conducted in situ.
Findings from multi-omics approaches (16S- 18S- and AD amplicon sequencing, genome resolved metagenomics and metabolomics) to track the taxon, BGCs and metabolome dynamics of surface
associated communities during marine biofilm succession suggested that the early marine biofilm formation favoured bacterial community members with higher BGC potential. This early phase of the biofilm succession, where furthermore associated with more metabolic features, while the later phase was dominated by multicellular eukaryotes and a reduction in microbial BGC potential.
In conclusion, this work has contributed to the understanding of microbial community assembly, highlighting the importance of temporal studies to display dynamic changes of the genetic microbial secondary metabolite potential and thus the possible production of secondary metabolites and their impact on microbial community succession.