Planctomycetes as a source of novel secondary metabolites: triggers and regulation of their biosynthesis and engineered production in native strains or heterologous hosts
Metabolism, Biochemistry and Genetics of Microorganisms
Final Report Abstract
Planctomycetes is a bacterial phylum with ecological and biotechnological relevance. Although members of the phylum occur ubiquitously, they are often found in higher abundance on various surfaces in aquatic environments. Previous studies demonstrated a striking association of planctomycetes and macroalgae. In particular in the oceans, the surfaces of algae and other aquatic phototrophs are competitive ecological niches, in which phototrophs as primary producers are amongst the rare sources of nutrients for heterotrophic bacteria. Planctomycetes turned out to be rather slow-growing bacteria, but unexpectedly, faster-growing bacterial competitors that live in the same environments fail to outcompete planctomycetes on the surfaces of phototrophs. In contrast, planctomycetes can even account for up to 80% of the bacterial community on such surfaces. This observation led to the hypothesis that planctomycetes form bioactive secondary metabolites with antibacterial properties to compensate for slower growth and thereby avoid being outcompeted. These compounds can potentially also be used as therapeutics for humans, hence, planctomycetes may also serve as an untapped source of urgently needed antibiotics. Although the first planctomycete was already described in 1926, these bacteria were long thought to be uncultivable and until 2005 only a small number of 10 planctomycetal strains were characterized. Based on the development of novel cultivation techniques and thanks to larger sampling and isolation campaigns targeting the phylum Planctomycetes, around 120 novel strains were described in the last 15 years. Part of the here described project was the effective publication of 79 novel planctomycetal strains that were isolated from various freshwater and seawater environments in the last 5-10 years. Metabolite analyses of planctomycete cultures also yielded the first sets of bioactive compounds. Planctomycetes produce carotenoids that find potential applications as feed additives or food colourants. I also contributed to the recent identification of a new group of compounds designated stieleriacines that act as surface-active compounds and allow planctomycetes to alter biophysical surface properties and thereby modulate the community composition of associated biofilms. The biotechnological exploitation of the suspected secondary metabolite portfolio of planctomycetes on a larger scale requires the establishment of genetic tools that allow for the overexpression or inactivation of genes in planctomycetal genomes. Experiments performed within the framework of this project demonstrated the feasibility to inactivate non-essential genes in the model planctomycete Planctopirus limnophila. However, the development of a replicative plasmid system applicable for members of the phylum remains a challenging task. The project identifies Escherichia coli as a suitable host for the heterologous expression of genes of planctomycetal origin. By using a suitable genetic background of the E. coli expression strain, three tested genes obtained from a planctomycetal genome mining approach were successfully expressed. Taken together, the results obtained within the project are a promising basis for a bioprospection approach based on the large set of novel planctomycete strains isolated in the last decade combined with the expression of secondary metabolite-associated genes or clusters in heterologous hosts acting as microbial cell factories for bioactive compound production in the future.
Publications
- (2019). Description of three bacterial strains belonging to the new genus Novipirellula gen. nov., reclassification of Rhodopirellula rosea and Rhodopirellula caenicola and readjustment of the genus threshold of the phylogenetic marker rpoB for Planctomycetaceae. Antonie van Leeuwenhoek 113: 1779-1795
Kallscheuer N, Wiegand S, Peeters SH, Jogler M, Boedeker C, Heuer A, Rast P, Jetten MSM, Rohde M, Jogler C
(See online at https://doi.org/10.1007/s10482-019-01374-5) - (2019). Pink‐and orange‐pigmented Planctomycetes produce saproxanthin‐type carotenoids including a rare C45 carotenoid. Environ Microbiol Rep 11: 741-748
Kallscheuer N, Moreira C, Airs R, Llewellyn CA, Wiegand S, Jogler C, Lage OM
(See online at https://doi.org/10.1111/1758-2229.12796) - (2020). Cultivation-Independent Analysis of the Bacterial Community Associated With the Calcareous Sponge Clathrina clathrus and Isolation of Poriferisphaera corsica gen. nov., sp. nov., Belonging to the Barely Studied Class Phycisphaerae in the Phylum Planctomycetes, Front Microbiol 11: 602250
Kallscheuer N, Wiegand S, Kohn T, Boedeker C, Jeske O, Rast P, Müller R-W, Brümmer F, Heuer A, Jetten MSM, Rohde M, Jogler M, Jogler C
(See online at https://doi.org/10.3389/fmicb.2020.602250) - (2020). The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms. Commun Biol 3: 303
Kallscheuer N, Jeske O, Sandargo B, Boedeker C, Wiegand S, Bartling P, Jogler M, Rohde M, Petersen J, Medema MH, Surup F, Jogler C
(See online at https://doi.org/10.1038/s42003-020-0993-2) - (2021). Analysis of bacterial communities in a municipal duck pond during a phytoplankton bloom and isolation of Anatilimnocola aggregata gen. nov., sp. nov., Lacipirellula limnantheis sp. nov. and Urbifossiella limnaea gen. nov., sp. nov. belonging to the phylum Planctomycetes. Environ Microbiol 23: 1379-1396
Kallscheuer N, Rast P, Jogler M, Wiegand S, Kohn T, Boedeker C, Jeske O, Heuer A, Quast C, Glöckner FO, Rohde M, Jogler C
(See online at https://doi.org/10.1111/1462-2920.15341)
