Developing Techniques for the Utilization of Planctomycetes As Producers of Bioactive Molecules

Abstract

Planctomycetes are conspicuous, ubiquitous, environmentally important bacteria. They can attach to various surfaces in aquatic habitats and form biofilms. Their unique FtsZ-independent budding cell division mechanism is associated with slow growth and doubling times from 6 h up to 1 month. Despite this putative disadvantage in the struggle to colonize surfaces, Planctomycetes are frequently associated with aquatic phototrophic organisms such as diatoms, cyanobacteria or kelp, whereby Planctomycetes can account for up to 50% of the biofilm-forming bacterial population. Consequently, Planctomycetes were postulated to play an important role in carbon utilization, for example as scavengers after phototrophic blooms. However, given their observed slow growth, such findings are surprising since other faster- growing heterotrophs tend to colonize similar ecological niches. Accordingly, Planctomycetes were suspected to produce antibiotics for habitat protection in response to the attachment on phototrophs. Recently, we demonstrated their genomic potential to produce non-ribosomal peptides, polyketides, bacteriocins, and terpenoids that might have antibiotic activities. In this study, we describe the development of a pipeline that consists of tools and procedures to cultivate Planctomycetes for the production of antimicrobial compounds in a chemically defined medium and a procedure to chemically mimic their interaction with other organisms such as for example cyanobacteria. We evaluated and adjusted screening assays to enable the hunt for planctomycetal antibiotics. As proof of principle, we demonstrate antimicrobial activities of planctomycetal extracts from Planctopirus limnophila DSM 3776, Rhodopirellula baltica DSM 10527, and the recently isolated strain Pan216. By combining UV/Vis and high resolution mass spectrometry data from high-performance liquid chromatography fractionations with growth inhibition of indicator strains, we were able to assign the antibiotic activity to candidate peaks related to planctomycetal antimicrobial compounds. The MS analysis points toward the production of novel bioactive molecules with novel structures. Consequently, we developed a large scale cultivation procedure to allow future structural elucidation of such compounds. Our findings might have implications for the discovery of novel antibiotics as Planctomycetes represent a yet untapped resource that could be developed by employing the tools and methods described in this study.

Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea

“…Two potential scenarios could be envisioned: either the giant genes of strain NH11 T fulfill other, maybe structural functions, or they might be involved in the formation of yet unknown secondary metabolites. While the latter hypothesis fits to the recent observation of novel antibiotic small molecules from Planctomycetes (Jeske et al, 2016), at least some giant genes are predicted to encode proteins with structural function such as the discussed Fuma_00096. While resolving this issue is beyond the scope of this study, we conclude that the genome of strain NH11 T differs in important aspects from its peers.…”

“…These organisms are capable of anaerobic ammonium oxidation, a trait extremely useful for wastewater treatment (Kartal et al, 2013). In particular, members of the order Planctomycetales were found to encode numerous secondary metabolite-related genes and gene clusters (Jeske et al, 2013), that were recently found to be active under conditions that chemically mimicked the interaction with eukaryotes (Jeske et al, 2016). Consequently, Planctomycetes were postulated to be “talented producers” of small molecules and they might represent a yet untapped resource of novel bioactive molecules (Jeske et al, 2016).…”

“…In particular, members of the order Planctomycetales were found to encode numerous secondary metabolite-related genes and gene clusters (Jeske et al, 2013), that were recently found to be active under conditions that chemically mimicked the interaction with eukaryotes (Jeske et al, 2016). Consequently, Planctomycetes were postulated to be “talented producers” of small molecules and they might represent a yet untapped resource of novel bioactive molecules (Jeske et al, 2016). Furthermore, the biotechnological application of planctomycetal enzymes such as sulfatases as biocatalysts was demonstrated (Wallner et al, 2005).…”

Pink‐ and orange‐pigmented Planctomycetes produce saproxanthin‐type carotenoids including a rare C 45 carotenoid

“…In this study, we were able to identify three carotenoids present in two pigmented planctomycetal strains, thus contributing to improved characterization of bioactive molecules with potential biotechnological relevance in this phylum of aquatic bacteria (Graca et al ., ; Jeske et al ., ).…”

Description of Polystyrenella longa gen. nov., sp. nov., isolated from polystyrene particles incubated in the Baltic Sea

“…Their periplasm is enlarged and forms large invaginations into the cytoplasm. Several planctomycetal strains are regarded as potential talented producers of as yet uncharacterised small bioactive molecules (Graça et al 2016;Jeske et al 2016;Wiegand et al 2018). Many Planctomycetes possess large numbers of giant genes (Kohn et al 2016;Reva et al 2008) and are amongst the bacterial phyla with the highest number of predicted genes of unknown function (Overmann et al 2017;Wiegand et al 2018).…”