Tapping into the potential of Planctomycetes Planctomycetes often hold a predominant position in their natural marine habitats, despite their relatively low growth rates. We spoke to Dr. Nicolai Kallscheuer about his work in characterising the metabolome of different recently isolated planctomycetal species, and its implications for the discovery of new bioactive small molecules with potential applications as antioxidants or antibiotics. Planctomycetes are uncommon Gram-negative bacteria, which are typically found on nutrient-rich surfaces within marine environments, such as algae and sponges. Species of the phylum Planctomycetes play an important role in the global carbon and nitrogen cycle. “Most parts of the ocean are oligotrophic. This means that nutrients are not present in high amounts. In contrast, surfaces of algae and kelp are quite nutrient-rich, compared to the water itself. This is why the bacteria like to grow on such surfaces,” explains Dr. Nicolai Kallscheuer. These nutrient-rich surfaces are highly competitive environments, so it is thought likely that competition between microorganisms essentially triggers the production of antimicrobials. This holds important implications in terms of the development of new drugs, an important motivating factor behind Dr. Kallscheuer’s work. Currently based in Christian Jogler´s lab at Radboud University in the Netherlands, Dr. Kallscheuer aims to build a deeper understanding
Planctomycetes as a source of novel secondary metabolites This research was funded by the German Research Foundation (DFG), grant KA 4967/1-1, project number 405562673. Dr. Nicolai Kallscheuer Radboud University, Institute for Water and Wetland Research, Department of Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands E: N.Kallscheuer@science.ru.nl W: https://www.ru.nl/microbiology/ department/people/nicolai-kallscheuer-dr/ Dr. Nicolai Kallscheuer
2008-2013: B.Sc. and M.Sc. at Aachen University of Applied Sciences, Campus Juelich, Germany; 2013-2018: PhD and Postdoc at Forschungszentrum Juelich / Heinrich-Heine-University Duesseldorf, Germany; since 2018: Postdoc at Radboud University Nijmegen, The Netherlands.
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Scanning electron microscopy picture of the not yet described strain Poly41 isolated from plastic particles in the Baltic Sea close to Heiligendamm, Germany in October 2015.
of the secondary metabolism of different, as yet uncharacterized, Planctomycetes. “We’re looking at between 5-10 Planctomycetes that were previously harvested and isolated from marine environments. We chose those strains that looked most promising in terms of secondary metabolites, and focused our attention on those,” he says. The Streptomyces genus is responsible for producing the majority of natural
different natural competitors, after which we extract the superior performer, and then also analyse which compounds are produced. We compare it to a culture that was not triggered by the presence of a competitor, then we try and identifty which specific molecules are only produced in the presence of that particular competitor,” says Dr. Kallscheuer. Planctomycetes grow quite slowly, so it might be expected that they would be outcompeted by faster-growing bacteria; however, in their natural habitats this is in fact not the case, and researchers have found that Planctomycetes are dominant on such surfaces. “This seems somehow counter-intuitive. One possibility is that their survival is mediated by a set of bioactive, anti-microbial secondary metabolites,” explains Dr. Kallscheuer. A second approach involves using database predictions to assess which gene clusters of Planctomycetes are of interest with respect to the production of certain compounds. While the majority of antibiotic compounds derived from different streptomycetal species are known, Planctomycetes represent a completely
We’re looking at between 5-10 Planctomycetes that were previously harvested and isolated from marine environments. In our bioprospection approach, we chose the Planctomycetes that appeared to be the most promising sources of compounds with health-promoting activities. antibiotics currently available; by comparing the physiology of Planctomycetes with Streptomyces, researchers hope to gain important insights. “It might be that certain Planctomycetes follow similar strategies for survival as Streptomycetes, including the production of bioactive molecules,” outlines Dr. Kallscheuer. Further analysis is required to harness their wider potential however, which forms a major part of Dr. Kallscheuer’s overall agenda. Researchers are using different approaches to investigate the metabolic diversity of different species. “One is through the co-cultivation of Planctomycetes with
untapped source, so Dr. Kallscheuer says there is vast scope for investigation. “There are many interesting compounds to be found,” he stresses. This holds important implications in the context of growing concern about antibiotic resistance, and while research is still at a relatively early stage, Dr. Kallscheuer is very much aware of the wider picture. “Every anti-microbial compound that is identified could be important in future. Many strains are becoming resistant to existing antibiotics, so there’s an urgent need to look for new bioactive compounds,” he continues. “This is why we decided to look into a completely new phylum.”
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