Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Sandra Wiegand - , Radboud University Nijmegen (Author)
  • Mareike Jogler - , German Collection of Microorganisms and Cell Cultures (Author)
  • Christian Boedeker - , German Collection of Microorganisms and Cell Cultures (Author)
  • Daniela Pinto - , Chair of General Microbiology (Author)
  • John Vollmers - , Karlsruhe Institute of Technology (Author)
  • Elena Rivas-Marín - , Pablo de Olavide University (Author)
  • Timo Kohn - , Radboud University Nijmegen (Author)
  • Stijn H Peeters - , Radboud University Nijmegen (Author)
  • Anja Heuer - , German Collection of Microorganisms and Cell Cultures (Author)
  • Patrick Rast - , German Collection of Microorganisms and Cell Cultures (Author)
  • Sonja Oberbeckmann - , Leibniz Institute for Baltic Sea Research Warnemunde (Author)
  • Boyke Bunk - , German Collection of Microorganisms and Cell Cultures (Author)
  • Olga Jeske - , German Collection of Microorganisms and Cell Cultures (Author)
  • Anke Meyerdierks - , Max Planck Institute for Marine Microbiology (Author)
  • Julia E Storesund - , University of Bergen (Author)
  • Nicolai Kallscheuer - , Radboud University Nijmegen (Author)
  • Sebastian Lücker - , Radboud University Nijmegen (Author)
  • Olga M Lage - , Lusófona University of Porto (Author)
  • Thomas Pohl - , Freiberg University of Mining and Technology (Author)
  • Broder J Merkel - , Freiberg University of Mining and Technology (Author)
  • Peter Hornburger - , German Collection of Microorganisms and Cell Cultures (Author)
  • Ralph-Walter Müller - , Free University of Applied Sciences Stuttgart - Waldorf Education Seminar (Author)
  • Franz Brümmer - , Free University of Applied Sciences Stuttgart - Waldorf Education Seminar (Author)
  • Matthias Labrenz - , Leibniz Institute for Baltic Sea Research Warnemunde (Author)
  • Alfred M Spormann - , Stanford University (Author)
  • Huub J M Op den Camp - , Radboud University Nijmegen (Author)
  • Jörg Overmann - , German Collection of Microorganisms and Cell Cultures (Author)
  • Rudolf Amann - , Max Planck Institute for Marine Microbiology (Author)
  • Mike S M Jetten - , Radboud University Nijmegen (Author)
  • Thorsten Mascher - , Chair of General Microbiology (Author)
  • Marnix H Medema - , Wageningen University & Research (WUR) (Author)
  • Damien P Devos - , Pablo de Olavide University (Author)
  • Anne-Kristin Kaster - , Karlsruhe Institute of Technology (Author)
  • Lise Øvreås - , University of Bergen (Author)
  • Manfred Rohde - , Helmholtz Centre for Infection Research (Author)
  • Michael Y Galperin - , Bethesda (Author)
  • Christian Jogler - , Radboud University Nijmegen (Author)

Abstract

When it comes to the discovery and analysis of yet uncharted bacterial traits, pure cultures are essential as only these allow detailed morphological and physiological characterization as well as genetic manipulation. However, microbiologists are struggling to isolate and maintain the majority of bacterial strains, as mimicking their native environmental niches adequately can be a challenging task. Here, we report the diversity-driven cultivation, characterization and genome sequencing of 79 bacterial strains from all major taxonomic clades of the conspicuous bacterial phylum Planctomycetes. The samples were derived from different aquatic environments but close relatives could be isolated from geographically distinct regions and structurally diverse habitats, implying that 'everything is everywhere'. With the discovery of lateral budding in 'Kolteria novifilia' and the capability of the members of the Saltatorellus clade to divide by binary fission as well as budding, we identified previously unknown modes of bacterial cell division. Alongside unobserved aspects of cell signalling and small-molecule production, our findings demonstrate that exploration beyond the well-established model organisms has the potential to increase our knowledge of bacterial diversity. We illustrate how 'microbial dark matter' can be accessed by cultivation techniques, expanding the organismic background for small-molecule research and drug-target detection.

Details

Original languageEnglish
Pages (from-to)126-140
Number of pages15
JournalNature microbiology
Volume5
Issue number1
Publication statusPublished - 18 Nov 2019
Peer-reviewedYes

External IDs

PubMedCentral PMC7286433
Scopus 85075401514

Keywords

Keywords

  • Bacteria/classification, Bacterial Physiological Phenomena, Cell Division, Ecosystem, Genetic Variation, Genome, Bacterial/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Secondary Metabolism, Signal Transduction

Library keywords