Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

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.

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Fig. 1: Sampling the phylum Planctomycetes.
Fig. 2: Current diversity of the planctomycetal phylum.
Fig. 3: Planctomycetal cell division.
Fig. 4: Signalling in planctomycetes.
Fig. 5: Secondary metabolite BGCs.

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Acknowledgements

We appreciate the help of C. Wiegand, A. Scharmach and B. Schink in naming the isolates appropriately according to community standards. We are also grateful to I. Lagkouvardos and A. Kioukis for enabling our analyses on the IMNGS platform. We thank L. van Niftrik for providing bacterial biomass from anaerobic lab-scale bioreactors. The GHOSTDABS project provided the left-most image in the upper panel of Fig. 1. We further thank J. Piel for scientific discussion and C. Spröer for help with the sequencing of the planctomycetal strains. This work was funded by the Deutsche Forschungsgemeinschaft (grant no. JO 893/4-1) and the Volkswagen foundation (experiment no. 89256). M.Y.G. was funded by the NIH IRP at the US National Library of Medicine. Work in the Mascher lab was supported by the Deutsche Forschungsgemeinschaft (grant no. MA2837/2-2) and the Bundeministerium für Bildung und Forschung in the framework of the ERAnet Synthetic Biology (project: ERASynBio2-ECFexpress). R.A. and A.M. were funded by the Max Planck Society.

Author information

S.W., M.J. and C.J. designed the study. M.J., T.K., A.H., P.R., J.E.S., O.M.L. and L.Ø. cultivated the planctomycetes and established axenic cultures. M.J., C.B., T.K., A.H., P.R., S.O., O.J., J.E.S., T.P., B.J.M., P.H., R.-W.M., F.B., M.L., A.M.S., A.-K.K., L.Ø., A.M. and C.J. were involved in the sampling, sample processing and basic enrichments. S.W., J.V. and B.B. sequenced and assembled the genomes. E.R.-M. and D.P.D. constructed the deletion mutants, A.M. and R.A. constructed the planctomycetal fosmid, S.L. obtained the planctomycetal MAGs and O.M.L. isolated DNA for sequencing. C.B., T.K., S.H.P., M.R. and C.J. performed the microscopy. H.O.d.C., M.S.M.J., T.M., J.O., M.H.M. and R.A. provided expertise and supervision. S.W., D.P., J.V., N.K., M.H.M., M.Y.G. and C.J. analysed and interpreted data. S.W. and C.J. wrote the manuscript with major contributions from M.J., C.B., D.P., J.V., S.O., N.K., R.A., M.H.M, L.Ø. and M.Y.G., and with help and approval from all authors.

Correspondence to Christian Jogler.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–46, Supplementary Tables 8, 9 and 11–13, Supplementary Table legends, Supplementary Video legends, Supplementary Data legends and Supplementary References.

Reporting Summary

Supplementary Table 1

Strain information.

Supplementary Table 2

16S rRNA gene identity-based similarity matrix.

Supplementary Table 3

Planctomycetal orthologous groups of strict and soft core genome genes.

Supplementary Table 4

Pan and core genome analysis of the defined planctomycetal clades.

Supplementary Table 5

Identification of genes related to cell division and peptidoglycan biosynthesis.

Supplementary Table 6

Signal transduction systems.

Supplementary Table 7

Results of the identification and analysis of ECF sigma factors.

Supplementary Table 10

Results of AntiSMASH 3.0 analysis.

Supplementary Data 1

16S rRNA gene sequence analysis of 9002 non-redundant Planctomycetes in Newick format.

Supplementary Data 2

Multilocus sequence analysis tree c90cov50ML in Newick format.

Supplementary Data 3

Multilocus sequence analysis tree c90cov50BI in Newick format.

Supplementary Data 4

Multilocus sequence analysis tree c90cov70ML in Newick format.

Supplementary Data 5

Multilocus sequence analysis tree c90cov70BI in Newick format.

Supplementary Data 6

Multilocus sequence analysis tree c95cov50ML in Newick format.

Supplementary Data 7

Multilocus sequence analysis tree c95cov50BI in Newick format.

Supplementary Data 8

Multilocus sequence analysis tree c95cov70ML in Newick format.

Supplementary Data 9

Multilocus sequence analysis tree c95cov70BI in Newick format.

Supplementary Data 10

Maximum likelihood 16S rRNA tree in Newick format.

Supplementary Data 11

Bayesian interference 16S rRNA tree in Newick format.

Supplementary Data 12

Maximum likelihood RpoB tree in Newick format.

Supplementary Data 13

Bayesian interference RpoB tree in Newick format.

Supplementary Data 14

Maximum likelihood ribosomal protein tree in Newick format.

Supplementary Data 15

Bayesian interference ribosomal protein tree in Newick format.

Supplementary Data 16

Binary gene content analysis tree in Newick format.

Supplementary Data 17

Amino acid identity Neighbour joining tree in Newick format.

Supplementary Data 18

Veto method supertree analysis in Newick format.

Supplementary Data 19

Voting method supertree analysis in Newick format.

Supplementary Video 1

Lateral budding of ‘Kolteria novifilia’ Pan216.

Supplementary Video 2

Division of ‘Saltatorellus ferox’ Poly30 by budding and binary fission.

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Wiegand, S., Jogler, M., Boedeker, C. et al. Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. Nat Microbiol 5, 126–140 (2020). https://doi.org/10.1038/s41564-019-0588-1

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