Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations


Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth’s environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.

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Fig. 1: Phylogenetic trees of Bacteria and Archaea.
Fig. 2: The size ranges for CPR and DPANN genomes compared with size ranges for the genomes of known bacterial symbionts as well as other bacteria and archaea.

Adapted from ref.61, Annual Reviews.

Fig. 3: Profile of presence or absence of certain metabolic or biosynthetic capacities.
Fig. 4: Maximum likelihood phylogenetic trees constructed for the catalytic subunits of NiFe hydrogenases and Rubisco.
Fig. 5: Central metabolism of some CPR and DPANN, examples of typical configurations.
Fig. 6: Central metabolism of some CPR and DPANN, examples of exceptions.

Part b adapted from ref.71, Springer Nature Limited. Part d adapted with permission from ref.2, Elsevier.

Fig. 7: Maximum likelihood phylogenetic tree of the catalytic subunit Elp3, which is found in genomes of some CPR bacteria and DPANN archaea.
Fig. 8: Examples of tRNA introns identified in some CPR bacteria genomes.

Change history

  • 04 October 2018

    In the original online version of this manuscript, the ORCID links for Cindy J. Castelle, Karthik Anantharaman, Alexander J. Probst and Jillian F. Banfield were omitted. These have now been added.


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Support was provided by grants from the Lawrence Berkeley National Laboratory’s Genomes-to-Watershed Scientific Focus Area. The US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research funded the work under contract DE-AC02-05CH11231, the DOE carbon cycling programme DOE-SC10010566, the Sloan Foundation Deep Life (grant number G-2016-20166041), the Innovative Genomics Institute at the University of California, Berkeley and the Chan Zuckerberg Biohub. Sequencing was conducted by the DOE Joint Genome Institute, a DOE Office of Science User Facility, supported under contract number DE-AC02-05CH11231.

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Nature Reviews Microbiology thanks B. Baker, P. López-García, M. Strous and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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C.J.C., J.F.B. and C.T.B. conducted new data analysis. C.T.B., K.A. and R.H.H. contributed to the discussion of content. C.J.C. and J.F.B. wrote the article, and J.F.B, C.J.C., C.T.B., K.A., A.J.P. and R.H.H. reviewed and edited the manuscript before submission.

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Correspondence to Jillian F. Banfield.

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Candidate phyla

A phylum that is defined on the basis of sequence information and lacks any isolated representative.


A group of organisms that arose from a common ancestor.


Symbionts that are attached to the surface of another cell.

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Castelle, C.J., Brown, C.T., Anantharaman, K. et al. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol 16, 629–645 (2018).

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