Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales

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Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.

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Data availability

Sequence data have been deposited in GenBank with the accession codes: P. primaurelia CyL4-1 partial 18S-ITS1-5.8S-ITS2-28S—MH185950,P. primaurelia CyL4-1 partial cytochrome oxidase subunit I gene—MH188082, Deianiraea vastatrix CyL4-1 partial 16S rRNA gene—MH197138; Deianiraea vastatrix CyL4-1 genome—CP028925.


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This work was funded by the European Commission FP7-PEOPLE-2009-IRSES grant 247658 (project CINAR-PATHOBACTER) to GP, the Human Frontier Science Programme Grant RGY0075/2017 to DS, the Italian Ministry of Education, University and Research (MIUR): Dipartimenti di Eccellenza Programme (2018–2022)—Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia to DS, and, for the work of the group from St. Petersburg, by the RSF grant 16-14-10157 to AP. We would like to thank A. Oren for advice in bacterial nomenclature and species description. S. Gabrielli and S. Lometto are acknowledged for assistance in graphical artwork and in phylogenomic analyses, respectively. Cultures were maintained in Culture Collection of Microorganisms (RC CCM), Saint Petersburg State University.

Author information

NL isolated the host cells and performed live experiments. ES performed TEM and fluorescence microscopy. KB performed AFM. OL, AP and GP performed molecular experiments and probe design. MC, OL and GP performed phylogeny. MC and OL performed IMNGS analyses. MC, AMF and DS performed genome assembly and analyses. MC, AMF, SG and DS performed metabolic and evolutionary analyses. General interpretation of the results and manuscript writing were performed by MC, DS and GP, and contributed by CB, LM, ES and AP. All the authors contributed to the interpretation and writing of the specific results, and to the discussions. GP planned and coordinated the whole project, with DS planning and coordinating the genomic analyses, and ES coordinating the microscopy.

Correspondence to Davide Sassera or Giulio Petroni.

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