Abstract
The bacterial family Rickettsiaceae includes a group of well-known etiological agents of many human and vertebrate diseases, including epidemic typhus-causing pathogen Rickettsia prowazekii. Owing to their medical relevance, rickettsiae have attracted a great deal of attention and their host-pathogen interactions have been thoroughly investigated. All known members display obligate intracellular lifestyles, and the best-studied genera, Rickettsia and Orientia, include species that are hosted by terrestrial arthropods. Their obligate intracellular lifestyle and host adaptation is reflected in the small size of their genomes, a general feature shared with all other families of the Rickettsiales. Yet, despite that the Rickettsiaceae and other Rickettsiales families have been extensively studied for decades, many details of the origin and evolution of their obligate host-association remain elusive. Here we report the discovery and single-cell sequencing of ‘Candidatus Arcanobacter lacustris’, a rare environmental alphaproteobacterium that was sampled from Damariscotta Lake that represents a deeply rooting sister lineage of the Rickettsiaceae. Intriguingly, phylogenomic and comparative analysis of the partial ‘Candidatus Arcanobacter lacustris’ genome revealed the presence chemotaxis genes and vertically inherited flagellar genes, a novelty in sequenced Rickettsiaceae, as well as several host-associated features. This finding suggests that the ancestor of the Rickettsiaceae might have had a facultative intracellular lifestyle. Our study underlines the efficacy of single-cell genomics for studying microbial diversity and evolution in general, and for rare microbial cells in particular.
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Acknowledgements
All sequencing was performed by the SNP and SEQ Technology Platform, Science for Life Laboratory at Uppsala University, a national infrastructure supported by the Swedish Research Council (VR-RFI) and the Knut and Alice Wallenberg Foundation. We thank the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) at Uppsala University for providing computational resources. We thank Ilias Lagkouvardos for help in the analysis of the environmental distribution of A. lacustris and Davide Sassera for providing the flagella data set. This work was supported by grants to TJGE and SGEA of the Swedish Research Council (621-2009-4813; 621-2011-4669) and to TJGE and MH of the European Research Council (ERC Starting grant 310039-PUZZLE_CELL and 281633-EvoChlamy). FS is a recipient of the DOC fellowship of the Austrian Academy of Sciences at the Division of Microbial Ecology, University of Vienna, Austria.
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Martijn, J., Schulz, F., Zaremba-Niedzwiedzka, K. et al. Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. ISME J 9, 2373–2385 (2015). https://doi.org/10.1038/ismej.2015.46
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DOI: https://doi.org/10.1038/ismej.2015.46
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