title: Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.
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.
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Joran
authors.initials: J
authors.lastname: Martijn
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors.forename: Frederik
authors.initials: F
authors.lastname: Schulz
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Zaremba-Niedzwiedzka
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Viklund
authors.affiliation: Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
authors.forename: Ramunas
authors.initials: R
authors.lastname: Stepanauskas
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Siv G E
authors.initials: SG
authors.lastname: Andersson
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Horn
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.|Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Lionel
authors.identifier: http://orcid.org/0000-0001-8354-2398
authors.initials: L
authors.lastname: Guy
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Thijs J G
authors.initials: TJ
authors.lastname: Ettema
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics*; D005075:Biological Evolution; D002633:Chemotaxis; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics; D060106:Lakes; D056186:Metagenomics; D010802:Phylogeny; D012287:Rickettsiaceae / Q000145:classification / Q000235:genetics*; D013045:Species Specificity; D014871:Water Microbiology
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