The evolutionary origin of host association in the Rickettsiales

Abstract

The evolution of obligate host-association of bacterial symbionts and pathogens remains poorly understood. The Rickettsiales are an alphaproteobacterial order of obligate endosymbionts and parasites that infect a wide variety of eukaryotic hosts, including humans, livestock, insects and protists. Induced by their host-associated lifestyle, Rickettsiales genomes have undergone reductive evolution, leading to small, AT-rich genomes with limited metabolic capacities. Here we uncover eleven deep-branching alphaproteobacterial metagenome assembled genomes from aquatic environments, including data from the Tara Oceans initiative and other publicly available datasets, distributed over three previously undescribed Rickettsiales-related clades. Phylogenomic analyses reveal that two of these clades, Mitibacteraceae and Athabascaceae, branch sister to all previously sampled Rickettsiales. The third clade, Gamibacteraceae, branch sister to the recently identified ectosymbiotic ‘Candidatus Deianiraea vastatrix’. Comparative analyses indicate that the gene complement of Mitibacteraceae and Athabascaceae is reminiscent of that of free-living and biofilm-associated bacteria. Ancestral genome content reconstruction across the Rickettsiales species tree further suggests that the evolution of host association in Rickettsiales was a gradual process that may have involved the repurposing of a type IV secretion system.

Host association and intracellularity evolved multiple times independently in theRickettsiales

“…The four families that include at least one characterised organism were highly supported, and mostly with a much increased representativity, thanks to novel genomes sequenced and MAGs identified in this study (novel taxa: 14/29 Rickettsiaceae ; 10/17 Midichloriaceae ; 1/14 Anaplasmataceae ; 5/6 Deianiraeaceae ). The inner relationships within Rickettsiaceae and Anaplasmataceae are overall consistent with previous phylogenetic and phylogenomic studies 8,10,12,15–17 . For Midichloriaceae , it was possible to infer a novel inner topology with a much higher support with respect to previous studies 14,15,20,21 .…”

“…The phyletic relationships among the families are in general consistent with the most recent and comprehensive studies 8,10,19 , with a single partial exception. The present study indicates a closer relationship between the DDG-clade and Anaplasmataceae with respect to Midichloriaceae , consistent with 16S rRNA gene phylogenies and some phylogenomic analyses 8,19 , while another study placed Anaplasmataceae and Midichloriaceae as sister groups 10 .…”

“…The phyletic relationships among the families are in general consistent with the most recent and comprehensive studies 8,10,19 , with a single partial exception. The present study indicates a closer relationship between the DDG-clade and Anaplasmataceae with respect to Midichloriaceae , consistent with 16S rRNA gene phylogenies and some phylogenomic analyses 8,19 , while another study placed Anaplasmataceae and Midichloriaceae as sister groups 10 . It should be considered that the number of available members of the DDG-clade progressively and largely increased in successive studies (in particular, this is the first study considering Diomedesiaceae ), with a potential significant influence on the results.…”

“…The three recently described families composed only by MAGs 10 , namely Gamibacteraceae, Athabascaceae , and Mitibacteraceae , were retrieved with a comparatively higher representativity (Fig. 1).…”

“…Third, metagenome binning recently allowed the discovery of further Rickettsiales sublineages, in particular two early-diverging families 10 . Their genetic repertoire (including nutrient uptake, detoxification, and multiple biosynthetic pathways) led the authors to hypothesise that these bacteria could be free-living, implying that adaptation to the interaction with host cells would have occurred in more “derived” Rickettsiales lineages.…”