Genomic diversity across the Rickettsia and ‘Candidatus Megaira’ genera and proposal of genus status for the Torix group

Davison, Helen Rebecca; Pilgrim, Jack; Wybouw, Nicky; Parker, Joseph; Pirro, Stacy; Hunter-Barnett, Simon; Campbell, Paul M; Blow, Frances; Darby, Alistair C.; Hurst, Gregory D. D.; Siozios, Stefanos

doi:10.1038/s41467-022-30385-6

Cited by 30 publications

(86 citation statements)

References 120 publications

(152 reference statements)

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“…According to the ribosomal protein phylogeny the genome belongs to the recently proposed genus ‘ Ca. Tisiphia’ (formerly Torix group Rickettsia ), a sister group of the genus Rickettsia [15] (Figure 3B). The phylogenetic placement is further corroborated by a 16S rRNA phylogeny (Figure S3).…”

Section: Resultsmentioning

confidence: 99%

“…The family Rickettsiaceae (Alphaproteobacteria) includes the well-known arthropod-transmitted vertebrate and human pathogens of the genus Rickettsia but also invertebrate-restricted endosymbionts that are not transferred to vertebrate hosts and were recently placed in a separate genus ‘Ca. Tisiphia’ (formerly Torix group Rickettsia) [14, 15]. Like Wolbachia and Cardinium, ‘Ca.…”

Section: Introductionmentioning

confidence: 99%

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One to host them all: genomics of the diverse bacterial endosymbionts of the spiderOedothorax gibbosus

Halter

Köstlbacher

Rattei

et al. 2022

Preprint

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Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well-known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analyzed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, ‘Candidatus Tisiphia’ (formerly Torix group Rickettsia), Cardinium, and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, ‘Ca. Tisiphia’ and Cardinium endosymbionts. We provide insights in the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, ‘Ca. Tisiphia’ and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on earth and show the usefulness of transposable elements as an evolutionary “contact-tracing” tool.Data summaryAll supporting data, code and protocols have been provided within the article or through supplementary data files. Seven supplementary figures and seven supplementary tables are available with the online version of this article. Sequencing data used in this study was generated and previously published by Hendrickx et al., 2021. Genome assemblies generated in this study have been deposited under the project PRJEB52003 at DDBJ/ENA/GenBank. The MAG of R. oedothoracis OV001 was deposited at DDBJ/ENA/GenBank under the sample SAMN28026840. The genome of ‘Candidatus Rhabdochlamydia oedothoracis W744×776’ was previously published by Halter et al., 2022 and is available at DDBJ/ENA/GenBank (accession: CP075587-CP075588). The collection of genomes and proteomes, all files for phylogenetic analyses including gene alignments, concatenated alignments, and tree files, and original output files of the HGT and SNP predictions used in this study are available at zenodo (https://doi.org/10.5281/zenodo.6362846).

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

One to host them all: genomics of the diverse bacterial endosymbionts of the spiderOedothorax gibbosus

Halter

Köstlbacher

Rattei

et al. 2022

Preprint

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“…Outside of clade A stains, NVVL01 is highly distinct, having over double the number of unique gene clusters compared to all other taxa; a large number of unique gene clusters were additionally observed in the other two non-A group strains, MegNdeciBESST, and JAFLDA01 (Figure 4). Rickettsia) [25,51]. MegNdeciBESST and JAFLDA01 have complete dTDP-L-Rhamnose pathways (Figure 5).…”

Section: Phylogeny and Evolutionmentioning

confidence: 99%

“…Rickettsiales-positive libraries were taken forward for metagenomic assembly and binning to extract full genome sequences as described in Davison et al (2022) [25]. Briefly, metagenomic assembly, binning and quality check was performed with Megahit, Metabat2 and CheckM [25,[28][29][30][31].…”

Section: Collection Of External Genomes For Metagenomics and Phylogen...mentioning

confidence: 99%

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‘CandidatusMegaira’ are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

Davison

Hurst

Siozios

2022

Preprint

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Symbiotic microbes from the genus Candidatus Megaira (Rickettsiales) are known to be common associates of algae and ciliates. However genomic resources for these bacteria are scarce, limiting our understanding of their diversity and biology. We therefore utilized SRA and metagenomic assemblies to explore the diversity of this genus. We successfully extracted four draft Ca. Megaira genomes including one complete scaffold for a Ca. Megaira and identified an additional 14 draft genomes from uncategorised environmental Metagenome-Assembled Genomes. We use this information to resolve the phylogeny for the hyper-diverse Ca. Megaira, with hosts broadly spanning ciliates, micro- and macro-algae, and find that the current single genus designation Ca. Megaira significantly underestimates their diversity. We also evaluate the metabolic potential and diversity of Ca. Megaira from this new genomic data and find no clear evidence of nutritional symbiosis. In contrast, we hypothesize a potential for defensive symbiosis in Ca. Megaira. Intriguingly, one symbiont genome revealed a proliferation of ORFs with ankyrin, tetratricopeptide and Leucine rich repeats like those observed in the genus Wolbachia where they are considered important for host-symbiont protein-protein interactions. Onward research should investigate the phenotypic interactions between Ca. Megaira and their various potential hosts, including the economically important Nemacystus decipiens, and target acquisition of genomic information to reflect the diversity of this massively variable group.

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Reassessment of the genetic basis of natural rifampin resistance in the genus Rickettsia

Amoros,

Fattar,

Buysse

et al. 2024

MicrobiologyOpen

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Rickettsia, a genus of obligate intracellular bacteria, includes species that cause significant human diseases. This study challenges previous claims that the Leucine‐973 residue in the RNA polymerase beta subunit is the primary determinant of rifampin resistance in Rickettsia. We investigated a previously untested Rickettsia species, R. lusitaniae, from the Transitional group and found it susceptible to rifampin, despite possessing the Leu‐973 residue. Interestingly, we observed the conservation of this residue in several rifampin‐susceptible species across most Rickettsia phylogenetic groups. Comparative genomics revealed potential alternative resistance mechanisms, including additional amino acid variants that could hinder rifampin binding and genes that could facilitate rifampin detoxification through efflux pumps. Importantly, the evolutionary history of Rickettsia genomes indicates that the emergence of natural rifampin resistance is phylogenetically constrained within the genus, originating from ancient genetic features shared among a unique set of closely related Rickettsia species. Phylogenetic patterns appear to be the most reliable predictors of natural rifampin resistance, which is confined to a distinct monophyletic subclade known as Massiliae. The distinctive features of the RNA polymerase beta subunit in certain untested Rickettsia species suggest that R. raoultii, R. amblyommatis, R. gravesii, and R. kotlanii may also be naturally rifampin‐resistant species.

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Genomic diversity across the Rickettsia and ‘Candidatus Megaira’ genera and proposal of genus status for the Torix group

Cited by 30 publications

References 120 publications

One to host them all: genomics of the diverse bacterial endosymbionts of the spiderOedothorax gibbosus

One to host them all: genomics of the diverse bacterial endosymbionts of the spiderOedothorax gibbosus

‘CandidatusMegaira’ are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

Reassessment of the genetic basis of natural rifampin resistance in the genus Rickettsia

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