Comparative analysis of novel Pseudobdellovibrionaceae genera and species yields insights into the genomics and evolution of bacterial predation mode

Maher, R. L.; Wülbern, J.; Zimmermann, J.; Yeh, E.; Benda, L.; Repnik, U.; Fuss, J.; Künzel, S.; Schulenburg, H.; Bohannan, B. J. M.; Adair, K. L.; Johnke, J.

doi:10.1101/2025.02.19.638989

bioRxiv · 10.1101/2025.02.19.638989

Comparative analysis of novel Pseudobdellovibrionaceae genera and species yields insights into the genomics and evolution of bacterial predation mode

Maher, R. L.·Wülbern, J.·Zimmermann, J.·Yeh, E.·Benda, L.·Repnik, U.·Fuss, J.·Künzel, S.·Schulenburg, H.·Bohannan, B. J. M.·Adair, K. L.·Johnke, J.

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Abstract

Bacteria of the family Pseudobdellovibrionaceae belong to a group of bacteria that kill and feed on other bacteria. The diversity of predation strategies, habitats, and genome characteristics of these bacteria are largely unexplored, despite their ecological and evolutionary importance in microbial communities. Therefore, we characterized new Pseudobdellovibrionaceae strains isolated from the direct environments of three animal hosts: the zebrafish (Danio rerio), the threespine stickleback fish (Gasterosteus aculeatus), and the nematode Caenorhabditis elegans. We used transmission electron microscopy (TEM) and genomic analyses to characterize the morphology and predation modes of our isolates. While most of our isolates exhibited periplasmic (i.e. endoparasitic) predation, one isolate clearly exhibited epibiotic (i.e. exoparasitic) predation and represents only the third confirmed epibiotic strain within its clade. Of our isolates, six are members of five new species in the genus Bdellovibrio and two strains likely represent new genera within the family Pseudobdellovibrionaceae. From metabarcoding data, we found indications that Pseudobdellovibrionaceae are widespread among our three animal hosts. Genomic analyses showed that epibiotic predators lack genes involved in host independence (i.e. prey-independent feeding) and peptidoglycan modification. However, genes unique to epibiotic predators may underlie this predation mode, particularly those involved in cell wall remodeling and recycling. With robust phylogenomic analyses, we show that our novel isolates cluster with previously described Pseudobdellovibrionaceae isolates according to predation mode. Further, by placing Pseudobdellovibrionaceae predators within a wider evolutionary history including other predatory and non-predatory bacteria, we postulate periplasmic predation as the ancestral mode, with more derived epibiotic predators exhibiting genome streamlining.

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Maher, R. L., Wülbern, J., Zimmermann, J., Yeh, E., Benda, L., Repnik, U., Fuss, J., Künzel, S., Schulenburg, H., Bohannan, B. J. M., Adair, K. L., Johnke, J.. 2025-02-20. Comparative analysis of novel Pseudobdellovibrionaceae genera and species yields insights into the genomics and evolution of bacterial predation mode. https://doi.org/10.1101/2025.02.19.638989

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