Candidatus Megaira are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

Abstract

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. Data SummaryGenomes assembled in this project have been deposited in bioproject PRJNA867165 Impact statementBacteria that live inside larger organisms commonly form symbiotic relationships that impact the hosts biology in fundamental ways, such as improving defences against natural enemies or altering host reproduction. Certain groups like ciliates and algae are known to host symbiotic bacteria commonly, but our knowledge of their symbionts evolution and function is limited. One such bacteria is Candidatus Megaira, a Rickettsiales that was first identified in ciliates, then later in algae. To improve the available data for this common but understudied group, we searched the genomes of potential hosts on online databases for Rickettsiales and assembled their genomes. We found 4 Ca. Megaira this way and then used these to find a further 14 genomes in environmental metagenomic data. Overall, we increased the number of known Ca. Megaira draft genomes from 2 to 20. These new genomes show us that Ca. Megaira is far more diverse than previously thought and that it is potentially involved in defensive symbioses. In addition, one genome shows striking resemblance to well characterized symbiont, Wolbachia, in encoding many proteins predicted to interact directly with host proteins. The genomes we have identified and examined here provide baseline resources for future work investigating the real-world interactions between the hyper diverse Ca. Megaira and its various potential hosts, like the economically important Nemacystus decipiens.