At the threshold of symbiosis: the genome of obligately endosymbiotic 'Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain

Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.

Cardinium inhibits Wolbachia in its mite host, Tyrophagus putrescentiae, and affects host fitness

Interactions among endosymbiotic bacteria inside their eukaryotic hosts are poorly understood, particularly in mites. The mite Tyrophagus putrescentiae is a common, medically important generalist species that has many intracellular and gut bacterial symbionts. In the experiments, we examined bacterial abundances and composition in mite populations obtained by controlled mixing of stock mite populations that differed in the presence/absence of the major intracellular bacteria Wolbachia and Cardinium. Changes in microbial communities were characterized using 16S ribosomal RNA high-throughput sequencing (pooled mite individuals) and quantitative PCR for key microbial taxa (individual mites). Mite fitness was estimated as a parameter of population growth. We detected that in mixed mite populations, Cardinium and Wolbachia can co-occur in the same mite individual. The presence of Cardinium was negatively correlated with the presence of Wolbachia and Bartonella, while the Bartonella and Wolbachia were positively correlated in individual level samples. Since mixed populations had lower abundances of Wolbachia, while the abundance of Cardinium did not change, we suggest that the presence of Cardinium inhibits the growth of Wolbachia. The mixed mite populations had lower population growth than parental populations. The possible effect of symbionts on the fitness of mixed population is discussed.