Comparative tissue-specific microbiome analyses identify keystone endosymbionts shaping pathogen interactions in dromedary camel ticks

Ticks are blood-feeding arthropods that carry diverse pathogenic and nonpathogenic microorganisms, yet their dynamics within tick tissues remain poorly understood. We compared the microbial communities in the haemolymph, saliva, ovaries, midgut, and salivary glands of individual Amblyomma gemma and Hyalomma rufipes sampled from dromedary camel using V1-V2 16S rRNA gene metabarcoding. The haemolymph exhibited the highest bacterial diversity, followed by the saliva and ovaries, while the midgut and salivary glands had lower diversities. Keystone taxa exhibited varied connectivity across different tissues and played a crucial role in structuring microbial communities in both tick species. We exclusively detected Rickettsia africae in Am. gemma and Rickettsia aeschlimannii in Hy. rufipes. Both Rickettsia species showed negative correlations with dominant endosymbionts and environmental bacteria across multiple tissues. Coxiella endosymbionts were detected solely in Am. gemma and were most abundant in the salivary glands, while Francisella endosymbionts were dominant in Hy. rufipes’ salivary glands. Francisella endosymbionts were less abundant when R. aeschlimannii was high. In Am. gemma’s haemolymph and saliva, Wolbachia endosymbionts were prevalent, where they were inversely associated with R. africae at the individual tick level. In Hy. rufipes, Wolbachia endosymbionts were present in the ovaries, but not in the midgut. Candidatus Midichloria mitochondrii was found in all tissues of Hy. rufipes and predominantly in saliva, but was only detected in the ovaries, midgut, and salivary glands of Am. gemma. Positive interactions were found between Ca. Midichloria mitochondrii and R. aeschlimannii in Hy. rufipes’ saliva and ovaries, and Ca. Midichloria mitochondrii and Francisella endosymbionts in Am. gemma’s ovaries. Rickettsiella spp. were found in the saliva and haemolymph but not the midgut in both tick species. Environmental bacteria, such as Pseudomonas, Acinetobacter, Staphylococcus, and Corynebacterium, whilst abundant in the haemolymph and saliva were scarce in other tissues. Tick tissue significantly influences bacterial composition, with tissue-specific interactions between pathogens and endosymbionts suggesting bacterial functional specialization. The complex interactions observed between key endosymbionts and Rickettsia pathogens across tissues, including negative correlations with Coxiella, Francisella, and Wolbachia endosymbionts, and positive correlations between Ca. Midichloria mitochondrii and R. aeschlimannii, require further investigation. Identified keystone taxa may serve as targets for anti-microbiota vaccines.