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Background  Microsporidia are highly specialized, parasitic fungi that infect a wide range of eukaryotic hosts from all major taxa. Infections cause a variety of damaging effects on host physiology from increased stress to death. The microsporidian  Facilispora margolisi  infects the Pacific salmon louse ( Lepeophtheirus salmonis oncorhynchi ), an economically and ecologically important ectoparasitic copepod that can impact wild and cultured salmonids.    Results  Vertical transmission of  F. margolisi  was demonstrated by using PCR and in situ hybridization to identify and localize microsporidia in female  L. salmonis  and their offspring. Spores and developmental structures of  F. margolisi  were identified in 77% of F 1  generation copepods derived from infected females while offspring from uninfected females all tested negative for the microsporidia. The transcriptomic response of the salmon louse to  F. margolisi  was profiled at both the copepodid larval stage and the pre-adult stage using microarray technology .  Infected copepodids differentially expressed 577 transcripts related to stress, ATP generation and structural components of muscle and cuticle. The infection also impacted the response of the copepodid to the parasiticide emamectin benzoate (EMB) at a low dose of 1.0 ppb for 24 h. A set of 48 transcripts putatively involved in feeding and host immunomodulation were up to 8-fold underexpressed in the  F. margolisi  infected copepodids treated with EMB compared with controls or either stressor alone. Additionally, these infected lice treated with EMB also overexpressed 101 transcripts involved in stress resistance and signalling compared to the other groups. In contrast, infected pre-adult lice did not display a stress response, suggesting a decrease in microsporidian virulence associated with lice maturity. Furthermore, copepodid infectivity and moulting was not affected by the microsporidian infection.    Conclusions  This study demonstrated that  F. margolisi  is transmitted vertically between salmon louse generations and that biological impacts of infection differ depending on the stage of the copepod host. The infection caused significant perturbations of larval transcriptomes and therefore must be considered in future studies in which impacts to host development and environmental factors are assessed. Fitness impacts are probably minor, although the interaction between pesticide exposure and microsporidian infection merits further study.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4040-8) contains supplementary material, which is available to authorized users.

bmc genomics

Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis)