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© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Paight, C., Johnson, M., Lasek‐Nesselquist, E., & Moeller, H. Cascading effects of prey identity on gene expression in a kleptoplastidic ciliate. Journal of Eukaryotic Microbiology, 70(1), (2022): e12940, https://doi.org/10.1111/jeu.12940., Kleptoplastidic, or chloroplast stealing, lineages transiently retain functional photosynthetic machinery from algal prey. This machinery, and its photosynthetic outputs, must be integrated into the host's metabolism, but the details of this integration are poorly understood. Here, we study this metabolic integration in the ciliate Mesodinium chamaeleon, a coastal marine species capable of retaining chloroplasts from at least six distinct genera of cryptophyte algae. To assess the effects of feeding history on ciliate physiology and gene expression, we acclimated M. chamaeleon to four different types of prey and contrasted well-fed and starved treatments. Consistent with previous physiological work on the ciliate, we found that starved ciliates had lower chlorophyll content, photosynthetic rates, and growth rates than their well-fed counterparts. However, ciliate gene expression mirrored prey phylogenetic relationships rather than physiological status, suggesting that, even as M. chamaeleon cells were starved of prey, their overarching regulatory systems remained tuned to the prey type to which they had been acclimated. Collectively, our results indicate a surprising degree of prey-specific host transcriptional adjustments, implying varied integration of prey metabolic potential into many aspects of ciliate physiology., This work was supported by a grant from the Simons Foundation (Award # 689265 to HVM). Research was sponsored by the U.S. Army Research Office and accomplished under contract W911NF-19-D-0001 for the Institute for Collaborative Biotechnologies.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Paight, C., Johnson, M., Lasek‐Nesselquist, E., & Moeller, H. Cascading effects of prey identity on gene expression in a kleptoplastidic ciliate. Journal of Eukaryotic Microbiology, 70(1), (2022): e12940, https://doi.org/10.1111/jeu.12940., Kleptoplastidic, or chloroplast stealing, lineages transiently retain functional photosynthetic machinery from algal prey. This machinery, and its photosynthetic outputs, must be integrated into the host's metabolism, but the details of this integration are poorly understood. Here, we study this metabolic integration in the ciliate Mesodinium chamaeleon, a coastal marine species capable of retaining chloroplasts from at least six distinct genera of cryptophyte algae. To assess the effects of feeding history on ciliate physiology and gene expression, we acclimated M. chamaeleon to four different types of prey and contrasted well-fed and starved treatments. Consistent with previous physiological work on the ciliate, we found that starved ciliates had lower chlorophyll content, photosynthetic rates, and growth rates than their well-fed counterparts. However, ciliate gene expression mirrored prey phylogenetic relationships rather than physiological status, suggesting that, even as M. chamaeleon cells were starved of prey, their overarching regulatory systems remained tuned to the prey type to which they had been acclimated. Collectively, our results indicate a surprising degree of prey-specific host transcriptional adjustments, implying varied integration of prey metabolic potential into many aspects of ciliate physiology., This work was supported by a grant from the Simons Foundation (Award # 689265 to HVM). Research was sponsored by the U.S. Army Research Office and accomplished under contract W911NF-19-D-0001 for the Institute for Collaborative Biotechnologies.

Nephromyces, a genus in the phylum Apicomplexa, has recently been described as having a mutualistic relationship with its host: tunicates in the Molgulidae family (Saffo et al. 2010). If true, Nephromyces would be the only known example of a mutualistic apicomplexan genus. In addition to the possible switch to mutualism, Nephromyces is one of a few apicomplexan groups containing bacterial endosymbionts. To test the hypothesis that endosymbiotic bacteria facilitated the transition of Nephromyces from parasitism, the metabolic capabilities of Nephromyces and its bacterial endosymbionts need to be determined. The transition from obligate parasite to endosymbiont is predicted to involve different selective pressures leading to wide spread genomic changes. Identifying these changes will lead to a better understanding of the dynamics between the different biological players in this system. Using data from Illumina HiSeq, we have assembled and annotated the transcriptomes of Nephromyces and Cardiosporidium cionae. Using data from a combination of platforms; Illumina MiSeq, HiSeq, and Pacific Biosciences, we have partially assembled a pan-genome for Nephromyces and have assembled the genomes of its bacterial endosymbionts. Using amplicon sequencing, we have estimated the genetic diversity and prevalence of multispecies infections of Nephromyces and its bacterial endosymbionts in its host Molgula manhattensis. In addition to the implementation of next-generation sequencing technologies, this work is also based on laboratory cultures and species isolation experiments. With the aforementioned data we are able to describe the transcriptome of Nephromyces and Cardiosporidium as well as the genomes of all three bacterial endosymbionts, providing a basic overview of the metabolism of this system. Nephromyces and Cardiosporidium both encode a complete purine degradation pathway, which enables them to break uric acid into pyruvate and glycine, additionally Nephromyces is also able t