The ciliated protozoan Tetrahymena exemplifies a recombinant system for the expression of heterologous nucleic acids, preferably on the plasma membrane surface. Integration of a heterlogous nucleic acid into the .beta.-tubulin gene, BTU1, of a paclitaxel-sensitive T. thermophila mutant that possesses btu1-IK350M .beta.-tubulin allele allows screening for transformants using negative selection, as transformants have restored paclitaxel resistance. Transgenic ciliated protozoa of the invention can serve as live vaccines. For example, transgenic Tetrahymena expressing Ichthyophthirius multifiliis i-antigen protein on their surface are effective vehicles for vaccination of freshwater fish against infection by I. multifiliis.