Full citation: Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, et al. (2013) Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLoS ONE 8(2): e47879. doi:10.1371/journal.pone.0047879
Basically, the paper describes the development and use of a PCR strategy to simultaneously characterize eukaryotic, bacterial and archaeal microbes from samples.
Primers used are summarized in Table 2
Definitely worth a look.