In short, "targeted metagenomics" can be possible by integrating a technique called stable-isotope probing with metagenomics. The context in which this question has been asked (marine fauna) make me think that you are planing to target some metabolic functions of the microbiota associated to that fauna. Anyway, the best reference I have for this is:
Coyotzi, Sara, et al. "Targeted metagenomics of active microbial populations with stable-isotope probing." Current opinion in biotechnology 41 (2016): 1-8.