Everything I'm going to write is a gross over simplification and more importantly, my opinion, so I wouldn't put much stock in it, but here it goes 
For as much as we talk about the ocean, our little boxes of water are a crude approximation at best. We often place animals that have never coexisted in the same environment. We select for the organisms we want and attempt to eliminate those we don't want- towards this end we tinker with animal selection, chemistry, nutrients, lighting, and flow. Since the majority of reefs are centered around the growth of corals, those organisms whose needs are more similar to the needs of the corals will tend to do better than those organisms with differing needs.
Many marine algae grow well within our environments, however their needs and preferences are not perfectly matched. Often, we can utilize these differences between the two organisms to select against the algae. For example, we often include animals that eat algaes and restrict access to those animals that eat corals. Similarly, we often select the wavelength of our lighting to best promote the coral, not the algae.
However, dinoflagellates, are an extremely diverse group. The corals and other animals that we are hoping to grow already contain endosymbiotic dinoflagellates in the form of zooxanthellae. Therefore, the selective pressure becomes harder- how does one target certain dinoflagellates without harming the dinoflagellates we wish to keep?

For as much as we talk about the ocean, our little boxes of water are a crude approximation at best. We often place animals that have never coexisted in the same environment. We select for the organisms we want and attempt to eliminate those we don't want- towards this end we tinker with animal selection, chemistry, nutrients, lighting, and flow. Since the majority of reefs are centered around the growth of corals, those organisms whose needs are more similar to the needs of the corals will tend to do better than those organisms with differing needs.
Many marine algae grow well within our environments, however their needs and preferences are not perfectly matched. Often, we can utilize these differences between the two organisms to select against the algae. For example, we often include animals that eat algaes and restrict access to those animals that eat corals. Similarly, we often select the wavelength of our lighting to best promote the coral, not the algae.
However, dinoflagellates, are an extremely diverse group. The corals and other animals that we are hoping to grow already contain endosymbiotic dinoflagellates in the form of zooxanthellae. Therefore, the selective pressure becomes harder- how does one target certain dinoflagellates without harming the dinoflagellates we wish to keep?
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