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The passage first introduces the coral reef as a kind of self-contained ecosystem that works "symbiotically" with certain types of algae to support life in water that is "clear"...and thus nutrient poor ("clear" refering to the fact that it doesn't have floaties in the water as much as other less "clear" water does).
After this, it introduces a problem that is threatening the Coral Reef ecosystem. Namely, humans moving in and pooping in the nice clean "clear" water...(hopefully the pooping is done indirectly through a toilet, but you never know). The extra "CRUD" in the water causes the delicate balance between the algae and the amount of stuff in the "clear" water to become disrupted to the point where something dies. Once one animal in a symbiotic relationship dies, the other dies. And thus if Algae dies, Coral dies, little fishy that lives in coral dies, shark that eats little fishy dies....etc.
I hope that helped.
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